From f6343ca948f9d9697cb414ec779ab00361ca0ca6 Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Fri, 26 May 2023 22:24:48 +0200
Subject: [PATCH] removed superflous print statements
---
PyNutil/coordinate_extraction.py | 12 +++---------
PyNutil/counting_and_load.py | 16 ++++++++--------
PyNutil/generate_target_slice.py | 1 -
PyNutil/main.py | 1 -
4 files changed, 11 insertions(+), 19 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index a2a4d8d..5df3143 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -138,14 +138,7 @@ def folder_to_atlas_space(
points_len = [len(points) for points in points_list]
centroids_len = [len(centroids) for centroids in centroids_list]
points = np.concatenate(points_list)
- print("points shape: ",points.shape)
centroids = np.concatenate(centroids_list)
- print("centroids shape: ",centroids.shape)
- print("Number of points: ", len(points))
- print("Number of centroids: ", len(centroids))
- print("points_len: ", points_len)
- print("points: ", points)
- print("points first: ", points[0])
return (
np.array(points),
@@ -195,7 +188,6 @@ def segmentation_to_atlas_space(
)
if method in ["per_pixel", "all"]:
scaled_y, scaled_x = get_scaled_pixels(segmentation, pixel_id, y_scale, x_scale)
- print(f"{segmentation_path} \nNumber of objects: {len(scaled_centroidsY)}\nNumber of pixels: {len(scaled_y)}")
if non_linear:
if "markers" in slice:
@@ -229,7 +221,9 @@ def segmentation_to_atlas_space(
centroids = transform_to_atlas_space(
slice["anchoring"], centroids_new_y, centroids_new_x, reg_height, reg_width
)
- print(f"Finished and points len is: {len(points)} and centroids len is: {len(centroids)}")
+ print(
+ f"Finished and points len is: {len(points)} and centroids len is: {len(centroids)}"
+ )
points_list[index] = np.array(points)
centroids_list[index] = np.array(centroids)
diff --git a/PyNutil/counting_and_load.py b/PyNutil/counting_and_load.py
index 1d2dfdd..2c7b46e 100644
--- a/PyNutil/counting_and_load.py
+++ b/PyNutil/counting_and_load.py
@@ -17,23 +17,23 @@ def label_points(points, label_volume, scale_factor=1):
x = points[:, 0]
y = points[:, 1]
z = points[:, 2]
- print(x[0], y[0], z[0])
- #make sure the points are within the volume
+ # make sure the points are within the volume
x[x < 0] = 0
y[y < 0] = 0
z[z < 0] = 0
- mask = (x > label_volume.shape[0] - 1) | (y > label_volume.shape[1] - 1) | (z > label_volume.shape[2] - 1)
+ mask = (
+ (x > label_volume.shape[0] - 1)
+ | (y > label_volume.shape[1] - 1)
+ | (z > label_volume.shape[2] - 1)
+ )
x[mask] = 0
y[mask] = 0
z[mask] = 0
- print('total mask: ')
- print(np.sum(mask))
+
# Get the label value for each point
- print(x[0], y[0], z[0])
labels = label_volume[x, y, z]
- print('label sum: ')
- print(np.sum(labels))
+
return labels
diff --git a/PyNutil/generate_target_slice.py b/PyNutil/generate_target_slice.py
index 2968338..074fcca 100644
--- a/PyNutil/generate_target_slice.py
+++ b/PyNutil/generate_target_slice.py
@@ -7,7 +7,6 @@ def generate_target_slice(alignment, volume):
bounds = [455, 527, 319]
X_size = np.sqrt(np.sum(np.square((Ux, Uy, Uz))))
Z_size = np.sqrt(np.sum(np.square((Vx, Vy, Vz))))
- print(X_size, Z_size)
X_size = np.round(X_size).astype(int)
Z_size = np.round(Z_size).astype(int)
# make this into a grid (0,0) to (320,456)
diff --git a/PyNutil/main.py b/PyNutil/main.py
index c65c8a8..b494488 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -272,7 +272,6 @@ class PyNutil:
self.segmentation_filenames,
self.per_section_df,
):
-
split_fn = fn.split("/")[-1].split(".")[0]
df.to_csv(
f"{output_folder}/per_section_reports/{split_fn}.csv",
--
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