diff --git a/histoqc/ClassificationModule.py b/histoqc/ClassificationModule.py index 44273c9..9567a49 100644 --- a/histoqc/ClassificationModule.py +++ b/histoqc/ClassificationModule.py @@ -184,7 +184,7 @@ def byExampleWithFeatures(s, params): # convert grayscale images into binary images if images are not binary format if mask.dtype.kind != 'b': # warning log - msg = f"Mask file '{ex[1]}' is not a binary image" + msg = f"Mask file '{ex[1]}' is not a binary image. Automatically converting to binary..." logging.warning(s['filename'] + ' - ' + msg) s["warnings"].append(msg) # convert to binary diff --git a/histoqc/DeconvolutionModule.py b/histoqc/DeconvolutionModule.py index 8c85732..dbb41f1 100644 --- a/histoqc/DeconvolutionModule.py +++ b/histoqc/DeconvolutionModule.py @@ -23,9 +23,9 @@ def separateStains(s, params): sys.exit(1) return - stain_matrix = getattr(sys.modules[__name__], stain, "") + stain_matrix = getattr(sys.modules[__name__], stain, None) - if stain_matrix == "": + if stain_matrix is None: logging.error(f"{s['filename']} - Unknown stain matrix specified in DeconolutionModule.separateStains") sys.exit(1) return