Standardise use of atlas vs standard space

brainreg_segment/napari.yaml

@@ -0,0 +1,11 @@
+name: brainreg-segment
+schema_version: 0.1.0
+contributions:
+  commands:
+  - id: brainreg-segment.SegmentationWidget
+    title: Open segmentation widget
+    python_name: brainreg_segment.segment:SegmentationWidget
+
+  widgets:
+  - command: brainreg-segment.SegmentationWidget
+    display_name: Region/track segmentation

brainreg_segment/paths.py

@@ -3,23 +3,14 @@ class Paths:
     A single class to hold all file paths that may be used.
     """
 
-    def __init__(
-        self, brainreg_directory, standard_space=True, atlas_space=False
-    ):
+    def __init__(self, brainreg_directory, atlas_space=False):
         self.brainreg_directory = brainreg_directory
         self.main_directory = self.brainreg_directory / "manual_segmentation"
 
         if atlas_space:
             self.segmentation_directory = self.main_directory / "atlas_space"
         else:
-            if standard_space:
-                self.segmentation_directory = (
-                    self.main_directory / "standard_space"
-                )
-            else:
-                self.segmentation_directory = (
-                    self.main_directory / "sample_space"
-                )
+            self.segmentation_directory = self.main_directory / "sample_space"
 
         self.regions_directory = self.join_seg_files("regions")
         self.region_summary_csv = self.regions_directory / "summary.csv"

brainreg_segment/segment.py

@@ -193,7 +193,7 @@ def add_loading_panel(self, row, column=0):
         self.load_button = add_button(
             "Load project (sample space)",
             self.load_data_layout,
-            self.load_brainreg_directory_sample,
+            self.load_brainreg_directory_sample_space,
             row=0,
             column=0,
             visibility=False,
@@ -205,10 +205,10 @@ def add_loading_panel(self, row, column=0):
             "the orientation of your chosen atlas.",
         )
 
-        self.load_button_standard = add_button(
+        self.load_button_atlas_space = add_button(
             "Load project (atlas space)",
             self.load_data_layout,
-            self.load_brainreg_directory_standard,
+            self.load_brainreg_directory_atlas_space,
             row=1,
             column=0,
             visibility=False,
@@ -229,7 +229,7 @@ def add_loading_panel(self, row, column=0):
         #  buttons made visible after adding to main widget, preventing them
         # from briefly appearing in a separate window
         self.load_button.setVisible(True)
-        self.load_button_standard.setVisible(True)
+        self.load_button_atlas_space.setVisible(True)
 
     def add_saving_panel(self, row):
         """
@@ -349,7 +349,7 @@ def load_atlas(self):
             opacity=0.3,
             visible=False,
         )
-        self.standard_space = True
+        self.atlas_space = True
         self.prevent_layer_edit()
 
     def reset_atlas_menu(self):
@@ -360,25 +360,23 @@ def reset_atlas_menu(self):
 
     # BRAINREG INTERACTION #################################################
 
-    def load_brainreg_directory_sample(self):
-        self.get_brainreg_directory(standard_space=False)
+    def load_brainreg_directory_sample_space(self):
+        self.get_brainreg_directory(atlas_space=False)
 
-    def load_brainreg_directory_standard(self):
-        self.get_brainreg_directory(standard_space=True)
+    def load_brainreg_directory_atlas_space(self):
+        self.get_brainreg_directory(atlas_space=True)
 
-    def get_brainreg_directory(self, standard_space):
+    def get_brainreg_directory(self, atlas_space):
         """
         Shows file dialog to choose output directory
         and sets global directory info
         """
-        if standard_space:
-            self.plugin = (
-                "brainglobe-napari-io.brainreg_read_dir_standard_space"
-            )
-            self.standard_space = True
+        if atlas_space:
+            self.plugin = "brainglobe-napari-io.brainreg_read_dir_atlas_space"
+            self.atlas_space = True
         else:
             self.plugin = "brainglobe-napari-io.brainreg_read_dir"
-            self.standard_space = False
+            self.atlas_space = False
 
         self.status_label.setText("Loading...")
         options = QFileDialog.Options()
@@ -415,7 +413,7 @@ def load_brainreg_directory(self):
             self.viewer.open(str(self.directory), plugin=self.plugin)
             self.paths = Paths(
                 self.directory,
-                standard_space=self.standard_space,
+                atlas_space=self.atlas_space,
             )
             self.initialise_loaded_data()
         except ValueError:
@@ -443,7 +441,7 @@ def initialise_loaded_data(self):
         self.metadata = self.base_layer.metadata
         self.atlas = self.metadata["atlas_class"]
         self.annotations_layer = self.viewer.layers[self.metadata["atlas"]]
-        if self.standard_space:
+        if self.atlas_space:
             self.hemispheres_data = self.atlas.hemispheres
         else:
             self.hemispheres_layer = self.viewer.layers[
@@ -497,7 +495,7 @@ def initialise_segmentation_interface(self):
         self.initialise_image_view()
         self.save_data_panel.setVisible(True)
         self.save_button.setVisible(True)
-        self.export_button.setVisible(self.standard_space)
+        self.export_button.setVisible(self.atlas_space)
         self.show_regionseg_button.setEnabled(True)
         self.show_trackseg_button.setEnabled(True)
         self.status_label.setText("Ready")

pyproject.toml

@@ -19,7 +19,7 @@ classifiers = [
 ]
 requires-python = ">=3.7"
 dependencies = [
-    "brainglobe-napari-io",
+    "brainglobe-napari-io >= 0.3.0",
     "dask >= 2.15.0",
     "imio",
     "brainglobe-utils",
@@ -52,6 +52,8 @@ dev = [
     "napari-time-slicer" # to test non ndarray-types
 ]
 
