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

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github BrancoLab / BrainRender / brainrender / atlases / celegans.py View on Github external
allowed = ["neuron", "individual", "ind", "pair", "class", "type"]

        if colorby not in allowed:
            raise ValueError(
                f"color by key should be one of {allowed} not {colorby}"
            )

        if colorby == "type":
            color = cs.neurons_metadata.loc[
                cs.neurons_metadata.neuron == neuron
            ]["type_color"].values[0]
            color = ImageColor.getrgb(color)
        elif (
            colorby == "individual" or colorby == "ind" or colorby == "neuron"
        ):
            color = get_random_colors()
        else:
            raise NotImplementedError

        return color
github BrancoLab / BrainRender / brainrender / Utils / parsers / mouselight.py View on Github external
else:
				raise ValueError("You need to pass either a neuron, or a soma region or a soma")
		else:
			self.alleninfo = None

		if soma_region is not None:
			soma_region = self.scene.get_structure_parent(soma_region)['acronym']
		else:
			soma_region = "root"

		if self.color_by_region:
			try:
				region_color = self.scene.structure_tree.get_structures_by_acronym([soma_region])[0]['rgb_triplet']
			except:
				print("could not find default color for region: {}. Using random color instead".format(soma_region))
				region_color = get_random_colors(n_colors=1)

			axon_color = soma_color = dendrites_color = region_color

		return soma_color, axon_color, dendrites_color, soma_region
github BrancoLab / BrainRender / brainrender / ABA / aba_utils.py View on Github external
:param neurons: str, list, dict. File(s) with neurons data or list of rendered neurons.
        :param color: default None. Can be:
                - None: each neuron is given a random color
                - color: rbg, hex etc. If a single color is passed all neurons will have that color
                - cmap: str with name of a colormap: neurons are colored based on their sequential order and cmap
                - dict: a dictionary specifying a color for soma, dendrites and axon actors, will be the same for all neurons
                - list: a list of length = number of neurons with either a single color for each neuron
                        or a dictionary of colors for each neuron
    """

    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:
github BrancoLab / BrainRender / brainrender / Utils / parsers / mouselight.py View on Github external
def _render_neuron_get_params(self, neuron_number, neuron=None, soma_region=None, soma=None):
		"""
		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:
github BrancoLab / BrainRender / brainrender / Utils / parsers / mouselight.py View on Github external
: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:
						dendrites_color = self.dendrites_color

			# check that the colors make sense
			if not check_colors([soma_color, axon_color, dendrites_color]):