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<|file_name|>app.py<|end_file_name|><｜fim▁begin｜>import web
urls = (
'/hello','Index'
)
app = web.application(urls,globals())
render = web.template.render('/usr/local/LPTHW/ex51/gothonweb/templates/',base="layout")
class Index(object):
<|fim_middle|>
if __name__ == '__main__':
app.run()
<｜fim▁end｜> | def GET(self):
return render.hello_form()
def POST(self):
form = web.input(name="Nobody",greet="Hello")
greeting = "%s,%s" % (form.greet,form.name)
return render.index(greeting = greeting) |
<|file_name|>app.py<|end_file_name|><｜fim▁begin｜>import web
urls = (
'/hello','Index'
)
app = web.application(urls,globals())
render = web.template.render('/usr/local/LPTHW/ex51/gothonweb/templates/',base="layout")
class Index(object):
def GET(self):
<|fim_middle|>
def POST(self):
form = web.input(name="Nobody",greet="Hello")
greeting = "%s,%s" % (form.greet,form.name)
return render.index(greeting = greeting)
if __name__ == '__main__':
app.run()
<｜fim▁end｜> | return render.hello_form() |
<|file_name|>app.py<|end_file_name|><｜fim▁begin｜>import web
urls = (
'/hello','Index'
)
app = web.application(urls,globals())
render = web.template.render('/usr/local/LPTHW/ex51/gothonweb/templates/',base="layout")
class Index(object):
def GET(self):
return render.hello_form()
def POST(self):
<|fim_middle|>
if __name__ == '__main__':
app.run()
<｜fim▁end｜> | form = web.input(name="Nobody",greet="Hello")
greeting = "%s,%s" % (form.greet,form.name)
return render.index(greeting = greeting) |
<|file_name|>app.py<|end_file_name|><｜fim▁begin｜>import web
urls = (
'/hello','Index'
)
app = web.application(urls,globals())
render = web.template.render('/usr/local/LPTHW/ex51/gothonweb/templates/',base="layout")
class Index(object):
def GET(self):
return render.hello_form()
def POST(self):
form = web.input(name="Nobody",greet="Hello")
greeting = "%s,%s" % (form.greet,form.name)
return render.index(greeting = greeting)
if __name__ == '__main__':
<|fim_middle|>
<｜fim▁end｜> | app.run() |
<|file_name|>app.py<|end_file_name|><｜fim▁begin｜>import web
urls = (
'/hello','Index'
)
app = web.application(urls,globals())
render = web.template.render('/usr/local/LPTHW/ex51/gothonweb/templates/',base="layout")
class Index(object):
def <|fim_middle|>(self):
return render.hello_form()
def POST(self):
form = web.input(name="Nobody",greet="Hello")
greeting = "%s,%s" % (form.greet,form.name)
return render.index(greeting = greeting)
if __name__ == '__main__':
app.run()
<｜fim▁end｜> | GET |
<|file_name|>app.py<|end_file_name|><｜fim▁begin｜>import web
urls = (
'/hello','Index'
)
app = web.application(urls,globals())
render = web.template.render('/usr/local/LPTHW/ex51/gothonweb/templates/',base="layout")
class Index(object):
def GET(self):
return render.hello_form()
def <|fim_middle|>(self):
form = web.input(name="Nobody",greet="Hello")
greeting = "%s,%s" % (form.greet,form.name)
return render.index(greeting = greeting)
if __name__ == '__main__':
app.run()
<｜fim▁end｜> | POST |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
<｜fim▁hole｜> (1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
<|fim_middle|>
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
<|fim_middle|>
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
<|fim_middle|>
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
<|fim_middle|>
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named'] |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
<|fim_middle|>
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
<|fim_middle|>
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
<|fim_middle|>
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
<|fim_middle|>
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) ) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
<|fim_middle|>
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors)) |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def <|fim_middle|>(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | parse |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def <|fim_middle|>(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | __colors |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def <|fim_middle|>(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | named |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def <|fim_middle|>(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def read_config():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | try_parse |
