How to use the brainrender.Utils.data_io.load_mesh_from_file function in brainrender

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github BrancoLab / BrainRender / brainrender / atlases / brainglobe.py View on Github external
def _get_structure_mesh(self, acronym, **kwargs):
        obj_path = self._get_from_structure(acronym, "mesh_filename")
        return load_mesh_from_file(obj_path, **kwargs)
github BrancoLab / BrainRender / brainrender / atlases / base.py View on Github external
def _get_structure_mesh(self, acronym, **kwargs):
        obj_path = self._get_from_structure(acronym, "mesh_filename")
        return load_mesh_from_file(obj_path, **kwargs)
github BrancoLab / BrainRender / brainrender / atlases / celegans.py View on Github external
color="black",
                                verbose=False,
                                alpha=0,
                                radius=self.synapses_radius * 4,
                                res=24,
                                col_names=col_names,
                            ),
                        )
                    )

                    # Get mesh points for neuron the synapses belong to
                    if neuron not in scene_store.keys():
                        neuron_file = [
                            f for f in self.neurons_files if neuron in f
                        ][0]
                        neuron_act = load_mesh_from_file(neuron_file, c=color)
                    else:
                        neuron_act, as_skeleton = scene_store[neuron]

                    # Draw post synapses as dark patches
                    if draw_patches:
                        if as_skeleton:
                            print(
                                "Can't display post synapses as dark spots when neron is rendered in skeleton mode"
                            )
                        else:
                            # Get faces that are inside the synapses spheres and color them darker
                            raise NotImplementedError("This needs some fixing")

                            # neuron_points = neuron_act.cellCenters()
                            # inside_points = spheres.insidePoints(
                            #     neuron_points, returnIds=True
github BrancoLab / BrainRender / brainrender / atlases / zfish.py View on Github external
"""
        if self.structures is None: 
            print("No atlas was loaded, use self.get_brain first")
            return None

        if region not in list(self.structures['name']):
            print(f"Acronym {region} not in available regions: {self.structures}")
            return None

        # Get obj file path
        obj_path = os.path.join(self.meshes_folder, "{}.vtk".format(region))

        # Load
        if self._check_obj_file(region, obj_path):
            mesh = load_mesh_from_file(obj_path, **kwargs)
            return mesh
        else:
            mesh = self.download_and_save_mesh(region, obj_path)
            return mesh
github BrancoLab / BrainRender / brainrender / atlases / sba.py View on Github external
Fetches the mesh for a brain region from the atlas.

        :param region: string, name of brain region
        :param **kwargs:

        """
        if region not in list(self.structures['acronym']):
            print(f"Acronym {region} not in available regions: {self.structures}")
            return None

        # Get obj file path
        obj_path = os.path.join(self.meshes_folder, "{}.vtk".format(region))

        # Load
        if self._check_obj_file(region, obj_path):
            mesh = load_mesh_from_file(obj_path, **kwargs)
            return mesh
        else:
            mesh = self.save_structure_mesh(region, obj_path)
            return mesh
github BrancoLab / BrainRender / brainrender / atlases / custom_atlases / insects_brains_db.py View on Github external
raise ValueError(
                f"Acronym {acronym} not in available regions: {self.structures}"
            )

        # Get obj file path
        if acronym != "root":
            mesh_format = self.mesh_format
        else:
            mesh_format = "vtk"
        obj_path = os.path.join(
            self.meshes_folder, "{}.{}".format(acronym, mesh_format)
        )

        # Load
        if self._check_obj_file(acronym, obj_path):
            mesh = load_mesh_from_file(obj_path, **kwargs)
            return mesh
        else:
            mesh = self.download_and_write_mesh(acronym, obj_path)
            return None
github BrancoLab / BrainRender / brainrender / atlases / celegans.py View on Github external
else:
                color = self.get_neuron_color(neuron, colorby=colorby)

                if as_skeleton:  # reconstruct skeleton from json
                    actor = self._parse_neuron_skeleton(neuron)

                else:  # load as .obj file
                    try:
                        neuron_file = [
                            f for f in self.neurons_files if neuron in f
                        ][0]
                    except:
                        print(f"Could not find .obj file for neuron {neuron}")
                        continue

                    actor = load_mesh_from_file(neuron_file)

                if actor is not None:
                    # Refine actor's look
                    actor.alpha(alpha).c(color)

            actors.append(actor)
            store[neuron] = (actor, as_skeleton)

        return actors, store
github BrancoLab / BrainRender / brainrender / atlases / atlas.py View on Github external
def _get_structure_mesh(self, acronym, **kwargs):
        obj_path = self._get_from_structure(acronym, "mesh_filename")
        return load_mesh_from_file(obj_path, **kwargs)