scripts/gen-annotations/dataset_specs.py

"""Per-dataset build recipes for build_dataset.py.

One entry per dataset in the MedVision catalogue. Everything that can be derived is
derived instead of listed here:

  - the annotation version comes from _ANNOTATION_INDEX in MedVision.py (see
    build_dataset.py); this file records no version numbers at all;
  - whether a preprocess step accepts --reorient2RAS follows from the task kind and,
    for biometry, from _BIOMETRY_FAMILY in MedVision.py;
  - figure rendering needs no entry: --visualization is on by default in every
    biometry script that has it.

Field reference
---------------
pkg                   directory under src/medvision_ds/datasets/ (underscored)
download              module name: "download_raw" (build from source) or "download"
supports_max_workers  whether the download module accepts --max_workers
steps                 preprocess stages, in the order they must run
reorient              "download" | "preprocess" -- see the long note below
requires_env          environment variables the download WILL fail without
optional_env          environment variables that override a working public default
note                  anything a reader would otherwise have to reconstruct

The dict key is the RUNTIME dataset name passed as -n and used as the directory name
under $MedVision_DATA_DIR/Datasets/. It differs from `pkg` for ten datasets, and there
is no mapping table anywhere in the package -- the authority is the dataset_info
["dataset"] literal at the top of each preprocess_*.py, cross-checked here against
_ANNOTATION_INDEX.


The `reorient` field
--------------------
Ground truth is read in voxel/index space, so every annotation must be computed against
images that are already in RAS+. There are two places that can happen, and which one a
dataset uses is not a style choice.

reorient="download" -- do NOT pass --reorient2RAS to any preprocess step.

    These 8 datasets reorient to RAS+ inside their own download_raw.py, via
    reorient_niigz_RASplus_batch_inplace(), BEFORE any annotation is computed. The
    annotation steps therefore already see RAS+ voxels, and passing the flag again would
    be a pure no-op -- _reorient_niigz_RASplus() early-returns on an already-RAS file and,
    in the in-place case, writes nothing at all.

    It has to live in the downloader rather than the planner because three of them --
    AFIDs, PDDCA, VerSe -- derive landmark VOXEL INDICES at download time, and the
    landmark-biometry planner has no reorient2RAS parameter at all. Any reorientation
    after those indices exist would move the voxels out from under them.

    MAMA-MIA and PI-CAI are the two that learned this the hard way: their v1.2.0 shipped
    without it, was withdrawn, and was reissued as v1.2.1. See doc/release-v1.2.1.md.

    Ordering constraint inside each downloader: reorientation must come AFTER
    copy_img_header_to_mask(), which overwrites the mask affine with the image affine.
    Reorienting first would leave the mask carrying a pre-flip affine.

reorient="preprocess" -- pass --reorient2RAS to every step that accepts it.

    The remaining datasets ship in their source orientation and are reoriented in place by
    the planner, on the first annotation step. The flag is passed to every accepting step
    rather than only the first: repeat calls cost one header read per file, and it makes
    each step independently correct if someone runs just one of them.

    Ceph-Biometrics-400 ends up receiving the flag nowhere, and that is correct rather
    than special-cased: its only task is landmark biometry, whose planner does not accept
    the flag. Its images are 2D X-rays stored as array_size [1, 1935, 2400] with an
    identity affine, so they are already RAS in all 400 cases.
"""

