From 94901c00ea1aeff5900025bfdf62865c0001abe8 Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Fri, 25 Oct 2024 10:08:59 +0200
Subject: [PATCH] Minor updates to testing file
Updated the workflow for running a test using a custom atlas
---
.gitignore | 3 +++
...custom_atlases.py => basic_example_custom_atlas.py} | 10 ++++++----
2 files changed, 9 insertions(+), 4 deletions(-)
rename workflows/{loading_custom_atlases.py => basic_example_custom_atlas.py} (66%)
diff --git a/.gitignore b/.gitignore
index adadd6b..67b99dd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -161,3 +161,6 @@ cython_debug/
#inputs
+
+#outputs
+test_result/
diff --git a/workflows/loading_custom_atlases.py b/workflows/basic_example_custom_atlas.py
similarity index 66%
rename from workflows/loading_custom_atlases.py
rename to workflows/basic_example_custom_atlas.py
index ca4fb16..a4f8335 100644
--- a/workflows/loading_custom_atlases.py
+++ b/workflows/basic_example_custom_atlas.py
@@ -9,15 +9,17 @@ from PyNutil import PyNutil
###The segmentations should be images which come out of ilastix, segmenting an object of interest
###The alignment json should be out of DeepSlice, QuickNII, or VisuAlign, it defines the sections position in an atlas
###The colour says which colour is the object you want to quantify in your segmentation. It is defined in RGB
-###Finally the atlas name is the relevant atlas from brainglobe_atlasapi you wish to use in Quantification.
+###The atlas_path is the path to the relevant atlas.nrrd
+###The label_path is the path to the corresponding atlas .csv
+###The object_cutoff is a cut-off for min object size
pnt = PyNutil(
segmentation_folder="../tests/test_data/nonlinear_allen_mouse/",
alignment_json="../tests/test_data/nonlinear_allen_mouse/alignment.json",
colour=[0, 0, 0],
- atlas_path="/mnt/z/HBP_analytics/PyNutil/metadata/annotation_volumes/annotation_25_reoriented_2017.nrrd",
- label_path="/mnt/z/HBP_analytics/PyNutil/metadata/annotation_volumes/allen2017_colours.csv",
+ atlas_path="../tests/test_data/allen_mouse_2017_atlas/annotation_25_reoriented_2017.nrrd",
+ label_path="../tests/test_data/allen_mouse_2017_atlas//allen2017_colours.csv",
)
pnt.get_coordinates(object_cutoff=0)
pnt.quantify_coordinates()
-pnt.save_analysis("../demo_data/PyNutil_nonlinear_noflat_custom")
+pnt.save_analysis("../demo_data/test_nonlinear_allen_mouse")
--
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