How to use the brainrender.colors.colorMap function in brainrender

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github BrancoLab / BrainRender / tests / test_scene_io.py View on Github external
for step in track(
        np.arange(N_FRAMES), total=N_FRAMES, description="Generating frames..."
    ):
        if step % N_frames_for_change == 0:  # change neurons every N framse

            # reset neurons from previous set of neurons
            for neuron in prev_neurons:
                for component, actor in neuron.items():
                    actor.alpha(minalpha)
                    actor.color(darkcolor)
            prev_neurons = []

            # highlight new neurons
            neurons = choices(neurons_actors, k=N_neurons_in_frame)
            for n, neuron in enumerate(neurons):
                color = colorMap(
                    n, "Greens_r", vmin=-2, vmax=N_neurons_in_frame + 3
                )
                for component, actor in neuron.items():
                    actor.alpha(1)
                    actor.color(color)
                prev_neurons.append(neuron)

        # Move scene camera between 3 cameras
        scene.plotter.moveCamera(cam1, cam2, frac[step])
        if frac[step] == 1:
            cam1 = cam3

        # Update rendered window
        time.sleep(0.1)
        scene.render(zoom=zoom[step], interactive=False, video=True)
    scene.close()
github BrancoLab / BrainRender / brainrender / morphology / visualise.py View on Github external
"""
        N = len(neurons)
        colors = dict(soma=None, axon=None, dendrites=None,)

        # If no color is passed, get random colors
        if color is None:
            cols = [self.default_neuron_color for n in np.arange(N)]
            colors = dict(
                soma=cols.copy(), axon=cols.copy(), dendrites=cols.copy(),
            )
        else:
            if isinstance(color, str):
                # Deal with a a cmap being passed
                if color in _mapscales_cmaps:
                    cols = [
                        colorMap(n, name=color, vmin=-2, vmax=N + 2)
                        for n in np.arange(N)
                    ]
                    colors = dict(
                        soma=cols.copy(),
                        axon=cols.copy(),
                        dendrites=cols.copy(),
                    )

                else:
                    # Deal with a single color being passed
                    cols = [getColor(color) for n in np.arange(N)]
                    colors = dict(
                        soma=cols.copy(),
                        axon=cols.copy(),
                        dendrites=cols.copy(),
                    )
github BrancoLab / BrainRender / brainrender / Utils / parsers / mouselight.py View on Github external
"""
		Modify neurons actors after they have been created, at render time.
		neurons should be a list of dictionaries with soma, dendrite and axon actors of each neuron.

	:param neurons: list of dictionaries with vtk actors for each neuron
	:param **kwargs: 

	"""
	soma_color, axon_color, dendrites_color = None, None, None
	for neuron in neurons:
		if "random_color" in kwargs:
			if kwargs["random_color"]:
				if not isinstance(kwargs["random_color"], str):
					color = get_random_colors(n_colors=1)
				else: # random_color is a colormap 
					color = colorMap(np.random.randint(1000), name=kwargs["random_color"], vmin=0, vmax=1000)
				axon_color = soma_color = dendrites_color = color
		elif "color_neurites" in kwargs:
			soma_color = neuron["soma"].color()
			if not kwargs["color_neurites"]:
				axon_color = dendrites_color = soma_color
			else:
				if not "axon_color" in kwargs:
					# print("no axon color provided, using somacolor")
					axon_color = soma_color
				else:
					axon_color = kwargs["axon_color"]

				if not "dendrites_color" in kwargs:
					# print("no dendrites color provided, using somacolor")
					dendrites_color = soma_color
				else:
github BrancoLab / BrainRender / brainrender / ABA / aba_utils.py View on Github external
N = len(neurons)
    colors = dict(soma=None, axon=None, dendrites=None,)

