Remove references to manual segmentation (#150)

README.md

@@ -11,7 +11,9 @@
 
 Segmentation of 1/2/3D brain structures in a common anatomical space
 
-`brainglobe-segmentation` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)).
+`brainglobe-segmentation` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing segmentation
+of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain
+region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)).
 `brainglobe-segmentation` is the successor to [`brainreg-segment`](https://github.com/brainglobe/brainreg-segmentation).
 
 `brainglobe-segmentation` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).

brainglobe_segmentation/paths.py

@@ -5,7 +5,7 @@ class Paths:
 
     def __init__(self, brainreg_directory, atlas_space=False):
         self.brainreg_directory = brainreg_directory
-        self.main_directory = self.brainreg_directory / "manual_segmentation"
+        self.main_directory = self.brainreg_directory / "segmentation"
 
         if atlas_space:
             self.segmentation_directory = self.main_directory / "atlas_space"

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "brainglobe-segmentation"
-description = "Manual segmentation of 3D brain structures in a common anatomical space"
+description = "Segmentation of anatomical structures in a common coordinate space"
 readme = "README.md"
 authors = [
     { name = "Adam Tyson, Horst Obenhaus", email = "[email protected]" },

tests/conftest.py

@@ -33,7 +33,7 @@ def segmentation_widget_with_data_atlas_space(tmp_path, segmentation_widget):
     Fixture to load a brainreg directory into the segmentation widget.
     Data is copied to tmpdir so that when it's loaded, so all the paths
     are set correctly.
-    The manual segmentation data is then deleted so that saving/export
+    The segmentation data is then deleted so that saving/export
     can be properly tested
     """
     tmp_input_dir = tmp_path / "brainreg_output"
@@ -44,6 +44,6 @@ def segmentation_widget_with_data_atlas_space(tmp_path, segmentation_widget):
     )
     segmentation_widget.directory = Path(tmp_input_dir)
     segmentation_widget.load_brainreg_directory()
-    # delete manual segmentation data to ensure it's saved correctly in tests
+    # delete segmentation data to ensure it's saved correctly in tests
     shutil.rmtree(segmentation_widget.paths.main_directory)
     return segmentation_widget

tests/tests/test_integration/test_gui/test_gui.py

@@ -100,27 +100,27 @@ def check_defaults(widget):
 
 
 def check_paths(widget):
-    assert widget.paths.main_directory == brainreg_dir / "manual_segmentation"
+    assert widget.paths.main_directory == brainreg_dir / "segmentation"
 
     assert (
         widget.paths.segmentation_directory
-        == brainreg_dir / "manual_segmentation" / "atlas_space"
+        == brainreg_dir / "segmentation" / "atlas_space"
     )
 
     assert (
         widget.paths.regions_directory
-        == brainreg_dir / "manual_segmentation" / "atlas_space" / "regions"
+        == brainreg_dir / "segmentation" / "atlas_space" / "regions"
     )
 
     assert (
         widget.paths.region_summary_csv
         == brainreg_dir
-        / "manual_segmentation"
+        / "segmentation"
         / "atlas_space"
         / "regions"
         / "summary.csv"
     )
     assert (
         widget.paths.tracks_directory
-        == brainreg_dir / "manual_segmentation" / "atlas_space" / "tracks"
+        == brainreg_dir / "segmentation" / "atlas_space" / "tracks"
     )

tests/tests/test_integration/test_gui/test_region_ui_functionality.py

@@ -9,15 +9,15 @@
 
 brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"
 validate_regions_dir = (
-    brainreg_dir / "manual_segmentation" / "atlas_space" / "regions"
+    brainreg_dir / "segmentation" / "atlas_space" / "regions"
 )
 
 
 @pytest.fixture
 def test_regions_dir(tmp_path):
     tmp_input_dir = tmp_path / "brainreg_output"
     test_regions_dir = (
-        tmp_input_dir / "manual_segmentation" / "atlas_space" / "regions"
+        tmp_input_dir / "segmentation" / "atlas_space" / "regions"
     )
     return test_regions_dir
 

tests/tests/test_integration/test_gui/test_track_ui_functionality.py

@@ -6,17 +6,13 @@
 import pytest
 
 brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"
-validate_tracks_dir = (
-    brainreg_dir / "manual_segmentation" / "atlas_space" / "tracks"
-)
+validate_tracks_dir = brainreg_dir / "segmentation" / "atlas_space" / "tracks"
 
 
 @pytest.fixture
 def test_tracks_dir(tmp_path):
     tmp_input_dir = tmp_path / "brainreg_output"
-    test_tracks_dir = (
-        tmp_input_dir / "manual_segmentation" / "atlas_space" / "tracks"
-    )
+    test_tracks_dir = tmp_input_dir / "segmentation" / "atlas_space" / "tracks"
     return test_tracks_dir
 
 

tests/tests/test_unit/test_regions/test_region_analysis.py

@@ -13,7 +13,7 @@
 )
 
 region_image_path = Path(
-    "tests/data/brainreg_output/manual_segmentation/"
+    "tests/data/brainreg_output/segmentation/"
     "sample_space/regions/region_0.tiff"
 )
 atlas_resolution = (50, 50, 50)