From 621821be85475d30b3c11c1d09de4e0bf5d4721f Mon Sep 17 00:00:00 2001
From: sharoncy <s.c.yates@medisin.uio.no>
Date: Fri, 25 Oct 2024 13:02:55 +0200
Subject: [PATCH] Add test_dataset
---
.../linear_allen_mouse/alignment_linear.json | 6 ++++++
.../segmentations/test_s001.png | Bin 0 -> 6768 bytes
.../segmentations/test_s002.png | Bin 0 -> 6768 bytes
.../segmentations/test_s003.png | Bin 0 -> 6768 bytes
.../segmentations/test_s004.png | Bin 0 -> 6768 bytes
.../segmentations/test_s005.png | Bin 0 -> 6768 bytes
workflows/basic_example_custom_atlas.py | 6 +++---
7 files changed, 9 insertions(+), 3 deletions(-)
create mode 100644 tests/test_data/linear_allen_mouse/alignment_linear.json
create mode 100644 tests/test_data/linear_allen_mouse/segmentations/test_s001.png
create mode 100644 tests/test_data/linear_allen_mouse/segmentations/test_s002.png
create mode 100644 tests/test_data/linear_allen_mouse/segmentations/test_s003.png
create mode 100644 tests/test_data/linear_allen_mouse/segmentations/test_s004.png
create mode 100644 tests/test_data/linear_allen_mouse/segmentations/test_s005.png
diff --git a/tests/test_data/linear_allen_mouse/alignment_linear.json b/tests/test_data/linear_allen_mouse/alignment_linear.json
new file mode 100644
index 0000000..9c56aa0
--- /dev/null
+++ b/tests/test_data/linear_allen_mouse/alignment_linear.json
@@ -0,0 +1,6 @@
+{"name":"PyNutil_testdataset","target":"ABA_Mouse_CCFv3_2017_25um.cutlas","target-resolution":[456.0, 528.0, 320.0],"slices":[
+{"filename":"test_s001.png","nr":1,"width":1500,"height":1000,"anchoring":[-5.145275115966797, 361.8014440433213, 331.1490739071843, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]},
+{"filename":"test_s002.png","nr":2,"width":1500,"height":1000,"anchoring":[-3.8589563369750977, 318.7157039711191, 340.24552914037605, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]},
+{"filename":"test_s003.png","nr":3,"width":1500,"height":1000,"anchoring":[-2.8942172527313232, 275.6299638989171, 350.0189942541106, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]},
+{"filename":"test_s004.png","nr":4,"width":1500,"height":1000,"anchoring":[-3.0282087922096252, 232.54422382671487, 364.1366059225139, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]},
+{"filename":"test_s005.png","nr":5,"width":1500,"height":1000,"anchoring":[-0.6163610816001892, 189.45848375451277, 374.2485759765199, 456.0, 0.0, 0.0, 0.0, 0.0, -320.0]}]}
\ No newline at end of file
diff --git a/tests/test_data/linear_allen_mouse/segmentations/test_s001.png b/tests/test_data/linear_allen_mouse/segmentations/test_s001.png
new file mode 100644
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diff --git a/tests/test_data/linear_allen_mouse/segmentations/test_s002.png b/tests/test_data/linear_allen_mouse/segmentations/test_s002.png
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diff --git a/workflows/basic_example_custom_atlas.py b/workflows/basic_example_custom_atlas.py
index a4f8335..5d9b9ed 100644
--- a/workflows/basic_example_custom_atlas.py
+++ b/workflows/basic_example_custom_atlas.py
@@ -14,12 +14,12 @@ from PyNutil import PyNutil
###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",
+ segmentation_folder="../tests/test_data/linear_allen_mouse/",
+ alignment_json="../tests/test_data/linear_allen_mouse/alignment_linear.json",
colour=[0, 0, 0],
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/test_nonlinear_allen_mouse")
+pnt.save_analysis("../test_result/test_linear_allen_mouse")
--
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