wip: flexible dicom indexer
This commit is contained in:
bpinsard
parent
b6774e2176
commit
a579defbb0
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@ -79,3 +79,12 @@ build_pydeface:
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- changes:
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- docker/pydeface/**/*
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- .gitlab-ci.yml
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build_dicom_indexer:
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extends: .build_tpl
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variables:
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IMAGE: $CI_REGISTRY_IMAGE/dicom_indexer
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rules:
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- changes:
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- docker/dicom_indexer/**/*
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- .gitlab-ci.yml
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@ -0,0 +1,10 @@
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FROM alpine:3.17.2
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RUN apk add --no-cache ca-certificates tzdata \
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python3 py3-pip git openssh-client git-annex curl bzip2 bash glab\
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&& cp /usr/share/zoneinfo/UTC /etc/localtime \
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&& apk del tzdata \
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&& rm -rf /tmp/* /var/cache/apk/*
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RUN pip install --no-cache-dir datalad ssh_agent_setup python-gitlab pydicom
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WORKDIR /work
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@ -0,0 +1,354 @@
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import os
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import dicom
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import argparse
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import pathlib
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import urllib.parse
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import datalad.api as dlad
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import shutil
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GITLAB_REMOTE_NAME = os.environ.get('GITLAB_REMOTE_NAME', 'gitlab')
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def sort_series(path: str) -> None:
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"""Sort series in separate folder
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Parameters
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----------
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path : str
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path to dicoms
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"""
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files = glob.glob(os.path.join(path, '*'))
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for f in files:
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if not os.path.isfile(f):
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continue
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dic = dicom.read_file(f, stop_before_pixels=True)
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# series_number = dic.SeriesNumber
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series_instance_uid = dic.SeriesInstanceUID
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subpath = os.path.join(path, series_instance_uid)
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if not os.path.exists(subpath):
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os.mkdir(subpath)
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os.rename(f, os.path.join(subpath, os.path.basename(f)))
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def _build_arg_parser() -> argparse.ArgumentParser:
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p = argparse.ArgumentParser(
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description="dicom_indexer - indexes dicoms into datalad")
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p.add_argument(
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'input', nargs='+',
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help='path/url of the dicom.')
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p.add_argument()
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p.add_argument(
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'gitlab_group_template',
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default='{ReferringPhysicianName}/{StudyDescription.replace('^','/')}'
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type=str)
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p.add_argument(
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'--storage-remote',
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help='url to the datalad remote')
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p.add_argument(
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"--sort-series",
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action="store_true",
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type=bool,
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default=True,
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help="sort dicom series in separate folders",
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)
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p.add_argument(
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"--fake-dates",
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type=bool,
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action="store_true",
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help="use fake dates for datalad dataset",
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)
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return p
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def main() -> None:
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parser = _build_arg_parser()
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args = parser.parse_args()
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input = urllib.parse.urlparse(args.input)
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output_remote = urllib.parse.urlparse(args.storage_remote)
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logger.info(f"input data: {input}")
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process(
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input,
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output_remote,
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sort_series=p.sort_series,
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fake_dates=p.fake_dates,
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)
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def process(
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input:urllib.parse.ParseResult,
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output_remote: urllib.parse.ParseResult,
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sort_series: bool,
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fake_dates: bool,
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p7z_opts: str,
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gitlab_url: urllib.parse.ParseResult,
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gitlab_group_template: str,
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force_export: bool=False,
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) -> None:
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"""Process incoming dicoms into datalad repo
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"""
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with tempfile.TemporaryDirectory() as tmpdirname:
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dicom_session_ds = dlad.create(tmpdirname, fake_dates=fake_dates)
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do_export = force_export
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if not input.scheme or input.scheme == 'file':
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dest = import_local_data(
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dicom_session_ds,
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pathlib.Path(input.path),
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sort_series=sort_series,
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p7z_opts=p7z_opts,
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)
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do_export = True
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elif input.scheme in ['http', 'https', 's3']:
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dest = import_remote_data(dicom_session_ds, input_url)
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# index dicoms files
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dicom_session_ds.add_archive_content(
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dest,
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strip_leading_dirs=True,
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commit=False,
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)
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# cannot pass message above so commit now
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dicom_session_ds.save(message='index dicoms from archive')#
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# optimize git index after large import
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dicom_session_ds.repo.gc() # aggressive by default
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session_metas = extract_session_metas(dicom_session_ds)
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if do_export:
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if output_remote.scheme == 'ria':
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export_to_ria(dicom_session_ds, output_remote, session_metas)
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elif output_remote.scheme == 's3':
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export_to_s3(dicom_session_ds, output_remote, session_metas)
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setup_gitlab_remote(dicom_session_ds, gitlab_url, session_metas)
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def setup_gitlab_repos(
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dicom_session_ds: dlad.Dataset,
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gitlab_url: urllib.parse.ParseResult,
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session_metas: dict,
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):
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gitlab_conn = connect_gitlab()
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gitlab_group_path = gitlab_group_template.format(session_metas)
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dicom_sourcedata_path = '/'.join([dicom_session_path, 'sourcedata/dicoms'])
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dicom_session_path = '/'.join([dicom_sourcedata_path, ['StudyInstanceUID']])
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dicom_study_path = '/'.join([dicom_sourcedata_path, 'study'])
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dicom_session_repo = get_or_create_gitlab_project(gl, dicom_session_path)
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ds.siblings(
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action='configure', # allow to overwrite existing config
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name=GITLAB_REMOTE_NAME,
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url=dicom_session_repo._attrs['ssh_url_to_repo'],
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)
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ds.push(to=GITLAB_REMOTE_NAME)
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study_group = get_or_create_group(gl, gitlab_group_path)
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bot_user = gl.users.list(username=GITLAB_BOT_USERNAME)[0]
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study_group.members.create({
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'user_id': bot_user.id,
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'access_level': gitlab.const.AccessLevel.MAINTAINER,
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})
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dicom_study_repo = get_or_create_project(gl, dicom_study_path)
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with tempfile.TemporaryDirectory() as tmpdir:
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dicom_study_ds = datalad.api.install(
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source = dicom_study_repo._attrs['ssh_url_to_repo'],
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path=tmpdir,
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)
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if dicom_study_ds.repo.get_hexsha() is None or dicom_study_ds.id is None:
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dicom_study_ds.create(force=True)
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dicom_study_ds.push(to='origin')
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# add default study DS structure.
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init_dicom_study(dicom_study_ds, PI, study_name)
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# initialize BIDS project
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init_bids(gl, PI, study_name, dicom_study_repo)
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create_group(gl, [PI, study_name, "derivatives"])
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create_group(gl, [PI, study_name, "qc"])
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dicom_study_ds.install(
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source=dicom_session_repo._attrs['ssh_url_to_repo'],
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path=session_meta['PatientName'],
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)
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dicom_study_ds.create_sibling_ria(
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UNF_DICOMS_RIA_URL,
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name=UNF_DICOMS_RIA_NAME,
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alias=study_name,
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existing='reconfigure')
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# Push to gitlab + local ria-store
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dicom_study_ds.push(to='origin')
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dicom_study_ds.push(to=UNF_DICOMS_RIA_NAME)
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SESSION_META_KEYS = [
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'StudyInstanceUID',
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'PatientID',
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'PatientName',
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'ReferringPhysicianName',
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'StudyDate',
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'StudyDescription',
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]
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def extract_session_metas(dicom_session_ds: dlad.Dataset):
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all_files = dicom_session_ds.repo.find('*')
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for f in all_files:
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try:
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dic = dicom.read_file(f, stop_before_pixels=True)
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except Exception: # TODO: what exception occurs when non-dicom ?