<|file_name|>config.py<|end_file_name|><｜fim▁begin｜>from collections import namedtuple
Resolution = namedtuple('Resolution', ['x', 'y'])
class Resolutions(object):
resolutions = [
(1920, 1200),
(1920, 1080),
(1680, 1050),
(1440, 900),
(1360, 768),
(1280, 800),
(1024, 640)
]
@classmethod
def parse(self, x, y):
if (x,y) not in self.resolutions:
resolutions = ', '.join(['%sx%s' % (a, b) for a,b in self.resolutions])
raise Exception('Resolution %s x %s not supported. Available resolutions: %s' % (x,y, resolutions) )
return Resolution(x, y)
class Color(object):
gray = (0.15, 0.15, 0.13, 1.0)
black = (0.0, 0.0, 0.0, 1.0)
white = (1.0, 1.0, 1.0, 1.0)
red = (1.0, 0.2, 0.0, 1.0)
orange = (1.0, 0.4, 0.0, 1.0)
yellow = (1.0, 0.9, 0.0, 1.0)
light_green = (0.4, 1.0, 0.0, 1.0)
green = (0.0, 1.0, 0.2, 1.0)
cyan = (0.0, 1.0, 0.4, 1.0)
light_blue = (0.0, 0.6, 1.0, 1.0)
blue = (0.0, 0.2, 1.0, 1.0)
purple = (0.4, 0.0, 1.0, 1.0)
pink = (1.0, 0.0, 0.8, 1.0)
@classmethod
def __colors(self):
return [key for key in self.__dict__.keys() if not key.startswith('_') and key != 'named']
@classmethod
def named(self, name):
if not hasattr(self, name):
colors = ', '.join(self.__colors())
raise Exception('Unknown color %s. Available colors are: %s' % (name, colors))
return getattr(self, name)
def try_parse(value):
try: return int(value)
except: return { 'true': True, 'false': False }.get(value.lower(), value)
def <|fim_middle|>():
with open('config.cfg', 'r') as cfg_file:
lines = cfg_file.readlines()
lines = [
line.strip().replace(' ', '').split('=')
for line in lines
if line.strip() and '=' in line
]
cfg = {key:try_parse(value) for key,value in lines}
return cfg
cfg = read_config()
NUM_CELLS = cfg.get('CELLS', 100)
RESOLUTION = Resolutions.parse(cfg.get('WINDOW_WIDTH', 1280), cfg.get('WINDOW_HEIGHT', 800))
limit = min(RESOLUTION)
PIXEL_PER_CELL = limit / NUM_CELLS
OFFSET_X = (RESOLUTION.x - (NUM_CELLS * PIXEL_PER_CELL)) / 2
OFFSET_Y = (RESOLUTION.y - (NUM_CELLS * PIXEL_PER_CELL)) / 2
SHOW_FULLSCREEN = cfg.get('FULLSCREEN', False)
SHOW_GRID = cfg.get('SHOW_GRID', True)
BACKGROUND_COLOR = Color.named(cfg.get('BACKGROUND_COLOR', 'black'))
GRID_BACKDROP_COLOR = Color.named(cfg.get('GRID_BACKDROP_COLOR', 'gray'))
GRID_LINE_COLOR = Color.named(cfg.get('GRID_LINE_COLOR', 'black'))
CELL_COLOR = Color.named(cfg.get('CELL_COLOR', 'green'))
CURSOR_COLOR = Color.named(cfg.get('CURSOR_COLOR', 'red'))<｜fim▁end｜> | read_config |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,<｜fim▁hole｜><｜fim▁end｜> | limit=100,
) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
<|fim_middle|>
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | """Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
<|fim_middle|>
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | """Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1 |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
<|fim_middle|>
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | """Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
<|fim_middle|>
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | """Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"]) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
<|fim_middle|>
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | """Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"]) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
<|fim_middle|>
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | """Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
<|fim_middle|>
<｜fim▁end｜> | """
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
<|fim_middle|>
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | logger.info(f"Merged {nv - sheet.Nv+1} vertices") |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
<|fim_middle|>
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | logger.info("Failed to detach, skipping") |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
<|fim_middle|>
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | logger.info(f"Detached {sheet.Nv - nv} vertices") |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
<|fim_middle|>
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
<|fim_middle|>