+[project.entry-points."napari.manifest"]
+cellfinder-napari = "brainreg_segment:napari.yaml"
 
 [project.scripts]
 brainreg-segment = "brainreg_segment.segment:main"

tests/conftest.py

@@ -38,9 +38,9 @@ def segmentation_widget_with_data_atlas_space(tmp_path, segmentation_widget):
     """
     tmp_input_dir = tmp_path / "brainreg_output"
     shutil.copytree(brainreg_dir, tmp_input_dir)
-    segmentation_widget.standard_space = True
+    segmentation_widget.atlas_space = True
     segmentation_widget.plugin = (
-        "brainglobe-napari-io.brainreg_read_dir_standard_space"
+        "brainglobe-napari-io.brainreg_read_dir_atlas_space"
     )
     segmentation_widget.directory = Path(tmp_input_dir)
     segmentation_widget.load_brainreg_directory()

tests/tests/test_integration/test_gui/test_gui.py

@@ -8,23 +8,23 @@
 
 
 def test_load_sample_space(segmentation_widget):
-    segmentation_widget.standard_space = False
+    segmentation_widget.atlas_space = False
     segmentation_widget.plugin = "brainglobe-napari-io.brainreg_read_dir"
     segmentation_widget.directory = brainreg_dir
     segmentation_widget.load_brainreg_directory()
     check_loaded_layers(segmentation_widget, 7)
-    check_not_editable(segmentation_widget, standard_space=False)
+    check_not_editable(segmentation_widget, atlas_space=False)
 
 
-def test_load_standard_space(segmentation_widget):
-    segmentation_widget.standard_space = True
+def test_load_atlas_space(segmentation_widget):
+    segmentation_widget.atlas_space = True
     segmentation_widget.plugin = (
-        "brainglobe-napari-io.brainreg_read_dir_standard_space"
+        "brainglobe-napari-io.brainreg_read_dir_atlas_space"
     )
     segmentation_widget.directory = brainreg_dir
     segmentation_widget.load_brainreg_directory()
     check_loaded_layers(segmentation_widget, 4)
-    check_not_editable(segmentation_widget, standard_space=True)
+    check_not_editable(segmentation_widget, atlas_space=True)
 
 
 def test_layer_deletion(segmentation_widget):
@@ -35,7 +35,7 @@ def test_layer_deletion(segmentation_widget):
     assert len(segmentation_widget.viewer.layers) == 0
     segmentation_widget.viewer.add_points(np.array([[1, 1], [2, 2]]))
     assert len(segmentation_widget.viewer.layers) == 1
-    segmentation_widget.standard_space = False
+    segmentation_widget.atlas_space = False
     segmentation_widget.plugin = "brainglobe-napari-io.brainreg_read_dir"
     segmentation_widget.directory = brainreg_dir
     segmentation_widget.load_brainreg_directory()
@@ -51,10 +51,10 @@ def check_loaded_layers(widget, num_layers):
     assert widget.annotations_layer.name == widget.atlas.atlas_name
 
 
-def check_not_editable(widget, standard_space=False):
+def check_not_editable(widget, atlas_space=False):
     assert widget.base_layer.editable is False
     assert widget.annotations_layer.editable is False
-    if not standard_space:
+    if not atlas_space:
         assert widget.viewer.layers["Hemispheres"].editable is False
 
 
@@ -72,9 +72,9 @@ def test_load_atlas(segmentation_widget, tmp_path):
 
 
 def test_general(segmentation_widget):
-    segmentation_widget.standard_space = True
+    segmentation_widget.atlas_space = True
     segmentation_widget.plugin = (
-        "brainglobe-napari-io.brainreg_read_dir_standard_space"
+        "brainglobe-napari-io.brainreg_read_dir_atlas_space"
     )
     segmentation_widget.directory = brainreg_dir
     segmentation_widget.load_brainreg_directory()
@@ -104,23 +104,23 @@ def check_paths(widget):
 
     assert (
         widget.paths.segmentation_directory
-        == brainreg_dir / "manual_segmentation" / "standard_space"
+        == brainreg_dir / "manual_segmentation" / "atlas_space"
     )
 
     assert (
         widget.paths.regions_directory
-        == brainreg_dir / "manual_segmentation" / "standard_space" / "regions"
+        == brainreg_dir / "manual_segmentation" / "atlas_space" / "regions"
     )
 
     assert (
         widget.paths.region_summary_csv
         == brainreg_dir
         / "manual_segmentation"
-        / "standard_space"
+        / "atlas_space"
         / "regions"
         / "summary.csv"
     )
     assert (
         widget.paths.tracks_directory
-        == brainreg_dir / "manual_segmentation" / "standard_space" / "tracks"
+        == brainreg_dir / "manual_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" / "standard_space" / "regions"
+    brainreg_dir / "manual_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" / "standard_space" / "regions"
+        tmp_input_dir / "manual_segmentation" / "atlas_space" / "regions"
     )
     return test_regions_dir
 

tests/tests/test_integration/test_gui/test_track_ui_functionality.py

@@ -7,15 +7,15 @@
 
 brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"
 validate_tracks_dir = (
-    brainreg_dir / "manual_segmentation" / "standard_space" / "tracks"
+    brainreg_dir / "manual_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" / "standard_space" / "tracks"
+        tmp_input_dir / "manual_segmentation" / "atlas_space" / "tracks"
     )
     return test_tracks_dir