moved duplicate cell selection code to App

regexport/actions/save_cells.py

@@ -18,6 +18,7 @@ def register(self, model: AppState):
     def submit(self, filename: Path, selected_regions_only: bool = False):
         print('File saving...')
 
+        df = self.model.selected_cells if selected_regions_only else self.model.cells
         types = {
             'Image': 'category',
             'BrainRegion': 'category',
@@ -28,10 +29,8 @@ def submit(self, filename: Path, selected_regions_only: bool = False):
         }
 
         types.update({col: 'uint16' for col in self.model.cells.columns if "Num Spots" in col})
-        df = self.model.cells.astype(types)
+        df = df.astype(types)
         df: pd.DataFrame = df.drop(columns=['BGIdx'])
-        if selected_regions_only:
-            df = df.iloc[self.model.selected_cell_ids]
 
         print(df.info())
         print(filename)

regexport/model.py

@@ -23,6 +23,7 @@ class AppState(HasTraits):
     column_to_plot = Unicode(default_value="BrainRegion")
     colormap_options = List(Unicode(), default_value=[cmap for cmap in plt.colormaps() if not cmap.endswith('_r')])#['tab20c', 'viridis'])
     selected_colormap = Unicode(default_value='tab20c')
+    selected_cells = Instance(pd.DataFrame, allow_none=True)
 
     @observe('cells')
     def _update_column_to_plot_options(self, change):
@@ -43,9 +44,11 @@ def _update_selected_cell_ids(self, change):
             return
         elif len(self.selected_region_ids) == 0:
             self.selected_cell_ids = self.cells.index.values
+            self.selected_cells = self.cells
         else:
             is_parented = self.cells.groupby('BGIdx', as_index=False).BGIdx.transform(
                 lambda ids: is_parent(ids.values[0], selected_ids=self.selected_region_ids, tree=self.atlas.hierarchy) if ids.values[0] != 0 else False
             )
             only_parented = is_parented[is_parented.BGIdx].index.values
             self.selected_cell_ids = only_parented
+            self.selected_cells = self.cells.iloc[only_parented]

regexport/utils/plotting.py

@@ -21,13 +21,13 @@ def __post_init__(self):
 
 
 @warn_if_slow()
-def plot_cells(positions: np.ndarray, colors: np.ndarray, indices: Tuple[int], cmap: str = 'tab20c') -> PointCloud:
+def plot_cells(positions: np.ndarray, colors: np.ndarray, cmap: str = 'tab20c') -> PointCloud:
     return PointCloud(
-        coords=positions[indices, :],
-        colors=(selected_colors := convert_values_to_colors(colors, getattr(plt.cm, cmap))[indices])[:, :3],
+        coords=positions,
+        colors=(selected_colors := convert_values_to_colors(colors, getattr(plt.cm, cmap)))[:, :3],
         alphas=selected_colors[:, 3:4],
     )
 
 
 def convert_values_to_colors(color_codes: np.ndarray, cmap: ListedColormap):
-    return cmap(color_codes / color_codes.max())[:, :4]
+    return cmap(color_codes / color_codes.max())[:, :4]

regexport/views/plot_3d.py

@@ -27,19 +27,18 @@ def register(self, model: AppState):
             lambda atlas: Path(str(atlas.structures[997]['mesh_filename'])) if atlas is not None else None
         )
         model.observe(self.link_cells_to_points, names=[
-            'selected_cell_ids', 'cells', 'selected_colormap', 'column_to_plot',
+            'selected_cells', 'selected_colormap', 'column_to_plot',
         ])
 
     def link_cells_to_points(self, change):
         model = self.model
-        if model.cells is None:
+        if model.selected_cells is None:
             self.points = PointCloud()
             return
-        color_col = model.cells[model.column_to_plot]
+        color_col = model.selected_cells[model.column_to_plot]
         points = plot_cells(
-            positions=model.cells[['X', 'Y', 'Z']].values * 1000,
+            positions=model.selected_cells[['X', 'Y', 'Z']].values * 1000,
             colors=color_col.cat.codes.values if color_col.dtype.name == 'category' else color_col.values,
-            indices=model.selected_cell_ids if model.selected_cell_ids is not None else (),
             cmap=self.model.selected_colormap
         )
         self.points = points
@@ -103,4 +102,4 @@ def render(self, change=None):
 
         self.plotter.show(actors, at=0)
         self.plotter.addInset(self._atlas_mesh, pos=(.9, .9), size=0.1, c='w', draggable=True)
-        # note: look at from vedo.applications import SlicerPlotter for inspiration
+        # note: look at from vedo.applications import SlicerPlotter for inspiration