    # If no color is passed, get random colors
    if color is None:
        cols = get_random_colors(N)
        if not isinstance(cols, list):
            cols = [cols]
        colors = dict(soma=cols, axon=cols, dendrites=cols,)
    else:
        if isinstance(color, str):
            # Deal with a a cmap being passed
            if color in _mapscales_cmaps:
                cols = [
                    colorMap(n, name=color, vmin=-2, vmax=N + 2)
                    for n in np.arange(N)
                ]
                colors = dict(
                    soma=cols.copy(), axon=cols.copy(), dendrites=cols.copy(),
                )

            else:
                # Deal with a single color being passed
                cols = [getColor(color) for n in np.arange(N)]
                colors = dict(
                    soma=cols.copy(), axon=cols.copy(), dendrites=cols.copy(),
                )
        elif isinstance(color, dict):
            # Deal with a dictionary with color for each component
            if "soma" not in color.keys():
                raise ValueError(
github BrancoLab / BrainRender / brainrender / Utils / parsers / mouselight.py View on Github external
"""
		Makes sure that all the parameters to specify how neurons should be rendered. 

		:param neuron_number: number of the neuron being rendered
		:param neuron: neuron's metadata (Default value = None)
		:param soma_region: str with the acronym of the region the soma is in (Default value = None)
		:param soma: list with XYZ coordinates of the neuron's soma. (Default value = None)

		"""
		# Define colors of different components
		if not self.color_by_region:
			if self.random_color:
				if not isinstance(self.random_color, str):
					color = get_random_colors(n_colors=1)
				else: # random_color is a colormap 
					color = colorMap(neuron_number, name=self.random_color, vmin=0, vmax=self.n_neurons)
				axon_color = soma_color = dendrites_color = color
			else:
				if self.soma_color is None:
					soma_color = get_random_colors(n_colors=1)

				if not self.color_neurites:
					axon_color = dendrites_color = soma_color = self.soma_color
				else:
					soma_color = self.soma_color
					if self.axon_color is None:
						axon_color = soma_color
					else:
						axon_color = self.axon_color
					if self.dendrites_color is None:
						dendrites_color = soma_color
					else:
github BrancoLab / BrainRender / brainrender / morphology / utils.py View on Github external
Modify neurons actors after they have been created, at render time.
        neurons should be a list of dictionaries with soma, dendrite and axon actors of each neuron.
    :param neurons: list of dictionaries with vtk actors for each neuron
    :param **kwargs: 
    """
    if not isinstance(neurons, (list, tuple)):
        neurons = [neurons]

    soma_color, axon_color, dendrites_color = None, None, None
    for neuron in neurons:
        if "random_color" in kwargs:
            if kwargs["random_color"]:
                if not isinstance(kwargs["random_color"], str):
                    color = get_random_colors(n_colors=1)
                else:  # random_color is a colormap
                    color = colorMap(
                        np.random.randint(1000),
                        name=kwargs["random_color"],
                        vmin=0,
                        vmax=1000,
                    )
                axon_color = soma_color = dendrites_color = color
        elif "color_neurites" in kwargs:
            soma_color = neuron["soma"].color()
            if not kwargs["color_neurites"]:
                axon_color = dendrites_color = soma_color
            else:
                if "axon_color" not in kwargs:
                    # print("no axon color provided, using somacolor")
                    axon_color = soma_color
                else:
                    axon_color = kwargs["axon_color"]
github BrancoLab / BrainRender / Examples / advanced / animated_scene.py View on Github external
for step in track(
    np.arange(N_FRAMES), total=N_FRAMES, description="Generating frames..."
):
    if step % N_frames_for_change == 0:  # change neurons every N framse

        # reset neurons from previous set of neurons
        for neuron in prev_neurons:
            for component, actor in neuron.items():
                actor.alpha(minalpha)
                actor.color(darkcolor)
        prev_neurons = []

        # highlight new neurons
        neurons = choices(scene.actors["neurons"], k=N_neurons_in_frame)
        for n, neuron in enumerate(neurons):
            color = colorMap(
                n, "Greens_r", vmin=-2, vmax=N_neurons_in_frame + 3
            )
            for component, actor in neuron.items():
                actor.alpha(1)
                actor.color(color)
            prev_neurons.append(neuron)

    # Move scene camera between 3 cameras
    scene.plotter.moveCamera(cam1, cam2, frac[step])
    if frac[step] == 1:
        cam1 = cam3

    # Update rendered window
    time.sleep(0.1)
    scene.render(zoom=zoom[step], interactive=False, video=True)