add saving to automatic tests and fix bug

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(

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"]

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")