Data Downloads

Helpers for downloading and verifying optional example datasets used by the tutorials and experiments.

Module Reference

Dataset download and verification helpers.

Slicer-Heart-CT, KCL-Heart-Model, CHOP-Valve4D, Chest-CT, TCIA-4DLung, and Duke-Heart-4DLabelmaps are downloaded automatically. Other datasets require manual download, and the verification helpers check the file layouts used by the repository tutorials, experiments, and tests.

class monai_physio.download_data.DownloadData[source]

Bases: object

Download and verify optional MONAI Physio example datasets.

SLICER_HEART_CT_URL = 'https://github.com/Project-MONAI/monai-physio/releases/download/2026.07.1/TruncalValve_4DCT.seq.nrrd'

SLICER_HEART_CT_FILENAME = 'TruncalValve_4DCT.seq.nrrd'

SLICER_HEART_CT_SLICE_BASENAME = 'slice'

static DownloadSlicerHeartCTData(dirname)[source]

Download the Slicer-Heart-CT 4-D CT sample into dirname.

Also splits the downloaded 4-D sequence into per-frame slice_???.mha volumes in the same directory (via ConvertImage4DTo3D), skipping the split if those files already exist.

Parameters:: dirname (Union[str, Path]) – Directory where TruncalValve_4DCT.seq.nrrd and the converted slice_???.mha files should live.
Return type:: Path
Returns:: Path to the downloaded or already-cached .seq.nrrd file.

static VerifySlicerHeartCTData(dirname)[source]

Return True when Slicer-Heart-CT has the expected 4-D CT file.

Return type:: bool

KCL_HEART_MODEL_MESH_COUNT = 20

KCL_HEART_MODEL_INDIVIDUAL_URL_TEMPLATE = 'https://zenodo.org/records/4590294/files/{index:02d}.tar.gz?download=1'

KCL_HEART_MODEL_AVERAGE_URL = 'https://zenodo.org/records/4593739/files/average.tar.gz?download=1'

static DownloadKCLHeartModelData(dirname)[source]

Download the KCL-Heart-Model dataset into dirname.

Downloads and extracts the 20 individual four-chamber heart meshes from https://zenodo.org/records/4590294 into dirname/input_meshes/01.vtk through 20.vtk, and the average heart mesh from https://zenodo.org/records/4593739 into dirname/average_mesh.vtk. Already-extracted files are reused.

Parameters:: dirname (Union[str, Path]) – Directory where the KCL-Heart-Model dataset should live.
Return type:: Path
Returns:: Path to dirname.

CHOP_VALVE4D_RELEASE_URL = 'https://github.com/Project-MONAI/monai-physio/releases/download/2026.07.1/'

CHOP_VALVE4D_ASSETS: ClassVar[dict[str, str]] = {'Alterra': 'CHOP-Valve4D-Alterra.zip', 'CT': 'CHOP-Valve4D-CT.zip', 'TPV25': 'CHOP-Valve4D-TPV25.zip'}

static DownloadCHOPValve4DData(dirname)[source]

Download the CHOP-Valve4D convenience release into dirname.

Downloads the three zip archives attached to the MONAI Physio 2026.07.1 GitHub release (https://github.com/Project-MONAI/monai-physio/releases/tag/2026.07.1) and extracts each into its matching subdirectory: Alterra/ and TPV25/ (valve mesh time series, >1 GB each) and CT/ (source CT volume and Simpleware segmentation). A subdirectory that already has its expected files (see _CHOPValve4DSubdirIsPopulated) is left alone, so re-running resumes an interrupted download without re-fetching a subdirectory a partial extraction left behind. See data/CHOP-Valve4D/README.md for what this converted data contains and how it relates to the original FEBio source model.

Parameters:: dirname (Union[str, Path]) – Directory where the CHOP-Valve4D dataset should live.
Return type:: Path
Returns:: Path to dirname.

static VerifyCHOPValve4DData(dirname)[source]

Return True when CHOP-Valve4D files referenced by the repo exist.

Accepted layouts are the CT volume used by Simpleware/model-to-patient experiments and the valve time-series folders used by VTK-to-USD experiments.

Return type:: bool

CHEST_CT_URL = 'https://github.com/Project-MONAI/monai-physio/releases/download/2026.07.1/Chest-CT.mha'

CHEST_CT_FILENAME = 'Chest-CT.mha'

static DownloadChestCTData(dirname)[source]

Download the Chest-CT sample volume into dirname.

Fetches Chest-CT.mha - an ungated 3-D chest CT - from the MONAI Physio 2026.07.1 GitHub release. An existing non-empty file is reused, so re-running resumes an interrupted download. See data/Chest-CT/README.md for the data source and required citation.

Parameters:: dirname (Union[str, Path]) – Directory where Chest-CT.mha should live.
Return type:: Path
Returns:: Path to the downloaded or already-cached Chest-CT.mha file.

static VerifyChestCTData(dirname)[source]

Return True when Chest-CT has its expected CT volume.

