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getColor("#ffffff")
getColor(7)
getColor(-7)
getColorName("#ffffff")
cols = colorMap([0, 1, 2])
if not isinstance(cols, (list, np.ndarray)):
raise ValueError
if len(cols) != 3:
raise ValueError
c = colorMap(3, vmin=-3, vmax=4)
check_colors(cols)
check_colors(c)
getColor("k")
getColor("#ffffff")
getColor(7)
getColor(-7)
getColorName("#ffffff")
cols = colorMap([0, 1, 2])
if not isinstance(cols, (list, np.ndarray)):
raise ValueError
if len(cols) != 3:
raise ValueError
c = colorMap(3, vmin=-3, vmax=4)
check_colors(cols)
check_colors(c)
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors, (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError(
"when passing colors as a list, the number of colors must match the number of brain regions"
)
for col in colors:
if not check_colors(col):
raise ValueError(
"Invalide colors in input: {}".format(col)
)
else:
if not check_colors(colors):
raise ValueError(
"Invalide colors in input: {}".format(colors)
)
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
if region in self.ignore_regions:
continue
if verbose:
print("Rendering: ({})".format(region))
# get the structure and check if we need to download the object file
if region not in self.lookup.acronym.values:
print(
:param others_color: str, color for not VIP data (Default value = "white")
"""
# check coloring mode used and prepare a list COLORS to use for coloring stuff
if color_by == "manual":
# check color argument
if color is None:
color = brainrender.TRACT_DEFAULT_COLOR
COLORS = [color for i in range(len(tractography))]
elif isinstance(color, list):
if not len(color) == len(tractography):
raise ValueError(
"If a list of colors is passed, it must have the same number of items as the number of tractography traces"
)
else:
for col in color:
if not check_colors(col):
raise ValueError(
"Color variable passed to tractography is invalid: {}".format(
col
)
)
COLORS = color
else:
if not check_colors(color):
raise ValueError(
"Color variable passed to tractography is invalid: {}".format(
color
)
)
else:
COLORS = [color for i in range(len(tractography))]
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]):
raise ValueError("The colors chosen are not valid: soma - {}, dendrites {}, axon {}".format(soma_color, dendrites_color, axon_color))
# check if we have lists of colors or single colors
if isinstance(soma_color, list):
if isinstance(soma_color[0], str) or isinstance(soma_color[0], list):
soma_color = soma_color[neuron_number]
if isinstance(dendrites_color, list):
if isinstance(dendrites_color[0], str) or isinstance(dendrites_color[0], list):
dendrites_color = dendrites_color[neuron_number]
if isinstance(axon_color, list):
if isinstance(axon_color[0], str) or isinstance(axon_color[0], list):
axon_color = axon_color[neuron_number]
# get allen info: it containes the allenID of each brain region
# each sample has the corresponding allen ID so we can recontruct in which brain region it is
if neuron is not None:
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors, (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError(
"when passing colors as a list, the number of colors must match the number of brain regions"
)
for col in colors:
if not check_colors(col):
raise ValueError(
"Invalide colors in input: {}".format(col)
)
else:
if not check_colors(colors):
raise ValueError(
"Invalide colors in input: {}".format(colors)
)
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
if verbose:
print("Rendering: ({})".format(region))
# get the structure and check if we need to download the object file
if region not in self.lookup_df.acronym.values:
print(
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
if alpha is None:
alpha = brainrender.DEFAULT_STRUCTURE_ALPHA
# check that we have a list
if not isinstance(brain_regions, list):
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors, (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError(
"when passing colors as a list, the number of colors must match the number of brain regions"
)
for col in colors:
if not check_colors(col):
raise ValueError(
"Invalide colors in input: {}".format(col)
)
else:
if not check_colors(colors):
raise ValueError(
"Invalide colors in input: {}".format(colors)
)
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
if region in self.ignore_regions:
continue
if verbose:
if alpha is None:
alpha = brainrender.DEFAULT_STRUCTURE_ALPHA
# check that we have a list
if not isinstance(brain_regions, list):
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors, (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError(
"when passing colors as a list, the number of colors must match the number of brain regions"
)
for col in colors:
if not check_colors(col):
raise ValueError(
"Invalide colors in input: {}".format(col)
)
else:
if not check_colors(colors):
raise ValueError(
"Invalide colors in input: {}".format(colors)
)
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
if verbose:
print("Rendering: ({})".format(region))
brain_regions = [brain_regions]
# check the colors input is correct
if colors is not None:
if isinstance(colors, (list, tuple)):
if not len(colors) == len(brain_regions):
raise ValueError(
"when passing colors as a list, the number of colors must match the number of brain regions"
)
for col in colors:
if not check_colors(col):
raise ValueError(
"Invalide colors in input: {}".format(col)
)
else:
if not check_colors(colors):
raise ValueError(
"Invalide colors in input: {}".format(colors)
)
colors = [colors for i in range(len(brain_regions))]
# loop over all brain regions
actors = {}
for i, region in enumerate(brain_regions):
if verbose:
print("Rendering: ({})".format(region))
# get the structure and check if we need to download the object file
if region not in self.lookup_df.acronym.values:
print(
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
)
COLORS = color
else:
if not check_colors(color):
raise ValueError(
"Color variable passed to tractography is invalid: {}".format(
color
)
)
else:
COLORS = [color for i in range(len(tractography))]
elif color_by == "target_region":
if VIP_color is not None:
if not check_colors(VIP_color) or not check_colors(others_color):
raise ValueError("Invalid VIP or other color passed")
try:
if include_all_inj_regions:
COLORS = [
VIP_color
if is_any_item_in_list(
[
x["abbreviation"]
for x in t["injection-structures"]
],
VIP_regions,
)
else others_color
for t in tractography
]
else: