From 859c8b82b47718bf7c8c6a807954a2b0e283f2ce Mon Sep 17 00:00:00 2001
From: Sharon Christine Yates <sharoncy@uio.no>
Date: Wed, 3 Apr 2024 14:16:38 +0200
Subject: [PATCH] Fix for "per_pixel"
PyNutil only worked for method = "all". Fix so that it works for "per_pixel" and "per_object".
---
PyNutil/coordinate_extraction.py | 1 +
testOOP.py | 4 +++-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/PyNutil/coordinate_extraction.py b/PyNutil/coordinate_extraction.py
index a459c06..761d01e 100644
--- a/PyNutil/coordinate_extraction.py
+++ b/PyNutil/coordinate_extraction.py
@@ -309,6 +309,7 @@ def segmentation_to_atlas_space(
region_areas = get_region_areas(use_flat, atlas_labels, flat_file_atlas, seg_width, seg_height, slice_dict, atlas_volume, triangulation)
y_scale, x_scale = transform_to_registration(seg_height, seg_width, reg_height, reg_width)
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"]:
diff --git a/testOOP.py b/testOOP.py
index 03b7a21..0cab45c 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -2,11 +2,13 @@ from PyNutil import PyNutil
import os
os.chdir("..")
+
+
pnt = PyNutil(settings_file=r"PyNutil/test/test10_PyNutil_web.json")
##Use flat can be set to True if you want to use the flat file
# instead of the visualign json (this is only useful for testing and will be removed)
-pnt.get_coordinates(object_cutoff=0, use_flat=False)
+pnt.get_coordinates(object_cutoff=0, method="per_pixel")
pnt.quantify_coordinates()
--
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