Download Example Data

The physiotwin4d-download-data command downloads example datasets used by PhysioTwin4D tutorials and demos.

Supported Datasets

Data name

Description

Slicer-Heart-CT

Public 4D cardiac CT sample from SlicerHeart.

KCL-Heart-Model

King’s College London four-chamber heart model dataset: 20 individual heart meshes plus an average mesh, from Zenodo.

CHOP-Valve4D

CHOP Jolley Lab transcatheter pulmonary valve model, converted from the original FEBio model to VTK/ITK and segmented with Simpleware, from the PhysioTwin4D GitHub release. See data/CHOP-Valve4D/README.md.

Chest-CT

Ungated 3D chest CT, a single static volume, from the PhysioTwin4D GitHub release. See data/Chest-CT/README.md for the data source and required citation.

Basic Usage

Download a dataset into its default location:

physiotwin4d-download-data Slicer-Heart-CT

Running the command with no arguments prints usage/help instead of downloading anything.

Options

physiotwin4d-download-data [Slicer-Heart-CT|KCL-Heart-Model|CHOP-Valve4D|Chest-CT] [--directory DIRECTORY]
data_name

Dataset to download. One of Slicer-Heart-CT, KCL-Heart-Model, CHOP-Valve4D, or Chest-CT. Required — omitting it prints help and exits.

--directory

Directory where the dataset is stored. Defaults to data/<data_name>.

Output

For Slicer-Heart-CT, the command downloads the 4-D sequence and splits it into per-phase 3-D volumes:

data/Slicer-Heart-CT/TruncalValve_4DCT.seq.nrrd
data/Slicer-Heart-CT/slice_000.mha ... slice_020.mha

The command uses physiotwin4d.data_download_tools.DataDownloadTools.DownloadSlicerHeartCTData(), so repeated runs reuse the existing non-empty file and skip the split once the slice_???.mha files are present.

For KCL-Heart-Model, the command downloads, extracts, and reuses:

data/KCL-Heart-Model/average_mesh.vtk
data/KCL-Heart-Model/input_meshes/01.vtk ... 20.vtk

The command uses physiotwin4d.data_download_tools.DataDownloadTools.DownloadKCLHeartModelData(), which fetches each per-model .tar.gz archive from Zenodo, extracts its mesh, and skips archives whose target .vtk file is already present.

For CHOP-Valve4D, the command downloads, extracts, and reuses:

data/CHOP-Valve4D/Alterra/   (valve mesh time series, >1 GB)
data/CHOP-Valve4D/TPV25/     (valve mesh time series, >1 GB)
data/CHOP-Valve4D/CT/        (source CT volume and Simpleware segmentation)

The command uses physiotwin4d.data_download_tools.DataDownloadTools.DownloadCHOPValve4DData(), which fetches each subdirectory’s zip archive from the PhysioTwin4D GitHub release and skips a subdirectory once it has its expected extracted files (the CT volume or Simpleware segmentation for CT/, .vtk meshes for Alterra/ and TPV25/) — a subdirectory left behind by an interrupted extraction is re-downloaded rather than treated as complete.

For Chest-CT, the command downloads and reuses a single volume:

data/Chest-CT/Chest-CT.mha

The command uses physiotwin4d.data_download_tools.DataDownloadTools.DownloadChestCTData(), which fetches the volume from the PhysioTwin4D GitHub release and reuses an existing non-empty file, so re-running resumes an interrupted download.

See Also

  • Tutorials — Slicer-Heart-CT drives Heart Tutorials 1, 3 and 4; KCL-Heart-Model drives Heart Tutorial 6; Chest-CT drives Lung Tutorial 7 and Tutorial 13. DirLab-4DCT — Lung Tutorials 1, 2, 3, 4, 6, 8 and 10-12, plus Heart Tutorial 7 — is manual-only, see data/DirLab-4DCT/README.md. Duke-Heart-4DLabelmaps, which drives the ten duke_heart variants, is being released soon; see data/Duke-Heart-4DLabelmaps/README.md.

  • Bring Your Own Data - DICOM, Images & VTK to USD

  • Heart Gated CT Processing

  • CLI & Scripts Overview