def __init__(self, atlas_name=None):
"""
Brainrender's Atlas class subclasses BrainGlobeAtlas
to add methods to get regions meshes as Actors
and to get a plane at a given point and normal.
:param atlas_name: str, atlas name from brainglobe's atlas API atlases
"""
atlas_name = atlas_name or settings.DEFAULT_ATLAS
BrainGlobeAtlas.__init__(self,
atlas_name=atlas_name,
print_authors=False)
def __init__(self, atlas_name, *args, base_dir=None, **kwargs):
# Create brainglobe atlas
BrainGlobeAtlas.__init__(self, *args, atlas_name=atlas_name, **kwargs)
# Add brainrender paths
Paths.__init__(self, base_dir=base_dir, **kwargs)
self.meshes_folder = (
None # where the .obj mesh for each region is saved
)
# If it's a mouse atlas, add extra functionality
if "Mus musculus" == self.metadata["species"]:
ABA.__init__(self)
def __init__(self, atlas_name, *args, base_dir=None, **kwargs):
# Create brainglobe atlas
BrainGlobeAtlas.__init__(
self, *args, atlas_name=atlas_name, print_authors=False, **kwargs
)
# Add brainrender paths
Paths.__init__(self, base_dir=base_dir, **kwargs)
Enhanced.__init__(self)
# If it's a mouse atlas, add extra functionality
if "Mus musculus" == self.metadata["species"]:
ABA.__init__(self)
def update_atlas(atlas_name, force=False):
"""Updates a bg_atlasapi atlas from the latest
available version online.
Arguments:
----------
atlas_name: str
Name of the atlas to update.
force: bool
If False it checks if the atlas is already at the latest version
and doesn't update if that's the case.
"""
atlas = BrainGlobeAtlas(atlas_name=atlas_name)
# Check if we need to update
if not force:
if atlas.check_latest_version():
rprint(
f"[b][magenta2]bg_atlasapi: {atlas.atlas_name} is already updated "
+ f"(version: {_version_str_from_tuple(atlas.local_version)})[/b]"
)
return
# Delete atlas folder
rprint(
f"[b][magenta2]bg_atlasapi: updating {atlas.atlas_name}[/magenta2][/b]"
)
fld = atlas.brainglobe_dir / atlas.local_full_name
shutil.rmtree(fld)
if fld.exists():
raise ValueError(
"Something went wrong while tryint to delete the old version of the atlas, aborting."
)
# Download again
atlas.download_extract_file()
# Check that everything went well
rprint(
f"[b][magenta2]bg_atlasapi: {atlas.atlas_name} updated to version: "
+ f"{_version_str_from_tuple(atlas.remote_version)}[/magenta2][/b]"
)
def test_local_search():
brainglobe_dir = tempfile.mkdtemp()
interm_download_dir = tempfile.mkdtemp()
atlas = BrainGlobeAtlas(
"example_mouse_100um",
brainglobe_dir=brainglobe_dir,
interm_download_dir=interm_download_dir,
)
assert atlas.atlas_name in atlas.local_full_name
# Make a copy:
copy_filename = atlas.root_dir.parent / (atlas.root_dir.name + "_2")
shutil.copytree(atlas.root_dir, copy_filename)
with pytest.raises(FileExistsError) as error:
_ = BrainGlobeAtlas("example_mouse_100um",
brainglobe_dir=brainglobe_dir)
assert "Multiple versions of atlas" in str(error)
shutil.rmtree(brainglobe_dir)
shutil.rmtree(interm_download_dir)
def reader_function(path):
"""Take a path or list of paths and return a list of LayerData tuples.
Readers are expected to return data as a list of tuples, where each tuple
is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
both optional.
Parameters
----------
path : str or list of str
Path to file, or list of paths.
Returns
-------
layer_data : list of tuples
A list of LayerData tuples where each tuple in the list contains
(data, metadata, layer_type), where data is a numpy array, metadata is
a dict of keyword arguments for the corresponding viewer.add_* method
in napari, and layer_type is a lower-case string naming the type of layer.
Both "meta", and "layer_type" are optional. napari will default to
layer_type=="image" if not provided
"""
print("Loading brainreg directory")
path = Path(os.path.abspath(path))
with open(path / "brainreg.json") as json_file:
metadata = json.load(json_file)
atlas = BrainGlobeAtlas(metadata["atlas"])
metadata["atlas_class"] = atlas
layers = []
layers = load_additional_downsampled_channels(
path,
layers,
search_string="downsampled_standard",
exlusion_string="downsampled_standard.tiff",
)
layers.append((
tifffile.imread(path / "downsampled_standard.tiff"),
{
"name": "Registered image",
"metadata": metadata
},
"image",
))
layers = load_atlas(atlas, layers)
return layers
def main():
start_time = datetime.now()
args = register_cli_parser().parse_args()
arg_groups = get_arg_groups(args, register_cli_parser())
args = define_pixel_sizes(args)
args, additional_images_downsample = prep_registration(args)
paths = Paths(args.brainreg_directory)
log_metadata(paths.metadata_path, args)
fancylog.start_logging(
paths.registration_output_folder,
program_for_log,
variables=[args],
verbose=args.debug,
log_header="BRAINREG LOG",
multiprocessing_aware=False,
)
logging.info("Starting registration")
atlas = BrainGlobeAtlas(args.atlas)
register(
atlas,
args.orientation,
args.image_paths,
paths,
arg_groups["NiftyReg registration backend options"],
x_pixel_um=args.x_pixel_um,
y_pixel_um=args.y_pixel_um,
z_pixel_um=args.z_pixel_um,
sort_input_file=args.sort_input_file,
n_free_cpus=args.n_free_cpus,
additional_images_downsample=additional_images_downsample,
backend=args.backend,
debug=args.debug,
)
logging.info("Finished. Total time taken: %s", datetime.now() - start_time)
def install_atlas(atlas_name):
"""Installs a BrainGlobe atlas from the latest
available version online.
Arguments
---------
atlas_name : str
Name of the atlas to update.
"""
# Check input:
if not isinstance(atlas_name, str):
raise ValueError(f"atlas name should be a string, not {atlas_name}")
# Check if already downloaded:
available_atlases = get_downloaded_atlases()
if atlas_name in available_atlases:
rprint(
f"[b][magenta2]Bg_atlasapi: installing {atlas_name}: atlas already installed![/magenta2][/b]"
)
return
# Istantiate to download:
BrainGlobeAtlas(atlas_name)
def atlas():
return BrainGlobeAtlas("example_mouse_100um")
def atlas_path():
return BrainGlobeAtlas("example_mouse_100um").root_dir