From 215e4325ebe7990c1285fd49ee3cded2c123298e Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Wed, 23 Oct 2024 21:56:15 +0200
Subject: [PATCH] add saving to automatic tests and fix bug
---
PyNutil/io/file_operations.py | 2 +-
tests/test_quantification.py | 2 ++
workflows/using_transform_jsons.py | 7 +++++--
3 files changed, 8 insertions(+), 3 deletions(-)
diff --git a/PyNutil/io/file_operations.py b/PyNutil/io/file_operations.py
index ac81ef4..41226a4 100644
--- a/PyNutil/io/file_operations.py
+++ b/PyNutil/io/file_operations.py
@@ -115,7 +115,7 @@ def _save_per_section_meshview(
write_points_to_meshview(
pixel_points[prev_pl : pl + prev_pl],
labeled_points[prev_pl : pl + prev_pl],
- f"{output_folder}/per_section_meshview/{split}_pixels.json",
+ f"{output_folder}/per_section_meshview/{split_fn}_pixels.json",
atlas_labels,
)
write_points_to_meshview(
diff --git a/tests/test_quantification.py b/tests/test_quantification.py
index 79c9fd5..da1cbd8 100644
--- a/tests/test_quantification.py
+++ b/tests/test_quantification.py
@@ -37,6 +37,8 @@ class TestQuantification(unittest.TestCase):
pnt.label_df["region_area"].values,
expected_region_area["region_area"].values,
)
+ save_path = os.path.join(self.test_case_dir, "..", "demo_data", "outputs")
+ pnt.save_analysis(save_path)
test_case_files = ["brainglobe_atlas.json", "custom_atlas.json"]
diff --git a/workflows/using_transform_jsons.py b/workflows/using_transform_jsons.py
index a559ba7..5077d9f 100644
--- a/workflows/using_transform_jsons.py
+++ b/workflows/using_transform_jsons.py
@@ -10,9 +10,12 @@ from PyNutil import PyNutil
###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.
+"""we must run this from the parent dir as the file has releative imports"""
+os.chdir('..')
+
pnt = PyNutil(
- settings_file=r"/home/harryc/github/PyNutil/tests/test_jsons/test6_artifical.json"
+ settings_file=r"tests/test_cases/brainglobe_atlas.json"
)
pnt.get_coordinates(object_cutoff=0)
pnt.quantify_coordinates()
-pnt.save_analysis("../tests/outputs/PyNutil_nonlinear_noflat")
+pnt.save_analysis("demo_data/PyNutil_nonlinear_noflat")
--
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