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continue
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# return at first dicom found
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return {k:getattr(dic, k) for k in SESSION_META_KEYS}
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def import_local_data(
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dicom_session_ds: dlad.Dataset,
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input_path: pathlib.Path,
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sort_series: bool=True,
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p7z_opts: str='-mx5'
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):
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dest = input_path.basename()
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if input_path.is_dir():
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dest = dest + '.7z'
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# create 7z archive with 1block/file parameters
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subprocess.run(
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['7z', 'u', str(dest), '.'] + p7z_opts,
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cwd=str(dicom_session_ds.path),
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)
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elif input_path.is_file():
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dest = dicom_session_ds.path / dest
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try: # try hard-linking to avoid copying
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os.link(str(input_path), str(dest))
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except OSError: #fallback if hard-linking not supported
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shutil.copyfile(str(input_path), str(dest))
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dicom_session_ds.save(dest, message='add dicoms archive')
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return dest
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def import_remote_data(
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dicom_session_ds:dlad.Dataset,
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input_url:urllib.parse.ParseResult):
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try:
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dest = pathlib.Path(url.path).basename
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dicom_session_ds.repo.add_url_to_file(dest, url)
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except Exception:
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... #TODO: check how things can fail here and deal with it.
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return dest
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def export_to_ria(
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ds: dlad.Dataset,
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ria_url:urllib.parse.ParseResult,
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session_metas: dict,
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):
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ria_name = pathlib.Path(ria_url.path).basename
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ds.create_sibling_ria(
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ria_url,
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name=ria_name,
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alias=session_meta['PatientID'],
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existing='reconfigure')
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ds.push(to=ria_name, data='nothing')
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ria_sibling_path = pathlib.Path(ds.siblings(name=ria_name)[0]['url'])
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archive_path = ria_sibling_path / 'archives' / 'archive.7z'
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ds.export_archive_ora(
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archive_path,
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opts=[f'-mx{COMPRESSION_LEVEL}'],
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missing_content='error')
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ds.repo.fsck(remote=f"{ria_url}-storage", fast=True) #index
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ds.push(to=ria_name, data='nothing')
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def export_to_s3(
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ds: dlad.Dataset,
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s3_url:urllib.parse.ParseResult,
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session_metas: dict,
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):
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...
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# git-annex initremote remotename ...
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# git-annex wanted remotename include=**.{7z,tar.gz,zip}
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# datalad push --data auto --to remotename
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def connect_gitlab(debug=False):
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"""
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Connection to Gitlab
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"""
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gl = gitlab.Gitlab(GITLAB_SERVER, private_token=GITLAB_TOKEN)
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if debug:
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gl.enable_debug()
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gl.auth()
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return gl
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def get_or_create_gitlab_group(gl, group_list):
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"""
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"""
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found = False
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for keep_groups in reversed(range(len(group_list)+1)):
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tmp_repo_path = '/'.join(group_list[0:keep_groups])
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logging.warning(tmp_repo_path)
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gs = gl.groups.list(search=tmp_repo_path)
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for g in gs:
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if g.full_path == tmp_repo_path:
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found = True
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break
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if found:
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break
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for nb_groups in range(keep_groups, len(group_list)):
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if nb_groups == 0:
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msg = "Creating group {}".format(group_list[nb_groups])
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logging.warning(msg)
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logging.warning(len(msg) * "=")
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g = gl.groups.create({'name': group_list[nb_groups],
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'path': group_list[nb_groups]})
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else:
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msg = 'Creating group {} from {}'.format(group_list[nb_groups],
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g.name)
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logging.warning(msg)
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logging.warning(len(msg) * "=")
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g = gl.groups.create({'name': group_list[nb_groups],
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'path': group_list[nb_groups],
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'parent_id': g.id})
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return g
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def get_or_create_gitlab_project(gl, project_name):
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"""
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"""
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if len(project_name) == 1:
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# Check if exists
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p = gl.projects.list(search=project_name[0])
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if not p:
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p = gl.projects.create({'name': project_name[0],
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'path': project_name[0]})
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return p.id
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else:
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return p[0].id
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repo_full_path = '/'.join(project_name)
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# Look for exact repo/project:
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p = gl.projects.list(search=project_name[-1])
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if p:
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for curr_p in p:
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if curr_p.path_with_namespace == repo_full_path:
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return curr_p
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g = get_or_create_gitlab_group(gl, project_name[:-1])
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p = gl.projects.create({'name': project_name[-1],
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'namespace_id': g.id})
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return p
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