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def test_default():
brainrender.DISPLAY_INSET
brainrender.DISPLAY_ROOT
brainrender.WHOLE_SCREEN
brainrender.BACKGROUND_COLOR
brainrender.SHOW_AXES
brainrender.WINDOW_POS
brainrender.CAMERA
brainrender.DEFAULT_SCREENSHOT_NAME
brainrender.DEFAULT_SCREENSHOT_TYPE
brainrender.DEFAULT_SCREENSHOT_SCALE
brainrender.SCREENSHOT_TRANSPARENT_BACKGROUND
brainrender.ROOT_COLOR
brainrender.ROOT_ALPHA
brainrender.DEFAULT_STRUCTURE_COLOR
brainrender.DEFAULT_STRUCTURE_ALPHA
brainrender.INJECTION_VOLUME_SIZE
brainrender.TRACTO_RADIUS
brainrender.TRACTO_ALPHA
brainrender.TRACTO_RES
brainrender.TRACT_DEFAULT_COLOR
brainrender.INJECTION_DEFAULT_COLOR
brainrender.STREAMLINES_RESOLUTION
brainrender.INJECTION_VOLUME_SIZE
brainrender.TRACTO_RADIUS
brainrender.TRACTO_ALPHA
brainrender.TRACTO_RES
brainrender.TRACT_DEFAULT_COLOR
brainrender.INJECTION_DEFAULT_COLOR
brainrender.STREAMLINES_RESOLUTION
brainrender.SHADER_STYLE
if not os.path.isfile(meshname):
raise FileExistsError(meshname)
if use_original_color:
c = entry["rgb"].values[0]
if isinstance(c, str):
c = c.replace("[", "")
c = c.replace("]", "")
cols = c.split(",")
color = [int(c) for c in cols]
else:
color = c
else:
if "color" in list(kwargs.keys()):
color = kwargs.pop("color", DEFAULT_STRUCTURE_COLOR)
elif "c" in list(kwargs.keys()):
color = kwargs.pop("c", DEFAULT_STRUCTURE_COLOR)
if "color" in list(kwargs.keys()): del kwargs["color"]
elif "c" in list(kwargs.keys()): del kwargs["c"]
mesh = load(meshname, c=color, **kwargs)
mesh = mesh.smoothLaplacian().subdivide(2)
meshes.append(mesh)
except:
print("Could not load rat region: {}".format(entry["Name"].values[0]))
return None
if not check:
return meshes[0]
else:
raise FileExistsError(meshname)
if use_original_color:
c = entry["rgb"].values[0]
if isinstance(c, str):
c = c.replace("[", "")
c = c.replace("]", "")
cols = c.split(",")
color = [int(c) for c in cols]
else:
color = c
else:
if "color" in list(kwargs.keys()):
color = kwargs.pop("color", DEFAULT_STRUCTURE_COLOR)
elif "c" in list(kwargs.keys()):
color = kwargs.pop("c", DEFAULT_STRUCTURE_COLOR)
if "color" in list(kwargs.keys()): del kwargs["color"]
elif "c" in list(kwargs.keys()): del kwargs["c"]
mesh = load(meshname, c=color, **kwargs)
mesh = mesh.smoothLaplacian().subdivide(2)
meshes.append(mesh)
except:
print("Could not load rat region: {}".format(entry["Name"].values[0]))
return None
if not check:
return meshes[0]
else:
return meshes
"""
:param region:
:param paths:
:param **kwargs:
"""
if not isinstance(region, (tuple, list)):
region = [region]
check = False
else: check = True
metadata = get_drosophila_regions_metadata(paths.metadata)
if "color" in list(kwargs.keys()):
color = kwargs.pop("color", DEFAULT_STRUCTURE_COLOR)
elif "c" in list(kwargs.keys()):
color = kwargs.pop("c", DEFAULT_STRUCTURE_COLOR)
if "color" in list(kwargs.keys()): del kwargs["color"]
elif "c" in list(kwargs.keys()): del kwargs["c"]
meshes = []
for reg in region:
if reg.lower() == "root":
meshname = drosophila_root ## UNDEFINED!!??
