Datasets:
[src] fix: fetch QC figures on every load and track them per annotation version
Browse filesThe fetch used to sit in _split_generators, which made it unreachable after a
config's first build: datasets consults the Arrow cache after _info() and skips
_split_generators on a hit, so a machine whose figures had gone stale could not
obtain the current ones by any means short of deleting that cache.
QC figures:
- move the fetch into _ensure_qc_figures and call it from BOTH _info() and
_split_generators. _info() is the only hook a warm-cache load reaches, since
DatasetBuilder.__init__ runs it before the cache directory is consulted --
the same reasoning that put the paused-annotation gate there
- defer in _info() while the dataset's files are absent, so a first install is
served by the _split_generators call site instead. That one runs after step
3.3, whose reorientation pass globs "<dataset_dir>/**/*.nii.gz" recursively and
would otherwise walk hundreds of thousands of freshly extracted PNGs per
dataset for nothing. The two conditions are complementary: a warm cache skips
_split_generators, but having been built at all implies the files are on disk
- memoise per (data root, dataset, requested version): _info() runs once per
config, a sweep constructs hundreds of them over a handful of datasets, and an
annotation-version bump fires both call sites, since planner_version changes
and the config_id is therefore cold
- not covered, and deliberately so: a data directory deleted while its HF cache
is kept. That state already yields rows whose image_file paths do not exist,
and MedVision_FORCE_DOWNLOAD_DATA=True rebuilds out of it
- record "qc_figures_<dataset>" in .downloaded_datasets.json as the biometry
annotation version the figures belong to rather than a bare true, so a release
that regenerates a dataset re-fetches its figures while one that leaves the
dataset alone re-pulls nothing; keying on the release version instead would
invalidate all 295 GB on every release
- resolve the wanted version from the dataset's declared biometry versions --
figures are generated with the biometry plans and their directories carry that
version (Landmarks-Label2-fig-v1.4.0) -- whatever task type the config loads
- fall back to reading those directories when the tracker names no usable
version, which is every install predating v1.4.0: the figures shipped inside
Datasets/<name>.zip then, so such a machine already holds the set but never ran
a figure download to record it
- treat a legacy `true` as "version unknown" so it neither forces a blanket
re-pull nor blocks a genuine refresh; MedVision_FORCE_DOWNLOAD_DATA still
overrides the skip
- keep _figure_versions bounded: os.scandir over only the two directory levels
the archives use, emptiness tested by first entry, so a directory holding
hundreds of thousands of PNGs is never enumerated; an empty one does not count,
since that is the shape a crashed extract leaves behind
- five datasets predate the -fig-v{X} naming (AFIDs, Ceph-Biometrics-400,
FeTA24, PDDCA, VerSe); for them presence is the only on-disk signal, and the
tracker entry is what still lets a later release invalidate them
- keep the directory regex identical to FIG_COMPONENT in
scripts/split_qc_figures.py, which decided what went into those archives
- wrap both call sites in _try_ensure_qc_figures so a Hub failure warns instead
of raising. _info() runs inside DatasetBuilder.__init__, so an exception there
blocked even a fully cached local dataset from loading. Swallowing is safe here
in a way it is not at step 3.2: the tracker entry is written last and only on a
clean pass, so a failure leaves it unwritten and the next load retries, rather
than stamping a marker later runs would trust
- create the data root explicitly rather than relying on filelock to make the
parent of the lock files it opens, which is not a documented guarantee
Configs:
- add the 8 DEEP-PSMA and 4 LNQ2023 tumour/lesion sagittal+coronal configs; every
other T/L dataset already published all three planes
- MedVision.py +464 -88
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@@ -452,6 +452,107 @@ def _discover_versions(dataset_dir, kind):
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return sorted(found, key=_version_tuple)
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| 455 |
def _check_biometry_family(dataset_name, task_type):
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"""Fail loudly if a dataset's biometry plan could be the wrong family."""
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| 457 |
if _PLAN_KIND_BY_TASKTYPE.get(task_type) != "biometry":
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@@ -786,6 +887,189 @@ def _enforce_release_ack(planner_version, latest_version, ack_value=None,
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)
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| 789 |
class MedVisionConfig(BuilderConfig):
|
| 790 |
"""BuilderConfig for MedVision."""
|
| 791 |
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|
@@ -9660,6 +9944,46 @@ class MedVision(GeneratorBasedBuilder):
|
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| 9660 |
split="test",
|
| 9661 |
),
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| 9662 |
# DEEP-PSMA:Tumor-Lesion-Size:Task01
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| 9663 |
MedVisionConfig(
|
| 9664 |
name="DEEP-PSMA_TumorLesionSize_Task01_Axial_Train",
|
| 9665 |
dataset_name="DEEP-PSMA",
|
|
@@ -9681,6 +10005,46 @@ class MedVision(GeneratorBasedBuilder):
|
|
| 9681 |
split="test",
|
| 9682 |
),
|
| 9683 |
# DEEP-PSMA:Tumor-Lesion-Size:Task02
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| 9684 |
MedVisionConfig(
|
| 9685 |
name="DEEP-PSMA_TumorLesionSize_Task02_Axial_Train",
|
| 9686 |
dataset_name="DEEP-PSMA",
|
|
@@ -10007,6 +10371,46 @@ class MedVision(GeneratorBasedBuilder):
|
|
| 10007 |
split="test",
|
| 10008 |
),
|
| 10009 |
# LNQ2023:Tumor-Lesion-Size:Task01
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|
| 10010 |
MedVisionConfig(
|
| 10011 |
name="LNQ2023_TumorLesionSize_Task01_Axial_Train",
|
| 10012 |
dataset_name="LNQ2023",
|
|
@@ -11184,6 +11588,56 @@ class MedVision(GeneratorBasedBuilder):
|
|
| 11184 |
_paused_versions(self.config.dataset_name, _kind),
|
| 11185 |
)
|
| 11186 |
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|
| 11187 |
# Define dataset information including feature schema
|
| 11188 |
dataset_description = f"You are using the configuration <{self.config.name}> of the <{self.config.dataset_name}> dataset."
