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1,409 | 11-pulse_and_rests_pos.opat | cac-t-u-s_om-sharp/help-patches/Score/Trees/11-pulse_and_rests_pos.opat |
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1,410 | 10-n-pulses_group-pulses.opat | cac-t-u-s_om-sharp/help-patches/Score/Trees/10-n-pulses_group-pulses.opat |
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1,414 | list-selection.opat | cac-t-u-s_om-sharp/help-patches/Interactive boxes/list-selection.opat |
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(:connection (:from (:box 23 :out 3)) (:to (:box 1 :in 2))))) | 34,938 | Common Lisp | .l | 1,547 | 15.826115 | 73 | 0.46237 | cac-t-u-s/om-sharp | 167 | 14 | 31 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 312e3cf98ef1b0fa82935a785bd306f2e5a83a8021518e613b8fd70c13ca28df | 1,419 | [
-1
] |
1,434 | package.lisp | ghollisjr_cl-ana/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana
(:use :cl))
(in-package :cl-ana)
(defvar *cl-ana-package-names*
(list :cl-ana.pathname-utils
:cl-ana.package-utils
:cl-ana.generic-math
:cl-ana.binary-tree
:cl-ana.csv-table
:cl-ana.math-functions
:cl-ana.calculus
:cl-ana.spline
:cl-ana.tensor
:cl-ana.error-propogation
:cl-ana.quantity
:cl-ana.file-utils
:cl-ana.fitting
:cl-ana.functional-utils
:cl-ana.gnuplot-interface
:cl-ana.gsl-cffi
:cl-ana.hdf-table
:cl-ana.hdf-typespec
:cl-ana.hdf-utils
:cl-ana.histogram
:cl-ana.linear-algebra
:cl-ana.list-utils
:cl-ana.array-utils
:cl-ana.lorentz
:cl-ana.macro-utils
:cl-ana.map
:cl-ana.hash-table-utils
:cl-ana.memoization
:cl-ana.ntuple-table
:cl-ana.plotting
:cl-ana.reusable-table
:cl-ana.statistics
:cl-ana.statistical-learning
:cl-ana.string-utils
:cl-ana.symbol-utils
:cl-ana.symbol-utils
:cl-ana.table
:cl-ana.table-utils
:cl-ana.table-viewing
:cl-ana.typed-table
:cl-ana.typespec
:cl-ana.int-char
:cl-ana.clos-utils
:cl-ana.serialization
;; makeres:
:cl-ana.makeres
:cl-ana.makeres-macro
:cl-ana.makeres-block
:cl-ana.makeres-progress
:cl-ana.makeres-table
:cl-ana.makeres-graphviz
:cl-ana.makeres-branch
:cl-ana.makeres-utils))
(loop
for p in *cl-ana-package-names*
do (cl-ana.package-utils:add-package-to-group p :cl-ana))
(cl-ana.package-utils:use-package-group :cl-ana)
| 2,603 | Common Lisp | .lisp | 81 | 25.765432 | 70 | 0.628923 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 611954f629496fdb2cca3878fe53d05fcc1efaee7730a5f7f2a5bc8f3945dcd4 | 1,434 | [
-1
] |
1,435 | install.lisp | ghollisjr_cl-ana/install.lisp | (require 'quicklisp)
(ql:quickload "cffi")
(ql:quickload "gsll")
(ql:quickload "alexandria")
(ql:quickload "iterate")
(ql:quickload "antik")
(ql:quickload "closer-mop")
(ql:quickload "cl-csv")
(ql:quickload "cl-fad")
(ql:quickload "external-program")
| 252 | Common Lisp | .lisp | 10 | 24.1 | 33 | 0.742739 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 2f850d4e10041135834a4707a18f4ec7e56430a7edfa4cf54a47ee50156aa05a | 1,435 | [
-1
] |
1,436 | package.lisp | ghollisjr_cl-ana/string-utils/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.string-utils
(:use :cl)
(:export :lines
:unlines
:mkstr
:lispify
:string-append
:words))
| 1,043 | Common Lisp | .lisp | 28 | 33.928571 | 70 | 0.67357 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | bb18169a7e482096a72022c22507f054dddca2e0e44907aad83f248918fe7e18 | 1,436 | [
-1
] |
1,437 | string-utils.lisp | ghollisjr_cl-ana/string-utils/string-utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.string-utils)
(defun lispify (symbol-or-string)
"Converts symbol or string into a string and replaces all spaces and
underscores with -, and convert to uppercase."
(string-upcase (map 'string
(lambda (c)
(case c
(#\Space #\-)
(#\_ #\-)
(otherwise c)))
(string symbol-or-string))))
(defun string-append (&rest strings)
(apply #'concatenate 'string strings))
;; Working with lines:
(defun lines (string)
"Splits a string into a list of the lines comprising the string."
(flet ((cut-newline (s)
(let ((length (length s)))
(if (not (zerop length))
(if (char= #\Newline (elt s (1- length)))
(subseq s 0 (1- length))
s)
""))))
(split-sequence:split-sequence
#\Newline
(cut-newline string))))
(defun unlines (lines &optional (trailing-newline-p t))
"Joins a list of lines into original string, with optional trailing
newline."
(if (null lines)
""
(let ((result
(reduce (lambda (str line)
(string-append str
(string #\Newline)
line))
(rest lines)
:initial-value (first lines))))
(if trailing-newline-p
(string-append result (string #\Newline))
result))))
;; Useful for getting the words out of a string:
(defun words (string)
"Returns the read words (symbols, numbers, etc.) contained in a
string"
(with-input-from-string (s string)
(do ((w (read s nil nil) (read s nil nil))
(res nil (cons w res)))
((null w) (nreverse res)))))
;;;; From let-over-lambda:
(defun mkstr (&rest args)
(let ((*print-pretty* nil))
(with-output-to-string (s)
(dolist (a args)
(princ a s)))))
| 2,864 | Common Lisp | .lisp | 75 | 30.52 | 70 | 0.585971 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 9928721ba512d9f5f241a0ea2140266fcbb91d3b82b74fde857382e56511548f | 1,437 | [
-1
] |
1,438 | package.lisp | ghollisjr_cl-ana/functional-utils/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.functional-utils
(:use :cl)
(:export :flip
:splice
:to-pair-function
:lfuncall
:min-by
:minimum
:max-by
:maximum
:iterate
:iterate-collect
:safe-funcall))
| 1,150 | Common Lisp | .lisp | 33 | 30.636364 | 70 | 0.657706 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 01374d90148f9a8038efaefa20d5980c843e2f12f14e8f3f936e735fa0478b78 | 1,438 | [
-1
] |
1,439 | functional-utils.lisp | ghollisjr_cl-ana/functional-utils/functional-utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.functional-utils)
(defun flip (f)
"Takes a function of two parameters and creates a new function which
takes the same parameters in reverse order; particularly useful in
conjunction with reduce."
(lambda (x y) (funcall f y x)))
(defun splice (xsplit fn1 fn2)
"Splices two functions togother at xsplit. If either function is
nil, returns the other function or nil if both are nil."
(cond
((and fn1
fn2)
(lambda (x)
(if (<= x xsplit)
(funcall fn1 x)
(funcall fn2 x))))
(fn1 fn1)
(fn2 fn2)
(t nil)))
;; (defun compose (&rest fs)
;; "Arbitrary number of functions composed"
;; (let ((f (first fs)))
;; (if (= 1 (length fs))
;; (first fs)
;; (lambda (&rest xs)
;; (funcall f (apply (apply #'compose (rest fs)) xs))))))
(defun to-pair-function (f)
"Makes f apply to a pair instead of two arguments"
(lambda (x) (funcall f (car x ) (cdr x))))
(defun lfuncall (fn &rest args)
"Applies a function which takes a single list argument to an
arbitrary number of arguments."
(funcall fn args))
;; Didn't really know where to put these, but they are higher-order
;; functions:
(defun min-by (x y &key (key #'identity))
(if (< (funcall key x)
(funcall key y))
x
y))
(defun minimum (xs &key (key #'identity))
(when xs
(reduce (lambda (x y) (min-by x y :key key))
xs)))
(defun max-by (x y &key (key #'identity))
(if (> (funcall key x)
(funcall key y))
x
y))
(defun maximum (xs &key (key #'identity))
(when xs
(reduce (lambda (x y) (max-by x y :key key))
xs)))
(defun iterate (fn initial count)
"Calls a function on its own result for count iterations. Returns
the final result."
(do* ((i 1 (1+ i))
(fnval initial (funcall fn fnval)))
((> i count) fnval)))
(defun iterate-collect (fn initial count)
"Calls a function on its own result for count iterations. Returns
the full list of results."
(do* ((i 1 (1+ i))
(fnval initial (funcall fn fnval))
(result nil (cons fnval result)))
((> i count) (nreverse result))))
(defun safe-funcall (key-args &rest args)
"Only calls a function when it is in fact a function, and returns
all other objects."
(if (functionp key-args)
(apply key-args args)
key-args))
| 3,229 | Common Lisp | .lisp | 92 | 31.467391 | 70 | 0.655139 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 842eb25c0d8c45983d417f34b1186bf0e0bd50c17839721b8c83767fc4244604 | 1,439 | [
-1
] |
1,440 | package.lisp | ghollisjr_cl-ana/makeres-progress/package.lisp | ;;;; makeres-progress is a Common Lisp make-like tool for computations.
;;;; Copyright 2015 Gary Hollis
;;;;
;;;; This file is part of makeres-progress.
;;;;
;;;; makeres-progress is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; makeres-progress is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with makeres-progress. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis via email at
;;;; [email protected]
(defpackage #:cl-ana.makeres-progress
(:use :cl
:cl-ana.makeres)
(:export :progresstrans
:*makeres-progress-results-only-p*))
(cl-ana.gmath:use-gmath :cl-ana.makeres-progress)
| 1,121 | Common Lisp | .lisp | 26 | 41 | 80 | 0.720952 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 66b6f2ac6be5b6b779b1b4b92cbadccc9543ae78aee8cb07bb536c03a922e468 | 1,440 | [
-1
] |
1,441 | progresstrans.lisp | ghollisjr_cl-ana/makeres-progress/progresstrans.lisp | ;;;; makeres-progress is a Common Lisp make-like tool for computations.
;;;; Copyright 2014 Gary Hollis
;;;;
;;;; This file is part of makeres-progress.
;;;;
;;;; makeres-progress is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; makeres-progress is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with makeres-progress. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis via email at
;;;; [email protected]
(in-package :cl-ana.makeres-progress)
(defparameter *makeres-progress-results-only-p* t
"Set to nil if you want progresstrans to print messages for every
target in given table, not just the ones also present in the project
target table (meaning that internal-use-only targets will have their
strange names printed).")
(defun progresstrans (target-table)
"Adds status printing message to any targets present in both
target-table and the project target table unless
*makeres-progress-results-only-p* is nil. See
*makeres-progress-results-only-p* for more details."
(let ((result-table (make-hash-table :test 'equal))
(progress-ids
(if *makeres-progress-results-only-p*
(loop
for id being the hash-keys in (target-table)
collecting id)
;; subtle difference, read carefully
(loop
for id being the hash-keys in target-table
collecting id))))
(loop
for id being the hash-keys in target-table
do
(if (member id progress-ids :test #'equal)
(let* ((target (gethash id target-table))
(expr (target-expr target)))
(setf (gethash id result-table)
(make-target id
`(progn
(let ((*print-pretty* nil))
(format t "Computing ~s~%"
',id))
,expr)
:val (target-val target)
:stat (target-stat target)
:timestamp (target-timestamp target))))
(setf (gethash id result-table)
(if *copy-target-table-p*
(copy-target (gethash id target-table))
(gethash id target-table)))))
result-table))
| 2,883 | Common Lisp | .lisp | 62 | 35.774194 | 80 | 0.596877 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 196dbbbc711f6de53925b121d5dfe3151188906d7d1a4cdbcfeef62c42e289dd | 1,441 | [
-1
] |
1,442 | test.lisp | ghollisjr_cl-ana/makeres-progress/test.lisp | (require 'cl-ana)
(in-package :cl-ana)
(in-project makeres-progress-test)
(settrans (list #'progresstrans) :op :set)
(defres a
(list 1 2 3))
(defres b
(list 2 3 4))
(defres c
(+ (res a)
(res b)))
| 213 | Common Lisp | .lisp | 11 | 16.818182 | 42 | 0.647959 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 0d6aa33140f0699162eb98ad828a73c21b16abb561f06407e16e2bc4ee555dcc | 1,442 | [
-1
] |
1,443 | package.lisp | ghollisjr_cl-ana/serialization/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.serialization
(:use :cl
:cffi
:cl-ana.histogram
:cl-ana.int-char
:cl-ana.hdf-utils
:cl-ana.error-propogation
:cl-ana.macro-utils
:cl-ana.typespec
:cl-ana.table
:cl-ana.hdf-table)
(:export :write-histogram
:read-histogram))
| 1,204 | Common Lisp | .lisp | 33 | 32.69697 | 70 | 0.671795 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 5824c075c996d33030eaa193b972b300db056ae435d4bac033ca27cd42595182 | 1,443 | [
-1
] |
1,444 | test.lisp | ghollisjr_cl-ana/serialization/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana)
(in-package :cl-ana)
(defun write-histogram-test ()
(with-open-hdf-file (file "/home/ghollisjr/hist.h5"
:direction :output
:if-exists :supersede
:if-does-not-exist :create)
(write-histogram
(make-contiguous-hist (list (list :name "x"
:low -5d0
:high 5d0
:nbins 10)))
file
"/histogram")))
(defun read-histogram-test ()
(with-open-hdf-file (file "/home/ghollisjr/hist.h5"
:direction :input
:if-does-not-exist :error)
(read-histogram file "/histogram")))
| 1,630 | Common Lisp | .lisp | 39 | 33.307692 | 70 | 0.592943 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 5d9eb777fe8b57c9fb4e8439d0c1f7ebcfa502f22363e74eb04ccf7b103b231c | 1,444 | [
-1
] |
1,445 | histogram.lisp | ghollisjr_cl-ana/serialization/histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.serialization)
(defparameter *histogram-data-path* "data")
(defparameter *histogram-bin-spec-path* "bin-specs")
(defun ->double-float (x)
(float x 0d0))
(defun write-histogram (histogram file hdf-path)
"Writes histogram to file. Supports histogram count values with
errors as well as simple numerical values.
Note that this function assumes that either all the dimensions have
names or none of them do."
(hdf-mkgroup file hdf-path)
(flet ((subpath (path)
(concatenate 'string
hdf-path
"/"
path)))
(let* ((raw-data (hist-bin-values histogram))
(errors? (typep (first (first raw-data))
'err-num))
(data (if (not errors?)
raw-data
(mapcar (lambda (datum)
(destructuring-bind (count &rest xs) datum
(list* (err-num-value count)
(err-num-error count)
xs)))
raw-data)))
(data-names-specs
;; had to change this to double-float to allow for
;; normalized histograms etc.
(append (if errors?
(list (cons "count" :double)
(cons "count-error" :double))
(list (cons "count" :double)))
(loop
for i from 0
for n in (hist-dim-names histogram)
collect (cons (if n
n
(with-output-to-string (s)
(format s "x~a" i)))
:double))))
(data-table-path
(subpath *histogram-data-path*))
(data-table (create-hdf-table
file data-table-path data-names-specs))
(data-field-symbols (table-field-symbols data-table))
(hist-dim-specs
(let ((result (hist-dim-specs histogram)))
(loop
for plist in result
for i from 0
do (when (not (getf plist :name))
(setf (getf plist :name)
(with-output-to-string (s)
(format s "x~a" i)))))
result))
(bin-spec-table-path (subpath *histogram-bin-spec-path*))
(max-string-length
(loop
for plist in hist-dim-specs
maximizing (length (getf plist :name))))
(bin-spec-names-specs
(list (cons "name" (list :array :char max-string-length))
(cons "name-length" :int)
(cons "nbins" :int)
(cons "low" :double)
(cons "high" :double)))
(bin-spec-table (create-hdf-table
file bin-spec-table-path
bin-spec-names-specs)))
;; write data table
(loop
for datum in data
do (progn
(loop
for i from 0
for field in datum
for sym in data-field-symbols
do (table-set-field data-table sym
(->double-float field)))
(table-commit-row data-table)))
(table-close data-table)
;; write bin-spec table
;; fix plists
(loop
for plist in hist-dim-specs
for i from 0
do (when (not (getf plist :name))
(setf (getf plist :name)
(with-output-to-string (s)
(format s "x~a" i)))))
(loop
for plist in hist-dim-specs
do (progn
(table-push-fields bin-spec-table
(|name| (getf plist :name))
(|name-length| (length (getf plist :name)))
(|nbins| (getf plist :nbins))
(|low| (->double-float (getf plist :low)))
(|high| (->double-float (getf plist :high))))))
(table-close bin-spec-table))))
;; utility function
(defun h5tget-member-name-as-lisp-string (hdf-type i)
(let* ((name (hdf5:h5tget-member-name hdf-type i))
(lisp-name (cffi:foreign-string-to-lisp name)))
(cffi:foreign-free name)
lisp-name))
;; new version which uses raw HDF5 functions
(defun read-histogram (file hdf-path &optional (type :sparse))
"Reads a histogram from an hdf-table with file and path.
type can be either :contiguous or :sparse for contiguous-histogram and
sparse-histogram respectively."
(flet ((subpath (path)
(concatenate 'string
hdf-path
"/"
path)))
(let* ((binspec-path
(subpath *histogram-bin-spec-path*))
(binspec-dataset
(hdf5:h5dopen2 file binspec-path hdf5:+H5P-DEFAULT+))
(binspec-datatype
(hdf5:h5dget-type binspec-dataset))
(binspec-dataspace
(hdf5:h5dget-space binspec-dataset))
(data-path
(subpath *histogram-data-path*))
(data-dataset
(hdf5:h5dopen2 file data-path hdf5:+H5P-DEFAULT+))
(data-datatype
(hdf5:h5dget-type data-dataset))
(data-dataspace
(hdf5:h5dget-space data-dataset))
binspec-chunk-size
nrows
ndims
binspec-row-size
binspec-buffer-size
binspecs
data-chunk-size
data-row-size
data-buffer-size
memspace
n-count-vars
hist)
(with-foreign-objects ((binspec-dataset-dims 'hdf5:hsize-t)
(binspec-chunk-dims 'hdf5:hsize-t)
(binspec-name-dims 'hdf5:hsize-t)
(data-dataset-dims 'hdf5:hsize-t)
(data-chunk-dims 'hdf5:hsize-t)
(memspace-dims 'hdf5:hsize-t)
(memspace-maxdims 'hdf5:hsize-t))
(let ((create-plist
(hdf5:h5dget-create-plist binspec-dataset)))
(hdf5:h5pget-chunk create-plist 1 binspec-chunk-dims))
(setf binspec-chunk-size
(mem-aref binspec-chunk-dims 'hdf5:hsize-t))
(hdf5:h5sget-simple-extent-dims binspec-dataspace
binspec-dataset-dims
(null-pointer))
(setf ndims
(mem-aref binspec-dataset-dims 'hdf5:hsize-t))
(hdf5:h5tget-array-dims2
(hdf5:h5tget-member-type binspec-datatype
0)
binspec-name-dims)
(setf binspec-row-size
(hdf5:h5tget-size binspec-datatype))
(setf binspec-buffer-size
(* binspec-chunk-size binspec-row-size))
(with-foreign-object (buffer :char binspec-buffer-size)
(loop
for chunk-index from 0
while (< (* chunk-index binspec-buffer-size)
ndims)
do
(let ((remaining-rows
(- ndims
(* chunk-index binspec-chunk-size))))
(if (< remaining-rows binspec-chunk-size)
(setf (mem-aref memspace-dims 'hdf5:hsize-t 0)
remaining-rows)
(setf (mem-aref memspace-dims 'hdf5:hsize-t 0)
binspec-chunk-size)))
(setf (mem-aref memspace-maxdims 'hdf5:hsize-t)
(mem-aref memspace-dims 'hdf5:hsize-t))
(with-foreign-objects ((start 'hdf5:hsize-t)
(stride 'hdf5:hsize-t)
(cnt 'hdf5:hsize-t)
(blck 'hdf5:hsize-t))
(setf (mem-aref start 'hdf5:hsize-t)
(* chunk-index
binspec-chunk-size))
(setf (mem-aref stride 'hdf5:hsize-t)
1)
(setf (mem-aref cnt 'hdf5:hsize-t)
1)
(setf (mem-aref blck 'hdf5:hsize-t)
(mem-aref memspace-dims 'hdf5:hsize-t))
(hdf5:h5sselect-hyperslab binspec-dataspace
:H5S-SELECT-SET
start
stride
cnt
blck)
(setf memspace
(hdf5:h5screate-simple 1 memspace-dims memspace-maxdims))
(hdf5:h5dread binspec-dataset
binspec-datatype
memspace
binspec-dataspace
hdf5:+H5P-DEFAULT+
buffer)
(loop
for i from 0 below (mem-aref memspace-dims 'hdf5:hsize-t)
do (let* ((buffer-index
(+ (* i binspec-row-size)
(* binspec-chunk-size chunk-index)))
(name-length
(mem-aref
(mem-aptr buffer :char
(+ (hdf5:h5tget-member-offset binspec-datatype
1)
buffer-index))
:int))
(name
(let ((result
(make-string name-length)))
(loop
for j below name-length
do
(setf (aref result j)
(int-char
(mem-aref
buffer :char
(+ (hdf5:h5tget-member-offset
binspec-datatype 0)
buffer-index
j)))))
result))
(nbins
(mem-aref
(mem-aptr buffer :char
(+ (hdf5:h5tget-member-offset
binspec-datatype 2)
buffer-index))
:int))
(low
(mem-aref
(mem-aptr buffer :char
(+ (hdf5:h5tget-member-offset
binspec-datatype 3)
buffer-index))
:double))
(high
(mem-aref
(mem-aptr buffer :char
(+ (hdf5:h5tget-member-offset
binspec-datatype 4)
buffer-index))
:double)))
(push (list :name name
:nbins nbins
:low low
:high high)
binspecs)))
(setf binspecs
(nreverse binspecs))
(setf hist
(if (eq type :sparse)
(make-sparse-hist binspecs)
(make-contiguous-hist binspecs))))))
(let ((create-plist
(hdf5:h5dget-create-plist data-dataset)))
(hdf5:h5pget-chunk create-plist 1 data-chunk-dims))
(setf data-chunk-size
(mem-aref data-chunk-dims 'hdf5:hsize-t))
(hdf5:h5sget-simple-extent-dims data-dataspace
data-dataset-dims
(null-pointer))
(setf nrows
(mem-aref data-dataset-dims
'hdf5:hsize-t))
(let ((second-field-name
(h5tget-member-name-as-lisp-string data-datatype 1)))
(if (equal second-field-name
"count-error")
(progn
(setf n-count-vars 2)
(if (eq type :sparse)
(setf hist
(make-sparse-hist
binspecs
:empty-bin-value
(+- 0 0)
:default-increment (+- 1 1)))
(setf hist
(make-contiguous-hist
binspecs
:empty-bin-value
(+- 0 0)
:default-increment (+- 1 1)))))
(setf n-count-vars 1)))
(setf data-row-size
(hdf5:h5tget-size data-datatype))
(setf data-buffer-size
(* data-row-size
(mem-aref data-dataset-dims 'hdf5:hsize-t)))
(with-foreign-object (buffer :char data-buffer-size)
(setf (mem-aref memspace-dims 'hdf5:hsize-t)
(mem-aref data-dataset-dims 'hdf5:hsize-t))
(setf (mem-aref memspace-maxdims 'hdf5:hsize-t)
(mem-aref memspace-dims 'hdf5:hsize-t))
(with-foreign-objects ((start 'hdf5:hsize-t)
(stride 'hdf5:hsize-t)
(cnt 'hdf5:hsize-t)
(blck 'hdf5:hsize-t))
(setf (mem-aref start 'hdf5:hsize-t)
0)
(setf (mem-aref stride 'hdf5:hsize-t)
1)
(setf (mem-aref cnt 'hdf5:hsize-t)
1)
(setf (mem-aref blck 'hdf5:hsize-t)
(mem-aref memspace-dims 'hdf5:hsize-t))
(hdf5:h5sselect-hyperslab data-dataspace
:H5S-SELECT-SET
start
stride
cnt
blck)
(setf memspace
(hdf5:h5screate-simple 1
memspace-dims
memspace-maxdims))
(hdf5:h5dread data-dataset
data-datatype
memspace
data-dataspace
hdf5:+H5P-DEFAULT+
buffer)
(loop
for i below (mem-aref memspace-dims 'hdf5:hsize-t)
do
(let* ((buffer-index
(* i data-row-size))
(count
(case n-count-vars
(1 (mem-aref
(mem-aptr buffer
:char
(+ buffer-index
(hdf5:h5tget-member-offset
data-datatype 0)))
:double))
(2 (+- (mem-aref
(mem-aptr
buffer
:char
(+ buffer-index
(hdf5:h5tget-member-offset data-datatype 0)))
:double)
(mem-aref
(mem-aptr
buffer
:char
(+ buffer-index
(hdf5:h5tget-member-offset data-datatype 1)))
:double)))))
(xs
(loop
for dim from 0 below ndims
collecting
(mem-aref (mem-aptr buffer
:char
(+ buffer-index
(hdf5:h5tget-member-offset
data-datatype
(+ n-count-vars dim))))
:double))))
(hins hist
xs
count))))))
hist)))
;;;; This version will work again (with possible modification to
;;;; function arguments) once the hdf-table library supports arbitrary
;;;; compound type structures and not just those produced by the C
;;;; compiler.
(defun old-read-histogram (file hdf-path &optional (type :sparse))
"Reads a histogram from an hdf-table with file and path.
type can be either :contiguous or :sparse for contiguous-histogram and
sparse-histogram respectively."
(flet ((subpath (path)
(concatenate 'string
hdf-path
"/"
path)))
(let* ((bin-spec-table
(open-hdf-table file
(subpath *histogram-bin-spec-path*)))
(bin-spec-table-field-names
(list "name" "name-length" "low" "high" "nbins"))
(hist-dim-specs
(let ((result ()))
(table-reduce bin-spec-table
bin-spec-table-field-names
(lambda (state name name-length low high nbins)
(push (list :name (char-vector->string name name-length)
:low low
:high high
:nbins nbins)
result)))
(nreverse result)))
(histogram
(cond
((equal type :contiguous)
(make-contiguous-hist hist-dim-specs))
((equal type :sparse)
(make-sparse-hist hist-dim-specs))
(t (error "Must specify :contiguous or :sparse for
type."))))
(data-table
(open-hdf-table file
(subpath *histogram-data-path*)))
(data-table-field-names
(table-field-names data-table)))
(if (equal (second data-table-field-names)
"count-error")
(table-reduce data-table
data-table-field-names
(lambda (state count count-error &rest xs)
(hist-insert histogram xs
(+- count count-error))))
(table-reduce data-table
data-table-field-names
(lambda (state count &rest xs)
(hist-insert histogram xs count))))
(table-close bin-spec-table)
(table-close data-table)
histogram)))
| 20,828 | Common Lisp | .lisp | 461 | 23.952278 | 88 | 0.41158 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | d79db6acce038a0cb1012da103ce41d095fa73ce0d9dcfd0dcb8f422c02bb3c0 | 1,445 | [
-1
] |
1,446 | hdf-table-chain.lisp | ghollisjr_cl-ana/hdf-table/hdf-table-chain.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.hdf-table)
(declaim (optimize (speed 2)
(safety 1)
(compilation-speed 0)
(debug 1)))
;;;; hdf-table-chain: A read-only chain of hdf-tables which can be
;;;; randomly accessed unlike the general table-chain.
(defclass hdf-table-chain (table)
((dataset-path
:initform ""
:initarg :dataset-path
:accessor hdf-table-chain-dataset-path
:documentation "Path to dataset within each file. The path should
be uniform if the hdf files truly are a chain.")
(active-table ; hdf-table in-memory
:initform ()
:accessor hdf-table-chain-active-table
:documentation "The in-memory hdf-table")
(active-file ; hdf-file currently opened
:initform nil
:accessor hdf-table-chain-active-file
:documentation "hdf-file currently opened by the active hdf-table.")
(file-paths
:initform ()
:initarg :file-paths
:accessor hdf-table-chain-file-paths
:documentation "List of file-paths which contain one hdf-table
each")
(table-lengths
:initform ()
:initarg :table-lengths
:accessor hdf-table-chain-table-lengths
:documentation "Length (in indices) of each table")
(table-index-offsets
:initform ()
:initarg :index-offsets
:accessor hdf-table-chain-table-index-offsets
:documentation "Start indexes for each table")
(current-table-index
:initform -1
:accessor hdf-table-chain-current-table-index
:type integer
:documentation "index for in-memory hdf-table in (virtual) list of tables")
(current-table-start
:initform -1
:accessor hdf-table-chain-current-table-start
:type integer
:documentation "starting row index for the current table")
(current-table-end
:initform -1
:accessor hdf-table-chain-current-table-end
:type integer
:documentation "last row index for the current table")
(table-index-binary-tree
:initform ()
:initarg :binary-tree
:accessor hdf-table-chain-binary-tree
:documentation "binary search tree storing the indeces for
efficient searching")
(read-row-index
:initarg :read-row-index
:initform -1
:accessor hdf-table-chain-read-row-index
:documentation "Index to row which should be sequentually read
next")
(nrows
:initarg :nrows
:initform nil
:accessor hdf-table-chain-nrows
:documentation "number of rows in hdf-table")))
;; table-nrows method:
(defmethod table-nrows ((table hdf-table-chain))
(hdf-table-chain-nrows table))
;; initialization:
;; For each path, read the dataset and get the number of entries in
;; each. Use this to create the offset list. Use the offset list to
;; create the hdf-table-chain-binary-tree. Use this to create
(defun open-hdf-table-chain (filename-list dataset-path)
"Creates and initializes hdf-table-chain given the filename-list and
dataset-path"
(labels
((get-nrows (filename dset-path)
(with-open-hdf-file (file
filename
:direction :input)
(let* ((dataset (hdf5:h5dopen2 file dset-path hdf5:+H5P-DEFAULT+))
(dataspace (hdf5:h5dget-space dataset))
(result
(with-foreign-objects ((space-dim 'hsize-t 1)
(space-max-dim 'hsize-t 1))
(hdf5:h5sget-simple-extent-dims
dataspace
space-dim
space-max-dim)
(mem-aref space-dim 'hsize-t 0))))
(hdf5:h5sclose dataspace)
(hdf5:h5dclose dataset)
result)))
(get-field-names (filename dataset-path)
(with-open-hdf-file (hdf-file
filename
:direction :input)
(let* ((hdf-table
(open-hdf-table hdf-file dataset-path))
(result (table-field-names hdf-table)))
(table-close hdf-table)
result)))
(get-field-specs (filename dataset-path)
(with-open-hdf-file (hdf-file
filename
:direction :input)
(let* ((hdf-table
(open-hdf-table hdf-file dataset-path))
(result (table-field-specs hdf-table)))
(table-close hdf-table)
result))))
(let* ((file-nrows (mapcar
(lambda (filename)
(get-nrows filename dataset-path))
filename-list))
(offsets (make-offsets file-nrows))
(index-binary-tree
(make-index-binary-tree offsets))
(table
(make-instance 'hdf-table-chain
:field-names (get-field-names
(first filename-list)
dataset-path)
;; :field-specs (get-field-specs
;; (first filename-list)
;; dataset-path)
:dataset-path dataset-path
:file-paths filename-list
:index-offsets offsets
:table-lengths file-nrows
:binary-tree index-binary-tree
:nrows (reduce #'+ file-nrows))))
(let* ((current-table (hdf-table-chain-active-table table))
(table-index 0)
(filename (elt (hdf-table-chain-file-paths table)
table-index))
(dataset-path (hdf-table-chain-dataset-path table)))
(setf (hdf-table-chain-active-file table)
(open-hdf-file filename :direction :input))
(setf (hdf-table-chain-active-table table)
(open-hdf-table (hdf-table-chain-active-file table)
dataset-path))
(setf (hdf-table-chain-current-table-start table)
(elt (hdf-table-chain-table-index-offsets table)
table-index))
(setf (hdf-table-chain-current-table-end table)
(+ (the integer
(elt (hdf-table-chain-table-lengths table)
table-index))
(hdf-table-chain-current-table-start table)
-1))
table))))
;; finalization:
(defmethod table-close ((table-chain hdf-table-chain))
"Closes the active hdf-table & file"
(with-accessors ((active-table hdf-table-chain-active-table)
(active-file hdf-table-chain-active-file))
table-chain
(table-close active-table)
(close-hdf-file active-file)))
;; table-get-field:
;; Procedure is to first check if index is within bounds. If so,
;; create table-index from raw index and call table-get-field on
;; the active table. If not, get table index from the raw index, get
;; the file path using this index, and read the appropriate table into
;; memory using open-hdf-table with the file path and dataset
;; path. Then store the appropriate current-table-start/end and
;; change the table index to match the new in-memory table. This
;; should be done before the call to table-get-field on the
;; active table.
(defmethod table-get-field ((table hdf-table-chain) field-symbol)
(with-accessors ((active-table hdf-table-chain-active-table))
table
(table-get-field active-table field-symbol)))
(defmethod table-load-next-row ((table hdf-table-chain))
(with-accessors ((row-number hdf-table-chain-read-row-index)
(nrows hdf-table-chain-nrows))
table
(incf row-number)
(when (< row-number nrows)
(let* ((current-table-start (hdf-table-chain-current-table-start
table))
(current-table-end (hdf-table-chain-current-table-end
table)))
(declare (integer current-table-start current-table-end))
(if (<= current-table-start
row-number
current-table-end)
(table-load-next-row (hdf-table-chain-active-table
table))
(let* ((current-table (hdf-table-chain-active-table table))
(table-index (get-tree-index
(hdf-table-chain-binary-tree table)
row-number))
(filename (elt (hdf-table-chain-file-paths table)
table-index))
(dataset-path (hdf-table-chain-dataset-path table)))
;; free resources from previous table:
(when current-table
(table-close current-table)
(close-hdf-file (hdf-table-chain-active-file table)))
;; establish next table:
(setf (hdf-table-chain-active-file table)
(open-hdf-file filename :direction :input))
(setf (hdf-table-chain-active-table table)
(open-hdf-table (hdf-table-chain-active-file table)
dataset-path))
(setf (hdf-table-chain-current-table-start table)
(elt (hdf-table-chain-table-index-offsets table)
table-index))
(setf (hdf-table-chain-current-table-end table)
(+ (the integer
(elt (hdf-table-chain-table-lengths table)
table-index))
(hdf-table-chain-current-table-start table)
-1))
(table-load-next-row
(hdf-table-chain-active-table table))))))))
(defmethod table-field-specs ((table hdf-table-chain))
(with-slots (active-table)
table
(table-field-specs active-table)))
;;; Behind the scenes functions:
(defun make-index-binary-tree (offsets)
(let ((offsets-copy (copy-list offsets)))
(make-balanced-tree
(zip (sort offsets-copy #'<)
(range 0 (1- (length offsets-copy))))
:test #'equal
:sorted t
:key #'car)))
;; if this returns nil, the table index is 0
(defun get-tree-index (binary-tree row-index)
(declare (integer row-index))
(labels
((get-tree-index-worker (binary-tree row-index lastright)
(declare (integer row-index))
(if binary-tree
(let* ((node-value (node-value binary-tree))
(node-start-index (car node-value)))
(declare (integer node-start-index))
(cond
((< row-index node-start-index)
(get-tree-index-worker
(node-left-child binary-tree)
row-index
lastright))
((= row-index node-start-index)
(cdr node-value))
(t
(get-tree-index-worker
(node-right-child binary-tree)
row-index
(cdr node-value)))))
(if lastright
lastright
0))))
(get-tree-index-worker binary-tree
row-index
nil)))
| 11,799 | Common Lisp | .lisp | 285 | 31.175439 | 79 | 0.593617 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 9cf3f694c08d6efaddc8b91f9a156c92f8af7d1de495867eb4a993b614d1b470 | 1,446 | [
-1
] |
1,447 | package.lisp | ghollisjr_cl-ana/hdf-table/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.hdf-table
(:use #:cl
#:cffi
#:alexandria
#:hdf5
#:cl-ana.list-utils
#:cl-ana.hdf-utils
#:cl-ana.table
#:cl-ana.typed-table
#:cl-ana.typespec
#:cl-ana.hdf-typespec
#:cl-ana.string-utils
#:cl-ana.functional-utils
#:cl-ana.binary-tree
#:cl-ana.memoization)
(:export :hdf-table
:hdf-table-nrows
:open-hdf-table
:create-hdf-table
:hdf-table-chain
:hdf-table-chain-nrows
:open-hdf-table-chain))
| 1,374 | Common Lisp | .lisp | 42 | 29.428571 | 70 | 0.676183 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | b5af1a8f247b61349219305c70904c2b66f0ada8faedc7ffde8ede39552d2eb6 | 1,447 | [
-1
] |
1,448 | hdf-table.lisp | ghollisjr_cl-ana/hdf-table/hdf-table.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.hdf-table)
;;; NOTE: HDF5 types are left open forever. I tried to implement a
;;; system of closing types and re-opening them on a table-by-table
;;; basis, but it turned out to be a complete hassle, so I'm leaving
;;; them open forever once opened at the moment. In the future this
;;; could be revisited. It poses only minimal memory overhead since
;;; I've memoized the typespec functions so that only one HDF5 type is
;;; used per typespec. I believe the HDF5 type closing mechanism is
;;; for safety in situations where it isn't so easy to memoize
;;; functions.
(declaim (optimize (speed 2)
(safety 1)
(compilation-speed 0)
(debug 1)))
(defclass hdf-table (typed-table)
((row-buffer-size
:initarg :buffer-size
:initform nil
:accessor hdf-table-buffer-size
:documentation "buffer size in number of rows")
(chunk-index
:initarg :chunk-index
:initform -1
:accessor hdf-table-chunk-index
:documentation "index to the in-memory chunk")
(row-buffer
:initarg :row-buffer
:initform nil
:accessor hdf-table-row-buffer
:documentation "Object for storing a row to be read from/written
to hdf table. It's stored as part of the table for efficiency
purposes and should not be handled directly by the user; use the
awesome higher level tools for that.")
(row-buffer-index
:initarg :row-buffer-index
:initform nil
:accessor hdf-table-row-buffer-index
:documentation "Index to the row in the buffer which is currently
being modified prior to writing.")
(hdf-dataset
:initarg :hdf-dataset
:initform nil
:accessor hdf-table-dataset
:documentation "hdf dataset which the table is reading from/writing
to.")
