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Make color deconvolution annotation optional #1132

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Merged
manthey merged 1 commit into from
Sep 17, 2024
Merged

Make color deconvolution annotation optional #1132

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20 changes: 12 additions & 8 deletions histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,15 @@ def colorDeconvolve(args):
# Write stain images to output
print('>> Outputting individual stain images')

print(args.outputStainImageFile_1)
sink0.write(args.outputStainImageFile_1)
print(args.outputStainImageFile_2)
sink1.write(args.outputStainImageFile_2)
print(args.outputStainImageFile_3)
sink2.write(args.outputStainImageFile_3)
if args.outputStainImageFile_1:
print(args.outputStainImageFile_1)
sink0.write(args.outputStainImageFile_1)
if args.outputStainImageFile_2:
print(args.outputStainImageFile_2)
sink1.write(args.outputStainImageFile_2)
if args.outputStainImageFile_3:
print(args.outputStainImageFile_3)
sink2.write(args.outputStainImageFile_3)

return region

Expand Down Expand Up @@ -129,8 +132,9 @@ def main(args):
if args.stain_2 == 'null':
annotation[1:2] = []

with open(args.outputAnnotationFile, 'w') as annotation_file:
json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)
if args.outputAnnotationFile:
with open(args.outputAnnotationFile, 'w') as annotation_file:
json.dump(annotation, annotation_file, separators=(',', ':'), sort_keys=False)


if __name__ == '__main__':
Expand Down