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Commit a24b6f80 authored by Sharon Yates's avatar Sharon Yates
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New test dataset - PyNutil nonlinear

Perform key test
parent e763c3c8
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tests/test_data/PyNutil_nonlinear_test/segmentations/test_s003.png

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tests/test_data/PyNutil_nonlinear_test/segmentations/test_s004.png

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tests/test_data/PyNutil_nonlinear_test/segmentations/test_s005.png

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......@@ -9,14 +9,14 @@ from PyNutil import PyNutil
###The colour says which colour is the object you want to quantify in your segmentation. It is defined in RGB
###Finally the atlas name is the relevant atlas from brainglobe_atlasapi you wish to use in Quantification.
pnt = PyNutil(
segmentation_folder='../tests/test_data/big_caudoputamen_test/',
alignment_json='../tests/test_data/big_caudoputamen.json',
segmentation_folder='../tests/test_data/PyNutil_nonlinear_test/',
alignment_json='../tests/test_data/PyNutil_testdataset_Nonlin_SY_fixed.json',
colour=[0, 0, 0],
atlas_name='allen_mouse_25um'
)
pnt.get_coordinates(object_cutoff=0)
pnt.quantify_coordinates()
pnt.save_analysis("../tests/outputs/test9_PyNutil_bigcaudoputamen_new")
pnt.save_analysis("../tests/outputs/PyNutil_nonlinear_noflat")
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