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1 |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
<|fim_middle|>
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | return |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
<|fim_middle|>
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | exchange(sheet, face, type1_transition_spec["geom"]) |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
<|fim_middle|>
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | return |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def <|fim_middle|>(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | reconnect |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def <|fim_middle|>(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | division |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def <|fim_middle|>(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | contraction |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def <|fim_middle|>(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | type1_transition |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def <|fim_middle|>(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | face_elimination |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def <|fim_middle|>(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def contraction_line_tension(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | check_tri_faces |
<|file_name|>basic_events.py<|end_file_name|><｜fim▁begin｜>"""
Small event module
=======================
"""
import numpy as np
import logging
logger = logging.getLogger(__name__)
from ...utils.decorators import face_lookup
from ...geometry.sheet_geometry import SheetGeometry
from ...topology.sheet_topology import cell_division
from .actions import (
exchange,
remove,
merge_vertices,
detach_vertices,
increase,
decrease,
increase_linear_tension,
)
def reconnect(sheet, manager, **kwargs):
"""Performs reconnections (vertex merging / splitting) following Finegan et al. 2019
kwargs overwrite their corresponding `sheet.settings` entries
Keyword Arguments
-----------------
threshold_length : the threshold length at which vertex merging is performed
p_4 : the probability per unit time to perform a detachement from a rank 4 vertex
p_5p : the probability per unit time to perform a detachement from a rank 5 or more vertex
See Also
--------
**The tricellular vertex-specific adhesion molecule Sidekick
facilitates polarised cell intercalation during Drosophila axis
extension** _Tara M Finegan, Nathan Hervieux, Alexander
Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte
Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932
"""
sheet.settings.update(kwargs)
nv = sheet.Nv
merge_vertices(sheet)
if nv != sheet.Nv:
logger.info(f"Merged {nv - sheet.Nv+1} vertices")
nv = sheet.Nv
retval = detach_vertices(sheet)
if retval:
logger.info("Failed to detach, skipping")
if nv != sheet.Nv:
logger.info(f"Detached {sheet.Nv - nv} vertices")
manager.append(reconnect, **kwargs)
default_division_spec = {
"face_id": -1,
"face": -1,
"growth_rate": 0.1,
"critical_vol": 2.0,
"geom": SheetGeometry,
}
@face_lookup
def division(sheet, manager, **kwargs):
"""Cell division happens through cell growth up to a critical volume,
followed by actual division of the face.
Parameters
----------
sheet : a `Sheet` object
manager : an `EventManager` instance
face_id : int,
index of the mother face
growth_rate : float, default 0.1
rate of increase of the prefered volume
critical_vol : float, default 2.
volume at which the cells stops to grow and devides
"""
division_spec = default_division_spec
division_spec.update(**kwargs)
face = division_spec["face"]
division_spec["critical_vol"] *= sheet.specs["face"]["prefered_vol"]
print(sheet.face_df.loc[face, "vol"], division_spec["critical_vol"])
if sheet.face_df.loc[face, "vol"] < division_spec["critical_vol"]:
increase(
sheet, "face", face, division_spec["growth_rate"], "prefered_vol", True
)
manager.append(division, **division_spec)
else:
daughter = cell_division(sheet, face, division_spec["geom"])
sheet.face_df.loc[daughter, "id"] = sheet.face_df.id.max() + 1
default_contraction_spec = {
"face_id": -1,
"face": -1,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": False,
"contraction_column": "contractility",
"unique": True,
}
@face_lookup
def contraction(sheet, manager, **kwargs):
"""Single step contraction event."""