(hdf-row-type
:initarg :hdf-row-type
:initform nil
:accessor hdf-table-row-type
:documentation "hdf type for the row data object")
(read-row-index
:initarg :read-row-index
:initform -1
:accessor hdf-table-read-row-index
:documentation "Index to row which should be sequentually read
next")
(nrows
:initarg :nrows
:initform nil
:accessor hdf-table-nrows
:documentation "number of rows in hdf-table")))
;; table-nrows method:
(defmethod table-nrows ((table hdf-table))
(hdf-table-nrows table))
;; define high-level table access from files here
(defun open-hdf-table (hdf-file dataset-name &key buffer-size)
(labels ((get-dataset-length (dataset)
(with-open-dataspace (dataspace dataset)
(let ((rank (hdf5:h5sget-simple-extent-ndims dataspace)))
(with-foreign-objects ((dims 'hsize-t rank)
(maxdims 'hsize-t rank))
(hdf5:h5sget-simple-extent-dims dataspace dims maxdims)
(mem-aref dims 'hsize-t 0))))))
(let* ((dataset (hdf5:h5dopen2 hdf-file dataset-name hdf5:+H5P-DEFAULT+))
(typespec (dataset-read-typespec dataset))
(cstruct (typespec->cffi-type typespec))
(hdf-row-type (hdf5:h5dget-type dataset))
(buffer-size
(if (null buffer-size)
;; get buffer-size from the dataset
;; chunk-size:
;; this needs cleaning up
(let* ((create-plist (hdf5:h5dget-create-plist dataset)))
(with-foreign-object (chunkdims 'hsize-t 1)
;; this needs cleaning up
(hdf5:h5pget-chunk create-plist
1
chunkdims)
(mem-aref chunkdims 'hsize-t 0)))
buffer-size))
(row-buffer
(typespec-foreign-alloc typespec buffer-size)))
(make-instance 'hdf-table
:field-names (typespec->field-names typespec)
:field-specs (typespec->field-specs typespec)
:row-buffer row-buffer
:row-pointer
(mem-aptr row-buffer
cstruct
0)
:hdf-dataset dataset
:hdf-row-type hdf-row-type
:row-cstruct cstruct
:buffer-size buffer-size
:access-mode :read
:nrows
(get-dataset-length dataset)))))
(defun create-hdf-table
(hdf-file dataset-path names-specs &key (buffer-size 1000))
"Creates a hdf-table for writing in hdf-file with dataset-path as
the path to the dataset in the hdf-file and the alist names-specs
which maps the field names to their typespecs (this is just
applying rest to the typespec for the table). Buffer size will be
used as both the chunksize for the hdf dataset and as the size of
the buffer for writing into the file."
(let* ((typespec (cons :compound names-specs))
(cstruct (typespec->cffi-type typespec))
(row-buffer ;; (foreign-alloc cstruct
;; :count
;; buffer-size)
(typespec-foreign-alloc typespec buffer-size))
(hdf-type (typespec->hdf-type typespec))
(dataset
(progn
(let (cparms)
(with-foreign-objects
((chunkdims 'hsize-t 1)
(dims 'hsize-t 1)
(maxdims 'hsize-t 1))
(setf cparms (hdf5:h5pcreate hdf5:+H5P-DATASET-CREATE+))
(setf (mem-aref chunkdims 'hsize-t 0) buffer-size)
(setf (mem-aref dims 'hsize-t 0) 0)
(setf (mem-aref maxdims 'hsize-t 0) hdf5:+H5S-UNLIMITED+)
(hdf5:h5pset-chunk cparms 1 chunkdims)
;; this needs cleaning up
(with-create-dataspace (dataspace 1 dims maxdims)
(hdf5:h5dcreate1 hdf-file
dataset-path
hdf-type
dataspace
cparms)))))))
(make-instance 'hdf-table
:row-cstruct cstruct
:row-pointer
(mem-aptr row-buffer
cstruct
0)
:field-names (mapcar #'car names-specs)
:field-specs
(mapcar #'cdr names-specs)
:row-buffer row-buffer
:buffer-size buffer-size
:chunk-index 0
:row-buffer-index 0
:hdf-row-type hdf-type
:hdf-dataset dataset
:access-mode :write)))
(defmethod table-close ((table hdf-table))
"Cleanup function only to be called on an hdf-table for writing.
Writes the last remaining data in the buffer to the file and closes
the dataset."
(with-accessors ((dataset hdf-table-dataset)
(row-buffer-index hdf-table-row-buffer-index)
(hdf-type hdf-table-row-type)
(fields-specs table-field-specs)
(chunk-index hdf-table-chunk-index)
(row-buffer hdf-table-row-buffer)
(buffer-size hdf-table-buffer-size)
(cstruct typed-table-row-cstruct)
(access-mode table-access-mode))
table
(when (equal access-mode :write)
(when (not (zerop row-buffer-index))
(with-foreign-objects ((start 'hsize-t 1)
(stride 'hsize-t 1)
(count 'hsize-t 1)
(blck 'hsize-t 1)
(dataspace-dims 'hsize-t 1)
(dataspace-maxdims 'hsize-t 1)
(memdims 'hsize-t 1)
(memmaxdims 'hsize-t 1))
(setf (mem-aref start 'hsize-t 0)
(* buffer-size chunk-index))
(setf (mem-aref stride 'hsize-t 0) 1)
(setf (mem-aref count 'hsize-t 0) 1)
(setf (mem-aref blck 'hsize-t 0) row-buffer-index)
(with-open-dataspace (dataspace dataset)
(hdf5:h5sget-simple-extent-dims
dataspace dataspace-dims dataspace-maxdims)
(incf (mem-aref dataspace-dims 'hsize-t 0)
row-buffer-index)
(hdf5:h5dset-extent dataset dataspace-dims))
(with-open-dataspace (dataspace dataset)
(setf (mem-aref memdims 'hsize-t 0) row-buffer-index)
(setf (mem-aref memmaxdims 'hsize-t 0) row-buffer-index)
(with-create-dataspace (memspace 1 memdims memmaxdims)
(hdf5:h5sselect-hyperslab
dataspace :H5S-SELECT-SET start stride count blck)
(hdf5:h5dwrite
dataset hdf-type memspace
dataspace hdf5:+H5P-DEFAULT+ row-buffer))))))
;; no type closing for now, it's a complete headache and is
;; causing problems with memoization etc.
;; (let ((typespec (cons :compound fields-specs)))
;; (print 'typespec->hdf-type)
;; (print (typespec->hdf-type :int))
;; (remhash (list typespec) (get-memo-map #'typespec->hdf-type)))
;; (print 'hdf-type->typespec)
;; (remhash (list hdf-type) (get-memo-map #'hdf-type->typespec))
(foreign-free row-buffer)))
(defmethod table-commit-row ((table hdf-table))
(with-accessors ((row-buffer hdf-table-row-buffer)
(row-pointer typed-table-row-pointer)
(row-buffer-index hdf-table-row-buffer-index)
(buffer-size hdf-table-buffer-size)
(chunk-index hdf-table-chunk-index)
(cstruct typed-table-row-cstruct)
(dataset hdf-table-dataset)
(hdf-type hdf-table-row-type))
table
(incf row-buffer-index)
(setf row-pointer
(mem-aptr row-buffer
cstruct
(mod row-buffer-index buffer-size)))
(when (zerop (mod row-buffer-index buffer-size)) ;; was rem
(with-foreign-objects ((start 'hsize-t 1)
(stride 'hsize-t 1)
(count 'hsize-t 1)
(blck 'hsize-t 1)
(dataspace-dims 'hsize-t 1)
(dataspace-maxdims 'hsize-t 1)
(memdims 'hsize-t 1)
(memmaxdims 'hsize-t 1))
(with-open-dataspace (dataspace dataset)
(hdf5:h5sget-simple-extent-dims
dataspace dataspace-dims dataspace-maxdims)
(incf (mem-aref dataspace-dims 'hsize-t 0) buffer-size)
(hdf5:h5dset-extent dataset dataspace-dims))
(with-open-dataspace (dataspace dataset)
(setf (mem-aref start 'hsize-t 0)
(* buffer-size chunk-index))
(setf (mem-aref stride 'hsize-t 0) 1)
(setf (mem-aref count 'hsize-t 0) 1)
(setf (mem-aref blck 'hsize-t 0) buffer-size)
(setf (mem-aref memdims 'hsize-t 0) buffer-size)
(setf (mem-aref memmaxdims 'hsize-t 0) buffer-size)
(with-create-dataspace (memspace 1 memdims memmaxdims)
(hdf5:h5sselect-hyperslab dataspace
:H5S-SELECT-SET
start stride count blck)
(hdf5:h5dwrite dataset hdf-type
memspace dataspace
hdf5:+H5P-DEFAULT+ row-buffer))))
(incf chunk-index)
(setf row-buffer-index 0))))
(defun table->cstruct (table)
"Function which, given an hdf-table, defines a cffi cstruct for use
in reading/writing from the hdf file."
(typespec->cffi-type (typed-table->typespec table)))
(defun table->hdf-type (table)
(typespec->hdf-type (typed-table->typespec table)))
(defun dataset-read-typespec (dataset)
"Reads the typespec from the dataset"
;; this needs cleaning up
(with-dataset-type (type dataset)
(hdf-type->typespec type)))
;; use foreign-slot-value to get the value of a slot
;; use foreign-alloc to create a foreign object; should use
;; foreign-free once the object is not needed
;; assumes:
;;
;; * The cstruct row object has already been created
;;
;; * The dataset has already been opened and its parameters set
;;
;; * The memory dataspace has already been created and its parameters set
;;
;; * The row object hdf type has been created
(defmethod table-load-next-row ((table hdf-table))
(with-accessors ((row-number hdf-table-read-row-index)
(row-buffer hdf-table-row-buffer)
(row-pointer typed-table-row-pointer)
(buffer-size hdf-table-buffer-size)
(cstruct typed-table-row-cstruct))
table
;;(print row-number)
(incf row-number)
(setf row-pointer
(mem-aptr row-buffer
cstruct
(mod row-number buffer-size)))
(load-chunk table row-number)))
(defun load-chunk (table row-number)
(labels ((get-chunk-index (row-index buffer-size)
(declare (fixnum buffer-size row-index))
(the fixnum
(floor row-index buffer-size))))
(with-accessors ((buffer-size hdf-table-buffer-size)
(current-chunk-index hdf-table-chunk-index)
(row-buffer hdf-table-row-buffer)
(cstruct typed-table-row-cstruct)
(nrows hdf-table-nrows))
table
(let ((chunk-index (get-chunk-index row-number buffer-size)))
(if (< row-number nrows)
(progn
(when (not (= current-chunk-index chunk-index))
;; read data from file:
(with-accessors ((row-hdf-type hdf-table-row-type)
(dataset hdf-table-dataset)
(table-length hdf-table-nrows))
table
(let ((chunk-size (min (- table-length
(* chunk-index
buffer-size))
buffer-size)))
(with-foreign-objects ((start 'hsize-t 1)
(stride 'hsize-t 1)
(count 'hsize-t 1)
(blck 'hsize-t 1)
(memdims 'hsize-t 1)
(memmaxdims 'hsize-t 1))
(setf (mem-aref start 'hsize-t 0)
(* chunk-index buffer-size))
(setf (mem-aref stride 'hsize-t 0) 1)
(setf (mem-aref count 'hsize-t 0) 1)
(setf (mem-aref blck 'hsize-t 0) chunk-size)
(setf (mem-aref memdims 'hsize-t 0) chunk-size)
(setf (mem-aref memmaxdims 'hsize-t 0) chunk-size)
(with-open-dataspace (dataspace dataset)
(hdf5:h5sselect-hyperslab dataspace
:H5S-SELECT-SET
start
stride
count
blck)
(with-create-dataspace
(memspace 1 memdims memmaxdims)
(hdf5:h5dread dataset
row-hdf-type
memspace
dataspace
hdf5:+H5P-DEFAULT+
row-buffer))
(setf (hdf-table-row-buffer table) row-buffer)
(setf (hdf-table-chunk-index table) chunk-index))))))
t)
nil)))))
| 16,492 | Common Lisp | .lisp | 369 | 32.00542 | 77 | 0.560758 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 81a74572c5943f4b829900785347bafbdde753afec009bc8cb80584b56638e79 | 1,448 | [
-1
] |
1,450 | test.lisp | ghollisjr_cl-ana/hdf-table/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana.hdf-table)
(in-package :cl-ana.hdf-table)
(defun hdf-type-test ()
(hdf-type->typespec
(typespec->hdf-type
'(:compound
("x" . :double)
("y" . :int)
("xs" . (:array :double 5))
("ys" . (:compound
("t" . :int)))))))
(defun hdf-type-test2 ()
(hdf-type->typespec
(typespec->hdf-type
'(:compound
("x" . :double)
("y" . :int)
("xs" . (:compound
("fs" . (:array :double 5))))
("ys" . (:compound
("t" . :int)))))))
(defvar *table* nil)
(defvar *hdf-typespec*)
(defvar *table-typespec*)
(defvar *hdf-size*)
(defvar *cstruct-size*)
(defvar *hdf-file*)
(defun hdf-read-data-test ()
(with-open-hdf-file (file "/home/ghollisjr/phys/research/phd/ana/hdffile.h5"
:direction :input)
(setf *table* (open-hdf-table file "/h10"))
(setf *hdf-file* file)
(let ((result 0)
(last-row-index 0))
(setf *table-typespec* (typed-table->typespec *table*))
(setf *hdf-size* (hdf5:h5tget-size (hdf-table-row-type *table*)))
(setf *hdf-typespec* (hdf-type->typespec (hdf-table-row-type *table*)))
(setf *cstruct-size* (foreign-type-size (typed-table-row-cstruct *table*)))
(do-table (row-index *table*)
("gpart")
(incf result gpart)
(setf last-row-index row-index))
(format t "last-row-index: ~a~%" last-row-index)
result)))
(defun hdf-write-table-test ()
(with-open-hdf-file (file
"/home/ghollisjr/hdfwork/test.h5"
:direction :output
:if-exists :supersede)
(let* ((table
(create-hdf-table file
"/test"
(list (cons "x" :int)
(cons "y" :float)))))
;;(print (typed-table-type-map table))
(dotimes (i 1000000)
(table-set-field table :|x| i)
(table-set-field table :|y| (sqrt i))
(table-commit-row table))
(table-close table))))
(defun hdf-read-test ()
(when *table*
(table-close *table*))
(setf *table* (open-hdf-table-chain (list "/home/ghollisjr/hdfwork/test.h5") "/test"))
(let ((sum 0))
(do-table (row-index *table*)
("x" "y")
(incf sum |x|)
(incf sum |y|))
(print sum)))
(defun hdf-table-test ()
(with-open-hdf-file (outfile "/home/ghollisjr/hdfwork/outfile.h5"
:direction :output
:if-exists :supersede)
(let ((output-table (create-hdf-table outfile "/output-dataset"
(zip (list "x" "y")
(list :int :float))))
(input-table
(open-hdf-table-chain (list "/home/ghollisjr/hdfwork/test.h5") "/test")))
;;(open-hdf-table infile "/test")))
(do-table (row-index input-table)
("x" "y")
;; (format t "~a ~a; ~a ~a~%"
;; row-index (sqrt row-index)
;; x y)
(when (> row-index (hdf-table-chain-nrows input-table))
(when (zerop (mod row-index 1000))
(print row-index)))
(when (<= 25 y 30)
(table-push-fields output-table
x
y)))
(table-close output-table)
(table-close input-table))))
(defun hdf-typed-table-test ()
(with-open-hdf-file (outfile "/home/ghollisjr/hdfwork/outfile.h5"
:direction :output
:if-exists :supersede)
(let ((output-table (create-hdf-table outfile "/output-dataset"
(zip (list "x" "y")
(list :int :float))))
(input-table
(open-hdf-table-chain (list "/home/ghollisjr/hdfwork/test.h5") "/test")))
(do-table (row-index input-table)
("x" "y")
(when (<= 25 y 30)
(table-set-field output-table :x x)
(table-set-field output-table :y y)
(table-commit-row output-table)))
(table-close output-table)
(table-close input-table))))
(defun array-test ()
(with-open-hdf-file (outfile "/home/ghollisjr/hdfwork/array.h5"
:direction :output
:if-exists :supersede
:if-does-not-exist :create)
(let* ((table
(create-hdf-table
outfile "/array"
(list (cons "x"
(list :array :float 4))))))
(loop
for i below 30
do (progn
(table-push-fields table
(x
(vector (float i 0f0) (sqrt (float i 0f0)) (float i 0f0)
(sqrt (float i)))))))
(table-close table))))
| 5,396 | Common Lisp | .lisp | 149 | 28.563758 | 88 | 0.563289 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 0eb19975cbbeb541be5f2004b523ffd181abe0391c5f55776f8762600ed9a7cf | 1,450 | [
-1
] |
1,451 | raw-hdf-table.lisp | ghollisjr_cl-ana/hdf-table/raw-hdf-table.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013-2015 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.hdf-table)
;;; NOTE: HDF5 types are left open forever. I tried to implement a
;;; system of closing types and re-opening them on a table-by-table
;;; basis, but it turned out to be a complete hassle, so I'm leaving
;;; them open forever once opened at the moment. In the future this
;;; could be revisited. It poses only minimal memory overhead since
;;; I've memoized the typespec functions so that only one HDF5 type is
;;; used per typespec. I believe the HDF5 type closing mechanism is
;;; for safety in situations where it isn't so easy to memoize
;;; functions.
(declaim (optimize (speed 2)
(safety 1)
(compilation-speed 0)
(debug 1)))
(defclass hdf-table (typed-table)
((row-buffer-size
:initarg :buffer-size
:initform nil
:accessor hdf-table-buffer-size
:documentation "buffer size in number of rows")
(chunk-index
:initarg :chunk-index
:initform -1
:accessor hdf-table-chunk-index
:documentation "index to the in-memory chunk")
(row-buffer
:initarg :row-buffer
:initform nil
:accessor hdf-table-row-buffer
:documentation "Object for storing a row to be read from/written
to hdf table. It's stored as part of the table for efficiency
purposes and should not be handled directly by the user; use the
awesome higher level tools for that.")
(row-buffer-index
:initarg :row-buffer-index
:initform nil
:accessor hdf-table-row-buffer-index
:documentation "Index to the row in the buffer which is currently
being modified prior to writing.")
(hdf-dataset
:initarg :hdf-dataset
:initform nil
:accessor hdf-table-dataset
:documentation "hdf dataset which the table is reading from/writing
to.")
(hdf-row-type
:initarg :hdf-row-type
:initform nil
:accessor hdf-table-row-type
:documentation "hdf type for the row data object")
(read-row-index
:initarg :read-row-index
:initform -1
:accessor hdf-table-read-row-index
:documentation "Index to row which should be sequentually read
next")
(nrows
:initarg :nrows
:initform nil
:accessor hdf-table-nrows
:documentation "number of rows in hdf-table")))
;; table-nrows method:
(defmethod table-nrows ((table hdf-table))
(hdf-table-nrows table))
;; define high-level table access from files here
(defun open-hdf-table (hdf-file dataset-name &key buffer-size)
(labels ((get-dataset-length (dataset)
(with-open-dataspace (dataspace dataset)
(let ((rank (hdf5:h5sget-simple-extent-ndims dataspace)))
(with-foreign-objects ((dims 'hsize-t rank)
(maxdims 'hsize-t rank))
(hdf5:h5sget-simple-extent-dims dataspace dims maxdims)
(mem-aref dims 'hsize-t 0))))))
(with-foreign-string (cdataset-name dataset-name)
(let* ((dataset (hdf5:h5dopen2 hdf-file cdataset-name hdf5:+H5P-DEFAULT+))
(typespec (dataset-read-typespec dataset))
(cstruct (typespec->cffi-type typespec))
(hdf-row-type (hdf5:h5dget-type dataset))
(buffer-size
(if (null buffer-size)
;; get buffer-size from the dataset
;; chunk-size:
;; this needs cleaning up
(let* ((create-plist (hdf5:h5dget-create-plist dataset)))
(with-foreign-object (chunkdims 'hsize-t 1)
;; this needs cleaning up
(hdf5:h5pget-chunk create-plist
1
chunkdims)
(mem-aref chunkdims 'hsize-t 0)))
buffer-size))
(row-buffer
(typespec-foreign-alloc typespec buffer-size)))
(make-instance 'hdf-table
:field-names (typespec->field-names typespec)
:field-specs (typespec->field-specs typespec)
:row-buffer row-buffer
:row-pointer
(mem-aptr row-buffer
cstruct
0)
:hdf-dataset dataset
:hdf-row-type hdf-row-type
:row-cstruct cstruct
:buffer-size buffer-size
:access-mode :read
:nrows (get-dataset-length dataset))))))
(defun create-hdf-table
(hdf-file dataset-path names-specs &key (buffer-size 1000))
"Creates a hdf-table for writing in hdf-file with dataset-path as
the path to the dataset in the hdf-file and the alist names-specs
which maps the field names to their typespecs (this is just
applying rest to the typespec for the table). Buffer size will be
used as both the chunksize for the hdf dataset and as the size of
the buffer for writing into the file."
(let* ((typespec (cons :compound names-specs))
(cstruct (typespec->cffi-type typespec))
(row-buffer ;; (foreign-alloc cstruct
;; :count
;; buffer-size)
(typespec-foreign-alloc typespec buffer-size))
(hdf-type (typespec->hdf-type typespec))
(dataset
(progn
(let (cparms)
(with-foreign-objects
((chunkdims 'hsize-t 1)
(dims 'hsize-t 1)
(maxdims 'hsize-t 1))
(setf cparms (hdf5:h5pcreate hdf5:+H5P-DATASET-CREATE+))
(setf (mem-aref chunkdims 'hsize-t 0) buffer-size)
(setf (mem-aref dims 'hsize-t 0) 0)
(setf (mem-aref maxdims 'hsize-t 0) hdf5:+H5S-UNLIMITED+)
(hdf5:h5pset-chunk cparms 1 chunkdims)
;; this needs cleaning up
(with-create-dataspace (dataspace 1 dims maxdims)
(hdf5:h5dcreate1 hdf-file
dataset-path
hdf-type
dataspace
cparms)))))))
(make-instance 'hdf-table
:row-cstruct cstruct
:row-pointer
(mem-aptr row-buffer
cstruct
0)
:field-names (mapcar #'car names-specs)
:field-specs
(mapcar #'cdr names-specs)
:row-buffer row-buffer
:buffer-size buffer-size
:chunk-index 0
:row-buffer-index 0
:hdf-row-type hdf-type
:hdf-dataset dataset
:access-mode :write)))
(defmethod table-close ((table hdf-table))
"Cleanup function only to be called on an hdf-table for writing.
Writes the last remaining data in the buffer to the file and closes
the dataset."
(with-accessors ((dataset hdf-table-dataset)
(row-buffer-index hdf-table-row-buffer-index)
(hdf-type hdf-table-row-type)
(fields-specs table-field-specs)
(chunk-index hdf-table-chunk-index)
(row-buffer hdf-table-row-buffer)
(buffer-size hdf-table-buffer-size)
(cstruct typed-table-row-cstruct)
(access-mode table-access-mode))
table
(when (equal access-mode :write)
(when (not (zerop row-buffer-index))
(with-foreign-objects ((start 'hsize-t 1)
(stride 'hsize-t 1)
(count 'hsize-t 1)
(blck 'hsize-t 1)
(dataspace-dims 'hsize-t 1)
(dataspace-maxdims 'hsize-t 1)
(memdims 'hsize-t 1)
(memmaxdims 'hsize-t 1))
(setf (mem-aref start 'hsize-t 0)
(* buffer-size chunk-index))
(setf (mem-aref stride 'hsize-t 0) 1)
(setf (mem-aref count 'hsize-t 0) 1)
(setf (mem-aref blck 'hsize-t 0) row-buffer-index)
(with-open-dataspace (dataspace dataset)
(hdf5:h5sget-simple-extent-dims
dataspace dataspace-dims dataspace-maxdims)
(incf (mem-aref dataspace-dims 'hsize-t 0)
row-buffer-index)
(hdf5:h5dset-extent dataset dataspace-dims))
(with-open-dataspace (dataspace dataset)
(setf (mem-aref memdims 'hsize-t 0) row-buffer-index)
(setf (mem-aref memmaxdims 'hsize-t 0) row-buffer-index)
(with-create-dataspace (memspace 1 memdims memmaxdims)
(hdf5:h5sselect-hyperslab
dataspace :H5S-SELECT-SET start stride count blck)
(hdf5:h5dwrite
dataset hdf-type memspace
dataspace hdf5:+H5P-DEFAULT+ row-buffer))))))
;; no type closing for now, it's a complete headache and is
;; causing problems with memoization etc.
;;(hdf5:h5tclose hdf-type)
;; (let ((typespec (cons :compound fields-specs)))
;; (print 'typespec->hdf-type)
;; (print (typespec->hdf-type :int))
;; (remhash (list typespec) (get-memo-map #'typespec->hdf-type)))
;; (print 'hdf-type->typespec)
;; (remhash (list hdf-type) (get-memo-map #'hdf-type->typespec))
(hdf5:h5dclose dataset)
(foreign-free row-buffer)))
(defmethod table-commit-row ((table hdf-table))
(with-accessors ((row-buffer hdf-table-row-buffer)
(row-pointer typed-table-row-pointer)
(row-buffer-index hdf-table-row-buffer-index)
(buffer-size hdf-table-buffer-size)
(chunk-index hdf-table-chunk-index)
(cstruct typed-table-row-cstruct)
(dataset hdf-table-dataset)
(hdf-type hdf-table-row-type))
table
(incf row-buffer-index)
(setf row-pointer
(mem-aptr row-buffer
cstruct
(mod row-buffer-index buffer-size)))
(when (zerop (mod row-buffer-index buffer-size)) ;; was rem
(with-foreign-objects ((start 'hsize-t 1)
(stride 'hsize-t 1)
(count 'hsize-t 1)
(blck 'hsize-t 1)
(dataspace-dims 'hsize-t 1)
(dataspace-maxdims 'hsize-t 1)
(memdims 'hsize-t 1)
(memmaxdims 'hsize-t 1))
(with-open-dataspace (dataspace dataset)
(hdf5:h5sget-simple-extent-dims
dataspace dataspace-dims dataspace-maxdims)
(incf (mem-aref dataspace-dims 'hsize-t 0) buffer-size)
(hdf5:h5dset-extent dataset dataspace-dims))
(with-open-dataspace (dataspace dataset)
(setf (mem-aref start 'hsize-t 0)
(* buffer-size chunk-index))
(setf (mem-aref stride 'hsize-t 0) 1)
(setf (mem-aref count 'hsize-t 0) 1)
(setf (mem-aref blck 'hsize-t 0) buffer-size)
(setf (mem-aref memdims 'hsize-t 0) buffer-size)
(setf (mem-aref memmaxdims 'hsize-t 0) buffer-size)
(with-create-dataspace (memspace 1 memdims memmaxdims)
(hdf5:h5sselect-hyperslab dataspace
:H5S-SELECT-SET
start stride count blck)
(hdf5:h5dwrite dataset hdf-type
memspace dataspace
hdf5:+H5P-DEFAULT+ row-buffer))))
(incf chunk-index)
(setf row-buffer-index 0))))
(defun table->cstruct (table)
"Function which, given an hdf-table, defines a cffi cstruct for use
in reading/writing from the hdf file."
(typespec->cffi-type (typed-table->typespec table)))
(defun table->hdf-type (table)
(typespec->hdf-type (typed-table->typespec table)))
(defun dataset-read-typespec (dataset)
"Reads the typespec from the dataset"
;; this needs cleaning up
(with-dataset-type (type dataset)
(hdf-type->typespec type)))
;; use foreign-slot-value to get the value of a slot
;; use foreign-alloc to create a foreign object; should use
;; foreign-free once the object is not needed
;; assumes:
;;
;; * The cstruct row object has already been created
;;
;; * The dataset has already been opened and its parameters set
;;
;; * The memory dataspace has already been created and its parameters set
;;
;; * The row object hdf type has been created
(defmethod table-load-next-row ((table hdf-table))
(with-accessors ((row-number hdf-table-read-row-index)
(row-buffer hdf-table-row-buffer)
(row-pointer typed-table-row-pointer)
(buffer-size hdf-table-buffer-size)
(cstruct typed-table-row-cstruct))
table
;;(print row-number)
(incf row-number)
(setf row-pointer
(mem-aptr row-buffer
cstruct
(mod row-number buffer-size)))
(load-chunk table row-number)))
(defun load-chunk (table row-number)
(labels ((get-chunk-index (row-index buffer-size)
(declare (fixnum buffer-size row-index))
(the fixnum
(floor row-index buffer-size))))
(with-accessors ((buffer-size hdf-table-buffer-size)
(current-chunk-index hdf-table-chunk-index)
(row-buffer hdf-table-row-buffer)
(cstruct typed-table-row-cstruct)
(nrows hdf-table-nrows))
table
(let ((chunk-index (get-chunk-index row-number buffer-size)))
(if (< row-number nrows)
(progn
(when (not (= current-chunk-index chunk-index))
;; read data from file:
(with-accessors ((row-hdf-type hdf-table-row-type)
(dataset hdf-table-dataset)
(table-length hdf-table-nrows))
table
(let ((chunk-size (min (- table-length
(* chunk-index
buffer-size))
buffer-size)))
(with-foreign-objects ((start 'hsize-t 1)
(stride 'hsize-t 1)
(count 'hsize-t 1)
(blck 'hsize-t 1)
(memdims 'hsize-t 1)
(memmaxdims 'hsize-t 1))
(setf (mem-aref start 'hsize-t 0)
(* chunk-index buffer-size))
(setf (mem-aref stride 'hsize-t 0) 1)
(setf (mem-aref count 'hsize-t 0) 1)
(setf (mem-aref blck 'hsize-t 0) chunk-size)
(setf (mem-aref memdims 'hsize-t 0) chunk-size)
(setf (mem-aref memmaxdims 'hsize-t 0) chunk-size)
(with-open-dataspace (dataspace dataset)
(hdf5:h5sselect-hyperslab dataspace
:H5S-SELECT-SET
start
stride
count
blck)
(with-create-dataspace
(memspace 1 memdims memmaxdims)
(hdf5:h5dread dataset
row-hdf-type
memspace
dataspace
hdf5:+H5P-DEFAULT+
row-buffer))
(setf (hdf-table-row-buffer table) row-buffer)
(setf (hdf-table-chunk-index table) chunk-index))))))
t)
nil)))))
| 16,265 | Common Lisp | .lisp | 371 | 32.102426 | 80 | 0.573786 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 3bbccb09cda585dafa738e2264a5ffaa7d5d472d13a4ab7f4bf208ea44a3a5d0 | 1,451 | [
-1
] |
1,452 | package.lisp | ghollisjr_cl-ana/typed-table/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.typed-table
(:use #:cl
#:cffi
#:alexandria
#:cl-ana.list-utils
#:cl-ana.string-utils
#:cl-ana.symbol-utils
#:cl-ana.table
#:cl-ana.typespec)
(:export :typed-table
:table-field-specs
:typed-table-row-cstruct
:typed-table-row-pointer
:typed-table-lisp->c-converter-map
:typed-table-c->lisp-converter-map
:typespec->field-names
:typespec->field-specs
:typed-table->typespec))
| 1,360 | Common Lisp | .lisp | 38 | 32.210526 | 70 | 0.679031 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | ae642b3d90514944aeddc8fe73170e552e1365f5dbec3e8d61bd74baea222349 | 1,452 | [
-1
] |
1,453 | typed-table.lisp | ghollisjr_cl-ana/typed-table/typed-table.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.typed-table)
(declaim (optimize (speed 3)
(safety 0)
(compilation-speed 0)
(debug 3)))
(defun gethash-keywordify (key hash-table)
(gethash (keywordify (string key)) hash-table))
(defun (setf gethash-keywordify) (value key hash-table)
(setf (gethash (keywordify (string key)) hash-table)
value))
(defclass typed-table (table)
((field-specs
:initarg :field-specs
:initform ()
;; renamed for intuitive-ness:
:accessor table-field-specs
:documentation "list of typespecs, one per field")
(row-cstruct
:initarg :row-cstruct
:initform nil
:accessor typed-table-row-cstruct
:documentation "CFFI cstruct type designator for the row object")
(row-pointer
:initarg :row-pointer
:initform nil
:accessor typed-table-row-pointer
:documentation "pointer to foreign object storing current row
information.")
(lisp->c-converter-map
:initarg :lisp->c-converter-map
:initform nil
:accessor typed-table-lisp->c-converter-map
:documentation "Hash table which maps the field symbols to the
lisp->c converter function for corresponding field.")
(c->lisp-converter-map
:initarg :c->lisp-converter-map
:initform nil
:accessor typed-table-c->lisp-converter-map
:documentation "Hash table which maps the field symbols to the
c->lisp converter function for corresponding field.")))
(defmethod initialize-instance :after ((table typed-table) &key)
(with-accessors ((field-specs table-field-specs)
(lisp->c-converter-map
typed-table-lisp->c-converter-map)
(c->lisp-converter-map
typed-table-c->lisp-converter-map))
table
(setf lisp->c-converter-map (make-hash-table :test 'eq))
(setf c->lisp-converter-map (make-hash-table :test 'eq))
(loop
for s in (table-field-symbols table)
for cs in field-specs
do
(progn
(setf (gethash s lisp->c-converter-map)
(typespec->lisp-to-c cs))
(setf (gethash s c->lisp-converter-map)
(typespec->c-to-lisp cs))))))
;;; These methods make it so that all you have to do is define methods
;;; on table-load-next-row and table-commit-row which properly set the
;;; row-pointer value to the current row (as well as allocating &
;;; freeing space as appropriate).
(defmethod table-set-field ((table typed-table) field-symbol value)
"Method on table-set-field that automatically converts the value
into the appropriate CFFI type for the field given by field-symbol.
Note that this function is still pedantic about which particular
numerical type you are giving it, e.g. float vs. integer. Use plists
to represent a structure (works for nested as well), and vectors to
represent foreign arrays."
(with-slots (lisp->c-converter-map
row-pointer
row-cstruct)
table
(funcall (gethash field-symbol lisp->c-converter-map)
value
(foreign-slot-pointer row-pointer
row-cstruct
field-symbol))))
(defmethod table-get-field ((table typed-table) field-symbol)
"Automatically converts field pointer to lisp value."
(with-accessors ((c->lisp-converter-map
typed-table-c->lisp-converter-map)
(row-pointer typed-table-row-pointer)
(row-cstruct typed-table-row-cstruct))
table
(funcall (gethash field-symbol c->lisp-converter-map)
(foreign-slot-pointer row-pointer
row-cstruct
field-symbol))))
(defun typespec->field-names (compound-typespec)
"Returns field names from the compound type designation."
(if (typespec-compound-p compound-typespec)
(mapcar #'car (rest compound-typespec))
(error "Non compound type given to typespec->field-names")))
(defun typespec->field-specs (compound-typespec)
"Returns field typespecs from the compound type designation."
(if (typespec-compound-p compound-typespec)
(mapcar #'cdr (rest compound-typespec))
(error "Non compound type given to typespec->field-specs")))
(defun typed-table->typespec (table)
"Creates a typespec from the table"
(append (list :compound)
(zip (table-field-names table)
(table-field-specs table))))
| 5,343 | Common Lisp | .lisp | 124 | 36.298387 | 70 | 0.669291 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 5e4172351e17779bc52462e719b07940e31fe4b3743596e627eab25f8bd29228 | 1,453 | [
-1
] |
1,454 | package.lisp | ghollisjr_cl-ana/columnar-table/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2019 Katherine Cox-Buday
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
(defpackage #:cl-ana.columnar-table
(:use :cl
:cl-ana.table
:cl-ana.reusable-table)
(:export :pivot
:columnar-table))
| 938 | Common Lisp | .lisp | 23 | 38.391304 | 70 | 0.701313 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 763ecc3e76fd9dfdbcecb4a6cecc6c818b4590f29e459ef6bc717bfa836a0a17 | 1,454 | [
-1
] |
1,455 | columnar-table.lisp | ghollisjr_cl-ana/columnar-table/columnar-table.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2019 Katherine Cox-Buday
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
(in-package :cl-ana.columnar-table)
(defun pivot (table create-table-fn open-table-fn)
"Pivot a table so that column values are accessible via rows.
CREATE-TABLE-FN should create the table of type, and open-table-fn
should open the same table again for reuse."
(check-type table reusable-table)
(check-type create-table-fn function)
(check-type open-table-fn function)
(let ((columnar-table (funcall create-table-fn
'("column-name" "my-values")))
(field-names (table-field-names table)))
(loop for field in (table-field-symbols table)
do (table-set-field columnar-table :|column-name| field)
(let ((col-vals (make-array 100 :adjustable t :fill-pointer 0)))
(do-table (rowidx table) ()
(vector-push-extend
(table-get-field table field)
col-vals
100))
(table-set-field columnar-table :|my-values|
(adjust-array col-vals (length col-vals))))
(table-commit-row columnar-table))
(table-close columnar-table)
(make-instance 'columnar-table
:field-names field-names
;; Fetching rows will involve scanning the
;; underlying table several times.
:backing-table (wrap-for-reuse
(funcall open-table-fn columnar-table)))))
(defclass columnar-table (table)
((backing-table
:initarg :backing-table
:initform (error ":backing-table not specified")
:accessor backing-table)
(row
:initarg :row
:initform nil
:accessor columnar-table-row)
(row-index
:initform 0
:accessor row-index)))
(defmethod table-get-field ((table columnar-table) field-symbol)
(with-accessors ((row columnar-table-row))
table
(getf row field-symbol)))
(defmethod table-load-next-row ((table columnar-table))
(with-accessors ((index row-index)
(backing-table backing-table)
(row columnar-table-row))
table
(incf index)
(let ((new-row (list)))
(do-table (rowidx backing-table) ()
(let* ((column-name (table-get-field backing-table :|column-name|))
(values-vector (table-get-field backing-table :|my-values|)))
(when (> index (length values-vector)) (return-from table-load-next-row nil))
(setf new-row (nconc new-row (list column-name (elt values-vector (- index 1)))))))
(setf row new-row))
row))
(defmethod field-values ((table columnar-table) field)
(with-accessors ((backing-table backing-table))
table
(do-table (row-index backing-table) ()
(when (equalp (table-get-field backing-table :|column-name|)
field)
(table-close backing-table)
(return-from field-values
(table-get-field backing-table :|my-values|)))))
(error "cannot find field ~a" field))
| 3,778 | Common Lisp | .lisp | 86 | 36.162791 | 93 | 0.636536 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | edab25081f7f5e9511aa1234895483bf0f6df2d2ae107484bae514574b0f77f0 | 1,455 | [
-1
] |
1,456 | package.lisp | ghollisjr_cl-ana/ntuple-table/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.ntuple-table
(:use :cl
:cffi
:cl-ana.table
:cl-ana.typed-table
:cl-ana.typespec)
(:export :open-ntuple-table
:create-ntuple-table))
| 1,046 | Common Lisp | .lisp | 28 | 35.464286 | 70 | 0.704031 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e0518aaf48058ec0b1cf2c259e5c9d7276d67ac0dca8f39917862e7369abf483 | 1,456 | [
-1
] |
1,457 | ntuple-table.lisp | ghollisjr_cl-ana/ntuple-table/ntuple-table.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.ntuple-table)
(defclass ntuple-table (typed-table)
((ntuple
:initarg :ntuple
:initform nil
:accessor ntuple-table-ntuple
:documentation "GSL handler for ntuple object")))
;;; Writing functions:
(defun create-ntuple-table (filename names-specs)
"Creates an ntuple-table with file located at the path corresponding
to filename and names-specs being an alist mapping the field names to
their typespecs."