|
| 11189 |
return DatasetInfo(
|
|
@@ -11592,96 +12046,18 @@ class MedVision(GeneratorBasedBuilder):
|
|
| 11592 |
_discover_versions(dataset_dir, _kind),
|
| 11593 |
)
|
| 11594 |
|
| 11595 |
-
# 3.5 QC figures
|
| 11596 |
-
#
|
| 11597 |
-
#
|
| 11598 |
-
#
|
| 11599 |
-
#
|
| 11600 |
-
#
|
| 11601 |
-
#
|
| 11602 |
-
#
|
| 11603 |
-
# single archive would again clear 50 GB.
|
| 11604 |
-
#
|
| 11605 |
-
# The archives carry the SAME arcnames the figures had inside the dataset
|
| 11606 |
-
# archive, so restoring them is the same extractall into the same root: every
|
| 11607 |
-
# figure lands back at the path it used to occupy. Nothing is relocated
|
| 11608 |
-
# afterwards, so there is no path mapping here that can drift out of step
|
| 11609 |
-
# with whatever wrote the archives. Shards are independent zips, not `zip -s`
|
| 11610 |
-
# volumes, so they extract in any order and a missing one costs only its own
|
| 11611 |
-
# figures.
|
| 11612 |
-
#
|
| 11613 |
-
# This sits OUTSIDE the `_needs_download` block deliberately. A user who sets
|
| 11614 |
-
# the flag on a machine whose annotations are already present takes the
|
| 11615 |
-
# "using existing dataset" branch above, and would otherwise never get the
|
| 11616 |
-
# figures at all.
|
| 11617 |
if download_qc_figures:
|
| 11618 |
-
|
| 11619 |
-
MedVision_data_dir,
|
| 11620 |
)
|
| 11621 |
-
with FileLock(_fig_lock_file):
|
| 11622 |
-
# Re-read the tracker inside the lock instead of trusting the copy
|
| 11623 |
-
# loaded at entry: a sibling config of the same dataset may have
|
| 11624 |
-
# fetched the figures while this process waited. Lock order stays
|
| 11625 |
-
# zip-lock -> tracker-lock, matching step 3.1, so it cannot invert.
|
| 11626 |
-
_figs_present = False
|
| 11627 |
-
with FileLock(dataset_cache_lock_file):
|
| 11628 |
-
if os.path.exists(dataset_cache_file):
|
| 11629 |
-
try:
|
| 11630 |
-
with open(dataset_cache_file, "r") as f:
|
| 11631 |
-
_figs_present = bool(
|
| 11632 |
-
json.load(f).get(f"qc_figures_{dataset_name}")
|
| 11633 |
-
)
|
| 11634 |
-
except Exception:
|
| 11635 |
-
_figs_present = False
|
| 11636 |
-
|
| 11637 |
-
if _figs_present and not force_download_data:
|
| 11638 |
-
logger.info(
|
| 11639 |
-
f" - QC figures for {dataset_name} already on disk; skipping"
|
| 11640 |
-
)
|
| 11641 |
-
else:
|
| 11642 |
-
logger.info(f"Downloading QC figures for {dataset_name}...")
|
| 11643 |
-
_datasets_root = os.path.join(MedVision_data_dir, "Datasets")
|
| 11644 |
-
snapshot_download(
|
| 11645 |
-
repo_id="YongchengYAO/MedVision",
|
| 11646 |
-
repo_type="dataset",
|
| 11647 |
-
allow_patterns=[
|
| 11648 |
-
f"Datasets/{dataset_name}_fig.zip",
|
| 11649 |
-
f"Datasets/{dataset_name}_fig.part*.zip",
|
| 11650 |
-
],
|
| 11651 |
-
local_dir=MedVision_data_dir,
|
| 11652 |
-
max_workers=self.config.num_proc,
|
| 11653 |
-
)
|
| 11654 |
-
_fig_zips = sorted(
|
| 11655 |
-
glob.glob(
|
| 11656 |
-
os.path.join(_datasets_root, f"{dataset_name}_fig.zip")
|
| 11657 |
-
)
|
| 11658 |
-
+ glob.glob(
|
| 11659 |
-
os.path.join(
|
| 11660 |
-
_datasets_root, f"{dataset_name}_fig.part*.zip"
|
| 11661 |
-
)
|
| 11662 |
-
)
|
| 11663 |
-
)