contraction_spec = default_contraction_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if (sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]) or (
sheet.face_df.loc[face, contraction_spec["contraction_column"]]
> contraction_spec["max_contractility"]
):
return
increase(
sheet,
"face",
face,
contraction_spec["contractile_increase"],
contraction_spec["contraction_column"],
contraction_spec["multiply"],
)
default_type1_transition_spec = {
"face_id": -1,
"face": -1,
"critical_length": 0.1,
"geom": SheetGeometry,
}
@face_lookup
def type1_transition(sheet, manager, **kwargs):
"""Custom type 1 transition event that tests if
the the shorter edge of the face is smaller than
the critical length.
"""
type1_transition_spec = default_type1_transition_spec
type1_transition_spec.update(**kwargs)
face = type1_transition_spec["face"]
edges = sheet.edge_df[sheet.edge_df["face"] == face]
if min(edges["length"]) < type1_transition_spec["critical_length"]:
exchange(sheet, face, type1_transition_spec["geom"])
default_face_elimination_spec = {"face_id": -1, "face": -1, "geom": SheetGeometry}
@face_lookup
def face_elimination(sheet, manager, **kwargs):
"""Removes the face with if face_id from the sheet."""
face_elimination_spec = default_face_elimination_spec
face_elimination_spec.update(**kwargs)
remove(sheet, face_elimination_spec["face"], face_elimination_spec["geom"])
default_check_tri_face_spec = {"geom": SheetGeometry}
def check_tri_faces(sheet, manager, **kwargs):
"""Three neighbourghs cell elimination
Add all cells with three neighbourghs in the manager
to be eliminated at the next time step.
Parameters
----------
sheet : a :class:`tyssue.sheet` object
manager : a :class:`tyssue.events.EventManager` object
"""
check_tri_faces_spec = default_check_tri_face_spec
check_tri_faces_spec.update(**kwargs)
tri_faces = sheet.face_df[(sheet.face_df["num_sides"] < 4)].id
manager.extend(
[
(face_elimination, {"face_id": f, "geom": check_tri_faces_spec["geom"]})
for f in tri_faces
]
)
default_contraction_line_tension_spec = {
"face_id": -1,
"face": -1,
"shrink_rate": 1.05,
"contractile_increase": 1.0,
"critical_area": 1e-2,
"max_contractility": 10,
"multiply": True,
"contraction_column": "line_tension",
"unique": True,
}
@face_lookup
def <|fim_middle|>(sheet, manager, **kwargs):
"""
Single step contraction event
"""
contraction_spec = default_contraction_line_tension_spec
contraction_spec.update(**kwargs)
face = contraction_spec["face"]
if sheet.face_df.loc[face, "area"] < contraction_spec["critical_area"]:
return
# reduce prefered_area
decrease(
sheet,
"face",
face,
contraction_spec["shrink_rate"],
col="prefered_area",
divide=True,
bound=contraction_spec["critical_area"] / 2,
)
increase_linear_tension(
sheet,
face,
contraction_spec["contractile_increase"],
multiply=contraction_spec["multiply"],
isotropic=True,
limit=100,
)
<｜fim▁end｜> | contraction_line_tension |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)<｜fim▁hole｜> try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()<｜fim▁end｜> | |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
<|fim_middle|>
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run() |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
<|fim_middle|>
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start() |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
<|fim_middle|>
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0) |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
<|fim_middle|>
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff))) |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
<|fim_middle|>
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK") |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
<|fim_middle|>
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = "" |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
<|fim_middle|>
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
<|fim_middle|>
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | print("Cleanup called")
self._setspeeds(0,0) |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
<|fim_middle|>
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | print("Starting motorserver")
super(motorserver, self).run() |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
<|fim_middle|>
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | self._setspeeds(0,0) |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
