fusion-tools 2.3.0__tar.gz → 2.3.2__tar.gz

{fusion_tools-2.3.0 → fusion_tools-2.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.3.0
+Version: 2.3.2
 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-2.3.0 → fusion_tools-2.3.2}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="fusion-tools",
-    version="2.3.0",
+    version="2.3.2",
     author="Sam Border",
     author_email="sam.border2256@gmail.com",
     description="Modular visualization and analysis dashboard creation for high-resolution microscopy images",

{fusion_tools-2.3.0 → fusion_tools-2.3.2}/src/fusion_tools/feature_extraction.py

@@ -43,6 +43,8 @@ class ParallelFeatureExtractor:
                  feature_list: list = [],
                  preprocess: Union[Callable,None] = None,
                  sub_mask: Union[Callable,None] = None,
+                 mask_names: Union[list,None] = None,
+                 channel_names: Union[list,None] = None,
                  n_jobs: None = None,
                  verbose: bool = False):
         """Constructor method
@@ -71,6 +73,8 @@ class ParallelFeatureExtractor:
         self.feature_list = feature_list
         self.preprocess = preprocess
         self.sub_mask = sub_mask
+        self.mask_names = mask_names
+        self.channel_names = channel_names
         self.n_jobs = n_jobs
         self.verbose = verbose
 
@@ -87,6 +91,38 @@ class ParallelFeatureExtractor:
                 a[key] = b[key]
         return a
     
+    def update_dict_keys(self,input_dict:dict):
+        
+        convert_key = {}
+        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)}
+
+        def convert_dict_key(pre_convert):
+            if pre_convert in convert_key:
+                return convert_key[pre_convert]
+            else:
+                return pre_convert
+            
+        def change_keys(obj, convert):
+            """
+            Recursively goes through the dictionary obj and replaces keys with the convert function.
+            """
+            if isinstance(obj, (str, int, float)):
+                return obj
+            if isinstance(obj, dict):
+                new = obj.__class__()
+                for k, v in obj.items():
+                    new[convert(k)] = change_keys(v, convert)
+            elif isinstance(obj, (list, set, tuple)):
+                new = obj.__class__(change_keys(v, convert) for v in obj)
+            else:
+                return obj
+            return new
+        
+        return change_keys(input_dict,convert_dict_key)
+ 
     def get_bbox(self, coords:list)->list:
 
         coords_array = np.squeeze(np.array(coords))
@@ -192,14 +228,20 @@ class ParallelFeatureExtractor:
         bbox = self.get_bbox(coords)
 
         return_dict = {
-            'min_x': bbox[0],
-            'min_y': bbox[1],
-            'max_x': bbox[2],
-            'max_y': bbox[3]
+            "bbox": {
+                'min_x': bbox[0],
+                'min_y': bbox[1],
+                'max_x': bbox[2],
+                'max_y': bbox[3]
+            }
         }
         for f in self.feature_list:
             # Each feature extraction function should accept three inputs, whether they are used or not
-            return_dict = self.merge_dict(return_dict,f(image_region, mask, coords))
+            new_features = f(image_region, mask, coords)
+            if not self.mask_names is None or not self.channel_names is None:
+                new_features = self.update_dict_keys(new_features)
+
+            return_dict = self.merge_dict(return_dict,new_features)
             
         return return_dict
 

{fusion_tools-2.3.0 → fusion_tools-2.3.2}/src/fusion_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusion-tools
-Version: 2.3.0
+Version: 2.3.2
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border