|
| 11664 |
-
# Roughly half the datasets have no figures at all. Record the
|
| 11665 |
-
# attempt anyway so a figure-less dataset does not re-query the
|
| 11666 |
-
# Hub on every single load; MedVision_FORCE_DOWNLOAD_DATA is the
|
| 11667 |
-
# way back if figures are published for it later.
|
| 11668 |
-
if not _fig_zips:
|
| 11669 |
-
logger.info(
|
| 11670 |
-
f" - No QC figures are published for {dataset_name}"
|
| 11671 |
-
)
|
| 11672 |
-
else:
|
| 11673 |
-
for _fig_zip in _fig_zips:
|
| 11674 |
-
with zipfile.ZipFile(_fig_zip, "r") as zip_ref:
|
| 11675 |
-
zip_ref.extractall(_datasets_root)
|
| 11676 |
-
os.remove(_fig_zip)
|
| 11677 |
-
logger.info(
|
| 11678 |
-
f" - QC figures restored to {dataset_dir} from "
|
| 11679 |
-
f"{len(_fig_zips)} archive(s)"
|
| 11680 |
-
)
|
| 11681 |
-
# Written last, and only on a clean pass: a crash mid-extract
|
| 11682 |
-
# leaves the flag unset, so the next load redoes the whole
|
| 11683 |
-
# download and extractall overwrites whatever landed.
|
| 11684 |
-
_update_download_status(f"qc_figures_{dataset_name}", True)
|
| 11685 |
|
| 11686 |
# 4. Get the benchmark planner file - this is config specific but should use existing files if possible
|
| 11687 |
# NOTE: MUST NOT move the import to the front, as the "medvision_ds" package may not be installed yet at the beginning
|
|
|
|
| 452 |
return sorted(found, key=_version_tuple)
|
| 453 |
|
| 454 |
|
| 455 |
+
# A path COMPONENT that is a QC-figure directory: "Landmarks-Label1-fig-v1.4.0",
|
| 456 |
+
# "Landmarks-fig", "Landmarks-fig-w-projection". Kept identical to FIG_COMPONENT
|
| 457 |
+
# in scripts/split_qc_figures.py, which is what decided the CONTENTS of the _fig
|
| 458 |
+
# archives: a probe that disagreed with the splitter would either call a dataset
|
| 459 |
+
# "already has figures" on directories the archives never carried, or miss the
|
| 460 |
+
# ones they did. The leading hyphen is what keeps this off innocent names --
|
| 461 |
+
# "config" contains "fig" but not "-fig".
|
| 462 |
+
_FIG_COMPONENT = re.compile(r"-fig(?:-|$)")
|
| 463 |
+
|
| 464 |
+
# The annotation version a figure directory belongs to. Figures are generated
|
| 465 |
+
# alongside the biometry plans and carry the same version, so
|
| 466 |
+
# "Landmarks-Label2-fig-v1.4.0" holds the figures for biometry v1.4.0. Five
|
| 467 |
+
# datasets (AFIDs, Ceph-Biometrics-400, FeTA24, PDDCA, VerSe) predate the
|
| 468 |
+
# convention and have only unversioned directories; they are handled separately
|
| 469 |
+
# rather than being forced into it.
|
| 470 |
+
_FIG_VERSION = re.compile(r"-fig-v(\d+\.\d+\.\d+)$")
|
| 471 |
+
|
| 472 |
+
|
| 473 |
+
def _figure_versions(dataset_dir):
|
| 474 |
+
"""QC-figure state on disk: (annotation versions present, any unversioned dir).
|
| 475 |
+
|
| 476 |
+
Answers a different question from the tracker's qc_figures_<name> key. The
|
| 477 |
+
tracker records which version was fetched HERE; this records what is actually
|
| 478 |
+
on disk, however it arrived. Only the second one covers an install made before
|
| 479 |
+
v1.4.0, when the figures shipped INSIDE Datasets/<name>.zip: such a machine
|
| 480 |
+
holds figures already, yet no figure download ever ran on it, so the key
|
| 481 |
+
cannot exist and the tracker alone would re-pull the entire set.
|
| 482 |
+
|
| 483 |
+
Bounded on purpose. Only the two directory levels the archives use are
|
| 484 |
+
scanned - <dataset>/<figdir> and <dataset>/<subset>/<figdir>, the latter for
|
| 485 |
+
the subset-bearing datasets (BraTS24/BraTS24-GLI/...). os.scandir, not glob:
|
| 486 |
+
glob would stat every sibling of every Images/ tree on the way past, and the
|
| 487 |
+
emptiness test stops at the first entry so a directory holding hundreds of
|
| 488 |
+
thousands of PNGs is never enumerated.
|
| 489 |
+
|
| 490 |
+
A figure directory that exists but is EMPTY does not count. That is the shape
|
| 491 |
+
a crashed extract leaves behind, and treating it as present would suppress
|
| 492 |
+
the retry forever. A half-filled one still counts - the same limitation the
|
| 493 |
+
tracker has always had, since it is written only after a clean pass and a
|
| 494 |
+
partial extract is indistinguishable from a complete one without a manifest.
|
| 495 |
+
"""
|
| 496 |
+
|
| 497 |
+
def _subdirs(path):
|
| 498 |
+
try:
|
| 499 |
+
with os.scandir(path) as it:
|
| 500 |
+
return [e for e in it if e.is_dir()]
|
| 501 |
+
except OSError:
|
| 502 |
+
return []
|
| 503 |
+
|
| 504 |
+
def _nonempty(path):
|
| 505 |
+
try:
|
| 506 |
+
with os.scandir(path) as it:
|
| 507 |
+
return any(True for _ in it)
|
| 508 |
+
except OSError:
|
| 509 |
+
return False
|
| 510 |
+
|
| 511 |
+
versions, unversioned = set(), False
|
| 512 |
+
|
| 513 |
+
def _record(name, path):
|
| 514 |
+
nonlocal unversioned
|
| 515 |
+
if not _nonempty(path):
|
| 516 |
+
return
|
| 517 |
+
match = _FIG_VERSION.search(name)
|
| 518 |
+
if match:
|
| 519 |
+
versions.add(match.group(1))
|
| 520 |
+
else:
|
| 521 |
+
unversioned = True
|
| 522 |
+
|
| 523 |
+
for _lvl1 in _subdirs(dataset_dir):
|
| 524 |
+
if _FIG_COMPONENT.search(_lvl1.name):
|
| 525 |
+
_record(_lvl1.name, _lvl1.path)
|
| 526 |
+
else:
|
| 527 |
+
for _lvl2 in _subdirs(_lvl1.path):
|
| 528 |
+
if _FIG_COMPONENT.search(_lvl2.name):
|
| 529 |
+
_record(_lvl2.name, _lvl2.path)
|
| 530 |
+
return versions, unversioned
|
| 531 |
+
|
| 532 |
+
|
| 533 |
+
def _figures_current(dataset_dir, target):
|
| 534 |
+
"""Whether the figures on disk cover the annotation version being loaded.
