Merge pull request #36 from HelmholtzAI-Consultants-Munich/fix-rescaling

fixed mask resizing to match original image size

src/server/dcp_server/fsimagestorage.py

@@ -148,7 +148,7 @@ def rescale_image(self, img, height, width, channel_ax=None, order=2):
         rescale_factor = max_dim/512
         return rescale(img, 1/rescale_factor, order=order, channel_axis=channel_ax)
 
-    def resize_image(self, img, height, width, order):
+    def resize_image(self, img, height, width, channel_ax=None, order=2):
         """resize image
 
         :param img: image
@@ -161,8 +161,13 @@ def resize_image(self, img, height, width, order):
         :type order: int
         :return: resized image
         :rtype: ndarray
-        """        
-        return resize(img, (height, width), order=order)
+        """ 
+        if channel_ax is not None:
+            n_channel_dim = img.shape[channel_ax]
+            output_size = [height, width]
+            output_size.insert(channel_ax, n_channel_dim)
+        else: output_size = [height, width]
+        return resize(img, output_size, order=order)
 
     def prepare_images_and_masks_for_training(self, train_img_mask_pairs):
         """Image and mask processing for training.

src/server/dcp_server/segmentationclasses.py

@@ -37,18 +37,17 @@ async def segment_image(self, input_path, list_of_images):
             height, width, z_axis = self.imagestorage.get_image_size_properties(img, utils.get_file_extension(img_filepath))
             img = self.imagestorage.rescale_image(img,
                                                   height,
-                                                  width,
-                                                  order=None)
+                                                  width)
             # Add channel ax into the model's evaluation parameters dictionary
             self.model.eval_config['segmentor']['z_axis'] = z_axis
             # Evaluate the model
             mask = await self.runner.evaluate.async_run(img = img)
             # Resize the mask
-            mask = self.imagestorage.rescale_image(mask, 
-                                                   height, 
-                                                   width,
-                                                   self.model.eval_config['mask_channel_axis'],
-                                                   order=0)
+            mask = self.imagestorage.resize_image(mask,
+                                                height,
+                                                width,
+                                                self.model.eval_config['mask_channel_axis'],
+                                                order=0)
             # Save segmentation
             seg_name = utils.get_path_stem(img_filepath) + setup_config['seg_name_string'] + '.tiff'
             self.imagestorage.save_image(os.path.join(input_path, seg_name), mask)