Return type:: bool

TCIA_4D_LUNG_RELEASE_URL = 'https://github.com/Project-MONAI/monai-physio/releases/download/2026.07.1/'

TCIA_4D_LUNG_ASSETS: ClassVar[list[str]] = ['TCIA-4DLung-Part1.zip', 'TCIA-4DLung-Part2.zip']

static DownloadTCIA4DLungData(dirname)[source]

Download the TCIA-4DLung converted-subset release into dirname.

Fetches the two zip archives attached to the MONAI Physio 2026.07.1 GitHub release and extracts them directly into dirname, giving the per-case <case>/<case>_g0??.nii.gz phase volumes the lung tutorials read. This is a tutorial subset of the full TCIA 4D-Lung collection; see data/TCIA-4DLung/README.md for how to obtain the full collection manually. Already-populated data is left alone, so re-running is a no-op once the subset is present.

Parameters:: dirname (Union[str, Path]) – Directory where the TCIA-4DLung dataset should live.
Return type:: Path
Returns:: Path to dirname.

static VerifyTCIA4DLungData(dirname)[source]

Return True when TCIA-4DLung has at least one case’s phase volumes.

Return type:: bool

DUKE_HEART_4D_LABELMAPS_URL = 'https://github.com/Project-MONAI/monai-physio/releases/download/2026.07.1/Duke-Heart-4DLabelmaps.zip'

static DownloadDukeHeart4DLabelmapsData(dirname)[source]

Download the Duke-Heart-4DLabelmaps release into dirname.

Fetches Duke-Heart-4DLabelmaps.zip from the MONAI Physio 2026.07.1 GitHub release and extracts it directly into dirname, giving the per-case pm00*/ directories of *_labelmap.nii.gz and *_landmark.mrk.json files. The labelmaps were generated with the ASCardio module of Simpleware (SegmentHeartSimplewareTrimmedBranches); models trained on them should only be applied to labelmaps generated the same way. See data/Duke-Heart-4DLabelmaps/README.md. Already-populated data is left alone, so re-running is a no-op once the data is present.

Parameters:: dirname (Union[str, Path]) – Directory where the Duke-Heart-4DLabelmaps dataset should live.
Return type:: Path
Returns:: Path to dirname.

static VerifyDukeHeart4DLabelmapsData(dirname)[source]

Return True when Duke-Heart-4DLabelmaps has at least one labelmap.

Return type:: bool

static VerifyDirLab4DCTData(dirname)[source]

Return True when a supported DirLab-4DCT case layout exists.

Return type:: bool

DIRLAB_4DCT_HU_OFFSET = 1024

DIRLAB_4DCT_HU_CLIP_RANGE = (-1024, 1024)

static FixDirLab4DCTData(dirname, output_dirname=None)[source]

Convert DirLab-4DCT raw intensities to clipped Hounsfield units.

DirLab-4DCT’s raw .img/.mhd volumes store intensities offset by +1024 from Hounsfield units. This finds every .mhd header under dirname (recursively) whose raw data has been downloaded, subtracts 1024, clips the result to DIRLAB_4DCT_HU_CLIP_RANGE, and writes the corrected volume with the same base filename but a .mha extension, compressed.

Parameters:

dirname (Union[str, Path]) – Directory to search recursively for .mhd headers.
output_dirname (Union[str, Path, None]) – Directory to write the .mha files into. Defaults to writing each result next to its source .mhd header.

Return type:

list[Path]

Returns:

Paths to the written .mha files.

PHYSICSNEMO_MGN_LUNG_MOTION_URL = 'https://github.com/Project-MONAI/monai-physio/releases/download/2026.07.1/physicsnemo_mgn_lung_motion.zip'

PHYSICSNEMO_MGN_LUNG_MOTION_DIRNAME = 'physicsnemo_mgn_lung_motion'

static DownloadPhysicsNeMoMGNLungMotionData(dirname)[source]

Download the pretrained lung-motion PhysicsNeMo MGN checkpoint.

Fetches physicsnemo_mgn_lung_motion.zip from the MONAI Physio 2026.07.1 GitHub release and extracts it into dirname, giving the physicsnemo_mgn_lung_motion/mgn_stage_model.pt checkpoint Tutorial 10 and later lung tutorials read. Already-extracted data is left alone, so re-running is a no-op once it is present.

Parameters:: dirname (Union[str, Path]) – Directory where physicsnemo_mgn_lung_motion/ should live, typically tutorials/network_weights.
Return type:: Path
Returns:: Path to dirname/physicsnemo_mgn_lung_motion.

static VerifyPhysicsNeMoMGNLungMotionData(dirname)[source]

Return True when the lung-motion PhysicsNeMo MGN checkpoint exists.

Return type:: bool

static VerifyKCLHeartModelData(dirname)[source]

Return True when KCL-Heart-Model has its expected mesh inputs.

Return type:: bool

Navigation

Test Tools | Utility Modules