|
| 535 |
+
|
| 536 |
+
`target` is the biometry version this request resolves to - figures track the
|
| 537 |
+
biometry plans, so that is the only version that can be asked about. A
|
| 538 |
+
dataset that publishes no biometry has no figures either, which is `target is
|
| 539 |
+
None` and is decided by the caller.
|
| 540 |
+
|
| 541 |
+
Exact membership, not ">=": the figure archive carries every version's
|
| 542 |
+
directories at once, so holding v1.4.0 but not the v1.2.0 a pin asked for
|
| 543 |
+
means the extract is incomplete, and re-fetching is the right answer.
|
| 544 |
+
|
| 545 |
+
The unversioned fallback exists for the five datasets whose figures predate
|
| 546 |
+
the "-fig-v{X}" convention. For them presence is the only signal available;
|
| 547 |
+
the tracker entry written alongside is what lets a later release still
|
| 548 |
+
invalidate them.
|
| 549 |
+
"""
|
| 550 |
+
versions, unversioned = _figure_versions(dataset_dir)
|
| 551 |
+
if versions:
|
| 552 |
+
return target in versions
|
| 553 |
+
return unversioned
|
| 554 |
+
|
| 555 |
+
|
| 556 |
def _check_biometry_family(dataset_name, task_type):
|
| 557 |
"""Fail loudly if a dataset's biometry plan could be the wrong family."""
|
| 558 |
if _PLAN_KIND_BY_TASKTYPE.get(task_type) != "biometry":
|
|
|
|
| 887 |
)
|
| 888 |
|
| 889 |
|
| 890 |
+
# QC figures already handled in THIS process, keyed by (data root, dataset,
|
| 891 |
+
# requested version). _info() runs once per config and a sweep constructs
|
| 892 |
+
# hundreds of them, all resolving to a handful of datasets; without this the
|
| 893 |
+
# directory scan and tracker read repeat for every one of them.
|
| 894 |
+
_QC_FIGURES_DONE = set()
|
| 895 |
+
|
| 896 |
+
|
| 897 |
+
def _tracker_read(data_dir, key):
|
| 898 |
+
"""One key out of .downloaded_datasets.json, or None."""
|
| 899 |
+
path = os.path.join(data_dir, ".downloaded_datasets.json")
|
| 900 |
+
with FileLock(path + ".lock"):
|
| 901 |
+
if os.path.exists(path):
|
| 902 |
+
try:
|
| 903 |
+
with open(path, "r") as f:
|
| 904 |
+
return json.load(f).get(key)
|
| 905 |
+
except Exception:
|
| 906 |
+
return None
|
| 907 |
+
return None
|
| 908 |
+
|
| 909 |
+
|
| 910 |
+
def _tracker_write(data_dir, key, value):
|
| 911 |
+
"""Set one key in .downloaded_datasets.json, preserving the rest."""
|
| 912 |
+
path = os.path.join(data_dir, ".downloaded_datasets.json")
|
| 913 |
+
with FileLock(path + ".lock"):
|
| 914 |
+
current = {}
|
| 915 |
+
if os.path.exists(path):
|
| 916 |
+
try:
|
| 917 |
+
with open(path, "r") as f:
|
| 918 |
+
current = json.load(f)
|
| 919 |
+
except Exception:
|
| 920 |
+
current = {}
|
| 921 |
+
current[key] = value
|
| 922 |
+
with open(path, "w") as f:
|
| 923 |
+
json.dump(current, f)
|
| 924 |
+
|
| 925 |
+
|
| 926 |
+
def _try_ensure_qc_figures(dataset_name, requested, data_dir, num_proc):
|
| 927 |
+
"""_ensure_qc_figures, but a failure warns instead of aborting the load.
|
| 928 |
+
|
| 929 |
+
The figures are review material -- nothing in this loader reads them and no
|
| 930 |
+
task needs them -- so a transient Hub error or a half-written archive must not
|
| 931 |
+
take down a dataset that is otherwise fine. It would otherwise do exactly
|
| 932 |
+
that: _info() runs inside DatasetBuilder.__init__, so raising here blocks even
|
| 933 |
+
a fully cached local dataset from loading at all.
|
| 934 |
+
|
| 935 |
+
Swallowing is safe here in a way it is NOT at step 3.2, which deliberately
|
| 936 |
+
lets failures out. That one guards the completion marker: a swallowed error
|
| 937 |
+
there would stamp "installed" onto a dataset with no images, and every later
|
| 938 |
+
run would trust it. Here the tracker entry is written last and only on a clean
|
| 939 |
+
pass, so a failure simply leaves it unwritten and the next load retries.
