From f387206645a5f74998d817727310a5c671df143f Mon Sep 17 00:00:00 2001
From: Sharon Christine Yates <sharoncy@uio.no>
Date: Mon, 25 Mar 2024 10:03:31 +0100
Subject: [PATCH] Update testing files
---
test/test8_PyNutil_bigcaudoputamen.json | 9 +++++++++
test/test8_PyNutil_fixed.json | 8 --------
testOOP.py | 6 +++---
3 files changed, 12 insertions(+), 11 deletions(-)
create mode 100644 test/test8_PyNutil_bigcaudoputamen.json
delete mode 100644 test/test8_PyNutil_fixed.json
diff --git a/test/test8_PyNutil_bigcaudoputamen.json b/test/test8_PyNutil_bigcaudoputamen.json
new file mode 100644
index 0000000..f790fdf
--- /dev/null
+++ b/test/test8_PyNutil_bigcaudoputamen.json
@@ -0,0 +1,9 @@
+{
+ "volume_path": "allen2017",
+ "label_path": "PyNutil/annotation_volumes/allen2017_colours.csv",
+ "segmentation_folder": "PyNutil/test_data/PyTest_seg",
+ "alignment_json": "PyNutil/test_data/PyNutil_testdataset_Nonlin_SY_fixed_bigcaudoputamen.json",
+ "nonlinear": true,
+ "colour": [0, 0, 0],
+ "points_json_path": "PyNutil/outputs/test8_PyNutil.json"
+}
diff --git a/test/test8_PyNutil_fixed.json b/test/test8_PyNutil_fixed.json
deleted file mode 100644
index 4b2d6a1..0000000
--- a/test/test8_PyNutil_fixed.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{ "volume_path": "allen2017",
- "label_path": "PyNutil/annotation_volumes/allen2017_colours.csv",
- "segmentation_folder": "PyNutil/test_data/PyTest_seg",
- "alignment_json": "PyNutil/test_data/PyNutil_testdataset_Nonlin_SY_fixed_bigcaudoputamen.json",
- "nonlinear": true,
- "colour": [0, 0, 0],
- "points_json_path": "PyNutil/outputs/test8_PyNutil_use_flat.json"
-}
\ No newline at end of file
diff --git a/testOOP.py b/testOOP.py
index ab1365d..4b752b1 100644
--- a/testOOP.py
+++ b/testOOP.py
@@ -1,13 +1,13 @@
from PyNutil import PyNutil
-pnt = PyNutil(settings_file=r"PyNutil/test/test8_PyNutil_fixed.json")
+pnt = PyNutil(settings_file=r"PyNutil/test/test8_PyNutil_bigcaudoputamen.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=True)
+pnt.get_coordinates(object_cutoff=0, use_flat=False)
pnt.quantify_coordinates()
-pnt.save_analysis("PyNutil/outputs/test8_PyNutil_bigcaudoputamen_newatlasmaps")
+pnt.save_analysis("PyNutil/outputs/test8_PyNutil_bigcaudoputamen_noflat")
# remove name, r, g, b, from pixel_
# add to region_areas df
--
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