From 7c93766a2ed716b71e68842f636e9544eeabc43f Mon Sep 17 00:00:00 2001 From: David Manthey Date: Tue, 17 Sep 2024 15:18:36 -0400 Subject: [PATCH] Make color deconvolution annotation optional (#1132) --- .../ColorDeconvolution/ColorDeconvolution.py | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py b/histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py index 01480a1ea..ff5e86208 100644 --- a/histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py +++ b/histomicstk/cli/ColorDeconvolution/ColorDeconvolution.py @@ -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 @@ -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__':