How to use the brainrender.Utils.data_manipulation.return_list_smart function in brainrender

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github BrancoLab / BrainRender / brainrender / scene.py View on Github external
def add_streamlines(self, *args, **kwargs):
        """
        Render streamline data.
        Check the function definition in ABA for more details
        """
        actors = self.atlas.get_streamlines(*args, **kwargs)
        self.actors.extend(actors)
        return return_list_smart(actors)
github BrancoLab / BrainRender / brainrender / atlases / brainglobe.py View on Github external
each item is the color of the brain region each point is in
        """
        if isinstance(p0[0], (float, int)):
            p0 = [p0]

        resolution = int(self.metadata["resolution"][0])

        colors = []
        for point in p0:
            point = np.round(np.array(point) / resolution).astype(int)
            try:
                struct = self.structure_from_coords(point, as_acronym=True)
            except KeyError:  # couldn't find any region
                struct = "root"
            colors.append(self._get_from_structure(struct, "rgb_triplet"))
        return return_list_smart(colors)
github BrancoLab / BrainRender / brainrender / scene.py View on Github external
def add_from_file(self, *filepaths, **kwargs):
        """
        Add data to the scene by loading them from a file. Should handle .obj, .vtk and .nii files.

        :param filepaths: path to the file. Can pass as many arguments as needed
        :param **kwargs:

        """
        actors = []
        for filepath in filepaths:
            actor = load_mesh_from_file(filepath, **kwargs)
            actor.name = Path(filepath).name
            self.actors.append(actor)
            actors.append(actor)
        return return_list_smart(actors)
github BrancoLab / BrainRender / brainrender / scene.py View on Github external
def add_tractography(self, *args, **kwargs):
        """
        Renders tractography data and adds it to the scene. 
        Check the function definition in ABA for more details
        """

        actors = self.atlas.get_tractography(*args, **kwargs)
        self.actors.extend(actors)
        return return_list_smart(actors)
github BrancoLab / BrainRender / brainrender / atlases / mouse.py View on Github external
if not display_dendrites:
                neuron_actors["dendrites"] = None
            _neurons_actors.append(neuron_actors)

        # Color actors
        colors = parse_neurons_colors(neurons, color)
        for n, neuron in enumerate(_neurons_actors):
            if neuron["axon"] is not None:
                neuron["axon"].c(colors["axon"][n])
            if neuron["soma"] is not None:
                neuron["soma"].c(colors["soma"][n])
            if neuron["dendrites"] is not None:
                neuron["dendrites"].c(colors["dendrites"][n])

        # Return
        return return_list_smart(_neurons_actors), None
github BrancoLab / BrainRender / brainrender / scene.py View on Github external
def add_actor(self, *actors, store=None):
        """
        Add a vtk actor to the scene

        :param actor:
        :param store: a list to store added actors

        """
        for actor in actors:
            if store is None:
                self.actors.append(actor)
            else:
                store.append(actor)
        return return_list_smart(actors)
github BrancoLab / BrainRender / brainrender / scene.py View on Github external
planes = [plane]

        actors = []
        for plane in planes:
            if isinstance(plane, str):
                plane = self.atlas.get_plane_at_point(plane=plane, **kwargs)
            else:
                if not isinstance(plane, Plane):
                    raise ValueError(
                        "The plane arguments should either be a Plane actor or"
                        + "a string with the name of predefined planes."
                        + f" Not: {plane.__type__}"
                    )
            actors.append(plane)
        self.add_actor(*actors)
        return return_list_smart(actors)
github BrancoLab / BrainRender / brainrender / atlases / atlas.py View on Github external
each item is the color of the brain region each point is in
        """
        if isinstance(p0[0], (float, int)):
            p0 = [p0]

        resolution = int(self.metadata["resolution"][0])

        colors = []
        for point in p0:
            point = np.round(np.array(point) / resolution).astype(int)
            try:
                struct = self.structure_from_coords(point, as_acronym=True)
            except KeyError:  # couldn't find any region
                struct = "root"
            colors.append(self._get_from_structure(struct, "rgb_triplet"))
        return return_list_smart(colors)
github BrancoLab / BrainRender / brainrender / morphology / visualise.py View on Github external
if not display_dendrites:
                neuron_actors["dendrites"] = None
            _neurons_actors.append(neuron_actors)

        # Color actors
        for n, neuron in enumerate(_neurons_actors):
            if neuron["axon"] is not None:
                neuron["axon"].c(colors["axon"][n])
            neuron["soma"].c(colors["soma"][n])
            if neuron["dendrites"] is not None:
                neuron["dendrites"].c(colors["dendrites"][n])

        # Add to actors storage
        self.actors.extend(_neurons_actors)

        return return_list_smart(_neurons_actors)