(let* ((typespec (cons :compound names-specs))
(cstruct (typespec->cffi-type typespec))
(field-names (mapcar #'car names-specs))
(field-specs (mapcar #'cdr names-specs))
(row-pointer (typespec-foreign-alloc typespec)))
(let ((ntuple (gsll:create-ntuple filename row-pointer cstruct)))
(make-instance 'ntuple-table
:field-names field-names
:field-specs field-specs
:ntuple ntuple
:row-cstruct cstruct
:row-pointer row-pointer))))
;; (defmethod table-set-field ((table ntuple-table) field-symbol value)
;; (with-accessors ((row typed-table-row-pointer)
;; (cstruct ntuple-table-cstruct))
;; table
;; (setf
;; (foreign-slot-value row
;; cstruct
;; field-symbol)
;; value)))
(defmethod table-commit-row ((table ntuple-table))
(with-accessors ((row typed-table-row-pointer)
(ntuple ntuple-table-ntuple))
table
(gsll:write-ntuple ntuple)))
;;; Reading functions:
(defun open-ntuple-table (filename names-specs)
"Opens a pre-existing ntuple data file. Must already know the
typespecs of each of the field types (and names); this is a
limitation of the ntuple file format itself."
(let* ((typespec (cons :compound names-specs))
(cstruct (typespec->cffi-type typespec))
(field-names (mapcar #'car names-specs))
(field-specs (mapcar #'cdr names-specs))
(row (typespec-foreign-alloc typespec)))
(let ((ntuple (gsll:open-ntuple filename row cstruct)))
(make-instance 'ntuple-table
:field-names field-names
:field-specs field-specs
:ntuple ntuple
:row-cstruct cstruct
:row-pointer row))))
(defmethod table-load-next-row ((table ntuple-table))
(with-accessors ((ntuple ntuple-table-ntuple))
table
(let ((read-status (cl-ana.gsl-cffi:gsl-ntuple-read ntuple)))
(not (equal read-status cl-ana.gsl-cffi:+GSL-EOF+)))))
;; (defmethod table-get-field ((table ntuple-table) field-symbol)
;; (with-accessors ((row typed-table-row-pointer)
;; (cstruct ntuple-table-cstruct))
;; table
;; (foreign-slot-value row
;; cstruct
;; field-symbol)))
;;; Cleanup:
(defmethod table-close ((table ntuple-table))
(with-accessors ((ntuple ntuple-table-ntuple)
(row typed-table-row-pointer))
table
(gsll:close-ntuple ntuple)
(foreign-free row)))
| 3,659 | Common Lisp | .lisp | 94 | 35.755319 | 71 | 0.699972 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 7d52611e47bff362edb371f1e7f4edfdfc7cf8d5324265f045530a785beeb2a7 | 1,457 | [
-1
] |
1,458 | test.lisp | ghollisjr_cl-ana/ntuple-table/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana.ntuple-table)
(in-package :cl-ana.ntuple-table)
(defparameter *table*
(create-ntuple-table "/home/ghollisjr/test.dat"
(list (cons "x" :int)
(cons "X" :int)
(cons "y" :double))))
(table-push-fields *table*
(|x| 3)
(x 4)
(|y| 5d0))
(table-push-fields *table*
(|x| 4)
(x 5)
(|y| 10d0))
(table-close *table*)
(setf *table*
(open-ntuple-table "/home/ghollisjr/test.dat"
(list (cons "x" :int)
(cons "X" :int)
(cons "y" :double))))
(do-table (row-index *table*)
("x"
"X"
"y")
(print |x|)
(print x)
(print |y|))
| 1,561 | Common Lisp | .lisp | 48 | 27.9375 | 70 | 0.614466 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 58221320c2bc626a5fd800ccf460d64cac02fbbf1dda55ae9c8c9fe84c1a5a76 | 1,458 | [
-1
] |
1,459 | package.lisp | ghollisjr_cl-ana/reusable-table/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.reusable-table
(:use :cl
:cl-ana.table)
(:export :wrap-for-reuse
:reusable-table
:make-reusable-table
:internal-table
:reusable-table-opener-form))
| 1,092 | Common Lisp | .lisp | 28 | 36.035714 | 70 | 0.688617 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 038319896c1f94c5f73ae65b7e75e55531ced618b3a019637aa2cf4fa01c2bd5 | 1,459 | [
-1
] |
1,460 | reusable-table.lisp | ghollisjr_cl-ana/reusable-table/reusable-table.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; reusable-table.lisp
;;;; reusable-table provides a wrapper macro which, when given the
;;;; form you would have evaluated to open your table for reading,
;;;; creates a closure which will be called whenever the table needs
;;;; reloading. The table object returned only defines minimal
;;;; interface, but this is a minor inconvenience as it is still
;;;; possible to access the raw table directly.
;;;;
;;;; It can safely be used with do-table since table-load-next-row
;;;; still returns nil when appropriate.
(in-package :cl-ana.reusable-table)
(defclass reusable-table ()
((creation-fn
:initarg :creation-fn
:initform nil
:accessor reusable-table-creation-fn
:documentation "Function which creates the table being wrapped.")
(creation-fn-form
:initarg :opener-form
:initform nil
:accessor reusable-table-opener-form
:documentation "Lisp form which returns the table opener function
when evaluated. A table opener An optional field which assists in serializing
reusable tables.")
(raw-table
:initarg :raw-table
:initform nil
:accessor internal-table
:documentation "The table which is being wrapped.")
(needs-reloading
:initform nil
:accessor reusable-table-needs-reloading
:documentation "Boolean which tells the wrapper when it needs to
close and re-open the table.")))
(defun make-reusable-table (creation-fn &optional opener-form)
"Returns result of creation-fn if reusable-table, else returns
reusable-table which will make use of creation-fn to generate new
copies when needed."
(let ((tab (funcall creation-fn)))
(if (typep tab 'reusable-table)
tab
(make-instance 'reusable-table
:creation-fn creation-fn
:opener-form opener-form
:raw-table tab))))
(defmacro wrap-for-reuse (table-creation-form &optional opener-form)
"Creates a reusable (when table-creation-from does not return a
reusable-table) table which places the table-creation-form into a
closure which will be evaluated each time the table gets re-read from
the beginning. If the creation form returns a reusable-table, simply
returns the table."
(let ((lambda-form
`(lambda () ,table-creation-form)))
`(make-reusable-table ,lambda-form
,opener-form)))
(defmethod table-load-next-row ((table reusable-table))
(with-slots (raw-table creation-fn needs-reloading)
table
(when needs-reloading
(when (table-open-p raw-table)
(table-close raw-table))
(setf raw-table (funcall creation-fn))
(setf needs-reloading nil))
(let ((status (table-load-next-row raw-table)))
(when (not status)
(setf needs-reloading t))
status)))
(defmethod table-get-field ((table reusable-table) field-symbol)
(with-slots (raw-table)
table
(table-get-field raw-table field-symbol)))
(defmethod table-field-names ((table reusable-table))
(with-slots (raw-table)
table
(table-field-names raw-table)))
;;; Cleanup:
(defmethod table-close ((table reusable-table))
"Closes the physical table; note that this is unsafe unless you know
the table needs closing."
(with-slots (raw-table needs-reloading)
table
(when (not needs-reloading)
(setf needs-reloading t))
(table-close raw-table)))
;; table-nrows method:
(defmethod table-nrows ((table reusable-table))
(table-nrows (internal-table table)))
;; access mode:
(defmethod table-access-mode ((table reusable-table))
(table-access-mode (internal-table table)))
| 4,477 | Common Lisp | .lisp | 110 | 36.454545 | 82 | 0.710835 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | f961303e770ecaf7611adcc57c099b31a6968410f8c71d22bb760ce2fcb85ab7 | 1,460 | [
-1
] |
1,461 | test.lisp | ghollisjr_cl-ana/reusable-table/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana.reusable-table)
(require 'cl-ana.hdf-table)
(in-package :cl-ana.hdf-table)
(use-package 'cl-ana.reusable-table)
(defvar *table*
(wrap-for-reuse
(open-hdf-table-chain (list "/home/ghollisjr/hdfwork/outfile.h5")
"/output-dataset")))
(do-table (i *table*)
("x" "y")
(when (zerop i)
(print "First pass: ")
(print x)
(print y)))
(do-table (i *table*)
("x" "y")
(when (zerop i)
(print "Second pass: ")
(print x)
(print y)))
| 1,380 | Common Lisp | .lisp | 40 | 31.575 | 70 | 0.666917 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 3a0f47157542298c2057d34c592b9bb5b025ce2dbdba381887d29a3b3247b47e | 1,461 | [
-1
] |
1,462 | package.lisp | ghollisjr_cl-ana/makeres-graphviz/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.makeres-graphviz
(:use :cl
:external-program
:cl-ana.makeres)
(:export
;; project graph -> dot code:
:dot-compile
:dot->ps
:dot->png
:dot->pdf))
| 1,074 | Common Lisp | .lisp | 30 | 33.466667 | 70 | 0.689358 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 62fa46fe656513a38216b45136ab1842f9929a2ae48e4aac5d915fd617512df8 | 1,462 | [
-1
] |
1,463 | dot.lisp | ghollisjr_cl-ana/makeres-graphviz/dot.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.makeres-graphviz)
(defun dot-compile (path &key
(if-exists :error)
(target-table (target-table))
posts)
"Writes target graph into a file located at path. Returns path of
dot output file. posts is a list of lines to append to the end of the
dot commands without semicolons."
(let ((*print-pretty* nil))
(ensure-directories-exist path)
(with-open-file (file path
:direction :output
:if-does-not-exist :create
:if-exists if-exists)
(format file "digraph \"~a\" {~%"
(project))
(loop
for id being the hash-keys in target-table
for tar being the hash-values in target-table
do (let ((deps (target-deps tar)))
(loop
for d in deps
do (format file " \"~a\" -> \"~a\";~%"
d id))))
(loop
for p in posts
do (format file "~a;~%" p))
(format file "}~%")
path)))
(defun dot->ps (from-path to-path
&key
;; can be one of
;;
;; :dot (normal)
;; :neato
;; :twopi
;; :circo
;; :fdp
;; :sfdp
;; :patchwork
;; :osage
(type :dot))
"Runs dot command to convert dot code in from-path to a ps file at
to-path"
(let* ((types
(list
:dot
:neato
:twopi
:circo
:fdp
:sfdp
:patchwork
:osage)))
(when (member type types)
(run (string-downcase (string type))
(list from-path
"-Tps"
"-o"
to-path)))))
(defun dot->png (from-path to-path
&key
;; can be one of
;;
;; :dot (normal)
;; :neato
;; :twopi
;; :circo
;; :fdp
;; :sfdp
;; :patchwork
;; :osage
(type :dot))
"Runs dot command to convert dot code in from-path to a png file at
to-path"
(let* ((types
(list
:dot
:neato
:twopi
:circo
:fdp
:sfdp
:patchwork
:osage)))
(when (member type types)
(run (string-downcase (string type))
(list from-path
"-Tpng"
"-o"
to-path)))))
(defun dot->pdf (from-path to-path
&key
;; can be one of
;;
;; :dot (normal)
;; :neato
;; :twopi
;; :circo
;; :fdp
;; :sfdp
;; :patchwork
;; :osage
(type :dot))
"Runs dot command to convert dot code in from-path to a pdf file at
to-path"
(let* ((types
(list
:dot
:neato
:twopi
:circo
:fdp
:sfdp
:patchwork
:osage)))
(when (member type types)
(run (string-downcase (string type))
(list from-path
"-Tpdf"
"-o"
to-path)))))
| 4,429 | Common Lisp | .lisp | 142 | 19.422535 | 70 | 0.453059 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 57990244b3a4d9de958871570710bb459f0f8bb898bca2dad316d9307bf98318 | 1,463 | [
-1
] |
1,464 | test.lisp | ghollisjr_cl-ana/makeres-graphviz/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana.makeres-graphviz)
(in-package :cl-ana.makeres-graphviz)
(in-project makeres-graphviz)
(defres src
(list 1 2 3 4 5))
(defres squares
(mapcar (lambda (x)
(expt x 2))
(res src)))
(defres mean
(mean (res src)))
(defres mean-squares
(mean (res squares)))
(defres variance
(- (res mean-squares)
(expt (res mean)
2)))
(defres standard-deviation
(sqrt (res variance)))
| 1,309 | Common Lisp | .lisp | 39 | 30.948718 | 70 | 0.689929 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 875cf772291d4ab8297de9891ded37cab6cc409811c80fdf25a529794e5e7df9 | 1,464 | [
-1
] |
1,465 | package.lisp | ghollisjr_cl-ana/array-utils/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2021 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.array-utils
(:use :cl)
(:export :for-array
:map-array))
| 959 | Common Lisp | .lisp | 24 | 38.125 | 70 | 0.699143 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 4c358d3bcf6e7c52bfc08260008541cb011053baf358f9241f0561e2984aac01 | 1,465 | [
-1
] |
1,466 | array-utils.lisp | ghollisjr_cl-ana/array-utils/array-utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2021 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.array-utils)
;; Looping over array
(defmacro for-array (binding dimensions &body body)
"Iterates over every possible index for an array with supplied
dimensions. If binding is an atom, then the index list will be set to
that variable as a list. If it is a list of symbols, then each symbol
will be bound to its corresponding element from the Cartesian product
element."
(alexandria:with-gensyms (sets dims setdims nsets
index
continue
incr dim)
`(let* ((,dims ,dimensions)
(,nsets (if (atom ,dims)
1
(length ,dims)))
(,setdims (if (atom ,dims)
(vector ,dims)
(map 'vector #'identity ,dims)))
(,index (make-array ,nsets :initial-element 0))
(,continue t))
(loop
while ,continue
do
;; execute body
,(if (atom binding)
`(let ((,binding (map 'list #'identity
,index)))
,@body)
`(destructuring-bind ,binding
(map 'list #'identity
,index)
,@body))
;; iterate
(let* ((,incr t)
(,dim 0))
(loop
while ,incr
do
(if (>= ,dim ,nsets)
(progn
(setf ,incr nil)
(setf ,continue nil))
(progn
(incf (aref ,index ,dim))
(if (>= (aref ,index ,dim)
(aref ,setdims ,dim))
(progn
(setf (aref ,index ,dim) 0)
(incf ,dim))
(setf ,incr nil))))))))))
(defun map-array (array fn)
"Map for arrays. fn should be of the form (lambda (value &rest
indices)...)"
(let* ((result (make-array (array-dimensions array))))
(for-array indices (array-dimensions array)
(setf (apply #'aref result indices)
(apply fn
(apply #'aref array indices)
indices)))
result))
| 3,252 | Common Lisp | .lisp | 81 | 27.493827 | 70 | 0.506313 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 6e9c8681f5cb8ad31e831881a48c58aa899615bae05a897d801b24048a4ac1ce | 1,466 | [
-1
] |
1,467 | package.lisp | ghollisjr_cl-ana/hdf-utils/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.hdf-utils
(:use #:cl
#:cffi
#:alexandria
#:hdf5
#:cl-ana.memoization
#:cl-ana.typespec
#:cl-ana.hdf-typespec
#:cl-ana.macro-utils
#:cl-ana.string-utils
#:cl-ana.pathname-utils)
(:export :with-cleanup ; general use for HDF5 objects
:with-open-dataspace ; opens a dataspace from a dataset
:with-create-dataspace ; creates a new dataspace
:with-dataset-type ; opens dataset datatype
:with-open-hdf-file ; opens/creates a file for reading/writing
:open-hdf-file
:close-hdf-file
:hdf-mkgroup))
| 1,534 | Common Lisp | .lisp | 39 | 34.794872 | 76 | 0.659973 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | f9893eca179b5b6f2152f74a14f4cc3072ed7f02b649aa7064788a66cc3bb5ec | 1,467 | [
-1
] |
1,468 | hdf-utils.lisp | ghollisjr_cl-ana/hdf-utils/hdf-utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis via email at
;;;; [email protected]
(in-package :cl-ana.hdf-utils)
;;;; Still need to fix the with-open-hdf-file macro to make use of the
;;;; open-hdf-file and close-hdf-file functions.
(declaim (optimize (speed 3)
(safety 1)
(compilation-speed 0)
(debug 1)))
(defmacro with-cleanup ((&rest specs) &body body)
"Executes body inside of a lexical environment where objects
described by specs are bound and then freed upon concluding the body.
Each spec is a list of 3 elements:
1. A symbol which will denote a variable inside the body,
2. A form which will be evaluated and its value bound to the symbol,
3. A function for cleaning up the object referenced by the symbol; it
will be given the symbol as the sole argument."
(multiple-value-bind (symbols inits cleanup-fns)
(loop
for (s i c) in specs
collecting s into symbols
collecting i into inits
collecting c into cleanup-fns
finally (return (values symbols inits cleanup-fns)))
(let ((lexical-bindings
(loop
for s in symbols
for i in inits
collecting `(,s ,i)))
(cleanup-forms
(loop
for s in symbols
for c in cleanup-fns
collecting `(funcall ,c ,s))))
(with-gensyms (result)
`(let ,lexical-bindings
(let ((,result
(progn ,@body)))
,@(reverse cleanup-forms)
,result))))))
(defmacro with-open-dataspace ((dataspace dataset) &body body)
"Safely work with dataspace taken from dataset"
`(with-cleanup
((,dataspace (hdf5:h5dget-space ,dataset)
#'hdf5:h5sclose))
,@body))
(defmacro with-create-dataspace ((dataspace rank dims maxdims)
&body body)
"Creates a new dataspace and cleans up after it"
`(with-cleanup
((,dataspace (hdf5:h5screate-simple ,rank ,dims ,maxdims)
#'hdf5:h5sclose))
,@body))
(defmacro with-dataset-type ((type dataset) &body body)
`(with-cleanup
((,type (hdf5:h5dget-type ,dataset)
#'hdf5:h5tclose))
,@body))
;;;; File utilities:
(defun open-hdf-file
(filename &key direction
(if-exists nil if-exists-supplied-p)
(if-does-not-exist nil if-does-not-exist-supplied-p)
(read-access-parameters hdf5:+H5P-DEFAULT+)
(write-access-parameters (list hdf5:+H5P-DEFAULT+ hdf5:+H5P-DEFAULT+)))
"Opens an hdf file, returning a handle to the file (hid-t).
direction can be :input or :output.
if-exists can be :supersede :error nil
if-does-not-exist can be :create :error nil"
(let ((filename
(namestring (->absolute-pathname filename))))
(case direction
(:input
;; I'm choosing the convention that when direction is :input, the
;; only meaningful if-does-not-exist are :error and nil
;; setup if-does-not-exist:
(when (not if-does-not-exist-supplied-p)
(setf if-does-not-exist :error))
(let ((file-exists-p (probe-file filename)))
(if file-exists-p
(hdf5:h5fopen filename hdf5:+H5F-ACC-RDONLY+ read-access-parameters)
(case if-does-not-exist
(:error (error "File does not exist"))
(nil nil)))))
(:output
;; default for if-exists is :error
;; can't ignore if-does-not-exist if I want to be consistent with
;; with-open-file, but default is to go ahead and create the file
;; setup if-exists & if-does-not-exist
(when (not if-exists-supplied-p)
(setf if-exists :error))
(when (not if-does-not-exist-supplied-p)
(setf if-does-not-exist :create))
(let ((file-exists-p (probe-file filename)))
(if file-exists-p
(case if-exists
(:error (error "File exists"))
(nil nil)
(:supersede
(delete-file filename)
(apply #'hdf5:h5fcreate
filename hdf5:+H5F-ACC-TRUNC+
write-access-parameters))
(:rename
(progn
;; rename "file" to "file.bak"
;; then create new file
(rename-file filename (concatenate 'string filename ".bak"))
(apply #'hdf5:h5fcreate
filename hdf5:+H5F-ACC-TRUNC+
write-access-parameters)))
(:append
(hdf5:h5fopen filename
hdf5:+H5F-ACC-RDWR+
read-access-parameters)))
(case if-does-not-exist
(:create
(apply #'hdf5:h5fcreate filename
hdf5:+H5F-ACC-TRUNC+ write-access-parameters))
(:error (error "file does not exist"))
(nil nil))))))))
(defun close-hdf-file (hdf-file)
"Closes all datatype objects associated with file along with the
file"
(reset-memo-map #'typespec->hdf-type)
(reset-memo-map #'hdf-type->typespec)
(let ((nobs (hdf5:h5fget-obj-count hdf-file hdf5:+H5F-OBJ-ALL+))
(ids nil))
(when (plusp nobs)
(with-foreign-object (raw-ids 'hid-t nobs)
(hdf5:h5fget-obj-ids hdf-file
hdf5:+H5F-OBJ-ALL+
nobs
raw-ids)
(setf ids
(loop
for i below nobs
collecting (mem-aref raw-ids 'hid-t i)))))
(loop
for id in ids
do
;; In the future, detect type instead of trying everything
(hdf5:h5fclose id)
(hdf5:h5dclose id)
(hdf5:h5gclose id)
(hdf5:h5tclose id)
(hdf5:h5aclose id)))
(hdf5:h5fclose hdf-file))
(defmacro with-open-hdf-file ((hdf-file
file-path-or-string
&key
direction
(if-exists nil if-exists-supplied-p)
(if-does-not-exist nil if-does-not-exist-supplied-p)
(read-access-parameters hdf5:+H5P-DEFAULT+)
(write-access-parameters (list hdf5:+H5P-DEFAULT+
hdf5:+H5P-DEFAULT+)))
&body body)
"Macro providing lispy access to hdf (HDF5) files. Use just like
you would with-open-file, just give a file and a path/string.
The usual key arguments for access mode, etc. are honored and
transformed into HDF5 terms.
The argument hdf-file is the symbol you'll use to refer to the file
handle inside of the macro body."
;; direction: :input :output
;; if-exists: :error :supersede nil :rename
;; if-does-not-exist: :error :create nil
(let* ((result (gensym))
(body-with-close
`(let ((,result
(progn ,@body)))
(close-hdf-file ,hdf-file)
,result)))
`(let ((,hdf-file
(open-hdf-file ,file-path-or-string
,@(when-keywords
direction
if-exists
if-does-not-exist
read-access-parameters
(:write-access-parameters
(cons 'list write-access-parameters))))))
,body-with-close)))
(defun hdf-mkgroup (file group-name)
"Creates a group with name group-name in hdf-file file; returns path
to group with final '/' included."
(let ((group-name
(if (not (equal (last-elt group-name) #\/))
group-name
(subseq group-name 0 (1- (length group-name))))))
(hdf5:h5gclose (hdf5:h5gcreate1 file group-name 0))
(string-append group-name "/")))
| 8,486 | Common Lisp | .lisp | 210 | 30.857143 | 83 | 0.589967 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | ebb0e4386cefa8c10ec6d8c061f3e6059763530170226f5a384dd2dfa6b357e8 | 1,468 | [
-1
] |
1,469 | conversion.lisp | ghollisjr_cl-ana/histogram/conversion.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.histogram)
(defun sparse->contiguous (histogram)
"converts a sparse histogram into a contiguous one. Note that this
is dangerous in cases where sparse histograms are actually necessary."
(if (typep histogram 'sparse-histogram)
(let* ((dim-spec-plists
(hist-dim-specs
histogram))
(bin-values
(hist-bin-values histogram))
(hist
(make-contiguous-hist dim-spec-plists
:empty-bin-value
(hist-empty-bin-value histogram)
:default-increment
(hist-default-increment histogram))))
(loop
for datum in bin-values
do (hist-insert hist (rest datum) (first datum)))
hist)
histogram))
(defun contiguous->sparse (histogram)
"converts a sparse histogram into a contiguous one. Note that this
is dangerous in cases where sparse histograms are actually necessary."
(if (typep histogram 'contiguous-histogram)
(let* ((dim-spec-plists
(hist-dim-specs
histogram))
(bin-values
(hist-bin-values histogram))
(hist
(make-sparse-hist dim-spec-plists)))
(loop
for datum in bin-values
do (hist-insert hist (rest datum) (first datum)))
hist)
histogram))
| 2,338 | Common Lisp | .lisp | 57 | 32.561404 | 73 | 0.618086 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 41681e73558d9c5ed21c2cc170c93dff14a8547c0c4e13255c5eefa18f7aa8a4 | 1,469 | [
-1
] |
1,470 | package.lisp | ghollisjr_cl-ana/histogram/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage :cl-ana.histogram
(:use #:cl
#:alexandria
;; #:iter
#:cl-ana.clos-utils
#:cl-ana.tensor
#:cl-ana.binary-tree
#:cl-ana.symbol-utils
#:cl-ana.string-utils
#:cl-ana.list-utils
#:cl-ana.hash-table-utils
#:cl-ana.macro-utils
#:cl-ana.functional-utils
#:cl-ana.fitting
#:cl-ana.map)
(:export :bin ; useful for quickly plotting small datasets
:histogram
:rectangular-histogram
:contiguous-histogram
:sparse-histogram
:categorical-histogram
:make-contiguous-hist
:make-chist
:make-sparse-hist
:make-shist
:make-categorical-hist
:make-cathist
:sparse->contiguous
:contiguous->sparse
:copy-hist ; returns a filled or empty copy of a histogram
:map-contiguous-hist
:rectangular-hist-bin-specs
:hist-dim-specs
:hist-ndims
:hist-dim-names
:hist-bin-widths
:hist-empty-bin-value
:hist-default-increment
:hist-total-integral
:hist-integrate
:hist-project
:hist-slice
:getslice
:hist-insert
:hist-insert-list
:hist-absorb
:hist-index-ref ; setf-able
:hist-point-ref ; setf-able
:hist-bin-values
;; Functional access:
:hist-map
:hist-filter
;; Abbreviations:
:hins ;; hist-insert
:htint ;; hist-total-integral
:hint ;; hist-integrate
:hproj ;; hist-project
:hslice ;; hist-slice
:hiref ;; hist-index-ref
:hpref ;; hist-point-ref
:hbv ;; hist-bin-values
:hdn ;; hist-dim-names
:hds ;; hist-dim-specs
:hbw
:normalize-histogram
;; For generating discrete dim-specs
:discrete-dim-spec
:dds
;; Variable binning histograms:
:variable-binning-histogram
:make-variable-binning-histogram
:make-vhist))
(cl-ana.gmath:use-gmath :cl-ana.histogram)
| 2,998 | Common Lisp | .lisp | 93 | 24.795699 | 70 | 0.605789 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | c62cb772e9d1af9d3d29b77f7187d3c626ce30a3a575b269c057c244f80cae6a | 1,470 | [
-1
] |
1,471 | rectangular-histogram.lisp | ghollisjr_cl-ana/histogram/rectangular-histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; rectangular-histogram.lisp
;;;; This probably needs a lot of work to make it logically clear
;;;; what's going on, but at the moment it does work and I don't feel
;;;; like breaking it while I try to do get plotting done.
;;;;
;;;; For example there is currently code duplication for generating
;;;; the bin-specs from the plists in the contiguous and sparse
;;;; histograms, so this should be placed in this histogram class.
(in-package :cl-ana.histogram)
(declaim (optimize (speed 3)))
;;;; Provides a rectangular histogram; i.e. the binning is fixed-width
;;;; and the width is uniform in every dimension.
(defclass rectangular-histogram (histogram)
((bin-specs
:accessor rectangular-hist-bin-specs
:initarg :bin-specs
:initform nil
:documentation "List of number of bins, bin low edge, and bin high
edge. Should be computed from a bin specification plist and then
stored in said order as a list (not a plist).")))
(defmethod hist-slice ((hist rectangular-histogram) &rest dims)
(let* ((empty-bin-value
(hist-empty-bin-value hist))
(default-increment
(hist-default-increment hist))
(type-constructor
(type-constructor hist))
(all-dim-specs
(hist-dim-specs hist))
(all-dims
(hdn hist))
(slice-indices (get-dim-indices all-dims dims))
(remaining-dim-specs
(except-at all-dim-specs slice-indices))
(remaining-indices
(except-at (range 0 (1- (hist-ndims hist)))
slice-indices))
(bin-values (hbv hist))
(result (make-hash-table :test 'equal)))
(loop
for (count . centers) in bin-values
do (let* ((slice-centers
(at-indices centers slice-indices))
(other-centers
(at-indices centers remaining-indices))
(h (gethash slice-centers result)))
(when (not h)
(setf h (funcall
type-constructor
remaining-dim-specs
:empty-bin-value empty-bin-value
:default-increment default-increment))
(setf (gethash slice-centers result)
h))
(hins h other-centers count)))
result))
(defun get-bin-index (data-list bin-specs)
"Computes the bin-index-list from the data-list (a data point).
Does so for all axes, returns nil if overflow/underflow occurs.
Make sure that data-list and bin-specs have the same length before
calling this function; it is unchecked in this respect for speed."
(labels
((get-bin-index-worker (data-list bin-specs &optional result)
(if data-list ; I'm intentionally ignoring length differences
; between data-list and bin-specs
(let* ((datum (first data-list))
(bin-spec (first bin-specs))
(nbins (the fixnum (first bin-spec)))
(bin-index (the fixnum
(get-axis-bin-index datum bin-spec))))
(when (not (or (minusp bin-index)
(>= bin-index nbins)))
(get-bin-index-worker (rest data-list)
(rest bin-specs)
(cons bin-index result))))
(nreverse result))))
(get-bin-index-worker data-list bin-specs)))
(defun get-axis-bin-index (value bin-spec)
"Computes the bin index (-1 underflow, binnum overflow) for value
given the bin-spec for a single axis/dimension."
(declare (list bin-spec)
(real value))
(destructuring-bind (nbins binlo binhi) bin-spec
(declare (fixnum nbins))
(let ((delta (cl:/ (cl:- binhi binlo) nbins)))
(the fixnum (floor (cl:- value binlo) delta)))))
(defun get-bin-center-worker (bin-spec index)
(let* ((nbins (first bin-spec))
(binlo (second bin-spec))
(binhi (third bin-spec))
(delta (cl:/ (cl:- binhi binlo) nbins)))
(declare (fixnum nbins))
(cl:+ binlo
(cl:/ delta 2)
(cl:* delta
index))))
(defun get-bin-center (bin-specs bin-index)
(mapcar #'get-bin-center-worker bin-specs bin-index))
(defun hist-dim-specs (histogram)
"Returns the plists denoting the name, nbins, low, and high for each
dimension in the histogram."
(loop
for bin-spec in (rectangular-hist-bin-specs histogram)
for dim-name in (hist-dim-names histogram)
collecting (destructuring-bind (nbins low high)
bin-spec
(list :name dim-name
:nbins nbins
:low low
:high high))))
(defun hist-bin-widths (hist)
(mapcar (lambda (lst)
(destructuring-bind (&key low high nbins &allow-other-keys)
lst
(cl:/ (cl:- high low) nbins)))
(hist-dim-specs hist)))
;; abbrevations:
(defun hds (histogram)
"Abbreviation for hist-dim-specs"
(hist-dim-specs histogram))
(defun hbw (histogram)
(hist-bin-widths histogram))
;; Ease of use:
;; nbins * delta + low = high
;; -> delta = (high - low)/nbins
;; if nbins = floor((high-low/delta)) then
;; newhigh = floor((high-low)/delta)*delta + low
(defun discrete-dim-spec (&key low high (delta 1d0))
"Returns dim-spec for discrete/integral data, e.g. digital event
counter readouts."
(let* ((newlow (cl:- low
(cl:* delta 0.5)))
(newnbins (1+ (floor (cl:- high low)
delta)))
(newhigh (cl:+ low
(cl:* (1- newnbins)
delta)
(cl:* delta 0.5))))
(list :low newlow
:high newhigh
:nbins newnbins)))
(defun dds (&rest args)
"Abbreviation for discrete-dim-spec"
(apply #'discrete-dim-spec args))
| 6,763 | Common Lisp | .lisp | 164 | 32.932927 | 74 | 0.60933 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 251626107aa44096bcce9b56d09b806276f0ad595c68f9758ff3e3122a26c53c | 1,471 | [
-1
] |
1,472 | contiguous-histogram.lisp | ghollisjr_cl-ana/histogram/contiguous-histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; Implements histograms with binning which is both contiguous and
;;;; uniform.
(in-package :cl-ana.histogram)
(defclass contiguous-histogram (rectangular-histogram)
((bin-values
:accessor contiguous-hist-bin-values
:initarg :bin-values
:initform nil
:documentation "Nested arrays representing the bin values")))
;; I was thinking about making this a method on initialize-instance,
;; but it seems cleaner to keep this as a distinct function, since if
;; I wish to directly copy histogram contents the initialize-instance
;; method would have to handle these two cases separately, or I would
;; have to implement the copying in a strange way.
(defun make-contiguous-hist (dim-spec-plists &key empty-bin-value default-increment)
"dim-spec-plist is a plist with the following
fields: :name :low :high :nbins, which specify the axis name,
bin-low-edge, bin-high-edge, and the number of bins on the axis
respectively.
Example usage: (make-contiguous-hist (list (list :name \"x\" :nbins
10 :low 50 :high 55))) would create a contiguous histogram with one
dimension named \"x\" with 10 bins, low bin edge 50 and high bin edge
55."
(let* ((dim-names (mapcar (lambda (spec) (getf spec :name))
dim-spec-plists))
(ndims (length dim-names))
(bin-specs (mapcar (lambda (s)
(list (getf s :nbins)
(getf s :low)
(getf s :high)))
dim-spec-plists))
(size-list (mapcar #'first bin-specs))
(default-args (progn
(let ((result ()))
(when empty-bin-value
(push empty-bin-value result)
(push :empty-bin-value result))
(when default-increment
(push default-increment result)
(push :default-increment result))
result)))
(result (apply #'make-instance 'contiguous-histogram
:ndims ndims
:dim-names dim-names
:bin-specs bin-specs
default-args))
(bin-values (make-contiguous-hist-contents size-list
(hist-empty-bin-value result))))
(setf (contiguous-hist-bin-values result) bin-values)
result))
(defun make-chist (dim-spec-plists &key empty-bin-value default-increment)
"Abbreviation for make-contiguous-hist"
#k(make-contiguous-hist dim-spec-plists
&when-keys
empty-bin-value
default-increment))
(defmethod empty-copy ((h contiguous-histogram))
(with-slots (empty-bin-value
default-increment)
h
(make-chist (hist-dim-specs h)
:empty-bin-value empty-bin-value
:default-increment default-increment)))
(defmethod hist-total-integral ((hist contiguous-histogram))
(let ((bin-values (hist-bin-values hist)))
(sum (mapcar #'car bin-values))))
(defmethod hist-integrate ((histogram contiguous-histogram) &rest axes)
(if axes
(with-accessors ((ndims hist-ndims)
(dim-names hist-dim-names)
(empty-bin-value hist-empty-bin-value)
(default-increment hist-default-increment)
(bin-values contiguous-hist-bin-values)
(bin-specs rectangular-hist-bin-specs))
histogram
(if (length-equal axes ndims)
(hist-total-integral histogram)
(flet ((index-key (x)
(if (listp x)
(first x)
x)))
(let* ((axis-name-or-indices (mapcar (lambda (x)
(if (listp x)
(first x)
x))
axes))
(dim-indices (get-dim-indices dim-names axis-name-or-indices))
(point-bounds
(mapcar (lambda (x)
(when (listp x)
(rest x)))
axes))
(index-bounds
(mapcar (lambda (point-bound bin-spec)
(when point-bound
(let ((low-index
(get-axis-bin-index (first point-bound)
bin-spec))
(high-index
(get-axis-bin-index (second point-bound)
bin-spec)))
(list (if (equal low-index :underflow)
0
low-index)
(if (equal high-index :overflow)
(1- (first bin-spec))
high-index)))))
point-bounds
bin-specs))
(index-specs (mapcar (lambda (x y)
(if y
(cons x y)
x))
dim-indices
index-bounds))
(index-specs-copy (copy-list index-specs))
(sorted-index-specs (sort index-specs-copy #'>
:key #'index-key))
(unique-sorted-index-specs
(reduce
(lambda (x y) (adjoin y x
:test #'equal
:key #'index-key))
sorted-index-specs
:initial-value ()))
(unique-sorted-indices
(mapcar (lambda (x)
(if (listp x)
(first x)
x))
unique-sorted-index-specs))
(new-ndims (- ndims (length unique-sorted-indices)))
(new-dim-names (except-at dim-names unique-sorted-indices
:uniquely-sorted t))
(new-bin-specs (except-at bin-specs unique-sorted-indices
:uniquely-sorted t)))
(make-instance 'contiguous-histogram
:ndims new-ndims
:dim-names new-dim-names
:empty-bin-value empty-bin-value
:default-increment default-increment
:bin-values (contiguous-hist-integrate-contents
bin-values
index-specs)
:bin-specs new-bin-specs)))))
histogram))
;; note that hist-insert is a stateful function, since this is the
;; only efficient way to implement it
(defmethod hist-insert ((hist contiguous-histogram) datum &optional weight)
(let ((data-list (mklist datum))
(weight-factor (if weight
weight
(hist-default-increment hist))))
(cond-setf (hist-point-ref hist data-list)
(+ (hist-point-ref hist data-list) weight-factor)
:place)
hist))
(defmethod hist-index-ref ((hist contiguous-histogram) index-list)
"Unchecked, assumes you know what the allowed index values are."
(with-accessors ((bin-values contiguous-hist-bin-values))
hist
(apply #'tensor-ref bin-values index-list)))
(defmethod (setf hist-index-ref) (value (hist contiguous-histogram) index-list)
"Unchecked, assumes you know what the allowed index values are."
(with-accessors ((bin-values contiguous-hist-bin-values))
hist
(setf (apply #'tensor-ref bin-values index-list)
value)))
(defmethod hist-point-ref ((hist contiguous-histogram) data-list)
"Checked access to the bin value via a point. Returns nil if the
point is not inside the histogram domain."
(with-accessors ((bin-specs rectangular-hist-bin-specs))
hist
(let ((bin-index (get-bin-index data-list bin-specs)))
(when bin-index
(hist-index-ref hist bin-index)))))
(defmethod (setf hist-point-ref) (value (hist contiguous-histogram) data-list)
"Checked setf to the bin value via a point. Does nothing & returns
nil if the point is not inside the histogram domain."