|
| 940 |
+
"""
|
| 941 |
+
try:
|
| 942 |
+
_ensure_qc_figures(dataset_name, requested, data_dir, num_proc)
|
| 943 |
+
except Exception as exc:
|
| 944 |
+
logger.warning(
|
| 945 |
+
"QC figures for %s could not be fetched (%s: %s). The dataset itself "
|
| 946 |
+
"is unaffected; the next load retries. Set "
|
| 947 |
+
"MedVision_DOWNLOAD_QC_FIGURES=False to stop trying.",
|
| 948 |
+
dataset_name, type(exc).__name__, exc,
|
| 949 |
+
)
|
| 950 |
+
|
| 951 |
+
|
| 952 |
+
def _ensure_qc_figures(dataset_name, requested, data_dir, num_proc):
|
| 953 |
+
"""Fetch the per-slice QC figures for one dataset, if they are not current.
|
| 954 |
+
|
| 955 |
+
Called from _info(), not from _split_generators: datasets consults the Arrow
|
| 956 |
+
cache after _info() and short-circuits _split_generators when it hits, so a
|
| 957 |
+
fetch placed there runs on a config's first build and never again. _info()
|
| 958 |
+
runs on every load, warm cache or cold.
|
| 959 |
+
|
| 960 |
+
Until v1.4.0 the figures shipped inside Datasets/<name>.zip. They are ~99% of
|
| 961 |
+
that payload -- 298 GB of PNG against 3 GB of annotation -- nothing in this
|
| 962 |
+
loader reads them, and they pushed BraTS24.zip to 72.6 GB and MSD.zip to
|
| 963 |
+
51.4 GB, past HuggingFace's 50 GB per-file limit, which is a hard publish
|
| 964 |
+
failure (HTTP 422). They now ship as Datasets/<name>_fig.zip, or
|
| 965 |
+
<name>_fig.partNN.zip where a single archive would again clear 50 GB.
|
| 966 |
+
|
| 967 |
+
The archives carry the SAME arcnames the figures had inside the dataset
|
| 968 |
+
archive, so restoring them is the same extractall into the same root: every
|
| 969 |
+
figure lands back at the path it used to occupy. Shards are independent zips,
|
| 970 |
+
not `zip -s` volumes, so they extract in any order and a missing one costs
|
| 971 |
+
only its own figures.
|
| 972 |
+
"""
|
| 973 |
+
_memo = (data_dir, dataset_name, requested)
|
| 974 |
+
if _memo in _QC_FIGURES_DONE:
|
| 975 |
+
return
|
| 976 |
+
force = (
|
| 977 |
+
os.environ.get("MedVision_FORCE_DOWNLOAD_DATA", "False").lower() == "true"
|
| 978 |
+
)
|
| 979 |
+
dataset_dir = os.path.join(data_dir, "Datasets", dataset_name)
|
| 980 |
+
# _split_generators creates the data root, but this can run before it -- and
|
| 981 |
+
# from _info(), which runs before _split_generators exists to be reached at
|
| 982 |
+
# all. The locks below are created INSIDE data_dir, and filelock only happens
|
| 983 |
+
# to make their parents; that is not a documented guarantee, so do not depend
|
| 984 |
+
# on the version installed.
|
| 985 |
+
os.makedirs(data_dir, exist_ok=True)
|
| 986 |
+
|
| 987 |
+
# Datasets/<name>_fig.zip is ONE shared path per dataset and HF's builder lock
|
| 988 |
+
# is per CONFIG, so two configs of one dataset would otherwise download the
|
| 989 |
+
# same gigabytes twice into the same staging path and race at os.remove.
|
| 990 |
+
# Lock order is always zip-lock -> tracker-lock, matching step 3.1.
|
| 991 |
+
with FileLock(os.path.join(data_dir, f".{dataset_name}_fig.zip.lock")):
|
| 992 |
+
_tracked = _tracker_read(data_dir, f"qc_figures_{dataset_name}")
|
| 993 |
+
|
| 994 |
+
# Which figures this request wants. Figures are generated with the
|
| 995 |
+
# biometry plans and carry their version, so the biometry resolution is
|
| 996 |
+
# what decides whether what is on disk is current -- whatever task type
|
| 997 |
+
# the config loads. Resolved per DATASET, exactly as annotations are: a
|
| 998 |
+
# release that did not regenerate this dataset leaves the version
|
| 999 |
+
# unchanged and must not invalidate its figures. Keying on the release
|
| 1000 |
+
# version instead would re-pull all 295 GB on every release.
|
| 1001 |
+
target = _resolve(_declared_versions(dataset_name, "biometry"), requested)
|
| 1002 |
+
|
| 1003 |
+
if target is None:
|
| 1004 |
+
# No biometry annotations, so no QC figures are published for this
|
| 1005 |
+
# dataset. Any truthy entry means the Hub was already asked; keep
|
| 1006 |
+
# taking that answer rather than re-querying on every load.
|
| 1007 |
+
current = bool(_tracked)
|
| 1008 |
+
else:
