remove threshold in countTissuePieces, fix the typo and add stats int…

…o the print list

histoqc/BaseImage.py

@@ -207,7 +207,7 @@ def getImgThumb(self, size: str):
         return self[key]
 
 '''
-the followings are helper functions 
+the following are helper functions 
 '''
 def getBestThumb(s: BaseImage, x: int, y: int, dims: Tuple[int, int], target_sampling_factor: float):
     osh = s["os_handle"]
@@ -344,11 +344,11 @@ def getDimensionsByOneDim(s: BaseImage, dim: int) -> Tuple[int, int]:
         return w, dim
 
 
-def getMaskReginsStats(img, area_threshold: int = 0)-> dict:
+def getMaskRegionsStats(img)-> dict:
 
     rps = measure.regionprops(morphology.label(img))
     if rps:
-        areas = np.asarray([rp.area for rp in rps if rp.area > area_threshold])
+        areas = np.asarray([rp.area for rp in rps])
         num = len(rps)
         area_min = areas.min()
         area_max = areas.max()

histoqc/BasicModule.py

@@ -1,6 +1,6 @@
 import logging
 import os
-from histoqc.BaseImage import printMaskHelper, getMaskReginsStats
+from histoqc.BaseImage import printMaskHelper, getMaskRegionsStats
 from skimage.morphology import remove_small_objects, binary_opening, disk
 from skimage import io, color, img_as_ubyte
 
@@ -71,8 +71,7 @@ def finalProcessingArea(s, params):
             f"After BasicModule.finalProcessingArea NO tissue remains detectable! Downstream modules likely to be incorrect/fail")
 
 
-def countTissuePieces(s, params):
-    area_thresh = int(params.get("area_threshold", "1000"))
+def countTissuePieces(s):
     mask = s["img_mask_use"]
-    stats = getMaskReginsStats(mask, area_threshold=area_thresh)
+    stats = getMaskRegionsStats(mask)
     s.addToPrintList("#pieces_of_tissue", str(stats.get('num', 0)))

histoqc/BlurDetectionModule.py

@@ -2,7 +2,7 @@
 import os
 
 import skimage
-from histoqc.BaseImage import printMaskHelper, getMaskReginsStats
+from histoqc.BaseImage import printMaskHelper, getMaskRegionsStats
 from skimage import io, img_as_ubyte, morphology, measure
 from skimage.color import rgb2gray
 from skimage.filters import rank
@@ -45,12 +45,12 @@ def identifyBlurryRegions(s, params):
     #     area_mean = areas.mean()
     # else:
     #     nobj = area_max = area_mean = 0
-    stat_rs = getMaskReginsStats(mask)
+    stat_rs = getMaskRegionsStats(mask)
 
-
-    # s.addToPrintList("blurry_removed_num_regions", str(nobj))
-    # s.addToPrintList("blurry_removed_mean_area", str(area_mean))
-    # s.addToPrintList("blurry_removed_max_area", str(area_max))
+    
+    s.addToPrintList("blurry_removed_num_regions", str(stat_rs.get('num', 0)))
+    s.addToPrintList("blurry_removed_mean_area", str(stat_rs.get('area_mean',0)))
+    s.addToPrintList("blurry_removed_max_area", str(stat_rs.get('area_max',0)))
 
 
     s.addToPrintList("blurry_removed_percent",

histoqc/MorphologyModule.py

@@ -1,7 +1,7 @@
 import logging
 import os
 import numpy as np
-from histoqc.BaseImage import printMaskHelper, getMaskReginsStats
+from histoqc.BaseImage import printMaskHelper, getMaskRegionsStats
 from skimage import io, morphology, img_as_ubyte, measure
 
 from scipy import ndimage as ndi
@@ -31,7 +31,7 @@ def removeSmallObjects(s, params):
     #     area_mean = areas.mean()
     # else:
     #     nobj = area_max = area_mean = 0
-    stats = getMaskReginsStats(img_small)
+    stats = getMaskRegionsStats(img_small)
 
 
     # s.addToPrintList("small_tissue_removed_num_regions", str(nobj))
@@ -99,7 +99,7 @@ def removeFatlikeTissue(s, params):
     #     area_mean = areas.mean()
     # else:
     #     nobj = area_max = area_mean = 0
-    stats = getMaskReginsStats(mask_fat)
+    stats = getMaskRegionsStats(mask_fat)
 
     # s.addToPrintList("fatlike_tissue_removed_num_regions", str(nobj))
     # s.addToPrintList("fatlike_tissue_removed_mean_area", str(area_mean))
@@ -141,7 +141,7 @@ def fillSmallHoles(s, params):
     #     area_mean = areas.mean()
     # else:
     #     nobj = area_max = area_mean = 0
-    stats = getMaskReginsStats(img_small)
+    stats = getMaskRegionsStats(img_small)
 
     # s.addToPrintList("small_tissue_filled_num_regions", str(nobj))
     # s.addToPrintList("small_tissue_filled_mean_area", str(area_mean))

histoqc/config/config_v2.1.ini

@@ -255,4 +255,3 @@ upper_threshold: 210
 invert: True
 
 [BasicModule.countTissuePieces]
-area_threshold:  500