(with-accessors ((bin-specs rectangular-hist-bin-specs)
(bin-values contiguous-hist-bin-values))
hist
(let ((bin-index (get-bin-index data-list bin-specs)))
(when bin-index
(setf (hist-index-ref hist bin-index)
value)))))
(defmethod hist-bin-values ((hist contiguous-histogram))
(with-accessors ((bin-specs rectangular-hist-bin-specs)
(bin-values contiguous-hist-bin-values))
hist
(let* ((nbin-list (mapcar #'first bin-specs))
(bin-indices (apply #'cartesian-product
(mapcar (lambda (x) (range 0 (1- x))) nbin-list))))
(mapcar (lambda (bin-index)
(cons (hist-index-ref hist bin-index)
(get-bin-center bin-specs bin-index)))
bin-indices))))
;;; Generic Math functions:
;; Note that I am still not sure how to handle summing when the axis
;; limits and bin sizes are not the same. It may be best to leave
;; this to the user and just provide naive arithmetic functions.
;;
;; In general you should be safe as long as your histograms have the
;; same axis limits & bin sizes.
(defun map-contiguous-hist (fn &rest histograms)
"Defines the map operation over contiguous histograms."
(let ((h1 (first histograms)))
(with-accessors ((bin-specs rectangular-hist-bin-specs)
(ndims hist-ndims)
(dim-names hist-dim-names)
(empty-bin-value hist-empty-bin-value)
(default-increment hist-default-increment))
h1
(make-instance
'contiguous-histogram
:ndims ndims
:dim-names dim-names
:empty-bin-value empty-bin-value
:default-increment default-increment
:bin-specs bin-specs
:bin-values
(apply #'tensor-map
fn
(mapcar
#'contiguous-hist-bin-values
histograms))))))
(defmethod add ((h1 contiguous-histogram) (h2 contiguous-histogram))
(map-contiguous-hist #'add h1 h2))
(defmethod sub ((h1 contiguous-histogram) (h2 contiguous-histogram))
(map-contiguous-hist #'sub h1 h2))
(defmethod mult ((h1 contiguous-histogram) (h2 contiguous-histogram))
(map-contiguous-hist #'mult h1 h2))
(defmethod div ((h1 contiguous-histogram) (h2 contiguous-histogram))
(map-contiguous-hist #'div h1 h2))
(defmethod unary-div ((h1 contiguous-histogram))
(map-contiguous-hist #'unary-div h1))
;; NOTE: This method differs from the usage of other protected-div
;; methods in that histograms have a default bin value. For this
;; reason, the default bin value for the first histogram is used by
;; default instead of 0.
(defmethod protected-div ((h1 contiguous-histogram)
(h2 contiguous-histogram)
&key
protected-value)
(let ((protected-value
(if protected-value
protected-value
(hist-empty-bin-value h1))))
(map-contiguous-hist
(lambda (x y) (protected-div
x y
:protected-value
protected-value))
h1 h2)))
;; See notes on protected-div
(defmethod protected-unary-div ((h contiguous-histogram)
&key
protected-value)
(let ((protected-value
(if protected-value
protected-value
(hist-empty-bin-value h))))
(map-contiguous-hist
(lambda (x) (protected-unary-div
x
:protected-value
protected-value))
h)))
;;; Internal-usage functions
(defun contiguous-hist-integrate-contents (hist index-specs)
"Assumes the index-specs are unique and sorted greatest to least."
(reduce #'contiguous-hist-integrate-contents-worker index-specs
:initial-value hist))
(defun contiguous-hist-integrate-contents-worker (hist index-spec)
(if (zerop (if (listp index-spec)
(first index-spec)
index-spec))
(reduce #'tensor-+ (if (listp index-spec)
(subseq hist (second index-spec) (1+ (third index-spec)))
hist))
(map (type-of hist)
(lambda (h)
(contiguous-hist-integrate-contents-worker
h (if (listp index-spec)
(cons (1- (first index-spec))
(rest index-spec))
(1- index-spec))))
hist)))
(defun make-contiguous-hist-contents (size-list initial-value)
(if size-list
(let ((size (first size-list)))
(if (single size-list)
(make-array (first size-list) :initial-element initial-value)
(let* ((result (make-array size)))
(loop for i from 0 below size
do (setf (elt result i)
(make-contiguous-hist-contents
(rest size-list) initial-value)))
result)))
nil))
(defun point-in-bounds (hist point)
(with-accessors ((bin-specs rectangular-hist-bin-specs))
hist
(let ((lower-bounds (mapcar #'second bin-specs))
(upper-bounds (mapcar #'third bin-specs)))
(every (lambda (x y z) (and (<= x y)
(< y z)))
lower-bounds point upper-bounds))))
(defmethod hist-reorder-dimensions ((histogram contiguous-histogram) dim-indices)
(if (equal dim-indices (range 0 (length dim-indices)))
histogram
(let ((result
(make-contiguous-hist (permute (hist-dim-specs histogram)
dim-indices)
:empty-bin-value
(hist-empty-bin-value histogram)
:default-increment
(hist-default-increment histogram))))
(loop
for bin-value in (hist-bin-values histogram)
do (hist-insert result
(permute (rest bin-value)
dim-indices)
(first bin-value)))
result)))
(defmethod type-constructor ((hist contiguous-histogram))
#'make-contiguous-hist)
| 15,409 | Common Lisp | .lisp | 347 | 31.659942 | 84 | 0.559577 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 2be28fb25e8c4ad51bb592ac73e1309f8b265046d9352fa834ccb1fd021d83c4 | 1,472 | [
-1
] |
1,473 | categorical-histogram.lisp | ghollisjr_cl-ana/histogram/categorical-histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.histogram)
;; I've realized that histograms are an instance of a more general
;; idea: Categorization/Grouping. The categories are the bin ranges,
;; and can be represented by the bin centers as long as all bin
;; properties are known from this (it seems obvious but it took a
;; while to realize).
;;
;; Also: sparse and contiguous histograms are provided for efficiency
;; reasons only, since categorical-histograms are general enough for
;; any histogramming, including nonuniform-binning
(defclass categorical-histogram (histogram)
((bin-table
:initarg :bin-table
:initform (make-hash-table :test 'equal)
:accessor cathist-bin-table)))
(defun make-categorical-hist
(dim-names
&key
default-increment
empty-bin-value)
#k(make-instance 'categorical-histogram
:dim-names dim-names
:ndims (length dim-names)
&when-keys
default-increment
empty-bin-value))
(defun make-cathist (&rest args)
"Short form of make-categorical-hist"
(apply #'make-categorical-hist args))
(defmethod type-constructor ((hist categorical-histogram))
#'make-cathist)
(defmethod empty-copy ((hist categorical-histogram))
(with-slots (dim-names default-increment empty-bin-value)
hist
(make-cathist dim-names
:default-increment default-increment
:empty-bin-value empty-bin-value)))
(defmethod hist-insert ((hist categorical-histogram)
datum &optional weight)
(with-slots (bin-table empty-bin-value default-increment)
hist
(let ((weight (if weight weight default-increment)))
(if (gethash datum bin-table)
(incf (gethash datum bin-table)
weight)
(setf (gethash datum bin-table)
(+ empty-bin-value weight)))))
hist)
(defmethod hist-point-ref ((hist categorical-histogram)
point)
(with-slots (bin-table)
hist
(aif (gethash point bin-table)
it
(hist-empty-bin-value hist))))
(defmethod hist-bin-values ((hist categorical-histogram))
(with-slots (bin-table)
hist
(loop
for k being the hash-keys in bin-table
for v being the hash-values in bin-table
collecting (cons v k))))
(defmethod hist-total-integral ((hist categorical-histogram))
(sum (mapcar #'car
(hist-bin-values hist))))
(defmethod hist-integrate ((hist categorical-histogram) &rest axes)
(with-slots (ndims
dim-names
empty-bin-value
default-increment)
hist
(let* ((indices
(get-dim-indices dim-names axes))
(remaining-dim-names
(except-at dim-names indices))
(remaining-indices
(except-at (range 0 (1- ndims)) indices))
(result
(make-cathist remaining-dim-names
:empty-bin-value empty-bin-value
:default-increment default-increment)))
(loop
for (count . centers) in (hist-bin-values hist)
do (hist-insert result
(at-indices centers remaining-indices)
count))
result)))
;; for hist-project
(defmethod hist-reorder-dimensions ((hist categorical-histogram)
dim-indices)
(let ((result (empty-copy hist)))
(loop
for (count . centers) in (hist-bin-values hist)
do (hist-insert result
(permute centers dim-indices)
count))
result))
(defmethod hist-slice ((hist categorical-histogram) &rest dims)
(let* ((empty-bin-value
(hist-empty-bin-value hist))
(default-increment
(hist-default-increment hist))
(type-constructor
(type-constructor hist))
(all-dim-names
(hist-dim-names hist))
(all-dims
(hdn hist))
(slice-indices (get-dim-indices all-dims dims))
(remaining-dim-names
(except-at all-dim-names slice-indices))
(remaining-indices
(except-at (range 0 (1- (hist-ndims hist)))
slice-indices))
(bin-values (hbv hist))
(result (make-hash-table :test 'equal)))
(loop
for (count . centers) in bin-values
do (let* ((slice-centers
(at-indices centers slice-indices))
(other-centers
(at-indices centers remaining-indices))
(h (gethash slice-centers result)))
(when (not h)
(setf h (funcall
type-constructor
remaining-dim-names
:empty-bin-value empty-bin-value
:default-increment default-increment))
(setf (gethash slice-centers result)
h))
(hins h other-centers count)))
result))
| 5,902 | Common Lisp | .lisp | 153 | 29.575163 | 70 | 0.610548 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 86ba8abc6ae013287045fdbac1339fa46a4373d70c12283fd40d6b2bbf5c1bdb | 1,473 | [
-1
] |
1,474 | uniform-binning.lisp | ghollisjr_cl-ana/histogram/uniform-binning.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; Provides common functions for contiguous-histogram and
;;;; sparse-histogram due to uniform binning
(in-package :cl-ana.histogram)
(defun get-bin-index (data-list bin-specs)
"Computes the bin-index-list from the data-list (a data point).
Does so for all axes, returns nil if overflow/underflow occurs.
Make sure that data-list and bin-specs have the same length before
calling this function; it is unchecked in this respect for speed."
(labels
((get-bin-index-worker (data-list bin-specs &optional result)
(if data-list ; I'm intentionally ignoring length differences
; between data-list and bin-specs
(let* ((datum (first data-list))
(bin-spec (first bin-specs))
(bin-index (get-axis-bin-index datum bin-spec)))
(if (not (or (equal bin-index :underflow)
(equal bin-index :overflow)))
(get-bin-index-worker (rest data-list)
(rest bin-specs)
(cons bin-index result))))
(nreverse result))))
(get-bin-index-worker data-list bin-specs)))
(defun get-axis-bin-index (value bin-spec)
"Computes the bin index (-1 underflow, binnum overflow) for value
given the bin-spec for a single axis/dimension."
(let* ((nbins (first bin-spec))
(binlo (second bin-spec))
(binhi (third bin-spec))
(delta (/ (- binhi binlo) nbins)))
(labels ((internal-bin (i)
(cond ((< i 0) :underflow)
((> i (- nbins 1)) :overflow)
(t i))))
(internal-bin
(floor
(/ (- value binlo) delta))))))
(defun get-bin-center-worker (bin-spec index)
(let* ((nbins (first bin-spec))
(binlo (second bin-spec))
(binhi (third bin-spec))
(delta (/ (- binhi binlo) nbins)))
(+ binlo
(/ delta 2)
(* delta
index))))
(defun get-bin-center (bin-specs bin-index)
(mapcar #'get-bin-center-worker bin-specs bin-index))
| 2,704 | Common Lisp | .lisp | 67 | 36.761194 | 70 | 0.680867 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e23b2045c452a269a4e074ebac25b370f5238ff77e4bc284fd4543a542bac41e | 1,474 | [
-1
] |
1,475 | sparse-histogram.lisp | ghollisjr_cl-ana/histogram/sparse-histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; Implements sparse histogram with uniform binning
(in-package :cl-ana.histogram)
(defclass sparse-histogram (rectangular-histogram)
((bin-value-map
:accessor sparse-hist-value-map
:initarg :value-map
:initform nil
:documentation "Hash table storing the histogram bin values which
have been set.")))
(defun make-sparse-hist (dim-spec-plists &key
empty-bin-value
default-increment
hash-table-test)
"dim-spec-plist is a plist with the following
fields: :name :low :high :nbins, which specify the axis name,
bin-low-edge, bin-high-edge, and the number of bins on the axis
respectively.
Example usage: (make-sparse-hist (list (list :name \"x\" :nbins
10 :low 50 :high 55))) would create a sparse histogram with one
dimension named \"x\" with 10 bins, low bin edge 50 and high bin edge
55."
(let* ((dim-names (mapcar (lambda (spec) (getf spec :name))
dim-spec-plists))
(ndims (length dim-names))
(bin-specs (mapcar (lambda (s)
(list (getf s :nbins)
(getf s :low)
(getf s :high)))
dim-spec-plists))
(default-args (progn
(let ((result ()))
(when empty-bin-value
(push empty-bin-value result)
(push :empty-bin-value result))
(when default-increment
(push default-increment result)
(push :default-increment result))
result))))
(apply #'make-instance 'sparse-histogram
:ndims ndims
:dim-names dim-names
:bin-specs bin-specs
:value-map (make-hash-table
:test (if hash-table-test
hash-table-test
'equal))
default-args)))
(defun make-shist (dim-spec-plists &key empty-bin-value default-increment)
"Abbreviation for make-sparse-hist"
#k(make-sparse-hist dim-spec-plists
&when-keys
empty-bin-value
default-increment))
(defmethod empty-copy ((h sparse-histogram))
(with-slots (empty-bin-value
default-increment)
h
(make-shist (hist-dim-specs h)
:empty-bin-value empty-bin-value
:default-increment default-increment)))
;; For now I'll use this; since I'm not taking into account empty bins
;; during the other calculations I guess I'm not going to do it here
;; either--emphasis on for now.
(defmethod hist-total-integral ((hist sparse-histogram))
(let ((bin-values (hist-bin-values hist)))
(if bin-values
(sum (mapcar #'car bin-values))
0)))
(defmethod hist-integrate ((histogram sparse-histogram) &rest axes)
(if axes
(with-accessors ((ndims hist-ndims)
(dim-names hist-dim-names)
(empty-bin-value hist-empty-bin-value)
(default-increment hist-default-increment)
(value-map sparse-hist-value-map)
(bin-specs rectangular-hist-bin-specs))
histogram
(if (length-equal axes ndims)
(hist-total-integral histogram)
(flet ((index-key (x)
(if (listp x)
(first x)
x)))
(let* ((axis-name-or-indices (mapcar (lambda (x)
(if (listp x)
(first x)
x))
axes))
(dim-indices (get-dim-indices dim-names axis-name-or-indices))
(point-bounds
(mapcar (lambda (x)
(when (listp x)
(rest x)))
axes))
(index-bounds
(mapcar (lambda (point-bound bin-spec)
(when point-bound
(let ((low-index
(get-axis-bin-index (first point-bound)
bin-spec))
(high-index
(get-axis-bin-index (second point-bound)
bin-spec)))
(list (if (equal low-index :underflow)
0
low-index)
(if (equal high-index :overflow)
(1- (first bin-spec))
high-index)))))
point-bounds
bin-specs))
(index-specs (mapcar (lambda (x y)
(if y
(cons x y)
x))
dim-indices
index-bounds))
(index-specs-copy (copy-list index-specs))
(sorted-index-specs (sort index-specs-copy #'>
:key #'index-key))
(unique-sorted-index-specs
(reduce
(lambda (x y) (adjoin y x
:test #'equal
:key #'index-key))
sorted-index-specs
:initial-value ()))
(unique-sorted-indices
(mapcar (lambda (x)
(if (listp x)
(first x)
x))
unique-sorted-index-specs))
(new-ndims (cl:- ndims (length unique-sorted-indices)))
(new-dim-names (except-at dim-names unique-sorted-indices
:uniquely-sorted t))
(new-bin-specs (except-at bin-specs unique-sorted-indices
:uniquely-sorted t)))
(make-instance 'sparse-histogram
:ndims new-ndims
:dim-names new-dim-names
:empty-bin-value empty-bin-value
:default-increment default-increment
:value-map (sparse-hist-integrate-contents
value-map
index-specs
;;unique-sorted-index-specs
empty-bin-value)
:bin-specs new-bin-specs)))))
histogram))
(defmethod hist-insert ((hist sparse-histogram) datum &optional weight)
(with-accessors ((value-map sparse-hist-value-map)
(empty-bin-value hist-empty-bin-value))
hist
(let ((point (mklist datum))
(weight-factor (if weight
weight
(hist-default-increment hist))))
(cond-setf (hist-point-ref hist point)
(+ (hist-point-ref hist point)
weight-factor)
:place)
hist)))
(defmethod hist-index-ref ((hist sparse-histogram) index-list)
"Unchecked, assumes you know what the allowed index values are."
(with-accessors ((value-map sparse-hist-value-map)
(empty-bin-value hist-empty-bin-value))
hist
(gethash index-list value-map empty-bin-value)))
(defmethod (setf hist-index-ref) (value (hist sparse-histogram) index-list)
"Unchecked, assumes you know what the allowed index values are."
(with-accessors ((value-map sparse-hist-value-map))
hist
(setf (gethash index-list value-map) value)))
(defmethod hist-point-ref ((hist sparse-histogram) point)
"Checked access to the bin value via a point. Returns nil if the
point is not inside the histogram domain."
(with-accessors ((bin-specs rectangular-hist-bin-specs)
(value-map sparse-hist-value-map)
(empty-bin-value hist-empty-bin-value))
hist
(let ((bin-index (get-bin-index point bin-specs)))
(when bin-index
(gethash bin-index value-map empty-bin-value)))))
(defmethod (setf hist-point-ref) (value (hist sparse-histogram) point)
"Checked setf to the bin value via a point. Does nothing & returns
nil if the point is not inside the histogram domain."
(with-accessors ((bin-specs rectangular-hist-bin-specs)
(value-map sparse-hist-value-map))
hist
(let ((bin-index (get-bin-index point bin-specs)))
(when bin-index
(setf (gethash bin-index value-map) value)))))
(defmethod hist-bin-values ((hist sparse-histogram))
(with-accessors ((value-map sparse-hist-value-map)
(bin-specs rectangular-hist-bin-specs))
hist
(iter:iter
(iter:for (key val) in-hashtable value-map)
(iter:collect (cons val (get-bin-center bin-specs key))))))
;;; Generic Math functions:
;; It may not be in the best style to implement mathematical functions
;; on sparse histograms. Reason: They use un-ordered containers (hash
;; tables) for the data. That means that, unless assumptions are made
;; about the default value, it will be extremely inefficient to try to
;; do computations using the sparse histograms. It would be better to
;; do computations with contiguous histograms by first integrating the
;; sparse histogram into a size small enough to be operated on. But I
;; may change my mind and implement the basic functions anyways.
;;; Internal use functions
(defun sparse-hist-integrate-contents (value-map index-specs empty-bin-value)
"Integrates over the bin value hash table according to the
index-specs."
(reduce (rcurry #'sparse-hist-integrate-contents-worker empty-bin-value)
index-specs
:initial-value value-map))
(defun sparse-hist-integrate-contents-worker (value-map index-spec empty-bin-value)
"Integrates the bin value hash table along the index in index-spec;
if index-spec is a list, then the axis index is taken from the first
value, and then the index low/high cutoffs are taken from the second
and third elements respectively."
(let* ((test (hash-table-test value-map))
(result (make-hash-table :test test)))
(if (listp index-spec)
;; handle case with bounds
(let ((axis (first index-spec))
(low-bound (second index-spec))
(high-bound (third index-spec)))
(iter:iter
(iter:for (key val) in-hashtable value-map)
(let ((this-axis (elt key axis)))
(when (and (<= low-bound this-axis)
(< this-axis high-bound))
(setf (gethash (except-nth key axis) result)
(+ (gethash (except-nth key axis) result empty-bin-value)
val))))))
;; handle the unbounded case
(let ((axis index-spec))
(iter:iter
(iter:for (key val) in-hashtable value-map)
(setf (gethash (except-nth key axis) result)
(+ (gethash (except-nth key axis) result empty-bin-value)
val)))))
result))
(defmethod hist-reorder-dimensions ((histogram sparse-histogram) dim-indices)
(if (equal dim-indices (range 0 (length dim-indices)))
histogram
(let ((result
(make-sparse-hist (permute (hist-dim-specs histogram)
dim-indices)
:empty-bin-value
(hist-empty-bin-value histogram)
:default-increment
(hist-default-increment histogram))))
(loop
for bin-value in (hist-bin-values histogram)
do (hist-insert result
(permute (rest bin-value)
dim-indices)
(first bin-value)))
result)))
(defmethod type-constructor ((hist sparse-histogram))
#'make-sparse-hist)
| 13,101 | Common Lisp | .lisp | 283 | 32.074205 | 83 | 0.541064 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 7729085475e486306a249307485b4c90097e8fccdb1e380b6f57f8c0c0a58821 | 1,475 | [
-1
] |
1,476 | variable-binning-histogram.lisp | ghollisjr_cl-ana/histogram/variable-binning-histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.histogram)
;; Each bin low edge is mapped to the count of for that bin. The low
;; edge is chosen so that
(defclass variable-binning-histogram (histogram)
((dim-specs
:accessor variable-binning-histogram-dim-specs
:initarg :dim-specs
:initform nil
:documentation "List of bin edges for each dimension")
(content
:accessor variable-binning-histogram-content
:initarg :content
:initform (make-hash-table :test #'equal)
:documentation "Hash table mapping from low-edge list to count")
;; internal usage:
(binary-trees
:accessor variable-binning-histogram-binary-trees
:initarg :binary-trees
:initform nil
:documentation "List of binary trees for each dimension used to
lookup bin content")
(maxes
:accessor variable-binning-histogram-maxes
:initarg :maxes
:initform nil
:documentation "List of maximum values for each dimension; for
optimization.")))
(defun make-variable-binning-histogram
(names-specs
&key
(empty-bin-value 0)
(default-increment 1))
"Creates a variable-binning-histogram. names-specs should be an
alist mapping from dimension name to the list of bin edges for that
dimension (i.e. a list of lists with the first elements being the
dimension names)."
(make-instance 'variable-binning-histogram
:ndims (length names-specs)
:dim-names (mapcar #'car names-specs)
:empty-bin-value empty-bin-value
:default-increment default-increment
:dim-specs (mapcar #'cdr names-specs)
:binary-trees (mapcar #'make-balanced-tree
(mapcar #'cdr names-specs))
:maxes (mapcar (lambda (x)
(first (last x)))
names-specs)))
(defun make-vhist (names-specs
&key
(empty-bin-value 0)
(default-increment 1))
(make-variable-binning-histogram
names-specs
:empty-bin-value empty-bin-value
:default-increment default-increment))
(defmethod hist-insert ((hist variable-binning-histogram)
datum
&optional
weight)
(with-accessors ((low-edges variable-binning-histogram-dim-specs)
(btrees variable-binning-histogram-binary-trees)
(content variable-binning-histogram-content)
(maxes variable-binning-histogram-maxes)
(empty-bin-value hist-empty-bin-value)
(default-increment hist-default-increment))
hist
(flet ((uncar (x)
(if (consp x)
(car x)
x)))
(let ((indices
(mapcar (lambda (bt d h)
(when (< d h)
(uncar (bref bt d))))
btrees datum maxes)))
(when (every #'identity indices)
(let ((weight (if weight
weight
default-increment))
(start (if (gethash indices content)
(gethash indices content)
empty-bin-value)))
(setf (gethash indices content)
(+ start weight)))))))
hist)
;; Map->alist
(defmethod map->alist ((obj variable-binning-histogram))
(let* ((edges-list
(variable-binning-histogram-dim-specs
obj))
(bin-widths-list
(mapcar (lambda (edges)
(- (rest edges) edges))
edges-list))
(edge->width-ht-list
(loop
for edges in edges-list
for bin-widths in bin-widths-list
collecting (let ((result (make-hash-table :test 'equal)))
(loop
for edge in edges
for width in bin-widths
do (setf (gethash edge result)
width))
result)))
(content
(variable-binning-histogram-content obj)))
(loop
for point being the hash-keys in content
for count being the hash-values in content
collecting (cons (loop
for p in point
for edge->width in edge->width-ht-list
collecting (+ p
(* 0.5
(gethash p edge->width))))
count))))
;; Copying
(defmethod copy-hist ((obj variable-binning-histogram)
&optional empty-p)
(let ((result (make-variable-binning-histogram
(zip (hist-dim-names obj)
(variable-binning-histogram-dim-specs
obj))
:empty-bin-value
(hist-empty-bin-value obj)
:default-increment
(hist-default-increment obj))))
(if empty-p
result
(let ((ht (variable-binning-histogram-content obj))
(result-ht
(variable-binning-histogram-content result)))
(loop
for indices being the hash-keys in ht
for count being the hash-values in ht
do (setf (gethash indices result-ht)
count))
result))))
;; Arithmetic functions:
;; Assumes that the histograms have congruent binnings
(defmethod add ((h1 variable-binning-histogram)
(h2 variable-binning-histogram))
(let ((h2-content
(variable-binning-histogram-content h2))
(result
(copy-hist h1)))
(loop
for indices being the hash-keys in h2-content
for count being the hash-values in h2-content
do
(hins result indices count))
result))
(defmethod sub ((h1 variable-binning-histogram)
(h2 variable-binning-histogram))
(let ((h2-content
(variable-binning-histogram-content h2))
(result
(copy-hist h1)))
(loop
for indices being the hash-keys in h2-content
for count being the hash-values in h2-content
do (hins result indices (- count)))
result))
(defmethod mult ((h1 variable-binning-histogram)
(h2 variable-binning-histogram))
(let ((h1-content
(variable-binning-histogram-content h1))
(h2-content
(variable-binning-histogram-content h2))
(result
(copy-hist h1 t)))
(loop
for indices being the hash-keys in h1-content
for count1 being the hash-values in h1-content
do (let ((count2 (gethash indices h2-content)))
(when count2
(hins result indices (mult count1 count2)))))
result))
(defmethod unary-div ((h variable-binning-histogram))
(let ((h-content
(variable-binning-histogram-content h))
(result
(copy-hist h t)))
(loop
for indices being the hash-keys in h-content
for count being the hash-values in h-content
do (hins result indices (unary-div count)))
result))
(defmethod div ((h1 variable-binning-histogram)
(h2 variable-binning-histogram))
(let ((h1-content
(variable-binning-histogram-content h1))
(h2-content
(variable-binning-histogram-content h2))
(result
(copy-hist h1 t)))
(loop
for indices being the hash-keys in h1-content
for count1 being the hash-values in h1-content
do (let ((count2 (gethash indices h2-content)))
(when count2
(hins result indices (div count1 count2)))))
result))
;; NOTE: This method differs from the usage of other protected-div
;; methods in that histograms have a default bin value. For this
;; reason, the default bin value for the first histogram is used by
;; default instead of 0.
(defmethod protected-div ((h1 variable-binning-histogram)
(h2 variable-binning-histogram)
&key protected-value)
(let* ((protected-value
(if protected-value
protected-value
(hist-empty-bin-value h1)))
(h1-content
(variable-binning-histogram-content h1))
(h2-content
(variable-binning-histogram-content h2))
(result
(copy-hist h1 t)))
(loop
for indices being the hash-keys in h1-content
for count1 being the hash-values in h1-content
do (let ((count2 (gethash indices h2-content)))
(when count2
(hins result indices
(protected-div count1 count2
:protected-value
protected-value)))))
result))
| 9,786 | Common Lisp | .lisp | 251 | 28.079681 | 70 | 0.576935 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 0f0ab2abcd9a31a132f6b8b1685a330fa239e85960951f0489cde0711b315716 | 1,476 | [
-1
] |
1,477 | test.lisp | ghollisjr_cl-ana/histogram/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana)
(in-package :cl-ana)
(defparameter *ndata* 1000000)
(defparameter *x-data* nil)
(defparameter *y-data* nil)
(defun fill-random ()
(setf *x-data* nil)
(setf *y-data* nil)
(iter
(for i from 0 to (1- *ndata*))
(push (* 2d0 (/ (random 100) 100)) *x-data*)
(push (* 2d0 (/ (random 100) 100)) *y-data*)))
(defun contiguous-hist-test ()
(defparameter *hist*
(make-contiguous-hist (list (list :name "x"
:nbins 10
:low 0d0
:high 5d0)
(list :name "y"
:nbins 3
:low 0
:high 2))
:default-increment (+- 1 1)))
;;(fill-random)
(defparameter *data*
(mapcar #'list *x-data* *y-data*))
(dolist (d *data*)
(hist-insert *hist* d))
(hist-integrate *hist* "x"))
(defun sparse-hist-test ()
(defparameter *hist*
(make-sparse-hist (list (list :name "x"
:nbins 10
:low 0d0
:high 5d0)
(list :name "y"
:nbins 3
:low 0
:high 2))
:default-increment (+- 1 1)))
(defparameter *ndata* 1000000)
;;(fill-random)
(defparameter *data*
(mapcar #'list *x-data* *y-data*))
(dolist (d *data*)
(hist-insert *hist* d))
(hist-integrate *hist* "x"))
| 2,144 | Common Lisp | .lisp | 67 | 27.238806 | 70 | 0.616699 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | c6657b569dcd23e75732d8c62961cd62c8972c25106219f77df63cec0387c992 | 1,477 | [
-1
] |
1,478 | histogram.lisp | ghollisjr_cl-ana/histogram/histogram.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; Histogram interface. Most of the interesting mathematical
;;;; features like summing, multiplying, scaling histograms are done
;;;; via the generic math (gmath) library.
(in-package :cl-ana.histogram)
(defclass histogram ()
((ndims
:accessor hist-ndims
:initarg :ndims
:initform 0
:documentation "Number of dimensions of the histogram")
(dim-names
:accessor hist-dim-names
:initarg :dim-names
:initform ()
:documentation "Names of the dimension axes")
(empty-bin-value
:accessor hist-empty-bin-value
:initarg :empty-bin-value
:initform 0
:documentation "Default value for a bin which has had no events
added")
(default-increment
:accessor hist-default-increment
:initarg :default-increment
:initform 1
:documentation "Default amount by which bins are incremented;
i.e. unless overridden by a weight factor.")))
(defgeneric hist-total-integral (histogram)
(:documentation "Returns the number of entries in the histogram,
i.e. the full integral of the histogram"))
(defgeneric hist-integrate (histogram &rest axes)
(:documentation "Integrates the histogram along the dimensions/axes
specified. Axes are specified using the lispified dimension name
(a string); specifying by index is for internal use but can be done.
Also in order to support partial domain integration, each axis in the
axes list can also be a list of three values: the axis name, the lower
bound over which to integrate, and the upper bound."))
(defgeneric hist-project (histogram &rest axes)
(:documentation "Projects the histogram onto specified axes by
integrating over the other axes. As with integrate, the axes are
specified using name. Comes with a default implementation that
should be good for most cases; specialize only if necessary.")
(:method (histogram &rest axes)
(with-accessors ((dim-names hist-dim-names)
(ndims hist-ndims))
histogram
(let* ((selected-axis-indices
(get-dim-indices dim-names axes))
(integrate-axes
(set-difference (range 0 (1- ndims))
selected-axis-indices))
(disordered-hist
(apply #'hist-integrate histogram integrate-axes))
(new-selected-axis-indices
(condense-indices selected-axis-indices)))
(hist-reorder-dimensions
disordered-hist
new-selected-axis-indices)))))
(defgeneric hist-reorder-dimensions (histogram dim-indices)
(:documentation "Re-arranges the data in the histogram so that the
dimensions are permuted according to dim-indices."))
(defgeneric hist-insert (histogram datum &optional weight)
(:documentation "Inserts a value specified by the datum (An atom for
1-D or a list of values for more dimensions) into the histogram;
i.e. increments the bin value by weight (which defaults to 1 or
whatever you set). Returns histogram (though it does change the
histogram state)."))
;;;; Not sure if index-ref functions are appropriate for all types of
;;;; histograms
(defgeneric hist-index-ref (histogram indices)
(:documentation "Like aref for an array, but for histograms using
the index list."))
(defgeneric (setf hist-index-ref) (value histogram indices)
(:documentation "hist-index-ref is setf-able"))
(defgeneric hist-point-ref (histogram point)
(:documentation "Like hist-index-ref but looks up the cell in which
point would lie.")
;; default method for non-histograms:
(:method (x point)
x))
(defgeneric (setf hist-point-ref) (value histogram point)
(:documentation "hist-point-ref is setf-able"))
(defgeneric hist-bin-values (histogram)
(:documentation "Returns a list of bin values consed to the bin
center of the bin"))
(defmethod map->alist ((hist histogram))
"Since fitting needs 1-D histograms to give not a list with the cdr
being a singleton list but a cons with the cdr being the actual bin
center, we have to do some footwork here."
(let* ((hist-bin-values (hist-bin-values hist))
(alist-maker
(if (single (cdr (first hist-bin-values)))
(lambda (x)
(let ((car (car x))
(cdr (first (cdr x))))
(cons cdr car)))
(lambda (x)
(let ((car (car x))
(cdr (cdr x)))
(cons cdr car))))))
(mapcar alist-maker
(hist-bin-values hist))))
(defgeneric hist-slice (hist &rest dims)
(:documentation "Slices up the histogram along each dimension in
dims. Returns a hash table mapping the bin center list for each
dimension in dims to a histogram of the same kind as hist which has
only the leftover dimensions."))
(defun getslice (slices bin)
"Function for finding a slice from (hist-slice hist) via minimizing
the sum of squares of the vector difference between bin and each slice
center."
(ensure-lists (bin)
(gethash (minimum (hash-keys slices)
:key (lambda (s)
(sum (expt (- s bin) 2))))
slices)))
;; Functional access to histograms:
(defun hist-map (fn hist)
"hist-map maps the function fn over the histogram hist bin-by-bin.
fn should take as its first argument the bin value and the rest the
bin center values for each dimension of the histogram as keyword
parameters. The keyword arguments should be the lispified dimension
names of the histogram. fn should return the new bin value for that
bin; for a bin to not be re-filled in the resulting histogram, return
nil.
Note that a particularly useful strategy is to use &allow-other-keys
so that you do not have to worry about all the dimensions in the
histogram."
(let* ((result
(funcall (type-constructor hist)
(hist-dim-specs hist)
:empty-bin-value
(hist-empty-bin-value hist)
:default-increment
(hist-default-increment hist)))
(dim-names (hist-dim-names hist))
(dim-keywords
(mapcar (compose #'keywordify #'lispify)
dim-names)))
(reduce (lambda (h x)
(when x
(hist-insert h
(car x)
(cdr x)))
h)
(mapcar
(lambda (x)
(let* ((key-args (mapcan #'list dim-keywords (rest x)))
(count (first x))
(result
(apply fn count key-args)))
(when result
(cons (rest x)
result))))
(hist-bin-values hist))
:initial-value result)))
;; I'm keeping the first argument as the bin count since I don't want
;; to clobber any dimensions of the histogram which might wish to be
;; called count or anything else I would happen to choose.
(defun hist-filter (fn hist)
"Re-fills entries in the histogram only when fn returns non-nil.
fn should take as its first argument the bin count and the rest of the
arguments being the bin centers for each dimension of the histogram as
keyword arguments. The keyword arguments should be the lispified
dimension names of the histogram."
(hist-map (lambda (count &rest xs)
(when (apply fn count xs)
count))
hist))
;;;; Ease of use functions:
(defun hist-insert-list (histogram data-list)
"Inserts each data list in data-lists into the histogram. Accepts
data as either atom for 1-D or lists for any dimensionality."
(loop
for datum in data-list
do (hist-insert histogram (mklist datum))))
;;;; Abbreviations:
(defun hins (histogram datum &optional weight)
"Abbreviation for hist-insert"
(apply #'hist-insert
histogram
datum
(when weight (list weight))))
(defun htint (histogram)
"Abbreviation for hist-total-integral"
(hist-total-integral histogram))
(defun hint (histogram &rest axes)
"Abbreviation for hist-integrate"
(apply #'hist-integrate histogram axes))
(defun hproj (histogram &rest axes)
"Abbreviation for hist-project"
(apply #'hist-project histogram axes))
(defun hslice (histogram &rest axes)
"Abbreviation for hist-slice"
(apply #'hist-slice histogram axes))
(defun hiref (histogram indices)
"Abbreviation for hist-index-ref"
(hist-index-ref histogram indices))
(defun (setf hiref) (value histogram indices)
(setf (hist-index-ref histogram indices)
value))
(defun hpref (histogram point)
"Abbreviation for hist-point-ref"
(hist-point-ref histogram point))
(defun (setf hpref) (value histogram point)
(setf (hist-point-ref histogram point)
value))
(defun hbv (histogram)
"Abbreviation for hist-bin-values"
(hist-bin-values histogram))
(defun hdn (histogram)
"Abbreviation for hist-dim-names"
(hist-dim-names histogram))
;;;; Generic math: (still need to handle functions with keyword
;;;; arguments)
(defmacro defhistmath-unary (fname)
(with-gensyms (a count centers a-bin-values result)
`(defmethod ,fname ((,a histogram))
(let ((,a-bin-values
(hist-bin-values ,a))
(,result (copy-hist ,a t)))
(loop
for (,count . ,centers) in ,a-bin-values
do (hist-insert ,result
,centers
(,fname ,count)))
,result))))
(defun empty-set (&optional (test 'equal))
(make-hash-table :test test))
(defun set-insert (set object)
(multiple-value-bind (val p)
(gethash object set)
(when (not p)
(setf (gethash object set)
t))
set))
(defun set->list (set)
(loop for x being the hash-keys in set
collecting x))
(defmacro defhistmath-binary (fname)
(with-gensyms (a
b
res
count
all-centers
centers
a-bin-values
b-bin-values
result)
(let ((lrbody
`(let ((,all-centers
(cl-ana.histogram::set->list
(let ((,res (cl-ana.histogram::empty-set)))
(reduce #'cl-ana.histogram::set-insert
(mapcar #'cdr (hbv ,a))
:initial-value ,res)
(reduce #'cl-ana.histogram::set-insert
(mapcar #'cdr (hbv ,b))
:initial-value ,res))))
(,result (copy-hist ,a t)))
(loop
for ,centers in ,all-centers
do (hist-insert ,result
,centers
(,fname (hist-point-ref ,a ,centers)
(hist-point-ref ,b ,centers))))
,result))
(lbody
`(let ((,a-bin-values
(hist-bin-values ,a))
(,result (copy-hist ,a t)))
(loop
for (,count . ,centers) in ,a-bin-values
do (hist-insert ,result
,centers
(,fname ,count (hist-point-ref ,b ,centers))))
,result))
(rbody
`(let ((,b-bin-values
(hist-bin-values ,b))
(,result (copy-hist ,b t)))
(loop
for (,count . ,centers) in ,b-bin-values
do (hist-insert ,result
,centers
(,fname (hist-point-ref ,a ,centers) ,count)))
,result)))
`(progn
(defmethod ,fname ((,a histogram) (,b histogram))
,lrbody)
(defmethod ,fname ((,a histogram) ,b)
,lbody)
(defmethod ,fname (,a (,b histogram))
,rbody)))))
(defun defhistmaths ()
(loop
for fname being the hash-keys in *gmath-generic-map*
for arglist being the hash-values in *gmath-generic-map*
do
(case (length arglist)
(1
(eval `(defhistmath-unary ,fname)))
(2
(eval `(defhistmath-binary ,fname))))))
(defhistmaths)
;; NOTE: This method differs from the usage of other protected-div
;; methods in that histograms have a default bin value. For this
;; reason, the default bin value for the first histogram is used by
;; default instead of 0.
