removed excessive print statements

PyNutil/coordinate_extraction.py

@@ -118,7 +118,6 @@ def folder_to_atlas_space(
     atlas_labels,
     pixel_id=[0, 0, 0],
     non_linear=True,
-    method="all",
     object_cutoff=0,
     atlas_volume=None,
     use_flat=False,
@@ -194,7 +193,6 @@ def folder_to_atlas_space(
                 centroids_list,
                 region_areas_list,
                 index,
-                method,
                 object_cutoff,
                 atlas_volume,
                 use_flat,
@@ -237,9 +235,7 @@ def folder_to_atlas_space(
 
 def load_segmentation(segmentation_path: str):
     """Load a segmentation from a file."""
-    print(f"working on {segmentation_path}")
     if segmentation_path.endswith(".dzip"):
-        print("Reconstructing dzi")
         return reconstruct_dzi(segmentation_path)
     else:
         return cv2.imread(segmentation_path)
@@ -282,7 +278,6 @@ def get_region_areas(
 def get_transformed_coordinates(
     non_linear,
     slice_dict,
-    method,
     scaled_x,
     scaled_y,
     centroids,
@@ -292,17 +287,15 @@ def get_transformed_coordinates(
 ):
     new_x, new_y, centroids_new_x, centroids_new_y = None, None, None, None
     if non_linear and "markers" in slice_dict:
-        if method in ["per_pixel", "all"] and scaled_x is not None:
+        if scaled_x is not None:
             new_x, new_y = transform_vec(triangulation, scaled_x, scaled_y)
-        if method in ["per_object", "all"] and centroids is not None:
+        if centroids is not None:
             centroids_new_x, centroids_new_y = transform_vec(
                 triangulation, scaled_centroidsX, scaled_centroidsY
             )
     else:
-        if method in ["per_pixel", "all"]:
-            new_x, new_y = scaled_x, scaled_y
-        if method in ["per_object", "all"]:
-            centroids_new_x, centroids_new_y = scaled_centroidsX, scaled_centroidsY
+        new_x, new_y = scaled_x, scaled_y
+        centroids_new_x, centroids_new_y = scaled_centroidsX, scaled_centroidsY
     return new_x, new_y, centroids_new_x, centroids_new_y
 
 
@@ -317,7 +310,6 @@ def segmentation_to_atlas_space(
     centroids_list=None,
     region_areas_list=None,
     index=None,
-    method="per_pixel",
     object_cutoff=0,
     atlas_volume=None,
     use_flat=False,
@@ -346,17 +338,14 @@ def segmentation_to_atlas_space(
     )
     centroids, points = None, None
     scaled_centroidsX, scaled_centroidsY, scaled_x, scaled_y = None, None, None, None
-    if method in ["per_object", "all"]:
-        centroids, scaled_centroidsX, scaled_centroidsY = get_centroids(
-            segmentation, pixel_id, y_scale, x_scale, object_cutoff
-        )
-    if method in ["per_pixel", "all"]:
-        scaled_y, scaled_x = get_scaled_pixels(segmentation, pixel_id, y_scale, x_scale)
+    centroids, scaled_centroidsX, scaled_centroidsY = get_centroids(
+        segmentation, pixel_id, y_scale, x_scale, object_cutoff
+    )
+    scaled_y, scaled_x = get_scaled_pixels(segmentation, pixel_id, y_scale, x_scale)
 
     new_x, new_y, centroids_new_x, centroids_new_y = get_transformed_coordinates(
         non_linear,
         slice_dict,
-        method,
         scaled_x,
         scaled_y,
         centroids,
@@ -364,11 +353,11 @@ def segmentation_to_atlas_space(
         scaled_centroidsY,
         triangulation,
     )
-    if method in ["per_pixel", "all"] and new_x is not None:
+    if new_x is not None:
         points = transform_to_atlas_space(
             slice_dict["anchoring"], new_y, new_x, reg_height, reg_width
         )
-    if method in ["per_object", "all"] and centroids_new_x is not None:
+    if centroids_new_x is not None:
         centroids = transform_to_atlas_space(
             slice_dict["anchoring"],
             centroids_new_y,
@@ -387,9 +376,6 @@ def get_centroids(segmentation, pixel_id, y_scale, x_scale, object_cutoff=0):
     centroids, area, coords = get_centroids_and_area(
         binary_seg, pixel_cut_off=object_cutoff
     )
-
-    print(f"using pixel id {pixel_id}")
-    print(f"Found {len(centroids)} objects in the segmentation")
     if len(centroids) == 0:
         return None, None, None
     centroidsX = centroids[:, 1]

PyNutil/counting_and_load.py

@@ -230,8 +230,7 @@ def flat_to_dataframe(
         image = read_flat_file(file)
     elif file.endswith(".seg"):
         image = read_seg_file(file)
-    print("datatype", image.dtype)
-    print("image shape open", image.shape)
+
 
     if rescaleXY:
         image_shapeY, image_shapeX = image.shape[0], image.shape[1]