DATASETS = {
    # ------------------------------------------------------------------ v1.0.0 era
    "ACDC": {
        "pkg": "ACDC",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "AMOS22": {
        "pkg": "AMOS22",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "AbdomenAtlas1.0Mini": {
        "pkg": "AbdomenAtlas__1_0__Mini",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "AbdomenCT-1K": {
        "pkg": "AbdomenCT_1K",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "BCV15": {
        "pkg": "BCV15",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": ["SYNAPSE_TOKEN"],
        "optional_env": [],
    },
    "BraTS24": {
        "pkg": "BraTS24",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": ["SYNAPSE_TOKEN"],
        "optional_env": [],
        "note": 'dataset_info["dataset"] is the empty string in all three preprocess '
                "scripts, so the name comes only from -n.",
    },
    "CAMUS": {
        "pkg": "CAMUS",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "Ceph-Biometrics-400": {
        "pkg": "Ceph_Biometrics_400",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["biometry"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
        "note": "Landmark biometry only, so --reorient2RAS is never passed (that planner "
                "does not accept it). 2D X-ray on an identity affine: already RAS.",
    },
    "CrossMoDA": {
        "pkg": "CrossMoDA",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "FLARE22": {
        "pkg": "FLARE22",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "FeTA24": {
        "pkg": "FeTA24",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": ["SYNAPSE_TOKEN"],
        "optional_env": [],
        "note": "Biometry reads Images-reoriented/, which download.py already produces in "
                "RAS+ via im_original_to_realigned(); the planner's recursive reorientation "
                "of the dataset directory is a no-op there.",
    },
    "HNTSMRG24": {
        "pkg": "HNTSMRG24",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "ISLES24": {
        "pkg": "ISLES24",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "KiPA22": {
        "pkg": "KiPA22",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": ["BiometricVQA_KiPA22_HF_ID"],
    },
    "KiTS23": {
        "pkg": "KiTS23",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "MSD": {
        "pkg": "MSD",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "OAIZIB-CM": {
        "pkg": "OAIZIB_CM",
        "download": "download",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "SKM-TEA": {
        "pkg": "SKM_TEA",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": ["MedVision_SKMTEA_HF_ID", "HF_TOKEN"],
        "note": "Downloads from a HuggingFace mirror; HF_TOKEN is needed only if that "
                "mirror is private for you.",
    },
    "ToothFairy2": {
        "pkg": "ToothFairy2",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": ["MedVision_ToothFairy2_HF_ID", "HF_TOKEN"],
        "note": "Same HuggingFace-mirror arrangement as SKM-TEA.",
    },
    "TopCoW24": {
        "pkg": "TopCoW24",
        "download": "download",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "TotalSegmentator": {
        "pkg": "TotalSegmentator",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    "autoPET-III": {
        "pkg": "autoPET_III",
        "download": "download_raw",
        "supports_max_workers": False,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "preprocess",
        "requires_env": [],
        "optional_env": [],
    },
    # ------------------------------------------- added in v1.2.0: reorient in download
    "AFIDs": {
        "pkg": "AFIDs",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
        "note": "Landmark biometry only. The 32 fiducials are converted to voxel indices "
                "at download time, which is why the reorientation must precede them.",
    },
    "DEEP-PSMA": {
        "pkg": "DEEP_PSMA",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
        "note": "Two tracers in separate image/mask folders so the subject-level split "
                "cannot put one patient's PSMA and FDG scans on opposite sides.",
    },
    "LIDC-IDRI": {
        "pkg": "LIDC_IDRI",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
    },
    "LNQ2023": {
        "pkg": "LNQ2023",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
    },
    "MAMA-MIA": {
        "pkg": "MAMA_MIA",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": ["SYNAPSE_TOKEN"],
        "optional_env": [],
        "note": "Upstream volumes are ('L','A','I') for DUKE and ('P','S','L') for "
                "ISPY1/NACT. The v1.2.0 annotations were recorded in those frames and "
                "withdrawn; v1.2.1 is the correction.",
    },
    "PDDCA": {
        "pkg": "PDDCA",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
        "note": "Only 33 of the 48 cases ship landmarks, so biometry uses its own "
                "Images-landmark/ folder while segmentation and detection use all 48.",
    },
    "PI-CAI": {
        "pkg": "PICAI",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
        "note": "Source .mha are LPS-derived. Same withdrawal and correction as MAMA-MIA.",
    },
    "VerSe": {
        "pkg": "VerSe",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
        "note": "Vertebral centroids are voxel indices in the NATIVE orientation and are "
                "mapped through native->world->RAS+ at download time. Only 250 of the 325 "
                "scans contain all of L1-L5, so biometry uses Images-lumbar/.",
    },
    # ------------------------------------------- added in v1.3.0: reorient in download
    "MSWAL": {
        "pkg": "MSWAL",
        "download": "download_raw",
        "supports_max_workers": True,
        "steps": ["segmentation", "detection", "biometry"],
        "reorient": "download",
        "requires_env": [],
        "optional_env": [],
        "note": "Upstream test split (210 cases) was never uploaded to HF; the 484 "
                "published imagesTr cases are re-split by the planner (seed 1024, 0.7).",
    },
}