From efde119e7668a5e7be4962eb2fe2b80b5e96c152 Mon Sep 17 00:00:00 2001
From: Sharon Christine Yates <sharoncy@uio.no>
Date: Wed, 3 Apr 2024 11:53:39 +0200
Subject: [PATCH] Add PyNutil_web test
Test dataset from data-proxy bucket
---
test/test10_PyNutil_web.json | 9 +
testOOP.py | 4 +-
test_data/PyNutil_test.json | 285 ++++++++++++++++++
test_data/PyNutil_test.waln | 1 +
.../PyTest_web/segmentations/test_s001.dzip | Bin 0 -> 15377 bytes
.../PyTest_web/segmentations/test_s002.dzip | Bin 0 -> 15377 bytes
.../PyTest_web/segmentations/test_s003.dzip | Bin 0 -> 15377 bytes
.../PyTest_web/segmentations/test_s004.dzip | Bin 0 -> 15377 bytes
.../PyTest_web/segmentations/test_s005.dzip | Bin 0 -> 15377 bytes
9 files changed, 297 insertions(+), 2 deletions(-)
create mode 100644 test/test10_PyNutil_web.json
create mode 100644 test_data/PyNutil_test.json
create mode 100644 test_data/PyNutil_test.waln
create mode 100644 test_data/PyTest_web/segmentations/test_s001.dzip
create mode 100644 test_data/PyTest_web/segmentations/test_s002.dzip
create mode 100644 test_data/PyTest_web/segmentations/test_s003.dzip
create mode 100644 test_data/PyTest_web/segmentations/test_s004.dzip
create mode 100644 test_data/PyTest_web/segmentations/test_s005.dzip
diff --git a/test/test10_PyNutil_web.json b/test/test10_PyNutil_web.json
new file mode 100644
index 0000000..81a2f91
--- /dev/null
+++ b/test/test10_PyNutil_web.json
@@ -0,0 +1,9 @@
+{
+ "volume_path": "allen2017",
+ "label_path": "PyNutil/annotation_volumes/allen2017_colours.csv",
+ "segmentation_folder": "PyNutil/test_data/PyTest_web",
+ "alignment_json": "PyNutil/test_data/PyNutil_test.waln",
+ "nonlinear": true,
+ "colour": [0, 0, 0],
+ "points_json_path": "PyNutil/outputs/test.json"
+}
diff --git a/testOOP.py b/testOOP.py
index 90f075e..03b7a21 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -2,7 +2,7 @@ from PyNutil import PyNutil
import os
os.chdir("..")
-pnt = PyNutil(settings_file=r"PyNutil/test/test9_PyNutil_linear_only.json")
+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)
@@ -10,7 +10,7 @@ pnt.get_coordinates(object_cutoff=0, use_flat=False)
pnt.quantify_coordinates()
-pnt.save_analysis("PyNutil/outputs/test9_PyNutil_linear_noflat_fix")
+pnt.save_analysis("PyNutil/outputs/test10_PyNutil_web")
# remove name, r, g, b, from pixel_
# add to region_areas df
diff --git a/test_data/PyNutil_test.json b/test_data/PyNutil_test.json
new file mode 100644
index 0000000..8b7002d
--- /dev/null
+++ b/test_data/PyNutil_test.json
@@ -0,0 +1,285 @@
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diff --git a/test_data/PyNutil_test.waln b/test_data/PyNutil_test.waln
new file mode 100644
index 0000000..a14a830
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diff --git a/test_data/PyTest_web/segmentations/test_s001.dzip b/test_data/PyTest_web/segmentations/test_s001.dzip
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GitLab