|
| 1009 |
+
# The tracker settles it only when it names a version at least as new
|
| 1010 |
+
# as the one wanted. A legacy `true` names none, so it falls through
|
| 1011 |
+
# to the disk -- which is version-aware, and so can still skip the
|
| 1012 |
+
# download when the figures really are there. That keeps the
|
| 1013 |
+
# pre-v1.4.0 installs (figures shipped inside Datasets/<name>.zip, no
|
| 1014 |
+
# key ever written) from re-pulling a set they already hold.
|
| 1015 |
+
current = (
|
| 1016 |
+
_is_version(_tracked)
|
| 1017 |
+
and _version_tuple(_tracked) >= _version_tuple(target)
|
| 1018 |
+
) or _figures_current(dataset_dir, target)
|
| 1019 |
+
|
| 1020 |
+
stamp = target if target is not None else True
|
| 1021 |
+
|
| 1022 |
+
if current and not force:
|
| 1023 |
+
logger.info(
|
| 1024 |
+
" - QC figures for %s already cover annotation v%s; skipping",
|
| 1025 |
+
dataset_name, target,
|
| 1026 |
+
)
|
| 1027 |
+
if _tracked != stamp:
|
| 1028 |
+
_tracker_write(data_dir, f"qc_figures_{dataset_name}", stamp)
|
| 1029 |
+
_QC_FIGURES_DONE.add(_memo)
|
| 1030 |
+
return
|
| 1031 |
+
|
| 1032 |
+
logger.info("Downloading QC figures for %s...", dataset_name)
|
| 1033 |
+
_datasets_root = os.path.join(data_dir, "Datasets")
|
| 1034 |
+
snapshot_download(
|
| 1035 |
+
repo_id="YongchengYAO/MedVision",
|
| 1036 |
+
repo_type="dataset",
|
| 1037 |
+
allow_patterns=[
|
| 1038 |
+
f"Datasets/{dataset_name}_fig.zip",
|
| 1039 |
+
f"Datasets/{dataset_name}_fig.part*.zip",
|
| 1040 |
+
],
|
| 1041 |
+
local_dir=data_dir,
|
| 1042 |
+
max_workers=num_proc,
|
| 1043 |
+
)
|
| 1044 |
+
_fig_zips = sorted(
|
| 1045 |
+
glob.glob(os.path.join(_datasets_root, f"{dataset_name}_fig.zip"))
|
| 1046 |
+
+ glob.glob(os.path.join(_datasets_root, f"{dataset_name}_fig.part*.zip"))
|
| 1047 |
+
)
|
| 1048 |
+
# Roughly half the datasets have no figures at all. Record the attempt
|
| 1049 |
+
# anyway so a figure-less dataset does not re-query the Hub on every
|
| 1050 |
+
# single load; MedVision_FORCE_DOWNLOAD_DATA is the way back if figures
|
| 1051 |
+
# are published for it later.
|
| 1052 |
+
if not _fig_zips:
|
| 1053 |
+
logger.info(" - No QC figures are published for %s", dataset_name)
|
| 1054 |
+
else:
|
| 1055 |
+
for _fig_zip in _fig_zips:
|
| 1056 |
+
with zipfile.ZipFile(_fig_zip, "r") as zip_ref:
|
| 1057 |
+
zip_ref.extractall(_datasets_root)
|
| 1058 |
+
os.remove(_fig_zip)
|
| 1059 |
+
logger.info(
|
| 1060 |
+
" - QC figures restored to %s from %d archive(s)",
|
| 1061 |
+
dataset_dir, len(_fig_zips),
|
| 1062 |
+
)
|
| 1063 |
+
# Written last, and only on a clean pass: a crash mid-extract leaves the
|
| 1064 |
+
# entry untouched, so the next load redoes the whole download and
|
| 1065 |
+
# extractall overwrites whatever landed. The value is the annotation
|
| 1066 |
+
# version these figures belong to, so a later release that regenerates
|
| 1067 |
+
# this dataset supersedes it; True only where the dataset publishes no
|
| 1068 |
+
# biometry at all and there is no version to name.
|
| 1069 |
+
_tracker_write(data_dir, f"qc_figures_{dataset_name}", stamp)
|
| 1070 |
+
_QC_FIGURES_DONE.add(_memo)
|
| 1071 |
+
|
| 1072 |
+
|
| 1073 |
class MedVisionConfig(BuilderConfig):
|
| 1074 |
"""BuilderConfig for MedVision."""
|
| 1075 |
|
|
|
|
| 9944 |
split="test",
|
| 9945 |
),
|
| 9946 |
# DEEP-PSMA:Tumor-Lesion-Size:Task01
|
| 9947 |
+
MedVisionConfig(
|
| 9948 |
+
name="DEEP-PSMA_TumorLesionSize_Task01_Sagittal_Train",
|
| 9949 |
+
dataset_name="DEEP-PSMA",
|
| 9950 |
+
taskType="Tumor-Lesion-Size",
|
| 9951 |
+
taskID="01",
|
| 9952 |
+
imageType="2D",
|
| 9953 |
+
features_dict=features_dict_TumorLesionSize,
|
| 9954 |
+
imageSliceType="sagittal",
|
| 9955 |
+
split="train",
|
| 9956 |
+
),
|
| 9957 |
+
MedVisionConfig(
|
| 9958 |
+
name="DEEP-PSMA_TumorLesionSize_Task01_Sagittal_Test",
|
| 9959 |
+
dataset_name="DEEP-PSMA",
|
| 9960 |
+
taskType="Tumor-Lesion-Size",
|
| 9961 |
+
taskID="01",
|
| 9962 |
+
imageType="2D",
|
| 9963 |
+
features_dict=features_dict_TumorLesionSize,
|
| 9964 |
+
imageSliceType="sagittal",
|
| 9965 |
+
split="test",
|
| 9966 |
+
),
|
| 9967 |
+
MedVisionConfig(
|
| 9968 |
+
name="DEEP-PSMA_TumorLesionSize_Task01_Coronal_Train",
|
| 9969 |
+
dataset_name="DEEP-PSMA",
|
| 9970 |
+
taskType="Tumor-Lesion-Size",
