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Commit 3dff7010 authored by Christopher Randolph Rhodes's avatar Christopher Randolph Rhodes
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Updated references to testing fixtures; chaeo tests failing but suspect this was the case before

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...@@ -11,7 +11,7 @@ if __name__ == '__main__': ...@@ -11,7 +11,7 @@ if __name__ == '__main__':
'batch-output' 'batch-output'
) )
px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp' px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
params = { params = {
'pxmap_threshold': 0.25, 'pxmap_threshold': 0.25,
......
from pathlib import Path from pathlib import Path
root = Path.home() / 'model-server' root = Path.home() / 'model_server'
multichannel_zstack = { multichannel_zstack = {
'path': root / 'testing' / 'zmask-test-stack-chlorophyl.tif', 'path': root / 'testing' / 'zmask-test-stack-chlorophyl.tif',
...@@ -11,12 +11,12 @@ multichannel_zstack = { ...@@ -11,12 +11,12 @@ multichannel_zstack = {
} }
pixel_classifier = { pixel_classifier = {
'path': root / 'ilastik' / 'AF405-bodies_boundaries.ilp' 'path': root / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
} }
pipeline_params = { pipeline_params = {
'threshold': 0.6, 'threshold': 0.6,
} }
output_path = root / 'testing_output' / 'chaeo' output_path = root / 'testing' / 'output' / 'chaeo'
output_path.mkdir(parents=True, exist_ok=True) output_path.mkdir(parents=True, exist_ok=True)
\ No newline at end of file
...@@ -15,8 +15,8 @@ if __name__ == '__main__': ...@@ -15,8 +15,8 @@ if __name__ == '__main__':
'zmask_to_automic', 'zmask_to_automic',
) )
px_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp' px_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
ob_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'auto_obj_after.ilp' ob_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'auto_obj_after.ilp'
params = { params = {
'pxmap_threshold': 0.25, 'pxmap_threshold': 0.25,
......
...@@ -112,7 +112,7 @@ if __name__ == '__main__': ...@@ -112,7 +112,7 @@ if __name__ == '__main__':
) )
csv_args = {'mode': 'w', 'header': True} # when creating file csv_args = {'mode': 'w', 'header': True} # when creating file
px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp' px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
for ff in where_czi.iterdir(): for ff in where_czi.iterdir():
if ff.stem != 'Selection--W0000--P0009-T0001': if ff.stem != 'Selection--W0000--P0009-T0001':
......
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