<|fim_middle|>
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | time.sleep(0)
return |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
<|fim_middle|>
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | return |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
<|fim_middle|>
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | self.message_received(self.input_buffer[:-2])
self.input_buffer = "" |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
<|fim_middle|>
<｜fim▁end｜> | import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run() |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def <|fim_middle|>(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | __init__ |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def <|fim_middle|>(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | check_data_reveived |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def <|fim_middle|>(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | _setspeeds |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def <|fim_middle|>(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | setspeeds |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def <|fim_middle|>(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | handle_serial_event |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def <|fim_middle|>(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | message_received |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def <|fim_middle|>(self):
print("Cleanup called")
self._setspeeds(0,0)
def run(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | cleanup |
<|file_name|>motorctrl.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import zmq
from zmq.eventloop import ioloop as ioloop_mod
import zmqdecorators
import time
SERVICE_NAME = "urpobot.motor"
SERVICE_PORT = 7575
SIGNALS_PORT = 7576
# How long to wait for new commands before stopping automatically
COMMAND_GRACE_TIME = 0.250
class motorserver(zmqdecorators.service):
def __init__(self, service_name, service_port, serialport):
super(motorserver, self).__init__(service_name, service_port)
self.serial_port = serialport
self.input_buffer = ""
self.evthandler = ioloop_mod.IOLoop.instance().add_handler(self.serial_port.fileno(), self.handle_serial_event, ioloop_mod.IOLoop.instance().READ)
self.last_command_time = time.time()
self.pcb = ioloop_mod.PeriodicCallback(self.check_data_reveived, COMMAND_GRACE_TIME)
self.pcb.start()
def check_data_reveived(self, *args):
if (time.time() - self.last_command_time > COMMAND_GRACE_TIME):
self._setspeeds(0,0)
def _setspeeds(self, m1speed, m2speed):
self.serial_port.write("S%04X%04X\n" % ((m1speed & 0xffff), (m2speed & 0xffff)))
@zmqdecorators.method()
def setspeeds(self, resp, m1speed, m2speed):
self.last_command_time = time.time()
#print("Got speeds %s,%s" % (m1speed, m2speed))
self._setspeeds(m1speed, m2speed)
# TODO: actually handle ACK/NACK somehow (we need to read it from the serialport but we can't block while waiting for it...)
resp.send("ACK")
def handle_serial_event(self, fd, events):
# Copied from arbus that was thread based
if not self.serial_port.inWaiting():
# Don't try to read if there is no data, instead sleep (yield) a bit
time.sleep(0)
return
data = self.serial_port.read(1)
if len(data) == 0:
return
#print("DEBUG: data=%s" % data)
# Put the data into inpit buffer and check for CRLF
self.input_buffer += data
# Trim prefix NULLs and linebreaks
self.input_buffer = self.input_buffer.lstrip(chr(0x0) + "\r\n")
#print "input_buffer=%s" % repr(self.input_buffer)
if ( len(self.input_buffer) > 1
and self.input_buffer[-2:] == "\r\n"):
# Got a message, parse it (sans the CRLF) and empty the buffer
self.message_received(self.input_buffer[:-2])
self.input_buffer = ""
def message_received(self, message):
#print("DEBUG: msg=%s" % message)
try:
# Currently we have no incoming messages from this board
pass
except Exception as e:
print "message_received exception: Got exception %s" % repr(e)
# Ignore indexerrors, they just mean we could not parse the command
pass
pass
def cleanup(self):
print("Cleanup called")
self._setspeeds(0,0)
def <|fim_middle|>(self):
print("Starting motorserver")
super(motorserver, self).run()
if __name__ == "__main__":
import serial
import sys,os
port = serial.Serial(sys.argv[1], 115200, xonxoff=False, timeout=0.01)
instance = motorserver(SERVICE_NAME, SERVICE_PORT, port)
instance.run()
<｜fim▁end｜> | run |