handling atlases on pytest

Tomaubier · Jan 27, 2025 · fa7417d · fa7417d
1 parent 6bde405
commit fa7417d
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Showing 2 changed files with 31 additions and 28 deletions.
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -20,6 +20,9 @@ jobs:
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
 
+      - name: Download test BrainGlobe atlas
+        brainglobe install -a example_mouse_100um
+
       - name: Installing CoperniFUS
         run: python -m pip install -e .
 

diff --git a/coperniFUS/modules/atlas.py b/coperniFUS/modules/atlas.py
@@ -16,10 +16,10 @@ class BrainAtlas(Module):
     def __init__(self, parent_viewer, skip_online_atlas_retreival=False, **kwargs) -> None:
         super().__init__(parent_viewer, 'atlas', **kwargs)
 
-        self.test_atlas = False
+        # self.test_atlas = False
         if 'running_test' in self.module_kwargs and self.module_kwargs['running_test']:
             print('running test')
-            self.test_atlas = True
+            # self.test_atlas = True
             self._DEFAULT_PARAMS['default_atlas_name'] = 'example_mouse_100um'
 
         self.skip_online_atlas_retreival = skip_online_atlas_retreival
@@ -182,33 +182,33 @@ def _add_atlas(self):
         #     bg_atlas = BrainGlobeAtlas(online_atlas_name, check_latest=True)
         #     self._add_atlas()
 
-        if self.test_atlas: # Only when testing application
-            pass # TEMPORARY TODO implement proper test
-        else:
-            if selected_atlas_description is None:
-                pass # TODO msg in status bar
-            elif selected_atlas_description.endswith('(DOWNLOADED)'):
-                offline_atlas_name = selected_atlas_description.split(' | ')[0]
-                self.parent_viewer.statusBar().showMessage(f'Loading offline {offline_atlas_name}', self.parent_viewer._STATUS_BAR_MSG_TIMEOUT)
-                self.bg_atlas = BrainGlobeAtlas(offline_atlas_name, check_latest=False)
-            elif selected_atlas_description.endswith('(online)'):
-                online_atlas_name = selected_atlas_description.split(' | ')[0]
+        # if self.test_atlas: # Only when testing application
+        #     pass # TEMPORARY TODO implement proper test
+        # else:
+        if selected_atlas_description is None:
+            pass # TODO msg in status bar
+        elif selected_atlas_description.endswith('(DOWNLOADED)'):
+            offline_atlas_name = selected_atlas_description.split(' | ')[0]
+            self.parent_viewer.statusBar().showMessage(f'Loading offline {offline_atlas_name}', self.parent_viewer._STATUS_BAR_MSG_TIMEOUT)
+            self.bg_atlas = BrainGlobeAtlas(offline_atlas_name, check_latest=False)
+        elif selected_atlas_description.endswith('(online)'):
+            online_atlas_name = selected_atlas_description.split(' | ')[0]
+
+            dialog = AcceptRejectDialog(parent=self.parent_viewer, title='Proceed with Brain Atlas download?', msg=f'Do you want to download {online_atlas_name} ?\nThis might take a few minutes')
+            dialog_result = dialog.exec()
+            if dialog_result == 1:
+                self.parent_viewer.statusBar().showMessage(f'Downloading {online_atlas_name}')
+
+                # TODO reimplement threaded download
+                # self.threaded_atlas_download = threading.Thread(
+                #     target=download_atlas_wrapper,
+                #     args=(online_atlas_name,))
+                # self.threaded_atlas_download.start()
+                # TODO allow thread interruption
+                self.bg_atlas = BrainGlobeAtlas(online_atlas_name, check_latest=True)
 
-                dialog = AcceptRejectDialog(parent=self.parent_viewer, title='Proceed with Brain Atlas download?', msg=f'Do you want to download {online_atlas_name} ?\nThis might take a few minutes')
-                dialog_result = dialog.exec()
-                if dialog_result == 1:
-                    self.parent_viewer.statusBar().showMessage(f'Downloading {online_atlas_name}')
-
-                    # TODO reimplement threaded download
-                    # self.threaded_atlas_download = threading.Thread(
-                    #     target=download_atlas_wrapper,
-                    #     args=(online_atlas_name,))
-                    # self.threaded_atlas_download.start()
-                    # TODO allow thread interruption
-                    self.bg_atlas = BrainGlobeAtlas(online_atlas_name, check_latest=True)
-
-                else:
-                    self.parent_viewer.statusBar().showMessage('Atlas Download Canceled!', self.parent_viewer._STATUS_BAR_MSG_TIMEOUT)
+            else:
+                self.parent_viewer.statusBar().showMessage('Atlas Download Canceled!', self.parent_viewer._STATUS_BAR_MSG_TIMEOUT)
 
         if self.bg_atlas is not None: