fusion-tools 2.3.2__tar.gz → 2.3.3__tar.gz

{fusion_tools-2.3.2 → fusion_tools-2.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.3.2
+Version: 2.3.3
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border

{fusion_tools-2.3.2 → fusion_tools-2.3.3}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="fusion-tools",
-    version="2.3.2",
+    version="2.3.3",
     author="Sam Border",
     author_email="sam.border2256@gmail.com",
     description="Modular visualization and analysis dashboard creation for high-resolution microscopy images",

{fusion_tools-2.3.2 → fusion_tools-2.3.3}/src/fusion_tools/feature_extraction.py

@@ -97,7 +97,7 @@ class ParallelFeatureExtractor:
         if not self.mask_names is None:
             convert_key = {f'Mask {float(idx+1)}': i for idx,i in enumerate(self.mask_names)}
         if not self.channel_names is None:
-            convert_key = convert_key | {f'Channel {float(idx+1)}': i for idx,i in enumerate(self.channel_names)}
+            convert_key = convert_key | {f'Channel {idx}': i for idx,i in enumerate(self.channel_names)}
 
         def convert_dict_key(pre_convert):
             if pre_convert in convert_key:
@@ -308,10 +308,10 @@ def color_features(image:np.ndarray, mask: np.ndarray, coords:list)->dict:
         mask_regions = (mask==m)
         masked_channels = image[mask_regions>0]
 
-        mean_vals = np.nanmean(masked_channels,axis=0).tolist()
-        median_vals = np.nanmedian(masked_channels,axis=0).tolist()
-        max_vals = np.nanmedian(masked_channels,axis=0).tolist()
-        std_vals = np.nanstd(masked_channels,axis=0).tolist()
+        mean_vals = np.nanmean(masked_channels,axis=0).astype(float).tolist()
+        median_vals = np.nanmedian(masked_channels,axis=0).astype(float).tolist()
+        max_vals = np.nanmedian(masked_channels,axis=0).astype(float).tolist()
+        std_vals = np.nanstd(masked_channels,axis=0).astype(float).tolist()
 
         feature_values[f'Mask {m}'] = {}
         for c_idx,(m1,m2,m3,s) in enumerate(zip(mean_vals, median_vals, max_vals, std_vals)):
@@ -350,7 +350,7 @@ def texture_features(image:np.ndarray, mask:np.ndarray, coords: list)->dict:
             for t in texture_features:
                 t_value = graycoprops(texture_matrix,t.lower())[0][0]
                 
-                feature_values[f'Mask {m}'][f'Channel {c}'][t] = t_value
+                feature_values[f'Mask {m}'][f'Channel {c}'][t] = float(t_value)
 
     return feature_values
 
@@ -383,10 +383,10 @@ def morphological_features(image:np.ndarray,mask:np.ndarray,coords:list)->dict:
         feature_values[f'Mask {m}'] = {'Count': props.shape[0]}
         for p in props.columns.tolist():
             feature_values[f'Mask {m}'][p] = {
-                'Mean': props[p].mean(),
-                'Median': props[p].median(),
-                'Max': props[p].max(),
-                'Min': props[p].min()
+                'Mean': float(props[p].mean()),
+                'Median': float(props[p].median()),
+                'Max': float(props[p].max()),
+                'Min': float(props[p].min())
             }
 
     return feature_values
@@ -413,11 +413,11 @@ def relative_distance(input_shapes:dict, other_shapes:Union[dict,list])->list:
             all_dist.extend(other_fc.distance(shape(f['geometry'])))
 
         distance_stats.append({
-            'Min': np.min(all_dist),
-            'Max': np.max(all_dist),
-            'Mean': np.mean(all_dist),
-            'Median': np.median(all_dist),
-            'Std': np.std(all_dist)
+            'Min': float(np.min(all_dist)),
+            'Max': float(np.max(all_dist)),
+            'Mean': float(np.mean(all_dist)),
+            'Median': float(np.median(all_dist)),
+            'Std': float(np.std(all_dist))
         })
 
     return distance_stats

{fusion_tools-2.3.2 → fusion_tools-2.3.3}/src/fusion_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.3.2
+Version: 2.3.3
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border

{fusion_tools-2.3.2 → fusion_tools-2.3.3}/tests/test_feature_extraction.py

@@ -151,6 +151,8 @@ def main():
         ],
         preprocess = None,
         sub_mask = lambda image,mask: stain_mask(image,mask),
+        mask_names = ['Nuclei','Eosinophilic','Luminal Space'],
+        channel_names = ['Red','Green','Blue'],
         n_jobs = 4,
         verbose = True
     )
@@ -158,6 +160,8 @@ def main():
     feature_df = feature_extractor.start(annotations[0]['features'])
 
     print(feature_df)
+    import json
+    print(json.dumps(feature_df.to_dict('records'),indent=4))
     feature_df.to_csv('.\\tests\\test_features.csv')