PyNutil/main.py

@@ -45,7 +45,7 @@ class PyNutil:
     def _check_atlas_name(self):
         if not self.atlas_name:
             raise ValueError("Atlas name must be specified")
-            
+
     def _load_settings(self, settings_file):
         if settings_file:
             with open(settings_file, "r") as f:
@@ -58,7 +58,6 @@ class PyNutil:
 
     def load_atlas_data(self, atlas_name):
         """Loads the atlas volume and labels from disk."""
-        print("loading atlas volume")
         atlas = brainglobe_atlasapi.BrainGlobeAtlas(atlas_name=atlas_name)
         atlas_structures = {
             "idx": [i["id"] for i in atlas.structures_list],
@@ -79,28 +78,23 @@ class PyNutil:
         return atlas_volume, atlas_labels
 
     def _process_atlas_volume(self, atlas):
-        if "allen_mouse_" in self.atlas_name:
-            print("reorienting allen atlas into quicknii space...")
-            return np.transpose(atlas.annotation, [2, 0, 1])[:, ::-1, ::-1]
-        else:
-            return atlas.annotation
+        print("reorienting brainglobe atlas into quicknii space...")
+        return np.transpose(atlas.annotation, [2, 0, 1])[:, ::-1, ::-1]
+ 
 
     def load_custom_atlas(self, atlas_path, label_path):
         atlas_volume = read_atlas_volume(atlas_path)
         atlas_labels = pd.read_csv(label_path)
         return atlas_volume, atlas_labels
 
-    def get_coordinates(self, non_linear=True, method="all", object_cutoff=0, use_flat=False):
+    def get_coordinates(self, non_linear=True, object_cutoff=0, use_flat=False):
         """Extracts pixel coordinates from the segmentation data."""
-        self._validate_method(method)
-        print("extracting coordinates with method:", method)
         pixel_points, centroids, region_areas_list, points_len, centroids_len, segmentation_filenames = folder_to_atlas_space(
             self.segmentation_folder,
             self.alignment_json,
             self.atlas_labels,
             pixel_id=self.colour,
             non_linear=non_linear,
-            method=method,
             object_cutoff=object_cutoff,
             atlas_volume=self.atlas_volume,
             use_flat=use_flat,
@@ -111,19 +105,14 @@ class PyNutil:
         self.centroids_len = centroids_len
         self.segmentation_filenames = segmentation_filenames
         self.region_areas_list = region_areas_list
-        self.method = method
 
-    def _validate_method(self, method):
-        valid_methods = ["per_pixel", "per_object", "all"]
-        if method not in valid_methods:
-            raise ValueError(f"method {method} not recognised, valid methods are: {', '.join(valid_methods)}")
 
     def quantify_coordinates(self):
         """Quantifies the pixel coordinates by region."""
         self._check_coordinates_extracted()
         print("quantifying coordinates")
-        labeled_points_centroids = self._label_points(self.centroids) if self.method in ["per_object", "all"] else None
-        labeled_points = self._label_points(self.pixel_points) if self.method in ["per_pixel", "all"] else None
+        labeled_points_centroids = self._label_points(self.centroids)
+        labeled_points = self._label_points(self.pixel_points) 
 
         self._quantify_per_section(labeled_points, labeled_points_centroids)
         self._combine_slice_reports()
@@ -146,8 +135,8 @@ class PyNutil:
         per_section_df = []
 
         for pl, cl, ra in zip(self.points_len, self.centroids_len, self.region_areas_list):
-            current_centroids = labeled_points_centroids[prev_cl : prev_cl + cl] if self.method in ["per_object", "all"] else None
-            current_points = labeled_points[prev_pl : prev_pl + pl] if self.method in ["per_pixel", "all"] else None
+            current_centroids = labeled_points_centroids[prev_cl : prev_cl + cl] 
+            current_points = labeled_points[prev_pl : prev_pl + pl] 
             current_df = pixel_count_per_region(current_points, current_centroids, self.atlas_labels)
             current_df_new = self._merge_dataframes(current_df, ra)
             per_section_df.append(current_df_new)
@@ -213,13 +202,9 @@ class PyNutil:
             prev_pl += pl
 
     def _save_per_section_meshview(self, output_folder, split_fn, pl, cl, prev_pl, prev_cl):
-        if self.method in ["per_pixel", "all"]:
             write_points_to_meshview(self.pixel_points[prev_pl : pl + prev_pl], self.labeled_points[prev_pl : pl + prev_pl], f"{output_folder}/per_section_meshview/{split_fn}_pixels.json", self.atlas_labels)
-        if self.method in ["per_object", "all"]:
             write_points_to_meshview(self.centroids[prev_cl : cl + prev_cl], self.labeled_points_centroids[prev_cl : cl + prev_cl], f"{output_folder}/per_section_meshview/{split_fn}_centroids.json", self.atlas_labels)
 
     def _save_whole_series_meshview(self, output_folder):
-        if self.method in ["per_pixel", "all"]:
             write_points_to_meshview(self.pixel_points, self.labeled_points, f"{output_folder}/whole_series_meshview/pixels_meshview.json", self.atlas_labels)
-        if self.method in ["per_object", "all"]:
             write_points_to_meshview(self.centroids, self.labeled_points_centroids, f"{output_folder}/whole_series_meshview/objects_meshview.json", self.atlas_labels)
\ No newline at end of file

tests/test_quantification.py

@@ -34,7 +34,6 @@ class TestQuantification(unittest.TestCase):
         np.testing.assert_array_almost_equal(
             pnt.label_df["region_area"].values, expected_region_area["region_area"].values
         )
-
 test_case_files = [
     "brainglobe_atlas.json"
 ]