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""" |
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Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine |
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License: GNU GPL 2.0 |
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""" |
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import copy |
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import pickle |
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import numpy as np |
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import pandas as pd |
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import pytest |
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from pathml.preprocessing import ( |
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BinaryThreshold, |
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BoxBlur, |
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CollapseRunsVectra, |
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GaussianBlur, |
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MedianBlur, |
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MorphClose, |
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MorphOpen, |
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Pipeline, |
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QuantifyMIF, |
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) |
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from pathml.utils import RGB_to_GREY |
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def test_pipeline_passthru(tileHE): |
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p = Pipeline() |
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assert p.apply(tileHE) == tileHE |
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def test_pipeline_repr(): |
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p = Pipeline() |
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p2 = Pipeline([MedianBlur()]) |
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repr(p) |
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repr(p2) |
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def test_pipeline_HE(tileHE): |
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pipe = Pipeline( |
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[ |
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MedianBlur(), |
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GaussianBlur(), |
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BoxBlur(), |
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BinaryThreshold(mask_name="testing"), |
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MorphOpen(mask_name="testing"), |
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MorphClose(mask_name="testing"), |
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] |
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) |
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assert len(pipe) == 6 |
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orig_im = tileHE.image |
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pipe.apply(tileHE) |
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im = MedianBlur().F(orig_im) |
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im = GaussianBlur().F(im) |
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im = BoxBlur().F(im) |
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m = BinaryThreshold().F(RGB_to_GREY(im)) |
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m = MorphOpen().F(m) |
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m = MorphClose().F(m) |
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assert np.array_equal(tileHE.image, im) |
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assert np.array_equal(tileHE.masks["testing"], m) |
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def test_pipeline_mif(tileVectra): |
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""" |
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Run MIF pipeline |
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""" |
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pytest.importorskip("deepcell") |
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from pathml.preprocessing.transforms import SegmentMIF |
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orig_tile = copy.copy(tileVectra) |
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pipe = Pipeline( |
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[ |
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CollapseRunsVectra(), |
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SegmentMIF( |
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model="mesmer", |
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nuclear_channel=0, |
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cytoplasm_channel=2, |
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image_resolution=0.5, |
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), |
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QuantifyMIF(segmentation_mask="cell_segmentation"), |
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] |
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) |
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assert len(pipe) == 3 |
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pipe.apply(tileVectra) |
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collapsed_im = CollapseRunsVectra().F(orig_tile.image) |
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cell_segmentation, nuclear_segmentation = SegmentMIF( |
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model="mesmer", nuclear_channel=0, cytoplasm_channel=2, image_resolution=0.5 |
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).F(collapsed_im) |
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orig_tile.image = collapsed_im |
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orig_tile.masks["segmentation_mask"] = cell_segmentation |
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adata = QuantifyMIF(segmentation_mask="segmentation_mask").F( |
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orig_tile.image, orig_tile.masks["segmentation_mask"], orig_tile.coords |
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) |
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assert np.array_equal(tileVectra.masks["cell_segmentation"], cell_segmentation) |
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pd.testing.assert_frame_equal(adata.obs, tileVectra.counts.obs) |
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def test_pipeline_save(tmp_path): |
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fp = tmp_path / "test" |
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pipeline = Pipeline([MedianBlur()]) |
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pipeline.save(fp) |
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pipeline_loaded = pickle.load(open(fp, "rb")) |
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assert repr(pipeline_loaded) == repr(pipeline) |
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assert type(pipeline_loaded) is type(pipeline) |
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