|
| 9971 |
+
taskID="01",
|
| 9972 |
+
imageType="2D",
|
| 9973 |
+
features_dict=features_dict_TumorLesionSize,
|
| 9974 |
+
imageSliceType="coronal",
|
| 9975 |
+
split="train",
|
| 9976 |
+
),
|
| 9977 |
+
MedVisionConfig(
|
| 9978 |
+
name="DEEP-PSMA_TumorLesionSize_Task01_Coronal_Test",
|
| 9979 |
+
dataset_name="DEEP-PSMA",
|
| 9980 |
+
taskType="Tumor-Lesion-Size",
|
| 9981 |
+
taskID="01",
|
| 9982 |
+
imageType="2D",
|
| 9983 |
+
features_dict=features_dict_TumorLesionSize,
|
| 9984 |
+
imageSliceType="coronal",
|
| 9985 |
+
split="test",
|
| 9986 |
+
),
|
| 9987 |
MedVisionConfig(
|
| 9988 |
name="DEEP-PSMA_TumorLesionSize_Task01_Axial_Train",
|
| 9989 |
dataset_name="DEEP-PSMA",
|
|
|
|
| 10005 |
split="test",
|
| 10006 |
),
|
| 10007 |
# DEEP-PSMA:Tumor-Lesion-Size:Task02
|
| 10008 |
+
MedVisionConfig(
|
| 10009 |
+
name="DEEP-PSMA_TumorLesionSize_Task02_Sagittal_Train",
|
| 10010 |
+
dataset_name="DEEP-PSMA",
|
| 10011 |
+
taskType="Tumor-Lesion-Size",
|
| 10012 |
+
taskID="02",
|
| 10013 |
+
imageType="2D",
|
| 10014 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10015 |
+
imageSliceType="sagittal",
|
| 10016 |
+
split="train",
|
| 10017 |
+
),
|
| 10018 |
+
MedVisionConfig(
|
| 10019 |
+
name="DEEP-PSMA_TumorLesionSize_Task02_Sagittal_Test",
|
| 10020 |
+
dataset_name="DEEP-PSMA",
|
| 10021 |
+
taskType="Tumor-Lesion-Size",
|
| 10022 |
+
taskID="02",
|
| 10023 |
+
imageType="2D",
|
| 10024 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10025 |
+
imageSliceType="sagittal",
|
| 10026 |
+
split="test",
|
| 10027 |
+
),
|
| 10028 |
+
MedVisionConfig(
|
| 10029 |
+
name="DEEP-PSMA_TumorLesionSize_Task02_Coronal_Train",
|
| 10030 |
+
dataset_name="DEEP-PSMA",
|
| 10031 |
+
taskType="Tumor-Lesion-Size",
|
| 10032 |
+
taskID="02",
|
| 10033 |
+
imageType="2D",
|
| 10034 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10035 |
+
imageSliceType="coronal",
|
| 10036 |
+
split="train",
|
| 10037 |
+
),
|
| 10038 |
+
MedVisionConfig(
|
| 10039 |
+
name="DEEP-PSMA_TumorLesionSize_Task02_Coronal_Test",
|
| 10040 |
+
dataset_name="DEEP-PSMA",
|
| 10041 |
+
taskType="Tumor-Lesion-Size",
|
| 10042 |
+
taskID="02",
|
| 10043 |
+
imageType="2D",
|
| 10044 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10045 |
+
imageSliceType="coronal",
|
| 10046 |
+
split="test",
|
| 10047 |
+
),
|
| 10048 |
MedVisionConfig(
|
| 10049 |
name="DEEP-PSMA_TumorLesionSize_Task02_Axial_Train",
|
| 10050 |
dataset_name="DEEP-PSMA",
|
|
|
|
| 10371 |
split="test",
|
| 10372 |
),
|
| 10373 |
# LNQ2023:Tumor-Lesion-Size:Task01
|
| 10374 |
+
MedVisionConfig(
|
| 10375 |
+
name="LNQ2023_TumorLesionSize_Task01_Sagittal_Train",
|
| 10376 |
+
dataset_name="LNQ2023",
|
| 10377 |
+
taskType="Tumor-Lesion-Size",
|
| 10378 |
+
taskID="01",
|
| 10379 |
+
imageType="2D",
|
| 10380 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10381 |
+
imageSliceType="sagittal",
|
| 10382 |
+
split="train",
|
| 10383 |
+
),
|
| 10384 |
+
MedVisionConfig(
|
| 10385 |
+
name="LNQ2023_TumorLesionSize_Task01_Sagittal_Test",
|
| 10386 |
+
dataset_name="LNQ2023",
|
| 10387 |
+
taskType="Tumor-Lesion-Size",
|
| 10388 |
+
taskID="01",
|
| 10389 |
+
imageType="2D",
|
| 10390 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10391 |
+
imageSliceType="sagittal",
|
| 10392 |
+
split="test",
|
| 10393 |
+
),
|
| 10394 |
+
MedVisionConfig(
|
| 10395 |
+
name="LNQ2023_TumorLesionSize_Task01_Coronal_Train",
|
| 10396 |
+
dataset_name="LNQ2023",
|
| 10397 |
+
taskType="Tumor-Lesion-Size",
|
| 10398 |
+
taskID="01",
|
| 10399 |
+
imageType="2D",
|
| 10400 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10401 |
+
imageSliceType="coronal",
|
| 10402 |
+
split="train",
|
| 10403 |
+
),
|
| 10404 |
+
MedVisionConfig(
|
| 10405 |
+
name="LNQ2023_TumorLesionSize_Task01_Coronal_Test",
|
| 10406 |
+
dataset_name="LNQ2023",
|
| 10407 |
+
taskType="Tumor-Lesion-Size",
|
| 10408 |
+
taskID="01",
|
| 10409 |
+
imageType="2D",
|
| 10410 |
+
features_dict=features_dict_TumorLesionSize,
|
| 10411 |
+
imageSliceType="coronal",
|
| 10412 |
+
split="test",
|
| 10413 |
+
),
|
| 10414 |
MedVisionConfig(
|
| 10415 |
name="LNQ2023_TumorLesionSize_Task01_Axial_Train",
|
| 10416 |
dataset_name="LNQ2023",
|
|
|
|
| 11588 |
_paused_versions(self.config.dataset_name, _kind),
|
| 11589 |
)