(defmethod protected-div ((a histogram) (b histogram)
&key (protected-value 0))
(let* ((protected-value
(if protected-value
protected-value
(hist-empty-bin-value a)))
(all-centers
(cl-ana.histogram::set->list
(let ((res (cl-ana.histogram::empty-set)))
(reduce #'cl-ana.histogram::set-insert
(mapcar #'cdr (hbv a))
:initial-value res)
(reduce #'cl-ana.histogram::set-insert
(mapcar #'cdr (hbv b))
:initial-value res))))
(result (copy-hist a t)))
(loop
for centers in all-centers
do (hist-insert result
centers
(protected-div (hist-point-ref a centers)
(hist-point-ref b centers)
:protected-value
protected-value)))
result))
(defgeneric copy-hist (hist &optional empty-p)
(:documentation "Returns a filled copy of hist for null empty-p,
otherwise returns empty copy")
(:method (hist &optional empty-p)
(hist-map (if empty-p
(constantly nil)
(lambda (count &key &allow-other-keys)
count))
hist)))
(defun hist-absorb (h1 h2)
"Absorbs the contents of h2 into h1 by filling the contents of h2
into h1"
(loop
for cons in (map->alist h2)
do (hist-insert h1 (car cons) (cdr cons)))
h1)
;; ease of use function:
(defun bin (data
&key
dim-names
mins
maxs
nbins
empty-bin-value
default-increment)
"Creates a sparse histogram determining min, max, and number of bins
from the data.
data can be a list of atoms for 1-D data or a list of lists for any
dimensionality.
dim-names is an optional list of dimension names
mins, maxs, and nbins can be alists mapping from dimension name/index
to a value, or if all dimensions have a value specified, just a list
of values taken to be given in order of dimension.
empty-bin-value and default-increment will be supplied to the
histogram if present."
(when data
(let* ((dimensionality
(let ((d (first data)))
(if (atom d)
1
(length d))))
(dim-names
(if dim-names
dim-names
(loop for i below dimensionality
collect nil))))
(flet ((mkspecs (specs)
(if specs
(if (consp (first specs))
;; alists
(labels ((rec (spcs names result)
;; spcs should be a hash-table mapping
;; from whatever is in names to a value
(if names
(let ((spec (gethash (first names)
spcs)))
(rec spcs (rest names) (cons spec result)))
(nreverse result))))
(rec (map->hash-table specs 'equal)
(if dim-names
dim-names
(range 0 (1- dimensionality)))
nil))
;; full spec list
specs)
(loop for i below dimensionality
collect nil))))
;; each spec has either an explicit value or nil for each
;; dimension
(let ((min-specs (mkspecs mins))
(max-specs (mkspecs maxs))
(nbin-specs (mkspecs nbins))
(data-per-dim
(transpose (mapcar #'mklist data))))
(when (or (not (length-equal min-specs dimensionality))
(not (length-equal max-specs dimensionality))
(not (length-equal nbin-specs dimensionality)))
(error "Inconsistent histogram dimensionality"))
;; final version of mins, maxs and nbins
(let* ((hist-specs
(loop
for min in min-specs
for max in max-specs
for n in nbin-specs
for name in dim-names
for d in data-per-dim
collect
(let ((mi
(if min
min
(minimum d)))
(ma
(if max
max
(maximum d)))
(n
(if n n (ceiling (sqrt (length d))))))
(let (real-min real-max)
(if (and min
max)
;; min & max both explicit
(progn
(setf real-min min)
(setf real-max max))
;; need delta
(let ((delta (/ (- ma mi) n)))
(setf real-min
(if min
min
(- mi (* 0.5 delta))))
(setf real-max
(if max
max
(+ ma (* 0.5 delta))))))
(list :low real-min
:high real-max
:nbins (floor n)
:name name)))))
(result
(apply #'make-sparse-hist
hist-specs
(when-keywords
empty-bin-value
default-increment))))
(loop
for d in data
do (hins result (mklist d)))
result))))))
;; Utility for normalizing histogram intelligently:
(defun normalize-histogram (h &optional (norm :integral))
"Normalizes a histogram using either the integral or setting a
point's value to 1. Set norm to be a bin point value to choose a
specific point, or to NIL for no normalization. Set norm to a
function to normalize via an integral over a filtered subset of a
histogram."
(flet ((hnorm (h) (/ h (htint h)))
(hinorm (h f)
(/ h (htint (hist-filter f h))))
(hpnorm (h p)
(/ h (hpref h (list p)))))
(let ((normfn
(cond
;; no normalization
((null norm)
#'identity)
;; normalization by integral
((eq norm :integral)
#'hnorm)
;; normalization by filtered integral
((functionp norm)
(lambda (h)
(hinorm h norm)))
;; normalization by W point
(t
(lambda (h)
(hpnorm h norm))))))
(funcall normfn h))))
;;;; Internal use:
(defun condense-indices (indices)
(let* ((sorted (sort (copy-list indices) #'<))
(map
(let ((result (make-hash-table :test 'equal)))
(loop
for i from 0
for s in sorted
do (setf (gethash s result)
i))
result)))
(mapcar (lambda (x)
(gethash x map))
indices)))
(defun get-dim-indices (dim-names axes)
"Converts axes from a list of either index or name into a list of
indices by looking up the name when necessary."
(mapcar
(lambda (s)
(if (stringp s)
(position s dim-names :test #'equal)
s))
axes))
| 21,414 | Common Lisp | .lisp | 534 | 28.479401 | 83 | 0.553208 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 4d1c66d695a4689a8d3b42da3520b6d0230459801ee33d661ad15287b3aff7a4 | 1,478 | [
-1
] |
1,479 | package.lisp | ghollisjr_cl-ana/memoization/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; package.lisp
(defpackage #:cl-ana.memoization
(:use #:cl
#:alexandria)
(:export :memolet
:memoize
:unmemoize
:defun-memoized
:get-memo-map
:reset-memo-map))
| 1,103 | Common Lisp | .lisp | 30 | 33.333333 | 70 | 0.672575 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e35288d24643488956a7983bda3f46837c8a142b33d786574ce6d640844a7827 | 1,479 | [
-1
] |
1,480 | memoization.lisp | ghollisjr_cl-ana/memoization/memoization.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;; Memoized functions remember the previous calls of the function and
;;; look-up the return value from the last time the function was
;;; called.
;;;
;;; This implementation uses hash tables to store the previous call values.
;;;
;;; I am still unsure whether or not to expose access to the
;;; memoization hash table, at the moment it is not exposed.
(in-package :cl-ana.memoization)
(eval-when (:compile-toplevel :load-toplevel :execute)
(defvar *memoized-map* (make-hash-table :test 'equal)
"Hash table mapping each memoized function to its value hash
table."))
(defun get-memo-map (memo-fn)
"Returns the memoized function's value hash table."
(gethash memo-fn *memoized-map*))
(defun reset-memo-map (memo-fn)
"Resets the memoization hash table for memo-fn"
(when (gethash memo-fn *memoized-map*)
(clrhash (gethash memo-fn *memoized-map*))))
(defmacro memoize (fn &key (test 'equal))
"Macro for memoizing any function; test argument allows you to
specify how arguments will be looked up."
(with-gensyms (memoized
lookup-value
lookup-stored-p
return-value
args
table
xs)
`(let* ((,table
(make-hash-table :test ',test))
(,memoized
(lambda (&rest ,xs)
(let ((,args ,xs)) ; for accidental capture
(multiple-value-bind
(,lookup-value ,lookup-stored-p)
(gethash ,args ,table)
(if ,lookup-stored-p
,lookup-value
(let ((,return-value
(apply ,fn ,args)))
(setf (gethash ,args ,table)
,return-value)
,return-value)))))))
(setf (gethash ,memoized *memoized-map*)
,table)
,memoized)))
(defmacro memolet (memo-fns &body body)
"A macro for defining mutually recursive memoized functions and
executing body with knowledge of them. Cannot access the lookup
tables via *memoized-map* in the body, since this would prevent
garbage collection of the memoized function hash tables."
(with-gensyms (tables lookup-value lookup-stored-p args)
(let ((tabs (loop for i in memo-fns
collecting '(make-hash-table :test 'equal)))
(gsyms (loop for i in memo-fns
collecting (gensym))))
`(let ,(loop for tab in tabs
for gsym in gsyms
collecting `(,gsym ,tab))
(labels
(,@(loop
for mf in memo-fns
for gsym in gsyms
collecting
(destructuring-bind (self args-list &body body)
mf
`(,self (&rest ,args)
(multiple-value-bind
(,lookup-value ,lookup-stored-p)
(gethash ,args ,gsym)
(if ,lookup-stored-p
,lookup-value
(setf (gethash ,args ,gsym)
(destructuring-bind ,args-list
,args
,@body))))))))
;; ,@(loop
;; for gsym in gsyms
;; for mf in memo-fns
;; collecting `(setf (gethash (function ,(first mf))
;; *memoized-map*)
;; ,gsym))
,@body)))))
(defun unmemoize (fn)
"Removes fn from the memoization lookup table; this prevents access
to the lookup map from outside the function but allows the function to
be garbage collected if necessary."
(remhash fn *memoized-map*))
(defmacro defun-memoized (function-name arg-list &body body)
"Macro for defining a memoized function. Note that currently there
is a small inconvenience in that lambda-lists are not automatically
added to the documentation used by things like SLIME."
(with-gensyms (raw-function memoized defuned xs)
`(let* ((,raw-function
(lambda (&rest ,xs)
(destructuring-bind (,@arg-list)
,xs
,@body)))
(,memoized
(memoize ,raw-function))
(,defuned
(defun ,function-name (&rest ,xs)
(apply ,memoized ,xs))))
(setf (gethash (symbol-function ,defuned) *memoized-map*)
(gethash ,memoized *memoized-map*))
,memoized
,defuned)))
| 5,584 | Common Lisp | .lisp | 129 | 32.24031 | 75 | 0.56188 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 2b3ba10bf929dc530d12ef625809bc1769710965e3fdedb9a4d4e3e1ea2324fe | 1,480 | [
-1
] |
1,481 | package.lisp | ghollisjr_cl-ana/quantity/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.quantity
(:use :cl
;; :alexandria
:cl-ana.list-utils
:cl-ana.macro-utils
:cl-ana.symbol-utils
:cl-ana.error-propogation
:cl-ana.math-functions)
(:export
;; Unit:
:define-unit
;; Quantity:
:quantity
:quantity-scale
:quantity-unit
;; Quantity methods:
:define-quantity-methods
;; Temperature
:convert-temperature
;; General unit conversion
:convert-units
;; Metric prefix functions:
:yotta
:zetta
:exa
:peta
:tera
:giga
:mega
:kilo
:hecto
:deca
:deci
:centi
:milli
:micro
:nano
:pico
:femto
:atto
:zepto
:yocto
;; Binary prefix functions:
:binary-kilo
:binary-mega
:binary-giga
:binary-tera
;; Constants:
:+c+
:+G+
:+h+
:+hbar+
:+mu0+
:+eps0+
:+Z0+
:+k-coulomb+
:+e+
:+mu-bohr+
:+a0+
:+r-electron+
:+me+
:+alpha+
:+mp+
:+mn+
:+md+
:+rydberg+
:+NA+
:+k-boltzmann+
:+R+
:+stefan-boltzmann+
:+gravitational-acceleration+
:+vsound+
:+T0+
;; Misc.
:reader-macro-units->quantity))
(cl-ana.gmath:use-gmath :cl-ana.quantity)
| 2,056 | Common Lisp | .lisp | 96 | 17.791667 | 70 | 0.636874 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | ec9577339e945aa49348801d2ccaa4d9c4442e8264cf3734587532b3c97e8f57 | 1,481 | [
-1
] |
1,482 | metric-non-si.lisp | ghollisjr_cl-ana/quantity/metric-non-si.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;; These are common metric units which do not officially belong to the
;; S.I. unit system.
(define-unit :gram
(milli :kilogram))
(define-unit :minute
(* 60 :second))
(define-unit :hour
(* 60 :minute))
(define-unit :day
(* 24 :hour))
(define-unit :year
(* 365.25 :day))
(define-unit :hectare
(expt (hecto :meter) 2))
(define-unit :liter
(expt (deci :meter) 3))
(define-unit :tonne
(expt (mega :gram)))
(define-unit :atomic-mass-unit
(* 1.6605388628d-27 :kilogram))
(define-unit :dalton :atomic-mass-unit)
(define-unit :angstrom
(/ (nano :meter) 10))
(define-unit :barn
(* 1d-28
(expt :meter 2)))
(define-unit :bar
(* 1d5 :pascal))
(define-unit :atmosphere
(* 101325 :pascal))
(define-unit :mmHg ;; the full name is way too long
(* 133.322387415d0 :pascal))
(define-unit :torr
(* 133.322368421d0 :pascal))
(define-unit :kph
(/ (kilo :meter) :hour))
(define-unit :rpm
(/ (* 2 pi)
:minute))
| 1,892 | Common Lisp | .lisp | 60 | 28.766667 | 70 | 0.674945 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e28f5773ea12a52967e161e418283f6b85da04a3fefcee60b3210f070cffe9ad | 1,482 | [
-1
] |
1,483 | binary.lisp | ghollisjr_cl-ana/quantity/binary.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
(defun binary-kilo (x)
(* x (expt 2 10)))
(defun binary-mega (x)
(* x (expt 2 20)))
(defun binary-giga (x)
(* x (expt 2 30)))
(defun binary-tera (x)
(* x (expt 2 40)))
| 1,083 | Common Lisp | .lisp | 29 | 35.758621 | 70 | 0.689228 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | dad5ffd1b96357594fe859bac0abd5653143eadef79b863ef6e56e620cd2738b | 1,483 | [
-1
] |
1,484 | unit.lisp | ghollisjr_cl-ana/quantity/unit.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;;;; Units
;;; Units are, in the context of this library, restricted to base
;;; units, i.e. those directly corresponding to the base dimensions.
;;; They are directly represented via keyword symbols; properties of
;;; units are stored in global tables.
;;; Default units are S.I. units
(defvar *default-units* (make-hash-table :test 'equal)
"Maps from dimension to the default unit for that dimension.")
(defun set-default-unit (dimension unit)
"Sets the default unit for a dimension."
(setf (gethash dimension *default-units* )
unit))
;;; Units utilities
(defun unit-symbol (unit)
(if (symbolp unit)
unit
(unit-symbol
(first unit))))
(defun unit-string (unit)
(string (unit-symbol unit)))
(defun unit-first< (unit1 unit2)
(string< (unit-string unit1)
(unit-string unit2)))
(defun unit-first= (unit1 unit2)
(string= (unit-string unit1)
(unit-string unit2)))
(defun unit-standard-order (unit)
(if (not (listp unit))
unit
(if (and (length-equal unit 2)
(numberp (second unit)))
(list unit)
(let* ((copy (copy-list unit)))
(sort copy #'string<
:key #'unit-string)))))
(defun ensure-explicit-exponent (u)
"Ensures that a unit is expressed as a list."
(if (symbolp u)
(list u 1)
u))
(defun unit-compound-form (u)
"Ensures that a unit is expressed as a compound unit list."
(if (symbolp u)
(list u)
(if (and (length-equal u 2)
(numberp (second u)))
(list u)
u)))
(defun unit-standard-form (u)
"Ensures that a unit is in compound form with each component unit
being expressed with explicit exponent."
(if (equal u 1)
(list (list 1 0))
(mapcar #'ensure-explicit-exponent
(unit-compound-form u))))
(defun un-singleton-zero (lst)
(remove-if #'null
(mapcar (lambda (x)
(if (and (listp x)
(numberp (second x)))
(cond
((= (second x) 1)
(first x))
((zerop (second x))
nil)
(t x))
x))
lst)))
(defun one-if-null (x)
(if (null x)
1
x))
(defun unwrap-single (l)
(if (single l)
(car l)
l))
(defun unit-simplify (u)
"Expects u to be in standard form"
(unwrap-single
(one-if-null
(un-singleton-zero u))))
(defun unit-mult (unit1 unit2)
(labels ((ucoef (u)
(if (symbolp u)
1
(second u)))
(umult (u1 u2)
(+ (ucoef u1)
(ucoef u2))))
(cond
((equal unit1 1)
unit2)
((equal unit2 1)
unit1)
(t
(when (not (unit-first< unit1 unit2))
(rotatef unit1 unit2))
(let ((ulst1 (unit-standard-form unit1))
(ulst2 (unit-standard-form unit2))
(result ()))
(unit-simplify
(do ()
((or (null ulst1)
(null ulst2))
(append result ulst1 ulst2))
(let ((u1 (first ulst1))
(u2 (first ulst2)))
(cond
((string< (unit-string u1)
(unit-string u2))
(push u1 result)
(setf ulst1 (rest ulst1)))
((string= (unit-string u1)
(unit-string u2))
(push (list (unit-symbol u1)
(umult u1 u2))
result)
(setf ulst1 (rest ulst1))
(setf ulst2 (rest ulst2)))
(t
(push u2 result)
(setf ulst2 (rest ulst2))))))))))))
(defun unit-div (unit1 unit2)
(labels ((negate-unit-coefs (u)
(cond
((equal u 1)
1)
((symbolp u)
(list u -1))
((and (length-equal u 2)
(numberp (second u)))
(list (first u)
(- (second u))))
(t
(mapcar #'negate-unit-coefs u)))))
(unit-mult unit1
(unit-simplify
(negate-unit-coefs
(unit-standard-form unit2))))))
(defun unit-expt (unit power)
(unit-simplify
(let ((unit (unit-standard-form unit)))
(mapcar (lambda (u)
(list (first u)
(* (second u)
power)))
unit))))
| 5,576 | Common Lisp | .lisp | 168 | 23.452381 | 70 | 0.521441 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 48fd98ce863979a87a002c3068b0db4f0660b412f7073c3d6b45ec0f593af4d2 | 1,484 | [
-1
] |
1,485 | convert-units.lisp | ghollisjr_cl-ana/quantity/convert-units.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
(defun convert-units (quantity new-units)
"Gets the scale of quantity if expressed in new-units.
new-units can be either a product unit (usual unit, e.g. meter/second)
or a list of product units which is interpreted as a sum of units.
Using a list of units results in a list of unit-scales, one element
per unit in the sum. The quantity value is the result of multiplying
the unit-scales with the corresponding product units and them summing.
Useful for expressing U.S. quantities like heights in feet and
inches."
(if (listp new-units)
(let ((units (butlast new-units))
(last-unit (first (last new-units)))
(result ())
(q quantity)
factor)
(dolist (unit units)
(setf factor (floor (/ q unit)))
(setf q (- q (* unit factor)))
(push factor result))
(push (/ q last-unit) result)
(nreverse result))
(/ quantity new-units)))
| 1,847 | Common Lisp | .lisp | 43 | 39.023256 | 70 | 0.684444 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 4835490facaec33b0042f1b866f598e2f1bd8eff107aab748fd53cf10d782e3a | 1,485 | [
-1
] |
1,486 | si.lisp | ghollisjr_cl-ana/quantity/si.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;;; base units
(defvar +si-base-units+
(list (cons :meter :length)
(cons :kilogram :mass)
(cons :second :time)
(cons :ampere :electric-current)
(cons :kelvin :temperature)
(cons :mole :amount-of-substance)
(cons :candela :luminuous-intensity)))
(loop
for (u . d) in +si-base-units+
do (set-default-unit d u))
;;; derived units
(define-unit :hertz
(/ :second))
(define-unit :newton
(* :kilogram
:meter
(expt :second -2)))
(define-unit :pascal
(/ :newton
(expt :meter 2)))
(define-unit :joule
(* :newton
:meter))
(define-unit :watt
(/ :joule
:second))
(define-unit :coulomb
(* :ampere :second))
(define-unit :volt
(/ :watt
:ampere))
(define-unit :farad
(/ :coulomb
:volt))
(define-unit :ohm
(/ :volt
:ampere))
(define-unit :siemens
(/ :ampere
:volt))
(define-unit :weber
(* :volt :second))
(define-unit :tesla
(/ :weber (expt :meter 2)))
(define-unit :henry
(/ :weber :ampere))
(define-unit :lumen
(quantity :candela)) ;; technically there's a steradian in there,
;; but that's just 1.
(define-unit :lux
(/ :lumen (expt :meter 2)))
(define-unit :becquerel
(/ :second))
(define-unit :gray
(/ :joule :kilogram))
(define-unit :sievert
(/ :joule :kilogram))
(define-unit :katal
(/ :mole :second))
| 2,312 | Common Lisp | .lisp | 82 | 24.47561 | 70 | 0.643699 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 7c17843509610320b7da09d8e9e1287343ef8529b9f6b4fc827b4e8e530e254f | 1,486 | [
-1
] |
1,487 | constants.lisp | ghollisjr_cl-ana/quantity/constants.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
(defvar +c+
(* 299792458 :meter (expt :second -1))
"Speed of light in vacuum")
(defvar +G+
#q(6.6738480d-11 (:meter 3)
(:kilogram -1)
(:second -2))
"Newton's gravitational constant")
(defvar +h+
(* 6.6260695729d-34 :joule :second)
"Planck's constant")
(defvar +hbar+
(* 1.05457172647d-34 :joule :second)
"Reduced Planck's constant")
(defvar +mu0+
(* 4 pi
1d-7
:newton
(/ (expt :ampere
2)))
"Permeability of free space")
(defvar +eps0+
(/ (* +mu0+
(expt +c+ 2)))
"Permittivity of free space")
(defvar +Z0+
(* +mu0+ +c+)
"Impedance of vacuum")
(defvar +k-coulomb+
(/ (* 4 pi +eps0+))
"Coulomb's constant")
(defvar +e+
(* 1.60217656535d-19 :coulomb)
"Elementary charge")
(defvar +mu-bohr+
(* 9.2740096820d-24 :joule (/ :tesla))
"Bohr magneton")
(defvar +a0+
#q(5.291772109217d-11 :meter)
"Bohr radius")
(defvar +r-electron+
(* 2.817940326727d-15 :meter)
"Classical electron radius")
(defvar +me+
(* 9.1093829140e-31 :kilogram)
"Electron mass")
(defvar +alpha+
(/ (expt +e+ 2)
(* 4 pi
+eps0+ +hbar+ +c+))
"Fine Structure Constant")
(defvar +mp+
(* 1.67262177774d-27 :kilogram)
"Proton mass")
(defvar +mn+
(* 1.67492735174d-27 :kilogram)
"Neutron Mass")
(defvar +md+
(* 3.34358348d-27 :kilogram)
"Deuteron Mass")
(defvar +rydberg+
(* (expt +alpha+ 2)
+me+ +c+
(/ (* 2 +h+)))
"Rydberg Constant")
(defvar +NA+
6.0221412927e23
"Avogadro's Number")
(defvar +k-boltzmann+
(* 1.380648813d-23 :joule (/ :kelvin))
"Boltzmann constant")
(defvar +R+
(* 8.314462175d0 :joule
(/ (* :kelvin :mole)))
"Ideal Gas Constant")
(defvar +stefan-boltzmann+
(* (expt pi 2)
(/ (expt +k-boltzmann+ 4)
(* 60
(expt +hbar+ 3)
(expt +c+ 2))))
"Stefan-Boltzmann Constant")
(defvar +gravitational-acceleration+
(* 9.80665d0 :meter (expt :second -2))
"Standard Gravitational Acceleration")
(defvar +vsound+
(* 340.29d0 (/ :meter :second)))
(defvar +T0+
#q(273.15d0 :kelvin)
"Freezing point of water")
| 3,029 | Common Lisp | .lisp | 111 | 23.891892 | 70 | 0.640733 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | d7511753ef248c179d41f5867b36341b2b8d9fe98ab9a38c66103a81d3745c3e | 1,487 | [
-1
] |
1,488 | temperature.lisp | ghollisjr_cl-ana/quantity/temperature.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;;;; Temperature units are: :fahrenheit, :celsius, :kelvin, and :rankine
(defun invert-linear (linear-coefs)
"Yields the coefficients of the inverse of a linear function; i.e. A
+ B*x -> -A/B + (1/B)*x"
(destructuring-bind (A B)
linear-coefs
(list (- (/ A B))
(/ B))))
(defun compose-linear (linear-coefs1 linear-coefs2)
"Yields the coefficients of the composition linear1(linear2(x))"
(destructuring-bind (A1 B1)
linear-coefs1
(destructuring-bind (A2 B2)
linear-coefs2
(list (+ A1
(* B1 A2))
(* B1 B2)))))
(defvar *linear-fn-coefs*
(make-hash-table :test 'equal))
(defun linear-coefs (xname yname)
"line-name is a keywordified symbol"
(if (eq xname yname)
(list 0d0 1d0)
(gethash (cons (keywordify xname)
(keywordify yname))
*linear-fn-coefs*)))
(defun linear-composition-chain (&rest var-chain)
"Takes a chain of variables and returns the linear function as a
result of sequentially evaluating the linear function required to move
from one variable to the next in the var-chain."
(reduce (let ((last-var (first var-chain)))
(lambda (coefs var)
(let ((new-coefs (linear-coefs last-var var)))
(setf last-var var)
(compose-linear new-coefs coefs))))
(rest var-chain)
:initial-value (list 0 1)))
(defun linear-funcall (coefs x)
"Evaluates a linear function with coefficients coefs at the point x"
(destructuring-bind (A B)
coefs
(+ A
(* B x))))
(defun linear-trans (independent-var dependent-var x)
"Evaluates the linear transformation (function) which takes the
independent-var to the dependent-var at the point x"
(linear-funcall (linear-coefs independent-var dependent-var)
x))
(defmacro deflinear (xname yname coefs)
"Defines two functions xname->yname and yname->xname which are the
linear function and its inverse based on coefs."
(flet ((trans (a b)
(intern (concatenate 'string (string a) "->" (string b)))))
(let ((fname (trans xname yname))
(finvname (trans yname xname))
(xsym (keywordify xname))
(ysym (keywordify yname)))
(alexandria:with-gensyms (invcs cs)
`(let* ((,cs ,coefs)
(,invcs (invert-linear ,cs)))
(setf (gethash (cons ,xsym ,ysym)
*linear-fn-coefs*)
,cs)
(setf (gethash (cons ,ysym ,xsym)
*linear-fn-coefs*)
,invcs))))))
(deflinear celsius fahrenheit
(list 32
9/5))
(deflinear celsius kelvin
(list (/ +T0+ :kelvin)
1))
(deflinear fahrenheit kelvin
(linear-composition-chain
'fahrenheit 'celsius 'kelvin))
(deflinear fahrenheit rankine
(list 459.67d0
1))
(deflinear celsius rankine
(linear-composition-chain
'celsius 'fahrenheit 'rankine))
(deflinear kelvin rankine
(linear-composition-chain
'kelvin 'celsius 'rankine))
(defmacro define-temperature-mult (temp-keyword)
`(progn
(defmethod-commutative mult ((x (eql ,temp-keyword)) (y number))
(with-slots (quantity-scale) x
(mult (linear-trans ,temp-keyword :kelvin y) :kelvin)))
(defmethod-commutative mult ((y number) (x (eql ,temp-keyword)))
(with-slots (quantity-scale) x
(mult (linear-trans ,temp-keyword :kelvin y) :kelvin)))))
(define-temperature-mult :fahrenheit)
(define-temperature-mult :celsius)
(define-temperature-mult :rankine)
(defmacro define-temperature-quantity (temp-keyword)
`(defmethod quantity ((x (eql ,temp-keyword)))
(mult 1 ,temp-keyword)))
(define-temperature-quantity :fahrenheit)
(define-temperature-quantity :celsius)
(define-temperature-quantity :rankine)
;;;; General temperature conversion function:
(defun convert-temperature (temp to-units)
"Converts the temperature quantity temp into the temperature units to-units.
Note that the result is unitless."
(let* ((raw-from-units (unit-standard-form (quantity-unit temp)))
(from-units (first (first raw-from-units))))
(linear-trans (keywordify from-units) (keywordify to-units)
(quantity-scale temp))))
| 5,155 | Common Lisp | .lisp | 130 | 34.023077 | 78 | 0.664801 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 2c05725612e5b73edc7f73d6c0cd63488043261d0be09e7cfc6d231d9b4c9506 | 1,488 | [
-1
] |
1,489 | macros.lisp | ghollisjr_cl-ana/quantity/macros.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013-2016 Gary Hollis, 2016 Elijah Malaby
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;;;; This is in its own file since it needs to be available at compile
;;;; time; easiest fix since it was already fairly sizable code
(defun lcons (x lst)
"conses x onto each element of lst, hence the name"
(mapcar (lambda (y) (cons x y)) lst))
(defun some-not-all (val n-slots slot-vals)
"Returns the list of combinations of slot values taken from
slot-vals which is of length n-slots and where each combination has
some but not all slot values equal to val."
(if (<= n-slots 1)
()
(loop
for sv in slot-vals
append
(if (equal sv val)
(lcons sv
(not-all val (1- n-slots) slot-vals))
(lcons sv
(just-some val (1- n-slots) slot-vals))))))
(defun not-all (val n-slots slot-vals)
"Helper function for some-not-all, same but doesn't require there to
be any slots of type val at all."
(if (= n-slots 1)
(mapcar #'list
(remove-if (lambda (x) (equal x val))
slot-vals))
(loop
for sv in slot-vals
append
(if (equal val sv)
(lcons sv
(not-all val (1- n-slots) slot-vals))
(lcons sv
(all-possible (1- n-slots) slot-vals))))))
(defun all-possible (n-slots slot-vals)
"Returns list of lists of length n-slots which represent all
possible ways to select with ordering and repeating values from
slot-vals."
(cond
((<= n-slots 0)
())
((= n-slots 1)
(mapcar #'list slot-vals))
(t
(loop
for sv in slot-vals
append (lcons sv (all-possible (1- n-slots) slot-vals))))))
(defun just-some (val n-slots slot-vals)
"Like some-not-all but drops the not-all requirement."
(cond
((<= n-slots 0)
())
((= n-slots 1)
(if (member val slot-vals)
(list (list val))
()))
(t
(loop
for sv in slot-vals
append (if (equal sv val)
(lcons sv
(all-possible (1- n-slots) slot-vals))
(lcons sv
(just-some val (1- n-slots) slot-vals)))))))
;; Elijah Malaby's with-quantities:
(defmacro with-quantities ((&rest args) &body body)
"Ensures all arguments are quantities and evaluates body in this
context and with a quantity-if-necessary call. Supports dual syntax
for arguments:
* Symbols: Simply binds the symbol to the quantity value.
* Lists of form (s u q): Binds quantity to q, scale to s, and unit to u."
(labels ((recursor (args)
(if args
(if (symbolp (car args))
`(let ((,(car args) (quantity ,(car args))))
,(recursor (cdr args)))
`(with-accessors ((,(caar args) quantity-scale)
(,(cadar args) quantity-unit))
(quantity ,(caddar args))
,(recursor (cdr args))))
`(progn ,@body))))
`(quantity-if-necessary
(block nil
;; Block here so that #'return still passes through
;; quantity-if-necessary, although #'return-from does
;; not (similar to loop)
,(recursor args)))))
;; (defvar *quantity-types* nil)
;; (list 'number
;; 'symbol
;; 'err-num
;; 'quantity))
;; (defmacro defquantity (type var &body body)
;; "Defines a method on quantity for transforming a value from a given
;; type into a quantity."
;; `(when (not (member ',type *quantity-types* :test #'equal))
;; (push ',type *quantity-types*)
;; (defmethod quantity ((,var ,type))
;; ,@body)))
;; (defmacro define-quantity-methods
;; (fname (&rest args) &body qbody)
;; "Defines all suitable methods on quantities using only the
;; quantity-only function body. Note that one should omit the
;; quantity-if-necessary call, as this is always a good idea and is
;; built into the generated methods.
;; The methods are implemented via the minimal set of necessary methods
;; to allow quantities to interact with numbers, symbols, quantities,
;; and err-nums.
;; The rules:
;; 1. Methods on quantities should only be invoked by the presence of a
;; symbol or quantity as an argument.
;; 2. Methods invoked via the presence of a quantity should have
;; explicit typing of all arguments.
;; 3. Methods invoked via the presence of a symbol should leave all
;; other argument types unspecified and simply call quantity on all
;; arguments to pass to the quantity-only method."
;; (flet ((lzip (xs ys)
;; (loop
;; for x in xs
;; for y in ys
;; collect (list x y))))
;; (let* ((q-only
;; `(defmethod ,fname
;; ,(loop
;; for a in args
;; collecting `(,a quantity))
;; (quantity-if-necessary
;; (let ,(loop
;; for a in args
;; collecting `(,a (quantity ,a)))
;; ,@qbody))))
;; (body-args
;; (loop
;; for a in args
;; collect `(quantity ,a)))
;; (q-types
;; (some-not-all 'quantity
;; (length args)
;; *quantity-types*))
;; (q-args
;; (mapcar (lambda (x) (lzip args x))
;; q-types))
;; (q-methods
;; (loop
;; for a in q-args
;; collect `(defmethod ,fname ,a
;; (,fname ,@body-args))))
;; (symbol-args
;; (let ((traversed-elements ())
;; (result ()))
;; (loop
;; for lst on args
;; do
;; (progn
;; (push (append (reverse traversed-elements)
;; (list (list (first lst)
;; 'symbol))
;; (rest lst))
;; result)
;; (push (first lst)
;; traversed-elements))
;; finally (return (nreverse result)))))
;; (symbol-methods
;; (loop
;; for a in symbol-args
;; collect `(defmethod ,fname ,a
;; (,fname ,@body-args)))))
;; `(progn
;; ,q-only
;; ,@q-methods
;; ,@symbol-methods))))
| 7,546 | Common Lisp | .lisp | 192 | 34.395833 | 73 | 0.536742 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 4528ee2f09fc88da5970c765869ce268760ad7a6cef2cbcc6eaff1e3bc37ee03 | 1,489 | [
-1
] |
1,490 | us.lisp | ghollisjr_cl-ana/quantity/us.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;;;; Customary units:
(define-unit :inch
(* 2.54d0 (centi :meter)))
(define-unit :foot
(* 12 :inch))
(define-unit :yard
(* 3 :foot))
(define-unit :mile
(* 5280 :foot))
(define-unit :nautical-mile
(* 1.151d0 :mile))
;; (define-unit :acre
;; #q(4046.873d0 (:meter 2)))
(define-unit :acre
(* 4046.873d0 (expt :meter 2)))
;;;; Fluid volumes:
(define-unit :teaspoon
(* 4.928921 (milli :liter)))
(define-unit :tablespoon
(* 3 :teaspoon))
(define-unit :fluid-ounce
(* 2 :tablespoon))
(define-unit :cup
(* 8 :fluid-ounce))
(define-unit :pint
(* 2 :cup))
(define-unit :quart
(* 2 :pint))
(define-unit :gallon
(* 4 :quart))
;;;; Mass
(define-unit :pound
(* 453.59237d0 :gram))
(define-unit :grain
(/ :pound 7000))
(define-unit :dram
(* (+ 27 11/32)
:grain))
(define-unit :ounce
(* 16 :dram))
(define-unit :ton
(* 2000 :pound))
(define-unit :long-ton
(* 2240 :pound))
;; Speed
(define-unit :mph
(/ :mile :hour))
;; Miscellaneous
;; U.S. commonly used size for a "cup" of coffee
(define-unit :coffee-cup
(* 6 :fluid-ounce))
| 2,037 | Common Lisp | .lisp | 72 | 25.583333 | 70 | 0.655653 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | c819578969bce4115fcbb94c5bc408bcc889f8584ad8756ca2fc45db836f2000 | 1,490 | [
-1
] |
1,491 | post-constants.lisp | ghollisjr_cl-ana/quantity/post-constants.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.quantity)
;;;; Energy:
(define-unit :electron-volt
(* +e+ :volt))
(define-unit :dyne
(* 10 (micro :newton)))
(define-unit :calorie
(* 4.184d0 :joule))
;; Food calorie
(define-unit :cal
(kilo :calorie))
;;;; U.S. force & power
(define-unit :pound-force
(* +graviational-acceleration+ :pound))
(define-unit :horsepower
(* 33000 :foot :pound-force (/ :minute)))
;;;; Astronomical Distance:
(define-unit :light-year
(* +c+ :year))
(define-unit :astronomical-unit
(* 149597870.700d0
(kilo :meter)))
(define-unit :parsec
(/ :astronomical-unit
(tan (/ pi
(* 180 3600)))))
| 1,532 | Common Lisp | .lisp | 46 | 30.586957 | 70 | 0.673677 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e503861f483dac455edc702a437f5ef8fcf1eb890199f1bb9a4ab4f5149ffcd6 | 1,491 | [
-1
] |
1,492 | package.lisp | ghollisjr_cl-ana/statistical-learning/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2019 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.statistical-learning
(:use :cl
:cl-ana.macro-utils
:cl-ana.map
:cl-ana.list-utils
:cl-ana.functional-utils
:cl-ana.histogram
:cl-ana.math-functions
:cl-ana.statistics
:cl-ana.linear-algebra)
(:export
;; Clustering
:k-means-cluster
:g-means-cluster
;; Least squares
:linear-least-squares
:ridge-regression
:data->polynomial-x
:fit-polynomial-least-squares
;; Kernel methods
:gaussian-kernel
:make-gaussian-kernel
:kernel-method
:kernel-polynomial-method))
(cl-ana.gmath:use-gmath :cl-ana.statistical-learning)
| 1,505 | Common Lisp | .lisp | 45 | 29.933333 | 70 | 0.69273 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 93eb6bbafcc47218ad54bf55278835811022ea88a6da7475635bf23c823a84fb | 1,492 | [
-1
] |
1,493 | statistical-learning.lisp | ghollisjr_cl-ana/statistical-learning/statistical-learning.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2019 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.statistical-learning)
;;;; Clustering
;; K-means clustering
(defun k-means-cluster (data init)
"Clusters the data using the k-means algorithm. init can be a
number specifying the number of clusters to partition the data into,
or a list of explicit initial guesses for the centroids.
Data should be a list of numbers or lists.
Returns:
* The clusters of data.
* The centroids.
* The number of iterations required."
