Cardiac atlases

cardiac-geometries also have support for downloading and converting geometries coming from atlases. Currently we only support data coming from the Bai et. al atlas which is found at https://zenodo.org/records/4506463

You can use the command

!cardiac-geometries atlas-bai --help

                                                                                
 Usage: cardiac-geometries atlas-bai [OPTIONS] N                                
                                                                                
 Create meshes from instances of https://zenodo.org/records/4506463             
                                                                                
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --outdir         -o  DIRECTORY  Output directory, default is 'bai-atlas'     │
│ --force          -f             Force regeneration of files                  │
│ --verbose        -v             Print more information                       │
│ --copy-original                 Copy original files into output directory    │
│ --create-fibers                 Create fibers with LDRB algorithm            │
│ --coarsening     -c             Coarsen the mesh                             │
│ --ffun                          Create facet function                        │
│ --help                          Show this message and exit.                  │
╰──────────────────────────────────────────────────────────────────────────────╯

to work with the atlas data. For example say you want to download data for instance number 4, then you can do

!cardiac-geometries atlas-bai 4 -o atlas-data

Downloading https://zenodo.org/records/4506463/files/instances_001_to_010.tar.gz?download=1 to /__w/cardiac-geometries/cardiac-geometries/docs/atlas-data/instances_001_to_010.tar.gz. This may take a while.

Done downloading.
Extracting...

INFO:cardiac_geometries.bai_atlas:Creating output directory: /__w/cardiac-geometries/cardiac-geometries/docs/atlas-data/instance_004
INFO:cardiac_geometries.bai_atlas:Converting /__w/cardiac-geometries/cardiac-geometries/docs/atlas-data/instances_001_to_010/instance_004.vtp to dolfin xdmf

Warning: Meshio cannot handle (type Strips) but we explicitly convert them to 
triangles here.

INFO:cardiac_geometries.bai_atlas:Converting /__w/cardiac-geometries/cardiac-geometries/docs/atlas-data/instances_001_to_010/instance_004.vtu to dolfin xdmf

which will output the data in the folder atlas-data

!ls -R atlas-data

atlas-data:
instance_004  instances_001_to_010  instances_001_to_010.tar.gz

atlas-data/instance_004:
original

atlas-data/instance_004/original:
mesh.h5    surface_data.h5    surface_mesh.h5	 volume_data.h5
mesh.xdmf  surface_data.xdmf  surface_mesh.xdmf  volume_data.xdmf

atlas-data/instances_001_to_010:
instance_001.vtp  instance_003.vtu  instance_006.vtp  instance_008.vtu
instance_001.vtu  instance_004.vtp  instance_006.vtu  instance_009.vtp
instance_002.vtp  instance_004.vtu  instance_007.vtp  instance_009.vtu
instance_002.vtu  instance_005.vtp  instance_007.vtu  instance_010.vtp
instance_003.vtp  instance_005.vtu  instance_008.vtp  instance_010.vtu

Now the data inside atlas-data/instance_004/original can be read by dolfin.