Merge pull request #272 from choosehappy/fix_classification_module

small deconvolution bug fix
choosehappy · Nov 22, 2023 · 8943838 · 8943838
2 parents 9b2753c + 69a99b0
commit 8943838
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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