(let* ((niter 0)
(data (mapcar #'->double-float data))
(centroids
(if (listp init)
(copy-list init)
(subseq data 0 (min (length data) init))))
(k (length centroids))
(changed-p t))
;; data length check
(when (<= (length data)
(length centroids))
(return-from k-means-cluster
(values (map 'list #'list centroids)
centroids
0)))
(let* ((categories (make-vector (length data)
:initial-element -1))
(clusters (make-vector k :initial-element nil))
(normfn (if (listp (first data))
(lambda (x c)
(sum (expt (- x (car c)) 2)))
(lambda (x c)
(expt (- x (car c)) 2)))))
;; iterative algorithm
(loop
while changed-p
do
(incf niter)
(setf changed-p nil)
(loop
for x in data
for i from 0
do (let* ((nearest
(minimum (zip centroids
(range 0 (1- k)))
:key (lambda (c)
(funcall normfn x c))))
(newcategory (cdr nearest)))
(when (not (= newcategory (elt categories i)))
(setf changed-p t)
(setf (elt categories i)
newcategory)
(setf (elt centroids newcategory)
(mean (loop
for x in data
for c across categories
when (= c newcategory)
collecting x)))))))
;; collect categorized data:
(loop
for x in data
for c across categories
do (push x (elt clusters c)))
(values (map 'list #'reverse clusters)
centroids
niter))))
;; G-means clustering
(defun g-means-cluster (data
&key (critical 2.492))
"Applies the G-means clustering algorithm based on the
Anderson-Darling normality test. The algorithm is a variant of
k-means where the number k is determined through finding the minimum
number of clusters required to have Gaussian distributed data when
projected along a single dimension. Critical selects the critical
value for the normality test.
Data should be a list of numbers or lists.
Returns:
* Clusters
* Centroids
* k"
(labels (;; project data onto new axis
(project (x vec)
(if (atom x)
x
(/ (euclidean-dot x vec)
(euclidean-norm vec))))
;; test for gaussian normality of a centroid
(g-test (cluster)
;; Get new centroids
(multiple-value-bind (clusters centroids niter)
(k-means-cluster cluster 2)
(declare (ignore clusters niter))
(let* (;; Find axis
(vec (apply #'- centroids))
;; Project data onto that axis
(projected (mapcar (lambda (x)
(project x vec))
cluster)))
;; apply normality test
(anderson-darling-normality-test projected
:critical critical)))))
(let* ((n (length data)))
(loop
for k from 1 to n
do (multiple-value-bind (clusters centroid niter)
(k-means-cluster data k)
(declare (ignore niter))
(let* ((g-tests
(loop
for cluster in clusters
collecting (g-test cluster))))
(when (every #'identity g-tests)
(return (values clusters centroid k)))))))))
;;;; Least squares
(defun linear-least-squares (data)
"Fits a linear function against the data alist. car can be a list,
but cdr should be an atom. Fitting a vector Y value is mathematically
equivalent to simultaneous indepedent linear fits so no functionality
is lost."
(when data
(let* ((coefs
(coerce
(loop
for cons in data
collecting (coerce (cons 1d0 (mklist (car cons))) 'vector))
'vector))
(coefstransposed
(matrix-transpose coefs))
(yvector
(cdrs data)))
(lu-solve (matrix-mult coefstransposed
coefs
'list)
(first (transpose
(matrix-mult coefstransposed
(map 'vector
(lambda (x)
(apply #'vector x))
(transpose (list yvector)))
'list)))))))
(defun ridge-regression (data lambda)
"Applies ridge regression fitting as a function of lambda."
(let* ((coefs (map 'vector (lambda (x)
(coerce (cons 1d0 (mklist x)) 'vector))
(cars data)))
(coefstransposed
(matrix-transpose coefs))
(ys (mapcar #'cdr data))
(newcoefs (matrix-mult coefstransposed coefs 'list))
(newys
(first (transpose
(matrix-mult coefstransposed
(map 'vector (lambda (y)
(apply #'vector y))
(transpose (list ys)))
'list)))))
(loop
for i below (1- (length newcoefs))
do (incf (tensor-ref newcoefs i i) lambda))
(lu-solve newcoefs newys)))
(defun data->polynomial-x (data order)
"Returns an alist of data suitable for least squares fitting against
a polynomial function using the existing linear-least-squares fit
function. order should be at least 0. Note that this is not as
efficient as a purpose-built polynomial least squares fit due to
algebraic simplifications to the matrix multiplication that are
possible."
(mapcar (lambda (cons)
(destructuring-bind (x . y) cons
(let* ((term 1d0))
(cons (loop
for i from 1 upto order
do (setf term (* term x))
collecting term)
y))))
data))
(defun fit-polynomial-least-squares (data degree)
"Fits a polynomial of specified degree against the data, returning
the list of parameters from least order to highest order."
(let* ((coefs
(loop
for k from 0 to degree
collecting
(loop
for j from 0 to degree
for pow = (+ k j)
collecting (loop
for (x . y) in data
summing (expt x pow)))))
(constants
(loop
for k from 0 to degree
collecting
(loop
for (x . y) in data
summing (* y (expt x k))))))
(lu-solve coefs constants)))
;;;; Kernel methods
(defun gaussian-kernel (x1 x2 lambda)
"Gaussian kernel for multi-dimensional x1 and x2"
(* (/ lambda)
(exp
(- (/ (if (sequencep x1)
(sum (expt (- x1 x2) 2d0))
(expt (- x1 x2) 2d0))
lambda)))))
(defun make-gaussian-kernel (lambda)
(lambda (x1 x2)
(gaussian-kernel x1 x2 lambda)))
(defun kernel-method (data fn kernel init-params)
"Returns a function which will compute the kernel method estimate
for a given point, using the init-params to fit on a point-by-point
basis."
(lambda (x)
(let* ((weights (mapcar (lambda (y)
(funcall kernel x y))
(cars data)))
;; X is now (x, y, sqrt(w)) and y is always 0
(ndata (mapcar (lambda (cons w)
(cons (list (car cons)
(cdr cons)
(sqrt w))
0d0))
data
weights))
(nfn (lambda (params k)
(destructuring-bind (x y w) k
(* w
(- (funcall fn params x) y)))))
(fit-results
(suppress-output
(multiple-value-list
(fit ndata nfn init-params))))
(fit-params (second fit-results)))
(funcall fn fit-params x))))
(defun kernel-polynomial-method (data kernel degree)
"Returns a function which will compute the kernel method estimate
for a given point, using a polynomial of the specified degree."
(lambda (x)
(let* ((weights (mapcar (lambda (y)
(funcall kernel x y))
(cars data)))
(coefs
(loop
for k from 0 to degree
collecting
(loop
for j from 0 to degree
for pow = (+ k j)
collecting (loop
for (x . y) in data
for w in weights
summing (* w (expt x pow))))))
(constants
(loop
for k from 0 to degree
collecting
(loop
for (x . y) in data
for w in weights
summing (* y w (expt x k)))))
(fit-params (lu-solve coefs constants)))
(polynomial fit-params x))))
| 11,312 | Common Lisp | .lisp | 285 | 25.926316 | 75 | 0.499455 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | aea12c7c60e7cd0a42de81b27769130f26c819f50dd05dd11f30744680d6cb4f | 1,493 | [
-1
] |
1,494 | package.lisp | ghollisjr_cl-ana/lorentz/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.lorentz
(:use :cl
:cl-ana.linear-algebra
:cl-ana.tensor
:iterate)
(:export :lorentz-vector
:make-lorentz-vector
:make-double-float-vector
:make-lorentz-boost
:lorentz-vector-spatial
:minkowski-dot
:minkowski-norm
:minkowski-norm2 ; minkowski-norm^2
:lorentz-phi
:lorentz-theta
:gamma
:gamma-from-beta2
:four-momentum-beta-vector))
(cl-ana.gmath:use-gmath :cl-ana.lorentz)
| 1,372 | Common Lisp | .lisp | 39 | 31.333333 | 70 | 0.681443 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 9c9199fa0c0aba72adf7fe2a35ff2f6e930a8554adc35994f74a648c9789e186 | 1,494 | [
-1
] |
1,495 | lorentz.lisp | ghollisjr_cl-ana/lorentz/lorentz.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.lorentz)
;;; This library of lorentz transformation-related utilities assumes
;;; dogmatically that
;;;
;;; 1. Time component is the zeroth element.
;;; 2. We are using the (+,-,-,...) Minkowski space metric.
;;;
;;; This implementation does lack a general lorentz transformation as
;;; it only provides the boost facilities. But: you can do any
;;; general lorentz transformation by using a boost followed by a
;;; rotation.
;;;
;;; The library also provides the useful reader macro for lorentz
;;; vectors: #L(...), which accepts exactly 4 values inside of the
;;; parentheses which will become the time, x, y, and z components
;;; respectively.
(defun minkowski-dot (left-vector right-vector)
"Computes the inner product using the Minkowski metric; only
requires the tensor-ref function to be defined and that the vectors each
have exactly 4 elements each."
(flet ((variance-flip-factor (i)
(if (zerop i)
1
-1)))
(let ((left-length (first (tensor-dimensions left-vector)))
(right-length (first (tensor-dimensions right-vector))))
(loop
for i from 0 below left-length
for j from 0 below right-length
summing (* (variance-flip-factor i)
(tensor-ref left-vector i)
(tensor-ref right-vector j))))))
(defun minkowski-norm (vector)
(sqrt (minkowski-norm2 vector)))
(defun minkowski-norm2 (vector)
(minkowski-dot vector vector))
(defun make-lorentz-boost (beta-vector)
"Construct lorentz boost matrix from beta vector"
(let* ((lorentz-boost (make-matrix 4 4))
(beta2 (euclidean-norm2 beta-vector))
(gamma (gamma-from-beta2 beta2)))
(if (zerop beta2)
(list (list 1 0 0 0)
(list 0 1 0 0)
(list 0 0 1 0)
(list 0 0 0 1))
;; matrix is symmetric, so we can fill one side and then set the
;; other to be the same main diagonal: top-left corner:
(progn
(setf (tensor-ref lorentz-boost 0 0)
gamma)
;; spatial diagonal:
(loop
for i from 1 to 3
do (setf (tensor-ref lorentz-boost i i)
(+ 1
(* (- gamma 1)
(/ (expt (tensor-ref beta-vector (1- i)) 2)
beta2)))))
;; spatial off-diagonal:
(loop
for i from 1 to 2
do (loop
for j from (1+ i) to 3
do (progn
(setf (tensor-ref lorentz-boost i j)
(* (- gamma 1)
(tensor-ref beta-vector (1- i))
(tensor-ref beta-vector (1- j))
(/ beta2)))
(setf (tensor-ref lorentz-boost j i)
(tensor-ref lorentz-boost i j)))))
;; rest of first row & first column
(loop
for i from 1 to 3
do (progn
(setf (tensor-ref lorentz-boost 0 i)
(- (* gamma
(tensor-ref beta-vector (1- i)))))
(setf (tensor-ref lorentz-boost i 0)
(tensor-ref lorentz-boost 0 i))))
lorentz-boost))))
;;; miscellaneous physics functions:
(defun gamma (beta)
"Returns gamma factor from beta"
(gamma-from-beta2 (expt beta 2)))
(defun gamma-from-beta2 (beta2)
"Computes gamma from beta^2, for efficiency purposes"
;; protection against infinities:
(when (not (= beta2 1))
(/ (sqrt (- 1
beta2)))))
(defun lorentz-vector-spatial (vector)
"Returns spatial part of the lorentz-vector"
(let* ((length (first (tensor-dimensions vector)))
(spatial-part (make-vector (1- length))))
(loop
for i from 1 below length
do (setf (tensor-ref spatial-part (1- i))
(tensor-ref vector i)))
spatial-part))
(defun four-momentum-beta-vector (four-momentum)
"Returns the beta vector from the four-momentum. Assumes that your
units are chosen such that c is effectively 1 (e.g. GeV/c^2 for mass,
GeV/c for momentum, etc.)"
(let ((momentum-vector (lorentz-vector-spatial four-momentum))
(energy (tensor-ref four-momentum 0)))
(div momentum-vector energy)))
;; Angles for lorentz spatial components:
(defun lorentz-phi (lorentz-vector)
(phi (lorentz-vector-spatial lorentz-vector)))
(defun lorentz-theta (lorentz-vector)
(theta (lorentz-vector-spatial lorentz-vector)))
| 5,381 | Common Lisp | .lisp | 133 | 32.909774 | 72 | 0.614826 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | c0d3821574ef387078aeed002d1baebfa42c1369d8e279d5302a9b298f810a22 | 1,495 | [
-1
] |
1,496 | package.lisp | ghollisjr_cl-ana/map/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; package.lisp
(defpackage #:cl-ana.map
(:use #:cl
#:cl-ana.hash-table-utils)
(:export :map->alist
:map->hash-table))
| 1,018 | Common Lisp | .lisp | 26 | 37.038462 | 70 | 0.690212 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 453dc8dcd7a5cad4730e205718336707481f1d70a39b3b97bb5bad044d7abb13 | 1,496 | [
-1
] |
1,497 | map.lisp | ghollisjr_cl-ana/map/map.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; map.lisp
(in-package :cl-ana.map)
;;;; A map is any object which represents or can be represented by the
;;;; mapping from one value to another; a two good examples are alists
;;;; and hash tables.
;;;;
;;;; These utilities are for the generic handling of maps so they can
;;;; be appropriately treated by things like fitting data or making
;;;; scatter plots.
(defgeneric map->alist (object)
(:documentation "Returns the values of a data-source as an alist
mapping the independent value to the dependent one.
Multidimensional independent variable data can be represented as a
list of values.")
(:method ((obj list))
obj)
(:method ((obj hash-table))
(hash-table->alist obj)))
(defun map->hash-table (object &optional test)
(alist->hash-table
(map->alist object)
test))
| 1,678 | Common Lisp | .lisp | 42 | 38.095238 | 70 | 0.718137 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | cd7fd2e655408d3840b597620a6eb3d090e575c84d900668b8dba1cbfed98567 | 1,497 | [
-1
] |
1,498 | package.lisp | ghollisjr_cl-ana/makeres-utils/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2016 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.makeres-utils
(:use :cl
:cl-ana.fitting
:cl-ana.makeres
:cl-ana.macro-utils
:cl-ana.list-utils
:cl-ana.symbol-utils
:cl-ana.map
:cl-ana.plotting
:cl-ana.string-utils
:cl-ana.functional-utils
:cl-ana.file-utils
:cl-ana.histogram
:cl-ana.pathname-utils
:cl-ana.table
:cl-ana.reusable-table)
(:export
;; Basic utilities:
:deffitres
:fit-results
:fit-params
:fit-plot
))
(cl-ana.gmath:use-gmath :cl-ana.makeres-utils)
| 1,433 | Common Lisp | .lisp | 44 | 28.477273 | 70 | 0.665465 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 9208d39b1df27a8de06ae8bc4bc838e3ebe04ce39f7020bba900aad5bb8f1365 | 1,498 | [
-1
] |
1,499 | makeres-utils.lisp | ghollisjr_cl-ana/makeres-utils/makeres-utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2016 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.makeres-utils)
(defmacro deffitres
(fit-id-prefix
data-form
fn-form
&key
fit-options
draw-p
(x-range '(cons "*" "*"))
(y-range '(cons "*" "*"))
flags
force-p
nparams
(param-init-value 1d0)
param-init-list)
"Defines fit result, fit parameter and fit function targets for
fitting a function against data. force-p non-NIL means defres is
used, whereas NIL means defres-uniq is used for defining the targets.
flags should be a list of identifiers appended to the created targets'
IDs. param-inits can be a constant or a list of initial parameter
guesses. draw-p NIL means don't draw the fit results, non-NIL means
draw in an interactive window. Note that drawing only works for
single parameter data at the moment. x-range and y-range apply to the
optional plot. param-init-value can be used to set a constant default
parameter value, whereas param-init-list can be used to specify a list
of default parameter values. If fn-form is a simple lambda form, then
the number of parameters can be inferred, otherwise param-init-list
needs to be specified explicitly. fit-options are supplied to fit.
Defines the following targets:
* (fit-id-prefix fit-results): fit results, parameters, and the rest from
the multiple fit values.
* (fit-id-prefix fit-params): fit parameters
* (fit-id-prefix fit): fit function with applied parameters
* (fit-id-prefix fit-plot): optional plot target"
(let* ((defres-op (if force-p
'defres
'defres-uniq))
(id-fit-results `(,fit-id-prefix fit-results ,@flags))
(id-fit-params `(,fit-id-prefix fit-params ,@flags))
(id-fit `(,fit-id-prefix fit ,@flags))
(id-fit-plot `(,fit-id-prefix fit-plot ,@flags))
(param-init-form
(cond
;; Explicit case
(param-init-list
param-init-list)
;; Implicit case
((numberp nparams)
`(list ,@(loop for i below nparams
collecting param-init-value)))
;; Error when neither works
(t
(error "Must supply explicit param init list with non-lambda fit function form")))))
`(progn
(,defres-op ,id-fit-results
(rest
(multiple-value-list
(fit ,data-form ,fn-form
,param-init-form
,@fit-options))))
(,defres-op ,id-fit-params
(first (res ,id-fit-results)))
(,defres-op ,id-fit
(let ((params (res ,id-fit-params))
(fit-fn ,fn-form))
(lambda (x)
(funcall fit-fn params x))))
,@(when draw-p
`((,defres-op ,id-fit-plot
(let* ((xr ,x-range)
(yr ,y-range)
(sampling-list
(if (and (numberp (car xr))
(numberp (cdr xr)))
(list :low (car xr)
:high (cdr xr)
:nsamples 1000)))
(data ,data-form)
(fn (res ,id-fit)))
(draw
(page (list
(plot2d (list
(line data
:style "points"
:title "data"
:color "red")
(apply #'line
fn
:title "fit"
:style "lines"
:color "black"
(when sampling-list
(list :sampling
sampling-list))))
:x-range xr
:y-range yr))))))))
)))
| 5,115 | Common Lisp | .lisp | 117 | 29.512821 | 97 | 0.510511 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e7070b1e03d496296b0b586e85c16e7fc4ed8b27ad70b7a8bed012b0c68b61d6 | 1,499 | [
-1
] |
1,500 | test.lisp | ghollisjr_cl-ana/makeres-utils/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013-2016 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana)
(in-package :cl-ana)
(defproject makeres-utils-test "/home/ghollisjr/test/makeres-utils-test"
(list #'macrotrans #'progresstrans)
(fixed-cache 5))
(defres data
'((1 . 2)
(2 . 3)
(3 . 5)
(4 . 5)
(6 . 4)))
(deffitres data
(res data)
#'polynomial
:force-p t
:x-range (cons 0 7)
:y-range (cons 0 7)
:draw-p t
:nparams 2
:flags (linear))
| 1,266 | Common Lisp | .lisp | 40 | 29.45 | 72 | 0.682488 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | d7899314c5771c48345212fea0a73abd1ff96427ab4b47f224401df618688b26 | 1,500 | [
-1
] |
1,501 | combinatorics.lisp | ghollisjr_cl-ana/math-functions/combinatorics.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.math-functions)
(defmath factorial (x)
(:documentation "Very naive factorial function")
(:method ((x number))
(labels ((rec (x &optional (result 1))
(if (<= x 1)
result
(rec (1- x) (* x result)))))
(rec x))))
(defmath npermutations (n r)
(:documentation "Returns nPr, the number of permutations of n objects
taken r at a time without repetition. Assumes reasonable values of n
and r. Returns 1 for nP0.")
(:method ((n number) (r number))
(loop
for k from (- n r) upto n
for result = 1 then (* result k)
finally (return result))))
(defmath npermutations-repeating (n r)
(:documentation "Returns n^r, the number of ways to permute r
objects from a set of n with allowed repetition. Assumes reasonable
values of n and r. Note that r can be greater than n.")
(:method ((n number) (r number))
(expt n r)))
(defmath ncombinations (n r)
(:documentation "Returns nCr, the number of combinations of n
objects taken r at a time without repetition. Assumes reasonable
values of n and r.")
(:method ((n number) (r number))
(cond
((zerop r)
1)
((= n r)
1)
(t
(let ((result 1)
(r (min r (- n r)))) ; symmetry optimization
(do ((num n (1- num))
(den 1 (1+ den)))
((> den r) result)
(setf result (* result num))
(setf result (truncate result den))))))))
(defun ncombinations-repeating (n r)
"Returns the number of combinations of n objects taken r at a time
with allowed repetition. Assumes reasonable values of n and r.
Note that r can be greater than n."
(ncombinations (1- (+ n r)) r))
(defun binomial (n r)
"Nickname for ncombinations; returns the binomial coefficient of n
and r."
(ncombinations n r))
(defun multinomial (&rest ms)
"Returns the multinomial coefficient where each element of ms is
taken to be the number of objects of a single type."
(let* ((n (sum ms))
(m NIL)
(j NIL)
(result 1))
(loop
while ms
do
(when (not m)
(setf m (first ms))
(setf j 1)
(setf ms (rest ms)))
(cond
((null ms) nil)
((< m j)
(setf m nil))
(t
(setf result (* result (1+ (decf n))))
(setf result (/ result (1- (incf j)))))))
result))
;;;; Useful macros for working with combinatorics
;;; Loop over all nPr permutations. E.g.,
;;;
;;; (for-permutations (indices 5 2) (print indices))
;;;
;;; would print out all of the possible 20 permutation index arrays.
;;;
;;; Note that for nP0, a single iteration of body is evaluated with an
;;; empty index array.
(defmacro for-permutations ((indexvar n r) &body body)
"Iterates over all permutations of r objects taken from n total,
binding an array of r index values to indexvar and evaluating body
with that binding. If you want to actually permute objects in a
list/array/sequence, use the bound index array to find permutations of
those objects. No safety checks are performed, so use reasonable
values of n and r."
(alexandria:with-gensyms (npr nn rr i j norder x k)
`(let* ((,nn ,n)
(,rr ,r))
;; safety check
(when (and (plusp ,nn)
(<= 0 ,rr ,nn))
(let* ((,npr (npermutations ,nn ,rr))
(,indexvar (make-array ,rr :element-type 'integer :initial-element 0)))
(loop
for ,i below ,npr
do
(loop
for ,j below ,rr
do
(let* ((,norder (- ,nn ,j))
(,x (mod ,i ,norder)))
(setf (aref ,indexvar ,j)
,x)
(loop
for ,k below ,j
when (>= ,x
(aref ,indexvar ,k))
do (incf (aref ,indexvar ,j)))))
(progn
,@body)))))))
;; Same but with allowed repetition
(defmacro for-permutations-repeating ((indexvar n r) &body body)
"Iterates over all permutations with allowed repitition of r objects
taken from n total, binding an array of r index values to indexvar
and evaluating body with that binding. If you want to actually
permute objects in a list/array/sequence, use the bound index array
to find permutations of those objects. No safety checks are
performed, so use reasonable values of n and r. Note that r can be
greater than n since repetition is allowed."
(alexandria:with-gensyms (npr nn rr i j)
`(let* ((,nn ,n)
(,rr ,r))
;; safety check
(when (and (plusp ,nn)
(>= ,rr 0))
(let* ((,npr (npermutations-repeating ,nn ,rr))
(,indexvar (make-array ,rr :element-type 'integer :initial-element 0)))
(loop
for ,i below ,npr
do
(loop
for ,j below ,rr
do
(setf (aref ,indexvar ,j)
(mod (truncate ,i (expt ,nn ,j))
,nn)))
(progn
,@body)))))))
;;; Loop over all nCr combinations. E.g.,
;;;
;;; (for-combinations (indices 5 2) (print indices))
;;;
;;; would print out all of the possible 10 combination index arrays.
;;;
;;; Note that for nC0, a single iteration of body is evaluated with an
;;; empty index array.
(defmacro for-combinations ((indexvar n r) &body body)
"Evaluates body for every combination of r objects taken from a set
of n without repetition and without caring about order of occurrence.
indexvar will be set to an index array denoting the selected
combination. For unreasonable values of n and r, no iterations are
performed. Note that for r=0, one evaluation of the body is performed
with an empty index array."
(alexandria:with-gensyms (n-r
nn rr i
lastindex currentindex state
current nextindex next
delta k)
`(let* ((,nn ,n)
(,rr ,r)
(,n-r (- ,nn ,rr))) ; useful for later
;; safety check
(when (and (plusp ,nn)
(<= 0 ,rr ,nn))
(let* ((,indexvar
(make-array ,rr :element-type 'integer :initial-element 0)))
;; init indices
(loop
for ,i below ,rr
do (setf (aref ,indexvar ,i) ,i))
;; strategy:
;;
;; Indices will be strictly ordered from least to greatest.
;; This makes finding the next valid combination of indices
;; simple.
;;
;; Iteration is accomplished through a state machine with the
;; following states:
;;
;; 0. Execute combination.
;; 1. Increment.
;; 2. Halt.
;;
;; There is an additional state variable: currentindex is the
;; index currently attempted to increment. If it's not the
;; last index, then successfully finding a valid slot means
;; needing to initialize all higher indices.
(let* ((,lastindex (1- ,rr))
(,currentindex ,lastindex)
(,state 0))
(symbol-macrolet ((,current
(aref ,indexvar ,currentindex))
(,nextindex (1+ ,currentindex))
(,next (aref ,indexvar (1+ ,currentindex))))
(loop
while (not (= ,state 2))
do
(case ,state
;; execute
(0
,@body
(setf ,currentindex ,lastindex)
(setf ,state 1))
;; increment
(1
(cond
;; out of combinations
((< ,currentindex 0)
(setf ,state 2))
;; out of room to grow for increasing currentindex
((< ,n-r
(- (1+ ,current) ,currentindex))
(decf ,currentindex))
;; can find combination
(t
(incf ,current)
(let* ((,delta (- ,current ,currentindex)))
(loop
for ,k from (1+ ,currentindex) below ,rr
do (setf (aref ,indexvar ,k)
(+ ,k ,delta))))
(setf ,state 0)
(setf ,currentindex ,lastindex)))))))))))))
(defmacro for-combinations-repeating ((indexvar n r) &body body)
"Evaluates body for every combination of r objects taken from a set
of n with allowed repetition but without caring about order of
occurrence. indexvar will be set to an index array denoting the
selected combination. For unreasonable values of n and r, no
iterations are performed. Note that for r=0, one evaluation of the
body is performed with an empty index array."
(alexandria:with-gensyms (n-1
nn rr i
lastindex currentindex state
current nextindex next
k)
`(let* ((,nn ,n)
(,rr ,r)
(,n-1 (1- ,nn))) ; useful for later
;; safety check
(when (and (plusp ,nn)
(>= ,rr 0))
(let* ((,indexvar
(make-array ,rr :element-type 'integer :initial-element 0)))
;; init indices
(loop
for ,i below ,rr
do (setf (aref ,indexvar ,i) 0))
;; strategy:
;;
;; Indices will be strictly ordered from least to greatest.
;; This makes finding the next valid combination of indices
;; simple.
;;
;; Iteration is accomplished through a state machine with the
;; following states:
;;
;; 0. Execute combination.
;; 1. Increment.
;; 2. Halt.
;;
;; There is an additional state variable: currentindex is the
;; index currently attempted to increment. If it's not the
;; last index, then successfully finding a valid slot means
;; needing to initialize all higher indices.
(let* ((,lastindex (1- ,rr))
(,currentindex ,lastindex)
(,state 0))
(symbol-macrolet ((,current
(aref ,indexvar ,currentindex))
(,nextindex (1+ ,currentindex))
(,next (aref ,indexvar (1+ ,currentindex))))
(loop
while (not (= ,state 2))
do
(case ,state
;; execute
(0
,@body
(setf ,currentindex ,lastindex)
(setf ,state 1))
;; increment
(1
(cond
;; out of combinations
((< ,currentindex 0)
(setf ,state 2))
;; out of room to grow for increasing currentindex
((<= ,n-1
,current)
(decf ,currentindex))
;; can find combination
(t
(incf ,current)
(loop
for ,k from (1+ ,currentindex) below ,rr
do (setf (aref ,indexvar ,k)
,current))
(setf ,state 0)
(setf ,currentindex ,lastindex)))))))))))))
| 13,138 | Common Lisp | .lisp | 323 | 28.074303 | 87 | 0.511913 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 0224239a368a90ed03bf4d6e5760100b293c0763eec73cc5b08689c7ae0fc8ed | 1,501 | [
-1
] |
1,502 | package.lisp | ghollisjr_cl-ana/math-functions/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage :cl-ana.math-functions
(:use :cl)
(:shadow :erf)
(:shadow :factorial)
(:export
;; distributions:
:erf
:sinc
:normal-pdf
:normal-cdf
:normal-cdf-inv
:uniform-cdf
:uniform-cdf-inv
;; combinatorics:
:factorial
:npermutations
:npermutations-repeating
:ncombinations
:ncombinations-repeating
:binomial
:multinomial
;; misc
:logistic
:logistic-derivative
;; utils:
:->double-float
:periodic-shift
:solve-interval-bisection
;; macros:
:for-permutations
:for-permutations-repeating
:for-combinations
:for-combinations-repeating
))
(cl-ana.gmath:use-gmath :cl-ana.math-functions)
| 1,553 | Common Lisp | .lisp | 55 | 25.381818 | 70 | 0.703877 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | a2eec3ef6bfca8bf0fc6ec7bb20f9976da19d10b34cad42c8a97bfea896f50c7 | 1,502 | [
-1
] |
1,503 | utils.lisp | ghollisjr_cl-ana/math-functions/utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.math-functions)
(defmath ->double-float (x)
(:documentation "Converts numerical object into a double-float form;
does not need to be an actual double-float result, but where
appropriate constituents are converted into double-float
values.")
(:method ((x real))
(float x 0d0))
(:method ((x complex))
(complex (float (realpart x) 0d0)
(float (imagpart x) 0d0))))
(defun periodic-shift (x lo hi)
"Shifts x into the range [lo, hi] through interval multiples of (-
hi lo). Useful for shifting angles into a different range or working
with periodic quantities in general."
(let* ((range (- hi lo))
(k (ceiling (/ (- lo x) range))))
(+ x (* k range))))
;;;; Solving 1-D problems with interval bisection
(defun solve-interval-bisection (fn interval
&key
(value 0d0)
(prec 1d-4))
(flet ((exists (x y)
(minusp (* (signum (- (funcall fn x) value))
(signum (- (funcall fn y) value)))))
(middle (x y)
(* 0.5d0 (+ x y))))
(let* ((xlo (car interval))
(xhi (cdr interval))
(diff (- xhi xlo)))
(cond
((zerop (- (funcall fn xlo) value))
xlo)
((zerop (- (funcall fn xhi) value))
xhi)
(t
(when (exists xlo xhi)
(let* ((iter 0))
(loop
while (> diff prec)
do (let* ((xm (middle xlo xhi)))
(incf iter)
(if (zerop (- (funcall fn xm) value))
(return-from solve-interval-bisection
xm)
(if (exists xlo xm)
(setf xhi xm)
(setf xlo xm)))
(setf diff (- xhi xlo))))
(values (middle xlo xhi)
iter))))))))
| 2,845 | Common Lisp | .lisp | 72 | 30.416667 | 70 | 0.553991 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | f49cc08caa6d74389b0b12e9a8b118b760b9506d5f2259a441be7448dd8ceff4 | 1,503 | [
-1
] |
1,504 | distributions.lisp | ghollisjr_cl-ana/math-functions/distributions.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.math-functions)
(defmath erf (x)
(:documentation "the error function")
(:method ((x number))
(gsll:erf (->double-float x))))
(defmath normal-pdf (x)
(:documentation "Standard normal probability density function")
(:method ((x number))
(/ (exp (/ (- (* x x))
2))
(sqrt (* 2
pi)))))
(defmath normal-cdf (x)
(:documentation "Standard normal cumulative density function")
(:method ((x number))
(gsll:gaussian-p (->double-float x) 1d0)))
(defmath normal-cdf-inv (x)
(:documentation "Inverse of normal CDF")
(:method ((x number))
(gsll:gaussian-pinv (->double-float x) 1d0)))
(defmath uniform-cdf (x lo hi)
(:documentation "CDF of uniform distribution between lo and hi.")
(:method ((x number) (lo number) (hi number))
(cond
((< x lo)
0)
((> x hi)
1)
(t
(/ (- x lo)
(- hi lo))))))
(defmath uniform-cdf-inv (x lo hi)
(:documentation "Inverse CDF of uniform distribution between lo and hi. Assumes x
is between 0 and 1.")
(:method ((x number) (lo number) (hi number))
(+ lo
(* x (- hi lo)))))
| 2,026 | Common Lisp | .lisp | 57 | 31.877193 | 84 | 0.64595 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 9c747ad292ecda362d7d8c0b8e209151666901e66525125847bd6dd486ec6805 | 1,504 | [
-1
] |
1,505 | misc.lisp | ghollisjr_cl-ana/math-functions/misc.lisp | (in-package :cl-ana.math-functions)
(defun logistic (x)
"Logistic sigmoid function"
(expt (+ 1 (exp (- x))) -1))
(defun logistic-derivative (x)
"Derivative of logistic sigmoid function"
(let ((f (logistic x)))
(* f (- 1 f))))
| 240 | Common Lisp | .lisp | 8 | 27.25 | 43 | 0.647826 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 3206fa5d92822e846a00c52f308b339c36d4d3134f3f45b0d3c5454488f39604 | 1,505 | [
-1
] |
1,506 | package.lisp | ghollisjr_cl-ana/list-utils/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.list-utils
(:use :cl
:alexandria
:cl-ana.string-utils
:cl-ana.functional-utils)
(:export :range
:zip
:lzip
:unzip
:unlzip
:mapzip
:tree-map
:intersperse
:transpose
:cartesian-product
:every-nth
:except-nth
:at-indices
:except-at
:compress
:list-less-than
:list-greater-than
:aref-by-list
:make-offsets
:ensure-lists
:partition
:tree-flatten
;;; alists
:cars
:cdrs
;; lists as sets
:list->set
:list->set-ht
;;; plists
:plist-select-fields
:plist->alist
:alist->plist
;; Useful looping macros over plists:
:do-plists
:do-plist
;; Paul Graham's stuff (and some of my improvements)
:length-equal
:single
:append1
:conc1
:mklist
:longer
:group
:prune
:find2
:before
:after
:duplicate
:permute
;; miscellaneous
:groupby
:reduceby
))
| 2,124 | Common Lisp | .lisp | 78 | 19.717949 | 70 | 0.56577 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 1ca5bc7f94df42b1791a9b90ca1e0a45446dfccf4832509e95a1d9252ae11986 | 1,506 | [
-1
] |
1,507 | list-utils.lisp | ghollisjr_cl-ana/list-utils/list-utils.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.list-utils)
(defun range (start end &optional (step 1))
(labels
((range-helper (s e st result)
(if (> s e)
result
(range-helper (+ s st)
e
st
(cons s result)))))
(nreverse (range-helper start end step ()))))
;; Sorry: I learned Haskell before Common Lisp, so I like
;; zipping/unzipping lists
;; Just found out that pairlis does exactly what my zip does, except
;; that (at least in sbcl) the resulting list comes in reverse order
(defun zip (x y)
(mapcar #'cons x y))
(defun lzip (&rest lists)
"Like zip, but uses lists instead of cons pairs thus allowing ntuples"
(transpose lists))
(defun unzip (xs)
"Returns a cons with the car being the cars of the zipped xs and the
cdr being the cdrs."
(labels
((unzip-helper (xs ls rs)
(if xs
(unzip-helper (cdr xs)
(cons (car (car xs)) ls)
(cons (cdr (car xs)) rs))
(cons (nreverse ls) (nreverse rs)))))
(unzip-helper xs () ())))
(defun unlzip (xs)
"lzip is an inverse (through apply) of itself, simply applies lzip
to its argument, returning a list of the previously zipped lists in
xs."
(apply #'lzip xs))
;; Useful for creating mappings from data to values:
(defun mapzip (fn &rest lists)
"Returns an alist mapping the list of corresponding elements from
each input list to the value of fn for those values; it's just zipping
together the arguments with the value of fn. If only one list is
given, the elements are mapped directly (i.e. not in a list)"
(apply #'mapcar
(if (single lists)
(lambda (x)
(cons x (funcall fn x)))
(lambda (&rest xs)
(cons xs (apply fn xs))))
lists))
;; Tree map
(defun tree-map (fn &rest trees)
"Maps function over identically structured trees (lists)"
(when trees
(cond
((null (first trees))
nil)
((or (atom (first trees))
(cdr (last (first trees))))
(apply fn trees))
((listp (first trees))
(apply #'mapcar
(lambda (&rest ts)
(apply #'tree-map fn ts))
trees)))))
(defun intersperse (obj lst)
"Inserts obj in between each pair of elements in lst"
(labels ((rec (lst &optional result)
(if (null (cdr lst))
(nreverse (cons (car lst)
result))
(rec (rest lst) (cons obj
(cons (car lst)
result))))))
(rec lst)))
(defun transpose (xs)
(labels
((transpose-worker (xs result)
(let* ((heads (remove-if #'null (mapcar #'car xs)))
(tails (remove-if #'null (mapcar #'cdr xs))))
(if xs
(transpose-worker tails (cons heads result))
result))))
(nreverse (transpose-worker xs ()))))
;; Can't go without the Cartesian Product
(defun cartesian-product (&rest xs)
(if xs
(if (single xs)
(mapcar #'list (car xs))
(mapcan
(lambda (c)
(mapcar
(lambda (x) (cons x c))
(car xs)))
(apply #'cartesian-product (cdr xs))))))
;; Selects every nth term from a list (including the first term):
(defun every-nth (list n &optional (start 0))
(labels ((every-nth-worker (list n i result)
;; assumes that n > 0
(if list
(if (= i 1)
(every-nth-worker (rest list)
n
n
(cons (first list)
result))
(every-nth-worker (rest list)
n
(1- i)
result))
(when result
(nreverse result)))))
(if (plusp n)
(every-nth-worker (subseq list start) n 1 ())
(error "Negative number given to every-nth"))))
;; Until I implement the Levi-Civita tensor again, I'm using this to
;; write certain things
(defun except-nth (x n)
(labels
((except-nth-helper (x n result)
(cond ((> n 0)
(except-nth-helper (cdr x) (1- n) (cons (car x) result)))
((= n 0)
(except-nth-helper (cdr x) (1- n) result))
((< n 0)
(append (reverse x) result)))))
(nreverse (except-nth-helper x n ()))))
(defun at-indices (lst indices)
"Returns the values from lst located at positions given by indices"
(loop
for i in indices
collecting (elt lst i)))
;; (defun at-indices (lst indices)
;; "Returns the values from lst located at positions given by indices"
;; (labels ((rec (xs inds &optional result (i 0))
;; (cond
;; ((or (null xs)
;; (null inds))
;; (nreverse result))
;; ((equal (first inds) i)
;; (rec (rest xs)
;; (rest inds)
;; (cons (first xs) result)
;; (1+ i)))
;; (t
;; (rec (rest xs)
;; inds
;; result
;; (1+ i))))))
;; (rec lst indices)))
(defun except-at (xs ns &key (test #'eql) uniquely-sorted)
"Yields the list of xs except for the elements at the positions in
ns. Set uniquely-sorted to t if you want except-at to assume the ns
are already unique and sorted least to greatest."
