From c2a6b684bdf245260d7092bf0388c3d6702ec9fd Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Fri, 26 May 2023 13:45:21 +0200
Subject: [PATCH] now saves objects to meshview as well" "
---
PyNutil/coordinate_extraction.py | 10 +++++----
PyNutil/main.py | 36 ++++++++++++++++++++------------
testOOP.py | 2 +-
3 files changed, 30 insertions(+), 18 deletions(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index c220e82..d16ae6f 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -84,7 +84,7 @@ def transform_to_atlas_space(anchoring, y, x, reg_height, reg_width):
# related to coordinate extraction
# This function returns an array of points
def folder_to_atlas_space(
- folder, quint_alignment, pixel_id=[0, 0, 0], non_linear=True, method="all"
+ folder, quint_alignment, pixel_id=[0, 0, 0], non_linear=True, method="all", object_cutoff=0
):
"""Apply Segmentation to atlas space to all segmentations in a folder."""
@@ -118,6 +118,7 @@ def folder_to_atlas_space(
centroids_list,
index,
method,
+ object_cutoff
),
)
threads.append(x)
@@ -145,6 +146,7 @@ def segmentation_to_atlas_space(
centroids_list=None,
index=None,
method="per_pixel",
+ object_cutoff=0
):
"""Combines many functions to convert a segmentation to atlas space. It takes care
of deformations."""
@@ -170,7 +172,7 @@ def segmentation_to_atlas_space(
centroids, points = None, None
if method in ["per_object", "all"]:
centroids, scaled_centroidsX, scaled_centroidsY = get_centroids(
- segmentation, pixel_id, y_scale, x_scale
+ segmentation, pixel_id, y_scale, x_scale, object_cutoff
)
print("Number of objects: ", len(scaled_centroidsY))
if method in ["per_pixel", "all"]:
@@ -212,10 +214,10 @@ def segmentation_to_atlas_space(
centroids_list[index] = np.array(centroids)
-def get_centroids(segmentation, pixel_id, y_scale, x_scale):
+def get_centroids(segmentation, pixel_id, y_scale, x_scale, object_cutoff=0):
binary_seg = segmentation == pixel_id
binary_seg = np.all(binary_seg, axis=2)
- centroids, area, coords = get_centroids_and_area(binary_seg, pixel_cut_off=0)
+ centroids, area, coords = get_centroids_and_area(binary_seg, pixel_cut_off=object_cutoff)
centroidsY = centroids[:, 1]
centroidsX = centroids[:, 0]
scaled_centroidsY, scaled_centroidsX = scale_positions(
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 2a2ea71..97ebdd4 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -132,7 +132,7 @@ class PyNutil:
print("atlas labels loaded ✅")
return atlas_volume, atlas_labels
- def get_coordinates(self, non_linear=True, method="all"):
+ def get_coordinates(self, non_linear=True, method="all", object_cutoff=0):
"""Extracts pixel coordinates from the segmentation data.
Parameters
@@ -142,6 +142,8 @@ class PyNutil:
method : str, optional
The method to use for extracting coordinates. Valid options are 'per_pixel', 'per_object', or 'all'.
Default is 'all'.
+ object_cutoff : int, optional
+ The minimum number of pixels per object to be included in the analysis. Default is 1.
Raises
------
@@ -164,6 +166,7 @@ class PyNutil:
pixel_id=self.colour,
non_linear=non_linear,
method=method,
+ object_cutoff=object_cutoff,
)
self.pixel_points = pixel_points
self.centroids = centroids
@@ -201,6 +204,7 @@ class PyNutil:
labeled_points, labeled_points_centroids, self.atlas_labels
)
self.labeled_points = labeled_points
+ self.labeled_points_centroids = labeled_points_centroids
print("quantification complete ✅")
@@ -224,22 +228,28 @@ class PyNutil:
if not hasattr(self, "pixel_points"):
raise ValueError("Please run get_coordinates before running save_analysis")
-
- self.label_df.to_csv(
- output_folder + "/counts.csv", sep=";", na_rep="", index=False
- )
-
if not hasattr(self, "label_df"):
print("no quantification found so we will only save the coordinates")
print(
"if you want to save the quantification please run quantify_coordinates"
)
- else:
- write_points_to_meshview(
- self.pixel_points,
- self.labeled_points,
- output_folder + "/pixels_meshview.json",
- self.atlas_labels,
- )
+ self.label_df.to_csv(
+ output_folder + "/counts.csv", sep=";", na_rep="", index=False
+ )
+
+
+
+ write_points_to_meshview(
+ self.pixel_points,
+ self.labeled_points,
+ output_folder + "/pixels_meshview.json",
+ self.atlas_labels,
+ )
+ write_points_to_meshview(
+ self.centroids,
+ self.labeled_points_centroids,
+ output_folder + "/objects_meshview.json",
+ self.atlas_labels,
+ )
print("analysis saved ✅")
diff --git a/testOOP.py b/testOOP.py
index 617dcf7..fe5173a 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -3,7 +3,7 @@ from PyNutil import PyNutil
pnt = PyNutil(settings_file=r"test/test4_2017.json")
# pnt.build_quantifier()
-pnt.get_coordinates()
+pnt.get_coordinates(object_cutoff=0)
pnt.quantify_coordinates()
--
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