Small changes

Author: Nikolas Schmitz

monai/data/wsi_reader.py

@@ -790,7 +790,7 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
         # -> Should not throw ValueError, instead just return the closest value; how to select tolerances?
 
         mpp_closest_lvl = mpp_list[closest_lvl]
-        closest_lvl_dim = wsi.resolutions['level_dimensions'][closest_lvl]  # x,y notation
+        closest_lvl_dim = wsi.resolutions['level_dimensions'][closest_lvl]
 
         print(f'Closest Level: {closest_lvl} with MPP: {mpp_closest_lvl}')
         mpp_closest_lvl_x, mpp_closest_lvl_y = mpp_closest_lvl
@@ -809,7 +809,7 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
         if within_tolerance:
             # Take closest_level and continue with returning img at level
             print(f'User-provided MPP lies within tolerance of level {closest_lvl}, returning wsi at this level.')
-            closest_lvl_wsi = wsi.read_region((0, 0), level=closest_lvl, size=closest_lvl_dim, num_workers=self.num_workers)  # size in x,y notation
+            closest_lvl_wsi = wsi.read_region((0, 0), level=closest_lvl, size=closest_lvl_dim, num_workers=self.num_workers)
 
         else:
             # If mpp_closest_level < mpp -> closest_level has higher res than img at mpp => downscale from closest_level to mpp
@@ -827,13 +827,13 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
                 target_res_x = int(np.round(closest_lvl_dim[1] * ds_factor_x))
                 target_res_y = int(np.round(closest_lvl_dim[0] * ds_factor_y))
 
-                closest_lvl_wsi = cucim_resize(wsi_arr, (target_res_x, target_res_y), order=0)  # output_shape in row, col notation
+                closest_lvl_wsi = cucim_resize(wsi_arr, (target_res_x, target_res_y), order=0)
                 print(f'Case 1: Downscaling using factor {(ds_factor_x, ds_factor_y)}')
 
             else:
                 # Else: increase resolution (ie, decrement level) and then downsample
                 closest_lvl = closest_lvl - 1
-                mpp_closest_lvl = mpp_list[closest_lvl]  # Update MPP
+                mpp_closest_lvl = mpp_list[closest_lvl]
                 mpp_closest_lvl_x, mpp_closest_lvl_y = mpp_closest_lvl
 
                 ds_factor_x = mpp_closest_lvl_x / user_mpp_x
@@ -1115,7 +1115,7 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
             else:
                 # Else: increase resolution (ie, decrement level) and then downsample
                 closest_lvl = closest_lvl - 1
-                mpp_closest_lvl = mpp_list[closest_lvl]  # Update MPP
+                mpp_closest_lvl = mpp_list[closest_lvl]
                 mpp_closest_lvl_x, mpp_closest_lvl_y = mpp_closest_lvl
 
                 ds_factor_x = mpp_closest_lvl_x / user_mpp_x
@@ -1127,7 +1127,7 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
                 target_res_x = int(np.round(closest_lvl_dim[0] * ds_factor_x))
                 target_res_y = int(np.round(closest_lvl_dim[1] * ds_factor_y))
 
-                closest_lvl_wsi = closest_lvl_wsi.resize((target_res_x, target_res_y), pil_image.BILINEAR)  # Output size in x,y notation
+                closest_lvl_wsi = closest_lvl_wsi.resize((target_res_x, target_res_y), pil_image.BILINEAR)
                 print(f'Case 2: Downscaling using factor {(ds_factor_x, ds_factor_y)}, now from level {closest_lvl}')
 
         wsi_arr = np.array(closest_lvl_wsi)
@@ -1289,9 +1289,9 @@ def get_mpp(self, wsi, level: int) -> tuple[float, float]:
             and wsi.pages[level].tags["YResolution"].value
         ):
             unit = wsi.pages[level].tags.get("ResolutionUnit")
-            if unit is not None:  # Needs to be extended
-                # unit = str(unit.value)[8:]
-                unit = str(unit.value.name).lower()  # TODO: Merge both methods
+            if unit is not None:  # Needs to be improved
+                unit = str(unit.value)[8:]
+                # unit = str(unit.value.name).lower()  # TODO: Merge both methods
 
             else:
                 warnings.warn("The resolution unit is missing. `micrometer` will be used as default.")
@@ -1309,8 +1309,10 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
         """
         Returns the representation of the whole slide image at a given micro-per-pixel (mpp) resolution.
         The optional tolerance parameters are considered at the level whose mpp value is closest to the one provided by the user.
-        If the user-provided mpp is larger than the mpp of the closest level the image is downscaled to a resolution that matches the user-provided mpp.
-        Otherwise, if the closest level's resolution is not sufficient to meet the user's requested resolution, the next lower level (which has a higher resolution) is chosen.
+        If the user-provided mpp is larger than the mpp of the closest level,
+        the image is downscaled to a resolution that matches the user-provided mpp.
+        Otherwise, if the closest level's resolution is not sufficient to meet the user's requested resolution,
+        the next lower level (which has a higher resolution) is chosen.
         The image from this level is then down-scaled to achieve a resolution at the user-provided mpp value.
 
         Args:
@@ -1329,7 +1331,7 @@ def get_img_at_mpp(self, wsi, mpp: tuple, atol: float = 0.00, rtol: float = 0.05
 
         mpp_closest_lvl = mpp_list[closest_lvl]
 
-        lvl_dims = [self.get_size(wsi, lvl) for lvl in range(len(wsi.pages))]  # Returns size in (height, width) 
+        lvl_dims = [self.get_size(wsi, lvl) for lvl in range(len(wsi.pages))]
         closest_lvl_dim = lvl_dims[closest_lvl]
         closest_lvl_dim = (closest_lvl_dim[1], closest_lvl_dim[0])