(labels ((except-at-worker (xs ns &optional result (current-index 0))
(if xs
(if ns
(if (= (first ns) current-index)
(except-at-worker (rest xs)
(rest ns)
result
(1+ current-index))
(except-at-worker (rest xs)
ns
(cons (first xs)
result)
(1+ current-index)))
;; cons xs onto result and return result
(nreverse
(reduce (flip #'cons) xs
:initial-value result)))
(nreverse result))))
(let ((uniquely-sorted-ns
(if uniquely-sorted
ns
(let ((ns-copy (copy-list ns)))
(reverse
(reduce (lambda (x y)
(adjoin y x
:test test))
(sort ns-copy #'<)
:initial-value ()))))))
(except-at-worker xs uniquely-sorted-ns))))
;; Compress a list into an alist where each car is the value and each
;; cdr is the count of said value. This is a shitty algorithm btw,
;; not useful for processing intensive stuff, but for the time being
;; it works for some of my other utilities.
(defun compress (list &key
(key #'identity)
(test 'eql)
sort-by
singleton-pairs)
"Compress list such that duplicate elements are combined into a
single pair entry which has as the car the element value and as the
cdr the count.
The singleton-pairs option controls whether single elements are still
placed inside a pair. This is useful when the elements of the list
you wish to compress are cons cells, as this would otherwise lead to
ambiguity in the result."
(let* ((result-table (make-hash-table :test test)))
(dolist (x list)
(if (gethash x result-table)
(incf (gethash x result-table))
(setf (gethash x result-table) 1)))
(let* ((map-fn (if singleton-pairs
(lambda (x c)
(cons x c))
(lambda (x c)
(if (= 1 c)
x
(cons x c)))))
(raw-alist
(loop
for k being the hash-keys of result-table
for v being the hash-values of result-table
collect (funcall map-fn k v))))
(if sort-by
(sort raw-alist sort-by
:key (if singleton-pairs
(lambda (x)
(funcall key (car x)))
(lambda (x)
(if (consp x)
(funcall key (car x))
(funcall key x)))))
raw-alist))))
(defun list-less-than (list1 list2)
(let ((x1 (car list1))
(x2 (car list2)))
(cond ((and (null list1) (null list2)) nil)
((null list1) t)
((null list2) nil)
((< x1 x2) t)
((= x1 x2) (list-less-than (cdr list1) (cdr list2)))
(t nil))))
(defun list-greater-than (list1 list2)
(let ((x1 (car list1))
(x2 (car list2)))
(cond ((and (null list1) (null list2)) nil)
((null list1) nil)
((null list2) t)
((> x1 x2) t)
((= x1 x2) (list-greater-than (cdr list1) (cdr list2)))
(t nil))))
(defun aref-by-list (array indexlist)
"Access array element via index list instead of individual indices"
(apply #'aref array indexlist))
(defun list-equal (list1 list2)
(if (and (consp list1) (consp list2))
(if (equal (first list1) (first list2))
(list-equal (rest list1) (rest list2))
nil)
nil))
(defun make-offsets (sizes)
"Takes a list of sizes and returns a list containing 0, (first
sizes), (+ (first sizes) (second sizes)), ... summing the sizes as the
list goes.
This pattern has turned out to be recurrent, and the result can be
interpreted as finding the starting index of the ith list in the
concatenation of n lists."
(nreverse
(rest
(reduce (lambda (x y)
(cons (+ y (car x)) x))
sizes
:initial-value (list 0)))))
;;; useful for alists:
(defun cdrs (xs)
(mapcar #'cdr xs))
(defun cars (xs)
(mapcar #'car xs))
;;; lists as sets utilities:
(defun list->set (list &optional (test #'eql))
"Returns list with duplicates removed"
(reduce (lambda (res el)
(adjoin el res :test test))
list
:initial-value nil))
(defun list->set-ht (list &optional (test 'eql))
(let* ((ht (make-hash-table :test test)))
(loop
for x in list
do (when (not (gethash x ht))
(setf (gethash x ht) t)))
ht))
;; Partitioning a list
(defun partition (list
&key
(key #'identity)
(test #'eql))
"Re-groups the contents of a list into partitions using the test
function provided. Guarantees that the elements of each group pass
test with every member of the partition as long as the test function
is transitive. Does not necessarily preserve order of partitions, but
preserves order of the elements relative to each partition.
This function supports two different conceptual approaches to partitioning:
* By relation: the test function is the equivalence relation operator
* By association: using a key function which maps into a set of index
values allows the user to partition according to association with
that value."
(let* (;; map from partition number to result list
(resultht (make-hash-table :test 'equal))
;; number of partitions currently found
(nparts 0))
(loop
for i in list
do
;; Find a matching partition
(let ((match nil))
(loop for n from 1 to nparts
when (funcall test
(funcall key i)
(funcall key
(first (gethash n resultht))))
do (setf match n)
and return nil)
;; Either add the match or create a new partition
(if match
(push i
(gethash match resultht))
(push i
(gethash (incf nparts)
resultht)))))
;; finally return the list:
(loop
for i from 1 to nparts
collecting (nreverse (gethash i resultht)))))
;; Collects all non-nil atoms inside a tree
(defun tree-flatten (tree)
"Collects all non-nil atoms in a tree and returns the list of them
as encountered during a depth-first search."
(cond
((null tree)
nil)
((atom tree)
(list tree))
(t
(append (tree-flatten (car tree))
(tree-flatten (cdr tree))))))
;;; Stuff (mostly) from Paul Graham's On Lisp, as well as some of my
;;; own improvements.
(declaim (inline single append1 conc1 mklist))
;; Would include last1, but Alexandria has last-elt, which is last1
;; for sequences
(defun length-equal (list length)
"Returns t/nil as soon as it is apparent that the list does not
contain exactly length elements."
(declare (integer length))
(labels ((rec (list length)
(if (zerop length)
(if (null list)
t
nil)
(if (consp list)
(length-equal (cdr list) (1- length))
nil))))
(if (< length 0)
nil
(rec list length))))
(defun single (list)
"Checks to see if list is a list with exactly one element."
(and (consp list)
(null (rest list))))
(defun append1 (list object)
"Creates a list containing object and appends list to it."
(append list (list object)))
(defun conc1 (list object)
"Like append1, but uses nconc instead of append"
(nconc list (list object)))
(defun mklist (object)
"Ensures that object is a list, if not object is packaged in a
list."
(if (listp object)
object
(list object)))
(defmacro ensure-lists ((&rest list-bindings) &body body)
"Ensures and rebinds variables as lists via mklist. Each
list-binding must be either a symbol or a list (symbol form); for a
symbol it will be bound to (mklist symbol) in the body; for a list the
first element of the list-binding will be bound to (mklist (second
list-binding))."
`(let ,(loop
for lb in list-bindings
collect (if (listp lb)
`(,(first lb)
(mklist ,(second lb)))
`(,lb (mklist ,lb))))
,@body))
(defun longer (x y)
"Efficiently compares two lists, or if they're not both lists simply
calls length on each and compares. This could be sped up a bit if one
argument is a list and the other not, so it's a work in progress."
(labels ((compare (x y)
(and (consp x)
(or (null y)
(compare (cdr x) (cdr y))))))
(if (and (listp x) (listp y))
(compare x y)
(> (length x) (length y)))))
;; filter is (IMO) not so necessary (as Paul Graham uses the term)
(defun group (source n)
"Takes a list and returns a list of lists of the elements in the
list grouped in lists of size n with the remainder in the last list."
(if (zerop n)
(error "zero length")
(labels ((group-worker (source acc)
(let ((rest (nthcdr n source)))
(if (consp rest)
(group-worker rest
(cons (subseq source 0 n) acc))
(nreverse (cons source acc))))))
(if source
(group-worker source nil)
nil))))
;; flatten is already provided by Alexandria. To reduce a tree just
;; flatten the list first and then reduce it.
(defun prune (test tree)
"Like remove-if, but for lists treated as trees."
(labels ((prune-worker (tree acc)
(cond ((null tree) (nreverse acc))
((consp (car tree))
(prune-worker
(cdr tree)
(cons (prune-worker (car tree) nil) acc)))
(t (prune-worker (cdr tree)
(if (funcall test (car tree))
acc
(cons (car tree) acc)))))))
(prune-worker tree nil)))
(defun find2 (fn list)
"Like find, but it returns two values: the list element and the
value that fn returned."
(if (null list)
nil
(let ((val (funcall fn (car list))))
(if val
(values (car list) val)
(find2 fn (cdr list))))))
(defun before (x y list &key (test #'eql))
"Tells you if x is found before y in list."
(and list
(let ((first (car list)))
(cond ((funcall test y first) nil)
((funcall test x first) list)
(t (before x y (cdr list) :test test))))))
(defun after (x y list &key (test #'eql))
"Tells you if x is found after y in list."
(let ((rest (before y x list :test test)))
(and rest (member x rest :test test))))
(defun duplicate (object list &key (test #'eql))
"Tells you if the object occurs more than once in the list."
(member object (cdr (member object list :test test))
:test test))
(defun permute (list permutation)
"Re-arranges the elements in list according to the permutation."
(mapcar (lambda (p)
(elt list p))
permutation))
;; split-if is provided by split-sequence:split-sequence-if
;;;; plist stuff
(defun plist->alist (plist)
"Forms an alist from a plist"
(do ((lst plist (rest (rest lst)))
(result nil (cons (cons (first lst)
(second lst))
result)))
((null lst) (nreverse result))))
(defun alist->plist (alist)
"Forms a plist from an alist"
(let ((result ()))
(dolist (x alist)
(push (car x) result)
(push (cdr x) result))
(nreverse result)))
(defun plist-select-fields (plist &rest fields)
"Returns a list of the fields from plist in the order specified; the
element will be nil if the field is not present."
(mapcar (lambda (x)
(getf plist x))
fields))
;; Operator for looping over a plist:
(defmacro do-plist ((field-symbol field-value plist) &body body)
"Executes body via looping over plist, binding each field symbol to
field-symbol and each field value to field-value. Returns nil."
(with-gensyms (lst)
`(do ((,lst ,plist (rest (rest ,lst))))
((null ,lst))
(let ((,field-symbol (first ,lst))
(,field-value (second ,lst)))
,@body))))
;; Operator for looping over a list of plists, binding variables
;; according to the field names of each plist
(defmacro do-plists (plists &body body)
"Loops over a plist, binding each field in the plist to a variable
of the same name as the field symbol but in the current package."
(with-gensyms (lst fs fv)
`(dolist (,lst ,plists)
(do-plist (,fs ,fv ,lst)
(set (intern (lispify ,fs)) ,fv))
,@body)))
;; Grouping and reducing by keys
;;
;; These support any sequences, but generate lists.
(defun groupby (data
&key
(groupkey #'identity)
(valuekey #'identity)
(test 'equal))
"Groups data using a hash-table and the group and value key
functions provided. Return value is an alist of keys and the grouped
values for each key."
(let* ((ht (make-hash-table :test test)))
(map nil
(lambda (d)
(let* ((k (funcall groupkey d)))
(push (funcall valuekey d)
(gethash k ht))))
data)
(loop
for k being the hash-keys in ht
for v being the hash-values in ht
collecting (cons k v))))
(defun reduceby (data fn
&rest groupby-args)
"Groups using groupby and then reduces each group using the
reduction function provided."
(let* ((grouped (apply #'groupby data groupby-args)))
(map 'list
(lambda (x)
(destructuring-bind (type &rest amounts) x
(list type (reduce fn amounts))))
grouped)))
| 20,164 | Common Lisp | .lisp | 551 | 29.067151 | 75 | 0.584796 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 815e8db67d484e809b696b3f1f2a17c43fb0cd0c28161dfb6bdccf7ef2652a20 | 1,507 | [
-1
] |
1,508 | package.lisp | ghollisjr_cl-ana/tensor/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
;;;; package.lisp
(defpackage #:cl-ana.tensor
(:use #:cl
#:alexandria
#:cl-ana.list-utils
#:cl-ana.symbol-utils
;; debug
#:cl-ana.macro-utils)
(:export :make-tensor
:function->tensor
:tensor-ref
:tref
:tensor-flat-ref ; for flattened-index reference
:tfref
:tensor-map
:tensor-+
:tensor--
:tensor-*
:tensor-/
:tensor-rank
:tensor-dimensions
:sequencep
:tensor-contract
:tensor-flatten
:tensor-unflatten))
(cl-ana.gmath:use-gmath :cl-ana.tensor)
| 1,463 | Common Lisp | .lisp | 46 | 27.543478 | 70 | 0.65583 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | bb9a8fd863990dbf939bdee3ded844daf524c893e787f7c9f8ec96f7c336db0d | 1,508 | [
-1
] |
1,509 | tensor.lisp | ghollisjr_cl-ana/tensor/tensor.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.tensor)
;;;; A tensor is just a recursively structured sequence of sequences
;;;; of .... It's useful for implementing things like contiguous
;;;; histograms, matrices, actual tensors, etc. The utilities
;;;; provided in this sublibrary make it convenient to use nested
;;;; sequences as multidimensional arrays in CL since the ones
;;;; provided are awkward/clumsy to use.
;;;;
;;;; To make use of the tensor functions, just define a list, or
;;;; vector of vectors, or even a list of vectors of lists of ..., you
;;;; get the idea.
;;;;
;;;; Of particular merit is the fact that everything is vectorized
;;;; automatically when using this library; you want to add a constant
;;;; value to a list? Just do (+ (list x y z ...) value). Want to
;;;; take the square root of an array of numbers? Just do (sqrt
;;;; array).
(declaim (optimize (speed 3)
(safety 1)
(compilation-speed 0)
(debug 1)))
;;; Reader macro: #t(fn tensor1 tensor2 ...) applies tensor-map to the
;;; arguments. Can use #' or (function) on fn or not, both cases are
;;; handled.
(defun tensor-map-transformer-reader-macro (stream subchar arg)
(let* ((expr (read stream t))
(raw-fn (first expr))
(fn (if (symbolp raw-fn)
`(function ,raw-fn)
raw-fn))
(args (rest expr)))
`(tensor-map ,fn ,@args)))
(set-dispatch-macro-character
#\# #\t #'tensor-map-transformer-reader-macro)
(defun define-tensor-methods ()
(loop
for f being the hash-keys in *gmath-generic-map*
for a being the hash-values in *gmath-generic-map*
do (define-tensor-method f a)))
(defun define-tensor-method (fname args)
(multiple-value-bind (tensor-args key-args)
(let ((key-pos (position "&KEY" args
:test #'equal
:key #'string)))
(if key-pos
(values (subseq args 0 key-pos)
(subseq args (1+ key-pos)))
(values args nil)))
(let* ((key-fields (mapcar #'keywordify key-args))
(key-applied-args
(loop
for a in key-args
for k in key-fields
append (list k a)))
(tensor-specialized-args
(mapcar (lambda (x)
`(,x sequence))
tensor-args))
(nil-specialized-args
(mapcar (lambda (x)
`(,x (eql NIL)))
tensor-args))
(arg-specs
(remove-if-not
(lambda (x) (some #'listp x))
(apply #'cartesian-product
(mapcar #'list
tensor-args
tensor-specialized-args))))
(nil-arg-specs
(remove-if-not
(lambda (x) (some #'listp x))
(apply #'cartesian-product
(mapcar #'list
tensor-args
nil-specialized-args)))))
(loop
for a in arg-specs
do
(multiple-value-bind (unspecialized specialized)
(loop for i in a
if (symbolp i)
collect i into unspecialized
else collect (first i) into specialized
finally (return (values unspecialized
specialized)))
;; this seems to be a necessary use of eval
(eval
`(defmethod ,fname
(,@a
,@(when key-args
(cons '&key key-args)))
(tensor-map
(lambda (,@specialized)
(apply (function ,fname) ,@tensor-args
(list ,@key-applied-args)))
,@specialized)))))
;; NIL methods:
(loop
for n in nil-arg-specs
do
(multiple-value-bind (unspecialized specialized)
(loop for i in n
if (symbolp i)
collect i into unspecialized
else collect (first i) into specialized
finally (return (values unspecialized
specialized)))
;; this seems to be a necessary use of eval
(eval
`(defmethod ,fname
(,@n
,@(when key-args
(cons '&key key-args)))
nil))))
)))
;; Define tensor methods; note that this should be done after all
;; generic math functions have been defined with defmath.
(define-tensor-methods)
;; This version is much faster than using subtypep
(defun sequencep (x)
(typep x 'sequence))
(defun tensor-simple-type (type)
(if (atom type)
type
(first type)))
;; This version does not handle type constraints on arrays, but I'm
;; keeping it here until testing is complete
;;
;; (defun make-tensor (dimension-list &key
;; (type 'vector)
;; (initial-element 0d0))
;; "Creates a tensor with each dimension in dimension-list denoting the
;; length of the sequence at that dimension with the type of the
;; sequences given by the optional type argument."
;; (if (single dimension-list)
;; (make-sequence type (first dimension-list) :initial-element initial-element)
;; (map type
;; (lambda (&rest xs)
;; (make-tensor (rest dimension-list) :type type :initial-element initial-element))
;; (make-sequence type (first dimension-list)))))
(defun make-tensor (dimension-list &key
(type 'vector)
(initial-element 0d0))
"Creates a tensor with each dimension in dimension-list denoting the
length of the sequence at that dimension with the type of the
sequences given by the optional type argument."
(if (single dimension-list)
(make-sequence (tensor-simple-type type) (first dimension-list) :initial-element initial-element)
(map type
(lambda (&rest xs)
(make-tensor (rest dimension-list) :type type :initial-element initial-element))
(make-sequence (tensor-simple-type type) (first dimension-list)))))
(defun function->tensor (dimension-list fn &key
(type 'vector))
(let* ((result (make-tensor dimension-list :type type))
(size (apply #'* dimension-list )))
(loop
for i below size
do (setf (tensor-flat-ref result i)
(apply fn
(unflatten-index i dimension-list))))
result))
;; (defgeneric tensor-ref (tensor &rest subscripts)
;; (:documentation "References an object as a tensor"))
;; (defmethod tensor-ref ((tensor sequence) &rest subscripts)
;; (reduce #'elt subscripts :initial-value tensor))
;; (defmethod tensor-ref (tensor &rest subscripts)
;; tensor)
(defun tensor-ref (tensor &rest subscripts)
"References tensor via subscripts"
(if (sequencep tensor)
(reduce #'elt subscripts :initial-value tensor)
tensor))
(defun tref (tensor &rest subscripts)
"Abbreviation for tensor-ref; setfable."
(apply #'tensor-ref tensor subscripts))
(defun unflatten-index (index dim-sizes)
(let ((sub index)
(result nil))
(do* ((rdim-sze (reverse dim-sizes) (rest rdim-sze))
(dim-size (first rdim-sze) (first rdim-sze)))
((null rdim-sze) result)
(push (mod sub dim-size)
result)
(setf sub (floor sub dim-size)))))
(defun tensor-flat-ref (tensor subscript)
"References tensor by single subscript; done in such a way to mimick
the way multidimensional arrays are stored in memory by e.g. C.
Assumes rectangular tensor."
(if (sequencep tensor)
(let* ((dim-list (tensor-dimensions tensor))
(subscripts (unflatten-index subscript dim-list)))
(apply #'tensor-ref tensor subscripts))
tensor))
(defun tfref (tensor subscript)
"Abbreviation for tensor-flat-ref; setfable."
(tensor-flat-ref tensor subscript))
(defun (setf tensor-flat-ref) (value tensor subscript)
(let* ((dim-list (tensor-dimensions tensor))
(subscripts (unflatten-index subscript dim-list)))
(setf (apply #'tensor-ref tensor subscripts)
value)))
(defun (setf tfref) (value tensor subscript)
(setf (tensor-flat-ref tensor subscript) value))
(defun (setf tensor-ref) (value tensor &rest subscripts)
(let* ((last-sequence
(apply #'tensor-ref tensor (butlast subscripts)))
(last-subscript (lastcar subscripts)))
(setf (elt last-sequence last-subscript) value)))
(defun (setf tref) (value tensor &rest subscripts)
(setf (apply #'tensor-ref tensor subscripts)
value))
(defun tensor-rank (tensor)
(labels ((tensor-rank-worker (tensor &optional (result 1))
(let ((first-elt (elt tensor 0)))
(if (sequencep first-elt)
(tensor-rank-worker first-elt (1+ result))
result))))
(if (sequencep tensor)
(tensor-rank-worker tensor)
0)))
(defun tensor-dimensions (tensor)
"Returns a list of the sizes of the tensor for each dimension."
(labels ((tensor-dimensions-worker (tensor &optional result)
(if (sequencep tensor)
(tensor-dimensions-worker (elt tensor 0)
(cons (length tensor) result))
(nreverse result))))
(tensor-dimensions-worker tensor)))
(defun tensor-size (tensor)
(reduce #'* (tensor-dimensions tensor)))
(defun map* (type fn &rest xs)
"map* behaves like map except that non-sequences are treated
as arbitrarily deep sequences with uniform value (that of the
object)."
(let* ((min-length
(reduce #'min
(loop
for x in xs
appending (mklist
(length x)))))
(result (make-tensor (list min-length) :type type)))
(if (zerop min-length)
nil
(progn
(loop
for i below min-length
do (setf (tensor-ref result i)
(apply fn
(mapcar (lambda (x)
(tensor-ref x i))
xs))))
result))))
(defun tensor-map (fn &rest xs)
"Maps fn across xs for arbitrarily deep sequences. Treats
non-sequences as sequences of arbitrary depth."
(let ((first-sequence
(find-if #'sequencep xs)))
(if first-sequence
(apply #'map*
(type-of first-sequence)
(curry #'tensor-map fn)
xs)
(apply fn xs))))
(defun tmap (fn &rest xs)
"Abbreviation for tensor-map"
(apply #'tensor-map fn xs))
(defun tensor-+ (&rest xs)
"Convenient nickname for mapping + over tensors."
(apply #'tensor-map #'+ xs))
(defun tensor-- (&rest xs)
"Convenient nickname for mapping - over tensors."
(apply #'tensor-map #'- xs))
(defun tensor-* (&rest xs)
"Convenient nickname for mapping * over tensors."
(apply #'tensor-map #'* xs))
(defun tensor-/ (&rest xs)
"Convenient nickname for mapping / over tensors."
(apply #'tensor-map #'/ xs))
;; I do apologize for this extremely ugly code, but it does in fact
;; work. If you touch this code there is something wrong with you.
;;
;; At the moment I have not implemented single tensor contraction
;; (i.e. contraction of multiple indices from a single tensor).
(defun tensor-contract (tensor-index-pairs &key (type 'vector))
"Contracts each tensor along the dimension specified by the
specified index, resulting in a tensor of recursively rectangular
sequences of type type.
Each tensor-index-pair is a cons with the car being the tensor to
contract and the cdr being the index denoting the dimension to
contract along for this tensor.
It is just the mathematical notion of tensor contraction.
Example: multiplying matrices:
A . B ==> (tensor-contract (list (cons A 1) (cons B 0)))
In words, contract tensors A and B along the second index of A and
the first index of B."
(let* ((tensors (mapcar #'car tensor-index-pairs))
(tensor-ranks (mapcar #'tensor-rank tensors))
(starting-indices (make-offsets (mapcar #'1- tensor-ranks)))
(contracted-dims (mapcar #'cdr tensor-index-pairs))
(ref-fns ; a ref-fn is a function taking the final index list
; and another index, returning the value of the
; tensor for that ref-fn along the contracted
; dimension at the second index using the
; appropriate indices from the final index list
(mapcar
(lambda (tensor starting-index tensor-rank dim)
(let ((ending-index (add starting-index (1- tensor-rank))))
(lambda (final-index-list contracting-index)
(let* ((applicable-indices (subseq final-index-list
starting-index
ending-index))
(left-indices (subseq applicable-indices 0 dim))
(right-indices
(when (< dim (- tensor-rank 1))
(subseq applicable-indices dim))))
(apply #'tensor-ref tensor
(append left-indices
(list contracting-index)
right-indices))))))
tensors starting-indices tensor-ranks contracted-dims))
(contracted-dimension-length
(reduce #'min
(mapcar (lambda (tensor dim)
(elt (tensor-dimensions tensor) dim))
tensors contracted-dims)))
(dimension-lists
(mapcar
(lambda (tensor tensor-rank dim)
(let ((dimensions (tensor-dimensions tensor)))
(append (subseq dimensions 0 dim)
(when (< dim (1- tensor-rank))
(subseq dimensions (1+ dim))))))
tensors tensor-ranks contracted-dims))
(result-dimension-list (apply #'append dimension-lists))
(final-indices (apply #'cartesian-product
(loop
for dim-length in result-dimension-list
collect (range 0 (1- dim-length)))))
(result (when final-indices
(make-tensor result-dimension-list :type type))))
(if final-indices
(loop
for final-index in final-indices
do
(setf (apply #'tensor-ref result final-index)
(apply #'+
(loop
for contracted-index
below contracted-dimension-length
collect
(apply
#'*
(mapcar (lambda (ref-fn)
(funcall ref-fn
final-index
contracted-index))
ref-fns))))))
(setf result
(apply #'+
(loop
for contracted-index
below contracted-dimension-length
collect
(apply #'*
(mapcar
(lambda (ref-fn)
(funcall ref-fn
nil
contracted-index))
ref-fns))))))
result))
;; Flatten a tensor into a rank 0 or 1 tensor
(defun tensor-flatten (x)
"Returns a flattened tensor along with the dimensions of original
tensor so that unflattening is possible."
(if (atom x)
(values x nil)
(let* ((dims (tensor-dimensions x))
(size (product dims))
(result (make-tensor (list size) :type (type-of x))))
(loop
for i from 0 below size
do (setf (tensor-ref result i)
(tensor-flat-ref x i)))
(values result
dims))))
;; Unflatten a tensor
(defun tensor-unflatten (x dims)
"Restores a flattened tensor to its original dimensionality."
(if (atom x)
x
(let* ((size (length x))
(result (make-tensor dims :type (type-of x))))
(loop
for i from 0 below size
do (setf (tensor-flat-ref result i)
(tensor-ref x i)))
result)))
| 17,472 | Common Lisp | .lisp | 420 | 31.183333 | 103 | 0.572991 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 696bf88b74856b5fba911393938aa7140d9f61977c4cba4fd4aa2d7494511b4a | 1,509 | [
-1
] |
1,510 | package.lisp | ghollisjr_cl-ana/typespec/package.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(defpackage #:cl-ana.typespec
(:use :cl
:alexandria
:cffi
:cl-ana.int-char
:cl-ana.list-utils
:cl-ana.string-utils
:cl-ana.symbol-utils
:cl-ana.tensor
:cl-ana.memoization)
(:export :typespec->cffi-type
:typespec-foreign-alloc
;; compound typespec utilities:
:typespec-compound-p
:typespec-compound-field-alist
:typespec-compound-field-names
:typespec-compound-field-specs
;; array typespec utilities:
:typespec-array-p
:typespec-array-element-type
:typespec-array-dim-list
:typespec-array-rank
:typespec-array-size
;; A function for setting the values of a foreign object
;; recursively; currently this is not directly provided by
;; CFFI
:typespec->lisp-to-c
;; Returns a function which, when applied to a C-pointer,
;; returns a lisp object corresponding to the C object
:typespec->c-to-lisp
;; I may decide to use this (with changes) for providing
;; automatic flattening of typespecs so that nested array
;; types can be used as well as directly specifying the
;; rank of a multi-array:
:typespec-flatten-arrays
;; Function for handling strings stored as character arrays:
:char-vector->string))
| 2,274 | Common Lisp | .lisp | 57 | 33.526316 | 71 | 0.656137 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 3261476de7332bca7cc478f54c593c6ed4c51ca7d77d5d8deb4f059dbb415df2 | 1,510 | [
-1
] |
1,511 | typespec.lisp | ghollisjr_cl-ana/typespec/typespec.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(in-package :cl-ana.typespec)
(declaim (optimize (speed 3)
(safety 1)
(compilation-speed 0)
(debug 1)))
;;; Typespec: A typespec (as I'm referring to it) is either
;;;
;;; 1. A symbol denoting the cffi type
;;;
;;; 2. A list with the first element denoting the container type and
;;; the subsequent elements describing the members of the container
;;; type.
;;;
;;; Container types:
;;;
;;; :compound would denote that the type is a structure and the
;;; subsequent elements would be lists of the names and typespecs of
;;; the elements. (This is just the symbol :compound consed onto an
;;; alist mapping names to typespecs.)
;;;
;;; :array would denote that the type is an array type. The following
;;; elements in the typespec list are the typespec of the array
;;; elements and then the size of the array along each dimension as
;;; the rest of the typespec. Note that multidimensional array
;;; typespecs need to be flattened if you intend to use
;;; convert-from-foreign. The function flatten-array-typespec is
;;; provided for this purpose.
;;;
;;; (Note that strings are difficult: C treats character arrays as
;;; strings, and it is farirly seemless to convert between them;
;;; additionally small integers are routinely encoded as characters.
;;; However: Lisp's CFFI treats them differently, and so I have
;;; implemented the following conventions:
;;;
;;; *** Character arrays are converted to Lisp as vectors of integers.
;;; You can apply char-vector->string to convert this raw character
;;; array into a string.
;;;
;;; *** String typespecs should be that of a character array; this is
;;; necessary since most binary storage requires a fixed size for the
;;; data type. The same treatment above is necessary when the string
;;; is being read back into Lisp.)
;;;
;;; Example 1: A structure with integer x and float y:
;;; (:compound ("x" . :int) ("y" . :float))
;;;
;;; Example 2: A 1-D array of 20 doubles:
;;; (:array :double 20)
;; Creates cstruct types recursively as per the typespec
(defun-memoized typespec->cffi-type (typespec)
(labels
((make-slot-spec (name-cstruct)
(let* ((name (car name-cstruct))
(cstruct (cdr name-cstruct))
(type (if (typespec-array-p cstruct)
(typespec-array-element-type cstruct)
cstruct))
(count (if (typespec-array-p cstruct)
(typespec-array-size cstruct)
1)))
;;(reduce #'* (fourth cstruct))))) ; array type
(list (keywordify (intern (string name)))
type
:count count))))
(if (listp typespec)
;; handle arrays and compound
(case (first typespec)
;;(:array typespec) ; not much to do
(:array
(list :array
(typespec->cffi-type
(typespec-array-element-type typespec))
(typespec-array-size typespec)))
(:compound
;; here's where the fun happens
(let* ((names (typespec-compound-field-names typespec))
(specs (typespec-compound-field-specs typespec))
(member-cstructs (mapcar #'typespec->cffi-type specs))
(names-cstructs (zip names member-cstructs))
(slotspecs (mapcar #'make-slot-spec names-cstructs)))
;; I'd like to find a better way to do this, but I have
;; to evaluate slotspecs and gensym and splice them into
;; code which will be evaluated, so a simple macro
;; doesn't seem to work.
(eval
`(defcstruct ,(gensym) ,@slotspecs)))))
typespec))) ; since the symbol types are already known to cffi
;;;; Compound utilities:
(defun typespec-compound-p (typespec)
"Tests a typespec for being a compound typespec."
(when (consp typespec)
(equal (first typespec) :compound)))
(defun typespec-compound-field-alist (typespec)
"Returns the alist mapping field name to typespec."
(when (typespec-compound-p typespec)
(rest typespec)))
(defun typespec-compound-field-names (typespec)
"Returns the field names for the compound type."
(when (typespec-compound-p typespec)
(mapcar #'car
(typespec-compound-field-alist typespec))))
(defun typespec-compound-field-specs (typespec)
"Returns the typespecs for the fields in the compound type."
(when (typespec-compound-p typespec)
(mapcar #'cdr
(typespec-compound-field-alist typespec))))
;;;; Array utilities:
(defun typespec-array-p (typespec)
"Tests a typespec for being an array typespec."
(when (consp typespec)
(equal (first typespec) :array)))
(defun typespec-array-element-type (typespec)
"Returns the element type for the array type."
(when (typespec-array-p typespec)
(second typespec)))
(defun typespec-array-dim-list (typespec)
"Returns the list of dimension sizes for the array type."
(when (typespec-array-p typespec)
(rest (rest typespec))))
(defun typespec-array-rank (typespec)
"Returns the number of dimensions (rank) of the array type."
(when (typespec-array-p typespec)
(length (typespec-array-dim-list typespec))))
(defun typespec-array-size (typespec)
"Returns the total number of elements in the array type."
(when (typespec-array-p typespec)
(reduce #'*
(typespec-array-dim-list typespec))))
;; This is for automatically translating vectors into foreign arrays;
;; only works for 1-D at the moment but that is ok. Note that I had
;; to look into the CFFI code to get to this solution, so if they
;; change it significantly this may cease to work.
;; (defmethod translate-to-foreign ((value simple-vector) type)
;; (let* ((size (reduce #'* (cffi::dimensions type)))
;; (element-type (cffi::element-type type))
;; (result (foreign-alloc element-type :count size)))
;; (loop
;; for i below size
;; do (setf (mem-aref result element-type i)
;; (elt value i)))
;; result))
(defun typespec-flatten-arrays (typespec)
"Flattens an array typespec if typespec is an array typespec,
otherwise returns typespec unchanged. Note that this operation
is recursive, in that if there are arrays in the typespec(s) of the
component type(s), then they are flattened as well."
(when typespec
(if (listp typespec)
(cond
((typespec-array-p typespec)
(list :array
(typespec-flatten-arrays
(typespec-array-element-type typespec))
(typespec-array-size typespec)))
((typespec-compound-p typespec)
(cons :compound
(mapcar
(lambda (cons)
(cons (car cons)
(typespec-flatten-arrays (cdr cons))))
(rest typespec)))))
typespec)))
(defun typespec-foreign-alloc (typespec &optional (count 1))
"Allocates space for count foreign objects of type specified by
typespec."
(foreign-alloc (typespec->cffi-type typespec) :count count))
(defun typespec->lisp-to-c (typespec)
"Returns a function which takes
1. a lisp object,
2. a corresponding C pointer
and sets the fields/values of the C object recursively. The pointer
to the C-object is returned."
(let ((cstruct (typespec->cffi-type typespec)))
(cond
;; Compound types:
((typespec-compound-p typespec)
(let ((field-setters
(loop
for field-spec in (typespec-compound-field-specs typespec)
collect (typespec->lisp-to-c field-spec))))
(lambda (plist c-pointer)
(do* ((lst plist (rest (rest lst)))
(fs (first lst) (first lst))
(fv (second lst) (second lst))
(setter-lst field-setters (rest setter-lst))
(field-setter (first setter-lst)
(first setter-lst)))
((or (null lst)
(null setter-lst))
c-pointer)
(funcall field-setter
fv
(foreign-slot-pointer c-pointer
cstruct
fs))))))
;; Array types:
((typespec-array-p typespec)
(let ((element-type (typespec-array-element-type
typespec))
(array-size (typespec-array-size typespec)))
(if (equal element-type :char)
;; handle strings:
(let ((field-setter (typespec->lisp-to-c element-type)))
(lambda (tensor c-pointer)
(let ((element-converter
(if (typep tensor 'string)
#'char-code
#'identity)))
(dotimes (i array-size)
(funcall field-setter
(funcall element-converter (tensor-flat-ref tensor i))
(mem-aptr c-pointer
element-type
i))))))
;; other arrays:
(let ((field-setter (typespec->lisp-to-c element-type)))
(lambda (tensor c-pointer)
(dotimes (i array-size)
(funcall field-setter
(tensor-flat-ref tensor i)
(mem-aptr c-pointer
element-type
i))))))))
;; Primitive types:
(t
(lambda (primitive c-pointer)
(setf (mem-aref c-pointer cstruct)
primitive))))))
(defun typespec->c-to-lisp (typespec)
"Returns a function which takes a c-pointer argument and returns a
lisp object containing the converted values."
(cond
;; compound
((typespec-compound-p typespec)
(multiple-value-bind (field-symbols field-getters)
(loop
for (field-name . field-spec)
in (typespec-compound-field-alist typespec)
collecting (keywordify (string field-name))
into field-symbols
collecting (typespec->c-to-lisp field-spec)
into field-getters
finally (return (values field-symbols
field-getters)))
(let ((cstruct (typespec->cffi-type typespec)))
(lambda (c-pointer)
(loop
for fs in field-symbols
for fg in field-getters
collecting fs into result
collecting
(funcall fg
(foreign-slot-pointer c-pointer
cstruct
fs))
into result
finally
(return result))))))
;; array
((typespec-array-p typespec)
(let* ((element-type (typespec-array-element-type typespec))
(dim-list (typespec-array-dim-list typespec))
;; these should be used whenever the lisp array version is used:
;; (dim-vector (coerce dim-list 'vector))
;; (ndims (length dim-list))
(num-elements (typespec-array-size typespec))
(element-cffi-type
(typespec->cffi-type element-type))
(element-getter
(typespec->c-to-lisp element-type)))
;; function which returns an array of appropriate dimensions
;; with the foreign content.
;; ;; This function is here as an example of how to do this
;; ;; with lisp arrays, faster than using the tensors but at
;; ;; the cost of the tensor functions.
;;
;; (lambda (c-pointer)
;; (let ((result-array
;; (make-array dim-list))
;; (indices (make-array (list (length dim-vector))
;; :initial-element 0)))
;; (labels ((inc-indices! ()
;; (inc-indices-worker! (1- ndims)))
;; (inc-indices-worker! (inc-index)
;; (if (>= (elt indices inc-index)
;; (1- (elt dim-vector inc-index)))
;; (when (plusp inc-index)
;; (setf (elt indices inc-index) 0)
;; (inc-indices-worker! (1- inc-index)))
;; (incf (elt indices inc-index)))))
;; (loop
;; for i below num-elements
;; do (progn
;; (setf (apply #'aref result-array (coerce indices 'list))
;; (funcall element-getter
;; (mem-aptr c-pointer
;; element-cffi-type
;; i)))
;; (inc-indices!)))
;; result-array)))
(lambda (c-pointer)
(let ((result-tensor
(make-tensor dim-list)))
(loop
for i below num-elements
do (setf (tensor-flat-ref result-tensor i)
(funcall element-getter
(mem-aptr c-pointer
element-cffi-type
i))))
result-tensor))
))
;; primitive
(t
(lambda (c-pointer)
(mem-aref c-pointer typespec)))))
(defun char-vector->string (char-vector &optional length)
"Returns a string version of a vector of integers interpreted as the
numerical codes for characters. If argument length is given, the
result contains only the first length characters, or if length is
longer than the char-vector, the char-vector interpreted into a string
as if length were not given."
(let* ((length (if length
(min length (length char-vector))
(length char-vector)))
(result (make-string length)))
(loop
for i from 0 below length
for c across char-vector
do (setf (elt result i)
(int-char c)))
result))
| 14,822 | Common Lisp | .lisp | 352 | 33.551136 | 84 | 0.590635 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 54e7730575551df0385a0b0b901462ae595c98f7edffa3aaaf4fe3d8eb237d58 | 1,511 | [
-1
] |
1,512 | test.lisp | ghollisjr_cl-ana/typespec/test.lisp | ;;;; cl-ana is a Common Lisp data analysis library.
