Merge pull request #316 from nanli-emory/fix_counttissuepieces_params

fix #315 - BasicModule.countTissuePieces does not define the `params` parameter
choosehappy · Aug 28, 2024 · 13a9439 · 13a9439
2 parents 26a98cb + 808908a
commit 13a9439
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Showing 5 changed files with 936 additions and 958 deletions.
diff --git a/histoqc/BasicModule.py b/histoqc/BasicModule.py
@@ -71,7 +71,7 @@ def finalProcessingArea(s, params):
             f"After BasicModule.finalProcessingArea NO tissue remains detectable! Downstream modules likely to be incorrect/fail")
 
 
-def countTissuePieces(s):
+def countTissuePieces(s, params):
     mask = s["img_mask_use"]
     stats = getMaskRegionsStats(mask)
-    s.addToPrintList("#pieces_of_tissue", str(stats.get('num', 0)))
+    s.addToPrintList("#pieces_of_tissue", str(stats.get('num', 0)))
diff --git a/histoqc/SaveModule.py b/histoqc/SaveModule.py
@@ -37,7 +37,7 @@ def saveFinalMask(s, params):
 
 
 def saveAssociatedImage(s, key:str, dim:int):
-    logging.info(f"{s['filename']} - \tsave{key.capitalize()}")
+    logging.info(f"{s['filename']}- save{key.capitalize()}")
     osh = s["os_handle"]
 
     if not key in osh.associated_images: