From f6d7ffaebcaed070f716cd2586151211baa25258 Mon Sep 17 00:00:00 2001
From: nanli-emory <40213692+nanli-emory@users.noreply.github.com>
Date: Thu, 4 Jan 2024 21:58:58 -0600
Subject: [PATCH 1/2] verify the mask is empty or not before computation in
 LocalTextureEstimationModule.py

---
 histoqc/LocalTextureEstimationModule.py | 43 ++++++++++++++-----------
 1 file changed, 24 insertions(+), 19 deletions(-)

diff --git a/histoqc/LocalTextureEstimationModule.py b/histoqc/LocalTextureEstimationModule.py
index 87186e2..39c738e 100644
--- a/histoqc/LocalTextureEstimationModule.py
+++ b/histoqc/LocalTextureEstimationModule.py
@@ -24,24 +24,29 @@ def estimateGreyComatrixFeatures(s, params):
     img = color.rgb2gray(img)
 
     mask = s[mask_name] if not invert else ~s[mask_name]
-    maskidx = mask.nonzero()
-    maskidx = np.asarray(maskidx).transpose()
-    idx = np.random.choice(maskidx.shape[0], npatches)
-
-    results = []
-
-    for id in idx:
-        r, c = maskidx[id, :]
-        patch = img[r:r + patch_size, c:c + patch_size]
-        glcm = graycomatrix(np.digitize(patch,np.linspace(0,1,num=nlevels),right=True), distances=[5],
-                            angles=[0], levels=nlevels, symmetric=True, normed=True)
-
-        results.append([graycoprops(glcm, prop=feat) for feat in feats])
-
-    results = np.asarray(results).squeeze()
-
-    for vals, feat in zip(results.transpose(), feats):
-        s.addToPrintList(f"{prefix}{feat}", str(vals.mean()))
-        s.addToPrintList(f"{prefix}{feat}_std", str(vals.std()))
+    if len(mask.nonzero()[0]) == 0:  # add warning in case the no tissus detected in mask
+        msg = f"LocalTextureEstimationModule.estimateGreyComatrixFeatures:{prefix} Can not estimate the empty mask since NO tissue remains detectable in mask"
+        logging.warning(f"{s['filename']} - {msg}")
+        s["warnings"].append(msg)  
+    else:
+        maskidx = mask.nonzero()
+        maskidx = np.asarray(maskidx).transpose()
+        idx = np.random.choice(maskidx.shape[0], npatches)
+
+        results = []
+
+        for id in idx:
+            r, c = maskidx[id, :]
+            patch = img[r:r + patch_size, c:c + patch_size]
+            glcm = graycomatrix(np.digitize(patch,np.linspace(0,1,num=nlevels),right=True), distances=[5],
+                                angles=[0], levels=nlevels, symmetric=True, normed=True)
+
+            results.append([graycoprops(glcm, prop=feat) for feat in feats])
+
+        results = np.asarray(results).squeeze()
+
+        for vals, feat in zip(results.transpose(), feats):
+            s.addToPrintList(f"{prefix}{feat}", str(vals.mean()))
+            s.addToPrintList(f"{prefix}{feat}_std", str(vals.std()))
 
     return

From df80baff91ce4b72e5a36c2fa1beec5db81469a4 Mon Sep 17 00:00:00 2001
From: nanli-emory <40213692+nanli-emory@users.noreply.github.com>
Date: Fri, 5 Jan 2024 11:20:25 -0600
Subject: [PATCH 2/2] improve code structure and make it easy to read and
 maintain

---
 histoqc/LocalTextureEstimationModule.py | 33 +++++++++++++------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/histoqc/LocalTextureEstimationModule.py b/histoqc/LocalTextureEstimationModule.py
index 39c738e..6d3733f 100644
--- a/histoqc/LocalTextureEstimationModule.py
+++ b/histoqc/LocalTextureEstimationModule.py
@@ -27,26 +27,27 @@ def estimateGreyComatrixFeatures(s, params):
     if len(mask.nonzero()[0]) == 0:  # add warning in case the no tissus detected in mask
         msg = f"LocalTextureEstimationModule.estimateGreyComatrixFeatures:{prefix} Can not estimate the empty mask since NO tissue remains detectable in mask"
         logging.warning(f"{s['filename']} - {msg}")
-        s["warnings"].append(msg)  
-    else:
-        maskidx = mask.nonzero()
-        maskidx = np.asarray(maskidx).transpose()
-        idx = np.random.choice(maskidx.shape[0], npatches)
+        s["warnings"].append(msg)
+        return
 
-        results = []
+    maskidx = mask.nonzero()
+    maskidx = np.asarray(maskidx).transpose()
+    idx = np.random.choice(maskidx.shape[0], npatches)
 
-        for id in idx:
-            r, c = maskidx[id, :]
-            patch = img[r:r + patch_size, c:c + patch_size]
-            glcm = graycomatrix(np.digitize(patch,np.linspace(0,1,num=nlevels),right=True), distances=[5],
-                                angles=[0], levels=nlevels, symmetric=True, normed=True)
+    results = []
 
-            results.append([graycoprops(glcm, prop=feat) for feat in feats])
+    for id in idx:
+        r, c = maskidx[id, :]
+        patch = img[r:r + patch_size, c:c + patch_size]
+        glcm = graycomatrix(np.digitize(patch,np.linspace(0,1,num=nlevels),right=True), distances=[5],
+                            angles=[0], levels=nlevels, symmetric=True, normed=True)
 
-        results = np.asarray(results).squeeze()
+        results.append([graycoprops(glcm, prop=feat) for feat in feats])
 
-        for vals, feat in zip(results.transpose(), feats):
-            s.addToPrintList(f"{prefix}{feat}", str(vals.mean()))
-            s.addToPrintList(f"{prefix}{feat}_std", str(vals.std()))
+    results = np.asarray(results).squeeze()
+
+    for vals, feat in zip(results.transpose(), feats):
+        s.addToPrintList(f"{prefix}{feat}", str(vals.mean()))
+        s.addToPrintList(f"{prefix}{feat}_std", str(vals.std()))
 
     return