;;;; Copyright 2013, 2014 Gary Hollis
;;;;
;;;; This file is part of cl-ana.
;;;;
;;;; cl-ana is free software: you can redistribute it and/or modify it
;;;; under the terms of the GNU General Public License as published by
;;;; the Free Software Foundation, either version 3 of the License, or
;;;; (at your option) any later version.
;;;;
;;;; cl-ana is distributed in the hope that it will be useful, but
;;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;;; General Public License for more details.
;;;;
;;;; You should have received a copy of the GNU General Public License
;;;; along with cl-ana. If not, see <http://www.gnu.org/licenses/>.
;;;;
;;;; You may contact Gary Hollis (me!) via email at
;;;; [email protected]
(require 'cl-ana.typespec)
(in-package :cl-ana.typespec)
(defparameter *ts* '(:compound
("x" . (:array :double 3 3))
("y" . :string)))
(defparameter *struct*
'(:x ((1d0 2d0 3d0) (4d0 5d0 6d0) (7d0 8d0 9d0))
:y "hello"))
(defparameter *x* (typespec-foreign-alloc *ts*))
(defparameter *lisp->c-converter* (typespec->lisp-to-c *ts*))
(funcall *lisp->c-converter* *struct* *x*)
(defparameter *c->lisp-converter*
(typespec->c-to-lisp *ts*))
(print (funcall *c->lisp-converter* *x*))
| 1,410 | Common Lisp | .lisp | 34 | 38.588235 | 70 | 0.671544 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 1f5528b0b4717b5a82c393178fae81a0381a692e7fb730fa2b3ca5add6034e39 | 1,512 | [
-1
] |
1,513 | common.lisp | ghollisjr_cl-ana/hdf-cffi/examples/common.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
(defpackage #:h5ex
(:documentation "hdf5-examples: Common helpers for hdf5-cffi examples.")
(:use #:cl)
(:export close-handle
close-handles
create-null-dataspace
create-scalar-dataspace
create-simple-dataspace
create-c-string-type
create-c-string-type-utf8
create-f-string-type
create-f-string-type-utf8
pos2D))
(in-package :h5ex)
;; handles
(defun close-handle (hnd)
"Close an HDF5 handle"
(unless (< 0 (hdf5:h5iis-valid hnd))
(error "Invalid handle found."))
(let ((type (hdf5:h5iget-type hnd)))
(cond ((eql type :H5I-ATTR) (hdf5:h5aclose hnd))
((eql type :H5I-DATASET) (hdf5:h5dclose hnd))
((eql type :H5I-DATASPACE) (hdf5:h5sclose hnd))
((eql type :H5I-DATATYPE) (hdf5:h5tclose hnd))
((eql type :H5I-FILE) (hdf5:h5fclose hnd))
((eql type :H5I-GENPROP-LST) (hdf5:h5pclose hnd))
((eql type :H5I-GROUP) (hdf5:h5gclose hnd))
(t (error (format nil "Can't close handle. ~a~%" type))))))
(defun close-handles (handles)
(declare (type list handles))
"Close a list of handles"
(dolist (h handles)
(close-handle h)))
;; dataspaces
(defun create-null-dataspace ()
"Create a null dataspace"
(hdf5:h5screate :H5S-NULL))
(defun create-scalar-dataspace ()
"Create a scalar dataspace"
(hdf5:h5screate :H5S-SCALAR))
(defun create-simple-dataspace (dims &optional maxdims)
"Create a simple dataspace"
;; list arguments expected
(unless (and (consp dims) (listp maxdims))
(error "List arguments expected."))
;; rank check
(when (and maxdims
(not (= (list-length dims) (list-length maxdims))))
(error "Rank mismatch in simple dataspace definition."))
(when (or (< (list-length dims) 1)
(> (list-length dims) 32))
(error "The dataspace rank must be between 1 and 32."))
;; element checks
(when (some #'(lambda (x) (or (not (integerp x)) (< x 1))) dims)
(error "The dimensions must be positive integers."))
(when (and maxdims
(some #'(lambda (x) (or (not (integerp x))
(and (not (eql x hdf5:+H5S-UNLIMITED+))
(< x 1))))
maxdims))
(error "The maximum dimensions must be positive integers."))
(when (and maxdims
(some #'null
(mapcar #'(lambda (x y) (if (eql y hdf5:+H5S-UNLIMITED+)
T (<= x y)))
dims maxdims)))
(error "A dimension must not exceed it's corresponding maximum."))
;; go
(let* ((rank (list-length dims))
(dims-ptr (cffi:foreign-alloc 'hdf5:hsize-t :count rank
:initial-contents dims))
(maxdims-ptr (if maxdims
(cffi:foreign-alloc 'hdf5:hsize-t :count rank
:initial-contents maxdims)
hdf5:+NULL+))
(space (hdf5:h5screate-simple rank dims-ptr maxdims-ptr)))
(cffi:foreign-free dims-ptr)
(when maxdims (cffi:foreign-free maxdims-ptr))
space))
;; common string datatypes
(defun create-c-string-type (&optional length)
"Create a C-style string datatype"
(when length
(unless (and (integerp length) (< 0 length))
(error "Length must be a positive integer.")))
(let ((result (hdf5:h5tcopy hdf5:+H5T-C-S1+)))
(hdf5:h5tset-size result (if length length hdf5:+H5T-VARIABLE+))
result))
(defun create-c-string-type-utf8 (&optional length)
(let ((result (create-c-string-type length)))
(hdf5:h5tset-cset result :H5T-CSET-UTF8)
result))
(defun create-f-string-type (&optional length)
"Create a FORTRAN-style string datatype"
(when length
(unless (and (integerp length) (< 0 length))
(error "Length must be a positive integer.")))
(let ((result (hdf5:h5tcopy hdf5:+H5T-FORTRAN-S1+)))
(hdf5:h5tset-size result (if length length hdf5:+H5T-VARIABLE+))
result))
(defun create-f-string-type-utf8 (&optional length)
(let ((result (create-f-string-type length)))
(hdf5:h5tset-cset result :H5T-CSET-UTF8)
result))
;; array access
(defun pos2D (cols i j)
(declare (optimize (speed 3) (safety 0)))
(declare (fixnum cols i j))
"2D array access function"
(the fixnum (+ (the fixnum (* cols i)) j)))
| 4,906 | Common Lisp | .lisp | 119 | 33.310924 | 78 | 0.611263 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 66a1b4208f8d1b562bc0552134f6480e009e931e492c1027894f0402d7db251d | 1,513 | [
-1
] |
1,514 | h5ex-d-checksum.lisp | ghollisjr_cl-ana/hdf-cffi/examples/datasets/h5ex-d-checksum.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
;;; This example shows how to read and write data to a dataset
;;; using the Fletcher32 checksum filter. The program first
;;; checks if the Fletcher32 filter is available, then if it
;;; is it writes integers to a dataset using Fletcher32, then
;;; closes the file. Next, it reopens the file, reads back
;;; the data, checks if the filter detected an error and
;;; outputs the type of filter and the maximum value in the
;;; dataset to the screen.
;;; http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api//hdf5-examples/1_8/C/H5D/h5ex_d_checksum.c
(in-package :hdf5)
(defparameter *FILE* (namestring (merge-pathnames "h5ex_d_checksum.h5" *load-pathname*)))
(defparameter *DATASET* "DS1")
(defparameter *DIM0* 32)
(defparameter *DIM1* 64)
(defparameter *CHUNK0* 4)
(defparameter *CHUNK1* 8)
(cffi:with-foreign-objects ((chunk 'hsize-t 2)
(filter-info :unsigned-int 1)
(flags :unsigned-int 1)
(nelmts 'size-t 1)
(wdata :int (* *DIM0* *DIM1*))
(rdata :int (* *DIM0* *DIM1*)))
(setf (cffi:mem-aref nelmts 'size-t 0) 0)
;; Check if the Fletcher32 filter is available and can be used for
;; both encoding and decoding. Normally we do not perform error
;; checking in these examples for the sake of clarity, but in this
;; case we will make an exception because this filter is an
;; optional part of the hdf5 library.
(if (< (h5zfilter-avail +H5Z-FILTER-FLETCHER32+) 1)
(error "Fletcher32 filter not available."))
(h5zget-filter-info +H5Z-FILTER-FLETCHER32+ filter-info)
(if (or (eql 0 (logand (cffi:mem-ref filter-info :unsigned-int)
+H5Z-FILTER-CONFIG-ENCODE-ENABLED+))
(eql 0 (logand (cffi:mem-ref filter-info :unsigned-int)
+H5Z-FILTER-CONFIG-DECODE-ENABLED+)))
(error "Fletcher32 filter not available for encoding and decoding."))
;; Initialize data.
(dotimes (i *DIM0*)
(dotimes (j *DIM1*)
(setf (cffi:mem-aref wdata :int (h5ex:pos2D *DIM1* i j)) (- (* i j) j))))
;; Create a new file using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fcreate *FILE* +H5F-ACC-TRUNC+ +H5P-DEFAULT+ fapl))))
(unwind-protect
(let* ((space (h5ex:create-simple-dataspace `(,*DIM0* ,*DIM1*)))
(dcpl (h5pcreate +H5P-DATASET-CREATE+))
;; Create the dataset using the dataset creation property
;; list.
(dset (progn
;; Create the dataset creation property list, add the
;; Fletcher32 filter and set the chunk size.
(h5pset-fletcher32 dcpl)
(setf (cffi:mem-aref chunk 'hsize-t 0) *CHUNK0*
(cffi:mem-aref chunk 'hsize-t 1) *CHUNK1*)
(h5pset-chunk dcpl 2 chunk)
;; Create the chunked dataset.
(h5dcreate2 file *DATASET* +H5T-STD-I32LE+ space
+H5P-DEFAULT+ dcpl +H5P-DEFAULT+))))
;; Write the data to the dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ space +H5P-DEFAULT+ wdata)
;; Close and release resources.
(h5ex:close-handles (list dset dcpl space)))
(h5ex:close-handles (list file fapl))))
;; Now we begin the read section of this example.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDONLY+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(dcpl (h5dget-create-plist dset))
;; Retrieve and print the filter type. Here we only retrieve
;; the first filter because we know that we only added one
;; filter.
(filter-type (h5pget-filter2 dcpl 0 flags nelmts +NULL+
0 +NULL+ filter-info)))
(format t "Filter type is: ")
(cond ((eql filter-type +H5Z-FILTER-DEFLATE+)
(format t "H5Z_FILTER_DEFLATE~%"))
((eql filter-type +H5Z-FILTER-SHUFFLE+)
(format t "H5Z_FILTER_SHUFFLE~%"))
((eql filter-type +H5Z-FILTER-FLETCHER32+)
(format t "H5Z_FILTER_FLETCHER32~%"))
((eql filter-type +H5Z-FILTER-SZIP+)
(format t "H5Z_FILTER_SZIP~%"))
((eql filter-type +H5Z-FILTER-NBIT+)
(format t "H5Z_FILTER_NBIT~%"))
((eql filter-type +H5Z-FILTER-SCALEOFFSET+)
(format t "H5Z_FILTER_SCALEOFFSET~%")))
;; Read the data using the default properties.
;; Check if the read was successful. Normally we do not perform
;; error checking in these examples for the sake of clarity, but in
;; this case we will make an exception because this is how the
;; fletcher32 checksum filter reports data errors.
(if (< (h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+
+H5P-DEFAULT+ rdata)
0)
(prog2 (h5ex:close-handles (list dcpl dset))
(error "Dataset read failed!")))
;; Find the maximum value in the dataset, to verify that it was
;; read correctly.
(format t "Maximum value in ~a is: ~a~%" *DATASET*
(reduce #'max
(mapcar #'(lambda (i) (cffi:mem-aref rdata :int i))
(loop for i from 0 to (1- (* *DIM0* *DIM1*))
collect i))))
;; Close and release resources.
(h5ex:close-handles (list dcpl dset)))
(h5ex:close-handles (list file fapl)))))
| 5,857 | Common Lisp | .lisp | 118 | 42.271186 | 104 | 0.638383 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 9b635e44a37aa76b781eb351bd9da77a9d3a8cfc72711c405f6cd6dacdf46f6f | 1,514 | [
-1
] |
1,515 | h5ex-d-alloc.lisp | ghollisjr_cl-ana/hdf-cffi/examples/datasets/h5ex-d-alloc.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
;;; This example shows how to set the space allocation time
;;; for a dataset. The program first creates two datasets,
;;; one with the default allocation time (late) and one with
;;; early allocation time, and displays whether each has been
;;; allocated and their allocation size. Next, it writes data
;;; to the datasets, and again displays whether each has been
;;; allocated and their allocation size.
;;; http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5D/h5ex_d_alloc.c
(in-package :hdf5)
(defparameter *FILE* (namestring (merge-pathnames "h5ex_d_alloc.h5" *load-pathname*)))
(defparameter *DATASET1* "DS1")
(defparameter *DATASET2* "DS2")
(defparameter *DIM0* 4)
(defparameter *DIM1* 7)
(defun print-space-status-et-storage-size (dset name)
(cffi:with-foreign-object (space-status 'h5d-space-status-t 1)
(h5dget-space-status dset space-status)
(format t "Space for ~a has~abeen allocated.~%"
name (if (eql :H5D-SPACE-STATUS-ALLOCATED
(cffi:mem-ref space-status
'h5d-space-status-t))
" "
" not "))
(format t "Storage size for ~a is: ~a bytes.~%" name
(h5dget-storage-size dset))))
(cffi:with-foreign-object (wdata :int (* *DIM0* *DIM1*))
;; initialize data
(dotimes (i *DIM0*)
(dotimes (j *DIM1*)
(setf (cffi:mem-aref wdata :int (h5ex:pos2D *DIM1* i j)) (- (* i j) j))))
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fcreate *FILE* +H5F-ACC-TRUNC+ +H5P-DEFAULT+ fapl))))
(format t "Creating datasets...~%")
(format t "~a has allocation time H5D_ALLOC_TIME_LATE~%"
*DATASET1*)
(format t "~a has allocation time H5D_ALLOC_TIME_EARLY~%~%"
*DATASET2*)
(unwind-protect
(let* ((space (h5ex:create-simple-dataspace `(,*DIM0* ,*DIM1*)))
(dcpl (h5pcreate +H5P-DATASET-CREATE+))
;; Create the dataset using the dataset creation property
;; list.
(dset1 (h5dcreate2 file *DATASET1* +H5T-STD-I32LE+ space
+H5P-DEFAULT+ +H5P-DEFAULT+ +H5P-DEFAULT+))
;; Set the allocation time to "early". This way we
;; can be sure that reading from the dataset
;; immediately after creation will return the fill value.
(dset2 (prog2 (h5pset-alloc-time dcpl :H5D-ALLOC-TIME-EARLY)
(h5dcreate2 file *DATASET2* +H5T-STD-I32LE+ space
+H5P-DEFAULT+ dcpl +H5P-DEFAULT+))))
;; Retrieve and print space status and storage size for dset1.
(print-space-status-et-storage-size dset1 *DATASET1*)
;; Retrieve and print space status and storage size for dset2.
(print-space-status-et-storage-size dset2 *DATASET2*)
(format t "~%Writing data...~%~%")
;; Write the data to the datasets
(h5dwrite dset1 +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
wdata)
(h5dwrite dset2 +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
wdata)
;; Retrieve and print space status and storage size for dset1.
(print-space-status-et-storage-size dset1 *DATASET1*)
;; Retrieve and print space status and storage size for dset2.
(print-space-status-et-storage-size dset2 *DATASET2*)
;; Close and release resources.
(h5ex:close-handles (list dset2 dset1 dcpl space)))
(h5ex:close-handles (list file fapl)))))
| 4,068 | Common Lisp | .lisp | 77 | 44.025974 | 100 | 0.629499 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 06ab3f5ec141235fc2e538bd45433aeb136907b9f502d05cfd5d162453110f71 | 1,515 | [
-1
] |
1,516 | h5ex-d-unlimmod.lisp | ghollisjr_cl-ana/hdf-cffi/examples/datasets/h5ex-d-unlimmod.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
;;; This example shows how to create and extend an unlimited
;;; dataset. The program first writes integers to a dataset
;;; with dataspace dimensions of DIM0xDIM1, then closes the
;;; file. Next, it reopens the file, reads back the data,
;;; outputs it to the screen, extends the dataset, and writes
;;; new data to the entire extended dataset. Finally it
;;; reopens the file again, reads back the data, and utputs it
;;; to the screen.
;;; http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5D/h5ex_d_unlimmod.c
(in-package :hdf5)
(defparameter *FILE* (namestring (merge-pathnames "h5ex_d_unlimmod.h5" *load-pathname*)))
(defparameter *DATASET* "DS1")
(defparameter *DIM0* 4)
(defparameter *DIM1* 7)
(defparameter *EDIM0* 6)
(defparameter *EDIM1* 10)
(defparameter *CHUNK0* 4)
(defparameter *CHUNK1* 4)
(defun print-data (data rows cols)
(dotimes (i rows)
(format t " [")
(dotimes (j cols)
(format t " ~3d" (cffi:mem-aref data :int (h5ex:pos2D cols i j))))
(format t "]~%")))
(cffi:with-foreign-objects ((dims 'hsize-t 2)
(extdims 'hsize-t 2)
(chunk 'hsize-t 2)
(wdata :int (* *DIM0* *DIM1*))
(wdata2 :int (* *EDIM0* *EDIM1*)))
;; initialize data
(dotimes (i *DIM0*)
(dotimes (j *DIM1*)
(setf (cffi:mem-aref wdata :int (h5ex:pos2D *DIM1* i j)) (- (* i j) j))))
;; Create a new file using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fcreate *FILE* +H5F-ACC-TRUNC+ +H5P-DEFAULT+ fapl))))
(unwind-protect
(let* ((space (h5ex:create-simple-dataspace `(,*DIM0* ,*DIM1*)
`(,+H5S-UNLIMITED+
,+H5S-UNLIMITED+)))
;; Create the dataset creation property list, and set the chunk
;; size.
(dcpl (let ((tmp (h5pcreate +H5P-DATASET-CREATE+)))
(setf (cffi:mem-aref chunk 'hsize-t 0) *CHUNK0*
(cffi:mem-aref chunk 'hsize-t 1) *CHUNK1*)
(h5pset-chunk tmp 2 chunk)
tmp))
;; Create the unlimited dataset.
(dset (h5dcreate2 file *DATASET* +H5T-STD-I32LE+ space
+H5P-DEFAULT+ dcpl +H5P-DEFAULT+)))
;; Write the data to the dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
wdata)
;; Close and release resources.
(h5ex:close-handles (list dcpl dset space)))
(h5ex:close-handles (list file fapl))))
;; In this next section we read back the data, extend the dataset,
;; and write new data to the entire dataset.
;; Open file and dataset using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2
(h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDWR+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(space (let ((tmp (h5dget-space dset)))
(h5sget-simple-extent-dims tmp dims +NULL+)
tmp))
(dims[0] (cffi:mem-aref dims 'hsize-t 0))
(dims[1] (cffi:mem-aref dims 'hsize-t 1)))
;; Allocate space for integer data.
(cffi:with-foreign-object (rdata :int (* dims[0] dims[1]))
;; Read the data using the default properties
(h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
rdata)
;; Output the data to the screen.
(format t "Dataset before extension:~%")
(print-data rdata dims[0] dims[1]))
;; Extend the dataset.
(setf (cffi:mem-aref extdims 'hsize-t 0) *EDIM0*
(cffi:mem-aref extdims 'hsize-t 1) *EDIM1*)
(h5dset-extent dset extdims)
;; Initialize data for writing to the extended dataset.
(dotimes (i *EDIM0*)
(dotimes (j *EDIM1*)
(setf (cffi:mem-aref wdata2 :int (h5ex:pos2D *EDIM1* i j)) j)))
;; Write the data to the extended dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
wdata2)
;; Close and release resources.
(h5ex:close-handles (list space dset)))
(h5ex:close-handles (list file fapl))))
;; Now we simply read back the data and output it to the screen.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDONLY+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(space (let ((tmp (h5dget-space dset)))
(h5sget-simple-extent-dims tmp dims +NULL+)
tmp))
(dims[0] (cffi:mem-aref dims 'hsize-t 0))
(dims[1] (cffi:mem-aref dims 'hsize-t 1)))
;; Get dataspace and allocate memory for the read buffer as before.
(cffi:with-foreign-object (rdata :int (* dims[0] dims[1]))
;; Read the data using the default properties
(h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
rdata)
;; Output the data to the screen.
(format t "~%Dataset after extension:~%")
(print-data rdata *EDIM0* *EDIM1*))
;; Close and release resources.
(h5ex:close-handles (list space dset)))
(h5ex:close-handles (list file fapl)))))
| 5,633 | Common Lisp | .lisp | 124 | 39.16129 | 103 | 0.636861 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 415ddbdae498fbc1e45a8ea74dc54645289c007f015d3e24e2bd35b115fa35aa | 1,516 | [
-1
] |
1,517 | h5ex-d-unlimgzip.lisp | ghollisjr_cl-ana/hdf-cffi/examples/datasets/h5ex-d-unlimgzip.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
;;; This example shows how to create and extend an unlimited
;;; dataset with gzip compression. The program first writes
;;; integers to a gzip compressed dataset with dataspace
;;; dimensions of DIM0xDIM1, then closes the file. Next, it
;;; reopens the file, reads back the data, outputs it to the
;;; screen, extends the dataset, and writes new data to the
;;; extended portions of the dataset. Finally it reopens the
;;; file again, reads back the data, and outputs it to the
;;; screen.
;;; http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5D/h5ex_d_unlimgzip.c
(in-package :hdf5)
(defparameter *FILE* (namestring (merge-pathnames "h5ex_d_unlimgzip.h5" *load-pathname*)))
(defparameter *DATASET* "DS1")
(defparameter *DIM0* 4)
(defparameter *DIM1* 7)
(defparameter *EDIM0* 6)
(defparameter *EDIM1* 10)
(defparameter *CHUNK0* 4)
(defparameter *CHUNK1* 4)
(defun print-data (data rows cols)
(dotimes (i rows)
(format t " [")
(dotimes (j cols)
(format t " ~3d" (cffi:mem-aref data :int (h5ex:pos2D cols i j))))
(format t "]~%")))
(cffi:with-foreign-objects ((dims 'hsize-t 2)
(extdims 'hsize-t 2)
(chunk 'hsize-t 2)
(start 'hsize-t 2)
(count 'hsize-t 2)
(nelmts 'size-t 1)
(filter-info :unsigned-int 1)
(flags :unsigned-int 1)
(wdata :int (* *DIM0* *DIM1*))
(wdata2 :int (* *EDIM0* *EDIM1*)))
(setf (cffi:mem-aref nelmts 'size-t 0) 0)
;; Check if gzip compression is available and can be used for both
;; compression and decompression. Normally we do not perform error
;; checking in these examples for the sake of clarity, but in this
;; case we will make an exception because this filter is an
;; optional part of the hdf5 library.
(if (< (h5zfilter-avail +H5Z-FILTER-DEFLATE+) 1)
(error "gzip filter not available."))
(h5zget-filter-info +H5Z-FILTER-DEFLATE+ filter-info)
(if (or (eql 0 (logand (cffi:mem-ref filter-info :unsigned-int)
+H5Z-FILTER-CONFIG-ENCODE-ENABLED+))
(eql 0 (logand (cffi:mem-ref filter-info :unsigned-int)
+H5Z-FILTER-CONFIG-DECODE-ENABLED+)))
(error "gzip filter not available for encoding and decoding."))
;; initialize data
(dotimes (i *DIM0*)
(dotimes (j *DIM1*)
(setf (cffi:mem-aref wdata :int (h5ex:pos2D *DIM1* i j)) (- (* i j) j))))
;; Create a new file using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fcreate *FILE* +H5F-ACC-TRUNC+ +H5P-DEFAULT+ fapl))))
(unwind-protect
(let* ((space (h5ex:create-simple-dataspace `(,*DIM0* ,*DIM1*)
`(,+H5S-UNLIMITED+
,+H5S-UNLIMITED+)))
;; Create the dataset creation property list, add the gzip
;; compression filter and set the chunk size.
(dcpl (let ((tmp (h5pcreate +H5P-DATASET-CREATE+)))
(h5pset-deflate tmp 9)
(setf (cffi:mem-aref chunk 'hsize-t 0) *CHUNK0*
(cffi:mem-aref chunk 'hsize-t 1) *CHUNK1*)
(h5pset-chunk tmp 2 chunk)
tmp))
;; Create the compressed unlimited dataset.
(dset (h5dcreate2 file *DATASET* +H5T-STD-I32LE+ space
+H5P-DEFAULT+ dcpl +H5P-DEFAULT+)))
;; Write the data to the dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
wdata)
;; Close and release resources.
(h5ex:close-handles (list dcpl dset space)))
(h5ex:close-handles (list file fapl))))
;; In this next section we read back the data, extend the dataset,
;; and write new data to the extended portions.
;; Open file and dataset using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDWR+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(space (let ((tmp (h5dget-space dset)))
(h5sget-simple-extent-dims tmp dims +NULL+)
tmp))
(dims[0] (cffi:mem-aref dims 'hsize-t 0))
(dims[1] (cffi:mem-aref dims 'hsize-t 1)))
;; Allocate space for integer data.
(cffi:with-foreign-object (rdata :int (* dims[0] dims[1]))
;; Read the data using the default properties
(h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
rdata)
;; Output the data to the screen.
(format t "~%Dataset before extension:~%")
(print-data rdata dims[0] dims[1]))
(h5sclose space)
;; Extend the dataset.
(setf (cffi:mem-aref extdims 'hsize-t 0) *EDIM0*
(cffi:mem-aref extdims 'hsize-t 1) *EDIM1*)
(h5dset-extent dset extdims)
;; Retrieve the dataspace for the newly extended dataset.
(setq space (h5dget-space dset))
;; Initialize data for writing to the extended dataset.
(dotimes (i *EDIM0*)
(dotimes (j *EDIM1*)
(setf (cffi:mem-aref wdata2 :int (h5ex:pos2D *EDIM1* i j)) j)))
;; Select the entire dataspace.
(h5sselect-all space)
;; Subtract a hyperslab reflecting the original dimensions from the
;; selection. The selection now contains only the newly extended
;; portions of the dataset.
(setf (cffi:mem-aref start 'hsize-t 0) 0
(cffi:mem-aref start 'hsize-t 1) 0
(cffi:mem-aref count 'hsize-t 0)
(cffi:mem-aref dims 'hsize-t 0)
(cffi:mem-aref count 'hsize-t 1)
(cffi:mem-aref dims 'hsize-t 1))
(h5sselect-hyperslab space :H5S-SELECT-NOTB start +NULL+ count
+NULL+)
;; Write the data to the selected portion of the dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ space +H5P-DEFAULT+ wdata2)
;; Close and release resources.
(h5ex:close-handles (list space dset)))
(h5ex:close-handles (list file fapl))))
;; Now we simply read back the data and output it to the screen.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDONLY+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(dcpl (h5dget-create-plist dset))
;; Retrieve and print the filter type. Here we only retrieve
;; the first filter because we know that we only added one
;; filter.
(filter-type (prog2 (setf (cffi:mem-aref nelmts 'size-t 0) 0)
(h5pget-filter2 dcpl 0 flags nelmts +NULL+
0 +NULL+ filter-info)))
(space (let ((tmp (h5dget-space dset)))
(h5sget-simple-extent-dims tmp dims +NULL+)
tmp))
(dims[0] (cffi:mem-aref dims 'hsize-t 0))
(dims[1] (cffi:mem-aref dims 'hsize-t 1)))
(format t "~%Filter type is: ")
(cond ((eql filter-type +H5Z-FILTER-DEFLATE+)
(format t "H5Z_FILTER_DEFLATE~%"))
((eql filter-type +H5Z-FILTER-SHUFFLE+)
(format t "H5Z_FILTER_SHUFFLE~%"))
((eql filter-type +H5Z-FILTER-FLETCHER32+)
(format t "H5Z_FILTER_FLETCHER32~%"))
((eql filter-type +H5Z-FILTER-SZIP+)
(format t "H5Z_FILTER_SZIP~%"))
((eql filter-type +H5Z-FILTER-NBIT+)
(format t "H5Z_FILTER_NBIT~%"))
((eql filter-type +H5Z-FILTER-SCALEOFFSET+)
(format t "H5Z_FILTER_SCALEOFFSET~%")))
;; Get dataspace and allocate memory for the read buffer as before.
(cffi:with-foreign-object (rdata :int (* dims[0] dims[1]))
;; Read the data using the default properties
(h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
rdata)
;; Output the data to the screen.
(format t "Dataset after extension:~%")
(print-data rdata *EDIM0* *EDIM1*))
;; Close and release resources.
(h5ex:close-handles (list space dset)))
(h5ex:close-handles (list file fapl)))))
| 8,225 | Common Lisp | .lisp | 179 | 40.083799 | 104 | 0.653865 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | ebe6ca5b1e98d9de7724d4cdb1163c159a8bf6d6d6b42365b8d40c4f999e9ebc | 1,517 | [
-1
] |
1,518 | h5ex-d-extern.lisp | ghollisjr_cl-ana/hdf-cffi/examples/datasets/h5ex-d-extern.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
;;; This example shows how to read and write data to an
;;; external dataset. The program first writes integers to an
;;; external dataset with dataspace dimensions of DIM0xDIM1,
;;; then closes the file. Next, it reopens the file, reads
;;; back the data, and outputs the name of the external data
;;; file and the data to the screen.
;;; http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5D/h5ex_d_extern.c
(in-package :hdf5)
(defvar *FILE* (namestring (merge-pathnames "h5ex_d_extern.h5" *load-pathname*)))
(defvar *EXTERNAL* (namestring (merge-pathnames "h5ex_d_extern.data" *load-pathname*)))
(defvar *DATASET* "DS1")
(defvar *DIM0* 4)
(defvar *DIM1* 7)
(defvar *NAME-BUF-SIZE* 32)
(cffi:with-foreign-objects ((name :char *NAME-BUF-SIZE*)
(wdata :int (* *DIM0* *DIM1*))
(rdata :int (* *DIM0* *DIM1*)))
;; Initialize data.
(dotimes (i *DIM0*)
(dotimes (j *DIM1*)
(setf (cffi:mem-aref wdata :int (h5ex:pos2D *DIM1* i j)) (- (* i j) j))))
;; Create a new file using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fcreate *FILE* +H5F-ACC-TRUNC+ +H5P-DEFAULT+ fapl))))
(unwind-protect
(let* ((space (h5ex:create-simple-dataspace `(,*DIM0* ,*DIM1*)))
(dcpl (h5pcreate +H5P-DATASET-CREATE+))
(dset (prog2
;; Create the dataset creation property list, and
;; set the external file.
(h5pset-external dcpl *EXTERNAL* 0 +H5F-UNLIMITED+)
;; Create the external dataset
(h5dcreate2 file *DATASET* +H5T-STD-I32LE+ space
+H5P-DEFAULT+ dcpl +H5P-DEFAULT+))))
;; Write the data to the dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ space +H5P-DEFAULT+ wdata)
;; Close and release resources.
(h5ex:close-handles (list dset dcpl space)))
(h5ex:close-handles (list file fapl))))
;; Now we begin the read section of this example.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDONLY+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(dcpl (h5dget-create-plist dset)))
;; Retrieve and print the name of the external file. Here we
;; manually set the last field in name to null, in case the name of
;; the file is longer than the buffer.
(h5pget-external dcpl 0 *NAME-BUF-SIZE* name +NULL+ +NULL+)
(setf (cffi:mem-aref name :char (1- *NAME-BUF-SIZE*)) 0)
(format t "~a is stored in file: ~a~%" *DATASET*
(cffi:foreign-string-to-lisp name))
;;Read the data using the default properties.
(h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
rdata)
;; Output the data to the screen.
(format t "~a:~%" *DATASET*)
(dotimes (i *DIM0*)
(format t " [")
(dotimes (j *DIM1*)
(format t " ~3d" (cffi:mem-aref rdata :int
(h5ex:pos2D *DIM1* i j))))
(format t "]~%"))
;; Close and release resources.
(h5ex:close-handles (list dcpl dset)))
(h5ex:close-handles (list file fapl)))))
| 3,783 | Common Lisp | .lisp | 77 | 41.974026 | 101 | 0.626424 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | 2da5fb4a353ea0f67bab6cbd308613e63b849e4bd555b0fc092ef38c9cc840e5 | 1,518 | [
-1
] |
1,519 | h5ex-d-nbit.lisp | ghollisjr_cl-ana/hdf-cffi/examples/datasets/h5ex-d-nbit.lisp | ;;;; Copyright by The HDF Group.
;;;; All rights reserved.
;;;;
;;;; This file is part of hdf5-cffi.
;;;; The full hdf5-cffi copyright notice, including terms governing
;;;; use, modification, and redistribution, is contained in the file COPYING,
;;;; which can be found at the root of the source code distribution tree.
;;;; If you do not have access to this file, you may request a copy from
;;;; [email protected].
;;; This example shows how to read and write data to a dataset
;;; using the N-Bit filter. The program first checks if the
;;; N-Bit filter is available, then if it is it writes
;;; integers to a dataset using N-Bit, then closes the file.
;;; Next, it reopens the file, reads back the data, and
;;; outputs the type of filter and the maximum value in the
;;; dataset to the screen.
;;; http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5D/h5ex_d_nbit.c
(in-package :hdf5)
(defparameter *FILE* (namestring (merge-pathnames "h5ex_d_nbit.h5" *load-pathname*)))
(defparameter *DATASET* "DS1")
(defparameter *DIM0* 32)
(defparameter *DIM1* 64)
(defparameter *CHUNK0* 4)
(defparameter *CHUNK1* 8)
(cffi:with-foreign-objects ((chunk 'hsize-t 2)
(filter-info :unsigned-int 1)
(flags :unsigned-int 1)
(nelmts 'size-t 1)
(wdata :int (* *DIM0* *DIM1*))
(rdata :int (* *DIM0* *DIM1*)))
(setf (cffi:mem-aref nelmts 'size-t 0) 0)
;; Check if N-Bit compression is available and can be used for both
;; compression and decompression. Normally we do not perform error
;; checking in these examples for the sake of clarity, but in this
;; case we will make an exception because this filter is an
;; optional part of the hdf5 library.
(if (< (h5zfilter-avail +H5Z-FILTER-NBIT+) 1)
(error "N-Bit filter not available."))
(h5zget-filter-info +H5Z-FILTER-NBIT+ filter-info)
(if (or (eql 0 (logand (cffi:mem-ref filter-info :unsigned-int)
+H5Z-FILTER-CONFIG-ENCODE-ENABLED+))
(eql 0 (logand (cffi:mem-ref filter-info :unsigned-int)
+H5Z-FILTER-CONFIG-DECODE-ENABLED+)))
(error "N-Bit filter not available for encoding and decoding."))
;; Initialize data.
(dotimes (i *DIM0*)
(dotimes (j *DIM1*)
(setf (cffi:mem-aref wdata :int (h5ex:pos2D *DIM1* i j)) (- (* i j) j))))
;; Create a new file using the default properties.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fcreate *FILE* +H5F-ACC-TRUNC+ +H5P-DEFAULT+ fapl))))
(unwind-protect
(let* ((space (h5ex:create-simple-dataspace `(,*DIM0* ,*DIM1*)))
;; Create the datatype to use with the N-Bit filter. It has an
;; uncompressed size of 32 bits, but will have a size of 16 bits
;; after being packed by the N-Bit filter.
(dtype (let ((tmp (h5tcopy +H5T-STD-I32LE+)))
(h5tset-precision tmp 16)
(h5tset-offset tmp 5)
tmp))
(dcpl (h5pcreate +H5P-DATASET-CREATE+))
;; Create the dataset using the dataset creation property
;; list.
(dset (progn
;; Create the dataset creation property list, add the
;; N-Bit filter and set the chunk size.
(h5pset-nbit dcpl)
(setf (cffi:mem-aref chunk 'hsize-t 0) *CHUNK0*
(cffi:mem-aref chunk 'hsize-t 1) *CHUNK1*)
(h5pset-chunk dcpl 2 chunk)
;; Create the chunked dataset.
(h5dcreate2 file *DATASET* dtype space
+H5P-DEFAULT+ dcpl +H5P-DEFAULT+))))
;; Write the data to the dataset.
(h5dwrite dset +H5T-NATIVE-INT+ +H5S-ALL+ space +H5P-DEFAULT+ wdata)
;; Close and release resources.
(h5ex:close-handles (list dset dcpl dtype space)))
(h5ex:close-handles (list file fapl))))
;; Now we begin the read section of this example.
(let* ((fapl (h5pcreate +H5P-FILE-ACCESS+))
(file (prog2 (h5pset-fclose-degree fapl :H5F-CLOSE-STRONG)
(h5fopen *FILE* +H5F-ACC-RDONLY+ fapl))))
(unwind-protect
(let* ((dset (h5dopen2 file *DATASET* +H5P-DEFAULT+))
(dcpl (h5dget-create-plist dset))
;; Retrieve and print the filter type. Here we only retrieve
;; the first filter because we know that we only added one
;; filter.
(filter-type (h5pget-filter2 dcpl 0 flags nelmts +NULL+
0 +NULL+ filter-info)))
(format t "Filter type is: ")
(cond ((eql filter-type +H5Z-FILTER-DEFLATE+)
(format t "H5Z_FILTER_DEFLATE~%"))
((eql filter-type +H5Z-FILTER-SHUFFLE+)
(format t "H5Z_FILTER_SHUFFLE~%"))
((eql filter-type +H5Z-FILTER-FLETCHER32+)
(format t "H5Z_FILTER_FLETCHER32~%"))
((eql filter-type +H5Z-FILTER-SZIP+)
(format t "H5Z_FILTER_SZIP~%"))
((eql filter-type +H5Z-FILTER-NBIT+)
(format t "H5Z_FILTER_NBIT~%"))
((eql filter-type +H5Z-FILTER-SCALEOFFSET+)
(format t "H5Z_FILTER_SCALEOFFSET~%")))
;; Read the data using the default properties.
(h5dread dset +H5T-NATIVE-INT+ +H5S-ALL+ +H5S-ALL+ +H5P-DEFAULT+
rdata)
;; Find the maximum value in the dataset, to verify that it was
;; read correctly.
(format t "Maximum value in ~a is: ~a~%" *DATASET*
(reduce #'max
(mapcar #'(lambda (i) (cffi:mem-aref rdata :int i))
(loop for i from 0 to (1- (* *DIM0* *DIM1*))
collect i))))
;; Close and release resources.
(h5ex:close-handles (list dcpl dset)))
(h5ex:close-handles (list file fapl)))))
| 5,663 | Common Lisp | .lisp | 117 | 41.153846 | 99 | 0.632808 | ghollisjr/cl-ana | 196 | 18 | 8 | GPL-3.0 | 9/19/2024, 11:25:22 AM (Europe/Amsterdam) | e3afdf0e176d91d40e871874b22c04ef077f2123df9482466b5216e28968c5dd | 1,519 | [
-1
] |