Warn user if data segmented in a different coordinate space (#107)

* Warn user if data segmented in a different coordinate space

* Add draft (failing) test

* Add simpler test

* rename test file

* Add warnings about different coordinate spaces

* Update tests/conftest.py

Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>

---------

Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>

brainreg_segment/segmentation_panels/regions.py

@@ -196,25 +196,52 @@ def run_region_analysis(self, override=False):
                 choice = display_warning(
                     self.parent,
                     "About to analyse regions",
+                    "Please ensure the regions were segmented in the same "
+                    "reference space as the currently open image. "
                     "Existing files will be will be deleted. Proceed?",
                 )
             else:
                 choice = True  # for debugging
 
             if choice:
                 print("Running region analysis")
-                worker = region_analysis(
+
+                if check_segmentation_in_correct_space(
                     self.parent.label_layers,
                     self.parent.annotations_layer.data,
-                    self.parent.atlas,
-                    self.parent.hemispheres_data,
-                    self.parent.paths.regions_directory,
-                    output_csv_file=self.parent.paths.region_summary_csv,
-                    volumes=self.calculate_volumes_checkbox.isChecked(),
-                    summarise=self.summarise_volumes_checkbox.isChecked(),
-                )
-                worker.start()
+                ):
+                    worker = region_analysis(
+                        self.parent.label_layers,
+                        self.parent.annotations_layer.data,
+                        self.parent.atlas,
+                        self.parent.hemispheres_data,
+                        self.parent.paths.regions_directory,
+                        output_csv_file=self.parent.paths.region_summary_csv,
+                        volumes=self.calculate_volumes_checkbox.isChecked(),
+                        summarise=self.summarise_volumes_checkbox.isChecked(),
+                    )
+                    worker.start()
+                else:
+                    display_incorrect_space_warning(self.parent)
+                    return
             else:
                 print("Preventing analysis as user chose 'Cancel'")
         else:
             print("No regions found")
+
+
+def check_segmentation_in_correct_space(label_layers, annotations_layer_image):
+    for label_layer in label_layers:
+        if label_layer.data.shape != annotations_layer_image.shape:
+            return False
+    return True
+
+
+def display_incorrect_space_warning(widget):
+    display_info(
+        widget,
+        "Incorrect coordinate space",
+        "One or more of the segmented images are not of the same size "
+        "as the registered image. Please ensure you segmented your "
+        "data in the same coordinate space as you wish to analyse it in. ",
+    )

brainreg_segment/segmentation_panels/tracks.py

@@ -286,6 +286,8 @@ def run_track_analysis(self, override=False):
                 choice = display_warning(
                     self.parent,
                     "About to analyse tracks",
+                    "Please ensure the tracks were defined in the same "
+                    "reference space as the currently open image. "
                     "Existing files will be will be deleted. Proceed?",
                 )
             else:

tests/conftest.py

@@ -1,9 +1,26 @@
+from pathlib import Path
+
 import pytest
 from bg_atlasapi import BrainGlobeAtlas
 
+from brainreg_segment.segment import SegmentationWidget
+
 atlas_name = "allen_mouse_50um"
+brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"
 
 
 @pytest.fixture
 def allen_mouse_50um_atlas():
     return BrainGlobeAtlas(atlas_name)
+
+
+@pytest.fixture
+def segmentation_widget(make_napari_viewer):
+    """
+    Create a viewer, add the segmentation widget, and return the widget.
+    The viewer can be accessed using ``widget.viewer``.
+    """
+    viewer = make_napari_viewer()
+    widget = SegmentationWidget(viewer)
+    viewer.window.add_dock_widget(widget)
+    return widget

tests/tests/test_integration/test_gui/test_gui.py

@@ -4,27 +4,12 @@
 
 import numpy as np
 import pandas as pd
-import pytest
-
-from brainreg_segment.segment import SegmentationWidget
 
 brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"
 
 ATLAS_NAME = "example_mouse_100um"
 
 
-@pytest.fixture
-def segmentation_widget(make_napari_viewer):
-    """
-    Create a viewer, add the curation widget, and return the widget.
-    The viewer can be accessed using ``widget.viewer``.
-    """
-    viewer = make_napari_viewer()
-    widget = SegmentationWidget(viewer)
-    viewer.window.add_dock_widget(widget)
-    return widget
-
-
 def test_load_sample_space(segmentation_widget):
     segmentation_widget.standard_space = False
     segmentation_widget.plugin = "brainglobe-napari-io.brainreg_read_dir"

tests/tests/test_unit/test_segmentation_panels/test_regions.py

@@ -0,0 +1,17 @@
+import numpy as np
+from napari.layers import Labels
+
+from brainreg_segment.segmentation_panels.regions import (
+    check_segmentation_in_correct_space,
+)
+
+
+def test_check_segmentation_in_correct_space():
+    labels_layer_10 = Labels(np.zeros((10, 10, 10), dtype=int))
+    labels_layer_15 = Labels(np.zeros((15, 15, 15), dtype=int))
+    assert check_segmentation_in_correct_space(
+        [labels_layer_10], labels_layer_10.data
+    )
+    assert not check_segmentation_in_correct_space(
+        [labels_layer_10], labels_layer_15.data
+    )