From c5a041f6b340aed57e1999999021627b8e2e17f4 Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Wed, 23 Oct 2024 20:18:20 +0200
Subject: [PATCH] removed excessive print statements
---
PyNutil/coordinate_extraction.py | 34 ++++++++++----------------------
PyNutil/counting_and_load.py | 3 +--
PyNutil/main.py | 33 +++++++++----------------------
tests/test_quantification.py | 1 -
4 files changed, 20 insertions(+), 51 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index 0b1e54b..3f29d1b 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/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]
diff --git a/PyNutil/counting_and_load.py b/PyNutil/counting_and_load.py
index ae09ecf..c678c9a 100644
--- a/PyNutil/counting_and_load.py
+++ b/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]
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 0b700a4..03ee539 100644
--- a/PyNutil/main.py
+++ b/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
diff --git a/tests/test_quantification.py b/tests/test_quantification.py
index 8bc8740..b9ddf55 100644
--- a/tests/test_quantification.py
+++ b/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"
]
--
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