mesh = load(meshname, c=color, **kwargs)
mesh = mesh.smoothLaplacian().subdivide(2)
meshes.append(mesh)
else:
if isinstance(reg, int):
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
continue
# Get path to .obj file
obj_file = str(self.meshfile_from_structure(region))
# check which color to assign to the brain region
if use_original_color:
color = [
x / 255
for x in self._get_from_structure(region, "rgb_triplet")
]
else:
if colors is None:
color = brainrender.DEFAULT_STRUCTURE_COLOR
elif isinstance(colors, list):
color = colors[i]
else:
color = colors
# Load the object file as a mesh and store the actor
if hemisphere is not None:
if (
hemisphere.lower() == "left"
or hemisphere.lower() == "right"
):
obj = self.get_region_unilateral(
region, hemisphere=hemisphere, color=color, alpha=alpha
)
else:
raise ValueError(
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
continue
# Get path to .obj file
obj_file = str(self.meshfile_from_structure(region))
# check which color to assign to the brain region
if use_original_color:
color = [
x / 255
for x in self._get_from_structure(region, "rgb_triplet")
]
else:
if colors is None:
color = brainrender.DEFAULT_STRUCTURE_COLOR
elif isinstance(colors, list):
color = colors[i]
else:
color = colors
# Load the object file as a mesh and store the actor
if hemisphere is not None:
if (
hemisphere.lower() == "left"
or hemisphere.lower() == "right"
):
obj = self.get_region_unilateral(
region, hemisphere=hemisphere, color=color, alpha=alpha
)
else:
raise ValueError(
alpha=None,
colors=None,
use_original_color=True,
**kwargs,
):
if alpha is None:
alpha = brainrender.DEFAULT_STRUCTURE_ALPHA
if not isinstance(brain_regions, (list, tuple)):
brain_regions = [brain_regions]
# check the colors input is correct
if not use_original_color:
if colors is None:
colors = [
brainrender.DEFAULT_STRUCTURE_COLOR
for reg in brain_regions
]
else:
if isinstance(colors, (list, tuple)):
if len(colors) != len(brain_regions):
raise ValueError("Wrong number of colors")
else:
colors = [colors for reg in brain_regions]
else:
colors = [self.get_region_color(reg) for reg in brain_regions]
actors = {}
for region, color in zip(brain_regions, colors):
actors[region] = self._get_structure_mesh(region, c=color)
return actors
f"The region {region} doesn't seem to belong to the atlas being used: {self.atlas_name}. Skipping"
)
continue
# Get path to .obj file
obj_file = str(self.meshfile_from_structure(region))
# check which color to assign to the brain region
if use_original_color:
color = [
x / 255
for x in self._get_from_structure(region, "rgb_triplet")
]
else:
if colors is None:
color = brainrender.DEFAULT_STRUCTURE_COLOR
elif isinstance(colors, list):
color = colors[i]
else:
color = colors
# Load the object file as a mesh and store the actor
if hemisphere is not None:
if (
hemisphere.lower() == "left"
or hemisphere.lower() == "right"
):
obj = self.get_region_unilateral(
region, hemisphere=hemisphere, color=color, alpha=alpha
)
else:
raise ValueError(
:param region:
:param paths:
:param **kwargs:
"""
if not isinstance(region, (tuple, list)):
region = [region]
check = False
else: check = True
metadata = get_drosophila_regions_metadata(paths.metadata)
if "color" in list(kwargs.keys()):
color = kwargs.pop("color", DEFAULT_STRUCTURE_COLOR)
elif "c" in list(kwargs.keys()):
color = kwargs.pop("c", DEFAULT_STRUCTURE_COLOR)
if "color" in list(kwargs.keys()): del kwargs["color"]
elif "c" in list(kwargs.keys()): del kwargs["c"]
meshes = []
for reg in region:
if reg.lower() == "root":
meshname = drosophila_root ## UNDEFINED!!??
mesh = load(meshname, c=color, **kwargs)
mesh = mesh.smoothLaplacian().subdivide(2)
meshes.append(mesh)
else:
if isinstance(reg, int):
entry = metadata.loc[metadata.Id == reg]
elif isinstance(reg, str):