attempt to get mouse brain geometry

denmanlab · Jul 17, 2024 · 904250d · 904250d
1 parent 24c828c
commit 904250d
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diff --git a/examples/BrainGeometryAPI/Brain.py b/examples/BrainGeometryAPI/Brain.py
@@ -39,6 +39,15 @@
 geometry = ossdbs.BrainGeometry("Sphere", nifti_image.bounding_box)
 geometry.geometry.WriteStep("geo_full_sphere.step")
 
+'''
+repeat format for mouse brain:
+'''
+geometry = ossdbs.BrainGeometry("Mouse", region_of_interest)
+geometry.geometry.WriteStep("geo_ROI_mouse.step")
+geometry = ossdbs.BrainGeometry("Mouse", nifti_image.bounding_box)
+geometry.geometry.WriteStep("geo_full_mouse.step")
+
+
 occgeo = occ.OCCGeometry(geometry.geometry)
 with TaskManager():
     mesh = Mesh(occgeo.GenerateMesh())

diff --git a/ossdbs/model_geometry/brain_geometry.py b/ossdbs/model_geometry/brain_geometry.py
@@ -99,6 +99,7 @@ def _create_shape(self) -> netgen.occ.Solid:
                 `import_geometry` or add it via the `set_geometry` method."""
             )
         else:
+
             raise NotImplementedError(
                 f"""The shape {self._shape} is not implemented.
                 Please choose among these shapes: Box, Sphere, Ellipsoid and Custom."""
@@ -122,6 +123,10 @@ def _create_sphere(self) -> netgen.occ.Solid:
     def _create_box(self) -> netgen.occ.Solid:
         box = netgen.occ.Box(self._bbox.start, self._bbox.end)
         return self._affine_trafo(box)
+
+    def _create_mouse(self) -> netgen.occ.Solid:
+        mouse = BrainGeometry.import_geometry('/Users/pareesharma/Denman Lab Summer/mouse_brain.stl')
+        return self._affine_trafo(mouse)
 
     def import_geometry(self, path_to_geo_file: str):
         """Import brain geometry from CAD file.