|
| 11590 |
|
| 11591 |
+
# QC figures, opt-in and off by default. This sits in _info() rather than
|
| 11592 |
+
# in _split_generators for the same reason the pause gate above does: this
|
| 11593 |
+
# is the only point EVERY load passes through. datasets calls _info() from
|
| 11594 |
+
# DatasetBuilder.__init__, before the cache directory is consulted, while a
|
| 11595 |
+
# config that already has an Arrow cache never reaches _split_generators at
|
| 11596 |
+
# all. Fetching figures there meant they were obtained on a config's first
|
| 11597 |
+
# build and never again, so a machine holding stale figures could not get
|
| 11598 |
+
# the current ones by any means short of deleting its cache.
|
| 11599 |
+
#
|
| 11600 |
+
# Ordering against the data download is not a concern: the figure archives
|
| 11601 |
+
# extract into Datasets/<name>/ on their own, and the version they are
|
| 11602 |
+
# checked against comes from _ANNOTATION_INDEX, which touches neither disk
|
| 11603 |
+
# nor network. Everything here is behind the opt-in flag, so the default
|
| 11604 |
+
# path is unchanged -- including MedVision_PLANNER_VERSION, which is only
|
| 11605 |
+
# required (via _normalize_requested) once the flag is on, and is required
|
| 11606 |
+
# for the load itself regardless.
|
| 11607 |
+
# Deferred when the dataset's own files are not on disk yet, because that
|
| 11608 |
+
# is a first install: no Arrow cache can exist for a config that has never
|
| 11609 |
+
# been built, so _split_generators is guaranteed to run and its call site
|
| 11610 |
+
# fetches the figures AFTER step 3.3. That ordering matters -- the
|
| 11611 |
+
# reorientation pass globs "<dataset_dir>/**/*.nii.gz" recursively, and
|
| 11612 |
+
# figures extracted before it turn that into a walk over hundreds of
|
| 11613 |
+
# thousands of PNGs per dataset. Nothing is modified (only .nii.gz
|
| 11614 |
+
# matches), it is purely wasted stat traffic.
|
| 11615 |
+
#
|
| 11616 |
+
# Conversely, a warm cache implies the dataset was built successfully,
|
| 11617 |
+
# which implies its files ARE on disk -- so the branch that skips
|
| 11618 |
+
# _split_generators is exactly the branch this one covers. A version bump
|
| 11619 |
+
# satisfies both: it changes planner_version in the config fingerprint, so
|
| 11620 |
+
# the cache is cold and both call sites fire, with _QC_FIGURES_DONE making
|
| 11621 |
+
# the second a no-op.
|
| 11622 |
+
#
|
| 11623 |
+
# Not covered: a data directory deleted while its HF cache is kept. That
|
| 11624 |
+
# state already yields rows whose image_file paths do not exist, and
|
| 11625 |
+
# MedVision_FORCE_DOWNLOAD_DATA=True rebuilds out of it.
|
| 11626 |
+
if (
|
| 11627 |
+
os.environ.get("MedVision_DOWNLOAD_QC_FIGURES", "False").lower()
|
| 11628 |
+
== "true"
|
| 11629 |
+
) and os.path.isdir(
|
| 11630 |
+
os.path.join(_data_root(), "Datasets", self.config.dataset_name)
|
| 11631 |
+
):
|
| 11632 |
+
_try_ensure_qc_figures(
|
| 11633 |
+
self.config.dataset_name,
|
| 11634 |
+
_normalize_requested(
|
| 11635 |
+
os.environ.get("MedVision_PLANNER_VERSION"), self.config.version
|
| 11636 |
+
),
|
| 11637 |
+
_data_root(),
|
| 11638 |
+
self.config.num_proc,
|
| 11639 |
+
)
|
| 11640 |
+
|
| 11641 |
# Define dataset information including feature schema
|
| 11642 |
dataset_description = f"You are using the configuration <{self.config.name}> of the <{self.config.dataset_name}> dataset."
|
| 11643 |
return DatasetInfo(
|
|
|
|
| 12046 |
_discover_versions(dataset_dir, _kind),
|
| 12047 |
)
|
| 12048 |
|
| 12049 |
+
# 3.5 QC figures -- one of TWO call sites, and the one that serves a first
|
| 12050 |
+
# install. It runs here, after step 3.3, so the reorientation glob above
|
| 12051 |
+
# does not walk the figure tree. _info() holds the other call site and
|
| 12052 |
+
# covers the case this method cannot: a config with a warm Arrow cache
|
| 12053 |
+
# never reaches _split_generators at all, so a fetch placed only here ran
|
| 12054 |
+
# on a config's first build and never again -- which is what made stale
|
| 12055 |
+
# figures impossible to refresh. _QC_FIGURES_DONE keeps whichever call
|
| 12056 |
+
# comes second from repeating the work.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 12057 |
if download_qc_figures:
|
| 12058 |
+
_try_ensure_qc_figures(
|
| 12059 |
+
dataset_name, _requested, MedVision_data_dir, self.config.num_proc
|
| 12060 |
)
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
| 12061 |
|
| 12062 |
# 4. Get the benchmark planner file - this is config specific but should use existing files if possible
|
| 12063 |
# NOTE: MUST NOT move the import to the front, as the "medvision_ds" package may not be installed yet at the beginning
|