diff --git a/README.md b/README.md index ca7a5f4..0f548ee 100644 --- a/README.md +++ b/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/). diff --git a/brainglobe_segmentation/paths.py b/brainglobe_segmentation/paths.py index f73ead0..791e011 100644 --- a/brainglobe_segmentation/paths.py +++ b/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" diff --git a/pyproject.toml b/pyproject.toml index a67e1aa..ef8e769 100644 --- a/pyproject.toml +++ b/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 = "code@adamltyson.com" }, diff --git a/tests/conftest.py b/tests/conftest.py index 35dd22d..0000534 100644 --- a/tests/conftest.py +++ b/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 diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/regions/summary.csv b/tests/data/brainreg_output/segmentation/atlas_space/regions/summary.csv similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/regions/summary.csv rename to tests/data/brainreg_output/segmentation/atlas_space/regions/summary.csv diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/regions/test_region.csv b/tests/data/brainreg_output/segmentation/atlas_space/regions/test_region.csv similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/regions/test_region.csv rename to tests/data/brainreg_output/segmentation/atlas_space/regions/test_region.csv diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/regions/test_region.obj b/tests/data/brainreg_output/segmentation/atlas_space/regions/test_region.obj similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/regions/test_region.obj rename to tests/data/brainreg_output/segmentation/atlas_space/regions/test_region.obj diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/regions/test_region.tiff b/tests/data/brainreg_output/segmentation/atlas_space/regions/test_region.tiff similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/regions/test_region.tiff rename to tests/data/brainreg_output/segmentation/atlas_space/regions/test_region.tiff diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/tracks/test_track.csv b/tests/data/brainreg_output/segmentation/atlas_space/tracks/test_track.csv similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/tracks/test_track.csv rename to tests/data/brainreg_output/segmentation/atlas_space/tracks/test_track.csv diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/tracks/test_track.npy b/tests/data/brainreg_output/segmentation/atlas_space/tracks/test_track.npy similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/tracks/test_track.npy rename to tests/data/brainreg_output/segmentation/atlas_space/tracks/test_track.npy diff --git a/tests/data/brainreg_output/manual_segmentation/atlas_space/tracks/test_track.points b/tests/data/brainreg_output/segmentation/atlas_space/tracks/test_track.points similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/atlas_space/tracks/test_track.points rename to tests/data/brainreg_output/segmentation/atlas_space/tracks/test_track.points diff --git a/tests/data/brainreg_output/manual_segmentation/sample_space/regions/region_0.tiff b/tests/data/brainreg_output/segmentation/sample_space/regions/region_0.tiff similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/sample_space/regions/region_0.tiff rename to tests/data/brainreg_output/segmentation/sample_space/regions/region_0.tiff diff --git a/tests/data/brainreg_output/manual_segmentation/sample_space/regions/region_1.tiff b/tests/data/brainreg_output/segmentation/sample_space/regions/region_1.tiff similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/sample_space/regions/region_1.tiff rename to tests/data/brainreg_output/segmentation/sample_space/regions/region_1.tiff diff --git a/tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_0.csv b/tests/data/brainreg_output/segmentation/sample_space/tracks/track_0.csv similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_0.csv rename to tests/data/brainreg_output/segmentation/sample_space/tracks/track_0.csv diff --git a/tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_0.points b/tests/data/brainreg_output/segmentation/sample_space/tracks/track_0.points similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_0.points rename to tests/data/brainreg_output/segmentation/sample_space/tracks/track_0.points diff --git a/tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_1.csv b/tests/data/brainreg_output/segmentation/sample_space/tracks/track_1.csv similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_1.csv rename to tests/data/brainreg_output/segmentation/sample_space/tracks/track_1.csv diff --git a/tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_1.points b/tests/data/brainreg_output/segmentation/sample_space/tracks/track_1.points similarity index 100% rename from tests/data/brainreg_output/manual_segmentation/sample_space/tracks/track_1.points rename to tests/data/brainreg_output/segmentation/sample_space/tracks/track_1.points diff --git a/tests/tests/test_integration/test_gui/test_gui.py b/tests/tests/test_integration/test_gui/test_gui.py index 0e7456c..08de52e 100644 --- a/tests/tests/test_integration/test_gui/test_gui.py +++ b/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" ) diff --git a/tests/tests/test_integration/test_gui/test_region_ui_functionality.py b/tests/tests/test_integration/test_gui/test_region_ui_functionality.py index acc1b7c..354832d 100644 --- a/tests/tests/test_integration/test_gui/test_region_ui_functionality.py +++ b/tests/tests/test_integration/test_gui/test_region_ui_functionality.py @@ -9,7 +9,7 @@ brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output" validate_regions_dir = ( - brainreg_dir / "manual_segmentation" / "atlas_space" / "regions" + brainreg_dir / "segmentation" / "atlas_space" / "regions" ) @@ -17,7 +17,7 @@ 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 diff --git a/tests/tests/test_integration/test_gui/test_track_ui_functionality.py b/tests/tests/test_integration/test_gui/test_track_ui_functionality.py index 6b72308..3bd094a 100644 --- a/tests/tests/test_integration/test_gui/test_track_ui_functionality.py +++ b/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 diff --git a/tests/tests/test_unit/test_regions/test_region_analysis.py b/tests/tests/test_unit/test_regions/test_region_analysis.py index d46efff..93dd4b5 100644 --- a/tests/tests/test_unit/test_regions/test_region_analysis.py +++ b/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)