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wip: dicom indexer

This commit is contained in:
bpinsard 2024-01-25 15:08:22 -05:00
parent c845c4fd64
commit 1c706dc5e5
1 changed files with 19 additions and 16 deletions
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35
docker/dicom_indexer/indexer/index_dicom.py
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@ -7,6 +7,7 @@ import datalad.api as dlad
import shutil import shutil
import gitlab import gitlab
import tempfile import tempfile
import logging
from contextlib import contextmanager from contextlib import contextmanager
@ -50,7 +51,7 @@ def _build_arg_parser() -> argparse.ArgumentParser:
) )
p.add_argument( p.add_argument(
"--gitlab-group-template", "--gitlab-group-template",
default="{ReferringPhysicianName}/{StudyDescription.replace('^','/' )}", default="{ReferringPhysicianName}/{StudyDescription}",
type=str, type=str,
help="string with placeholder for dicom tags", help="string with placeholder for dicom tags",
) )
@ -110,6 +111,7 @@ def main() -> None:
gitlab_url=gitlab_url, gitlab_url=gitlab_url,
dicom_session_tag=args.session_name_tag, dicom_session_tag=args.session_name_tag,
session_metas=session_metas, session_metas=session_metas,
gitlab_group_template=args.gitlab_group_template
) )
@ -165,17 +167,18 @@ def setup_gitlab_repos(
gitlab_url: urllib.parse.ParseResult, gitlab_url: urllib.parse.ParseResult,
session_metas: dict, session_metas: dict,
dicom_session_tag: str, dicom_session_tag: str,
gitlab_group_template: str,
) -> None: ) -> None:
gitlab_conn = connect_gitlab(gitlab_url) gitlab_conn = connect_gitlab(gitlab_url)
gitlab_group_path = gitlab_group_template.format(session_metas) gitlab_group_path = gitlab_group_template.format(**session_metas)
dicom_sourcedata_path = "/".join([dicom_session_path, "sourcedata/dicoms"]) dicom_sourcedata_path = "/".join([gitlab_group_path, "sourcedata/dicoms"])
dicom_session_path = "/".join( dicom_session_path = "/".join(
[dicom_sourcedata_path, session_metas["StudyInstanceUID"]] [dicom_sourcedata_path, session_metas["StudyInstanceUID"]]
) )
dicom_study_path = "/".join([dicom_sourcedata_path, "study"]) dicom_study_path = "/".join([dicom_sourcedata_path, "study"])
dicom_session_repo = get_or_create_gitlab_project(gl, dicom_session_path) dicom_session_repo = get_or_create_gitlab_project(gitlab_conn, dicom_session_path)
ds.siblings( ds.siblings(
action="configure", # allow to overwrite existing config action="configure", # allow to overwrite existing config
name=GITLAB_REMOTE_NAME, name=GITLAB_REMOTE_NAME,
@ -183,8 +186,8 @@ def setup_gitlab_repos(
) )
ds.push(to=GITLAB_REMOTE_NAME) ds.push(to=GITLAB_REMOTE_NAME)
study_group = get_or_create_group(gl, gitlab_group_path) study_group = get_or_create_group(gitlab_conn, gitlab_group_path)
bot_user = gl.users.list(username=GITLAB_BOT_USERNAME)[0] bot_user = gitlab_conn.users.list(username=GITLAB_BOT_USERNAME)[0]
study_group.members.create( study_group.members.create(
{ {
"user_id": bot_user.id, "user_id": bot_user.id,
@ -206,10 +209,10 @@ def setup_gitlab_repos(
# add default study DS structure. # add default study DS structure.
init_dicom_study(dicom_study_ds, gitlab_group_path) init_dicom_study(dicom_study_ds, gitlab_group_path)
# initialize BIDS project # initialize BIDS project
init_bids(gl, dicom_study_repo, gitlab_group_path) init_bids(gitlab_conn, dicom_study_repo, gitlab_group_path)
# create subgroup for QC and derivatives repos # create subgroup for QC and derivatives repos
create_group(gl, f"{gitlab_group_path}/derivatives") create_group(gitlab_conn, f"{gitlab_group_path}/derivatives")
create_group(gl, f"{gitlab_group_path}/qc") create_group(gitlab_conn, f"{gitlab_group_path}/qc")
dicom_study_ds.install( dicom_study_ds.install(
source=dicom_session_repo._attrs["ssh_url_to_repo"], source=dicom_session_repo._attrs["ssh_url_to_repo"],
@ -278,15 +281,15 @@ SESSION_META_KEYS = [
def extract_session_metas(dicom_session_ds: dlad.Dataset) -> dict: def extract_session_metas(dicom_session_ds: dlad.Dataset) -> dict:
all_files = dicom_session_ds.repo.find("*") all_files = dicom_session_ds.repo.get_files()
for f in all_files: for f in all_files:
try: try:
dic = dicom.read_file(f, stop_before_pixels=True) dic = dicom.read_file(dicom_session_ds.pathobj/f, stop_before_pixels=True)
except Exception: # TODO: what exception occurs when non-dicom ? except Exception as e: # TODO: what exception occurs when non-dicom ?
continue continue
# return at first dicom found # return at first dicom found
return {k: getattr(dic, k) for k in SESSION_META_KEYS} return {k: str(getattr(dic, k)).replace('^','/') for k in SESSION_META_KEYS}
raise InputError('no dicom found')
def import_local_data( def import_local_data(
dicom_session_ds: dlad.Dataset, dicom_session_ds: dlad.Dataset,
@ -372,7 +375,7 @@ def get_or_create_gitlab_group(
group_path: str, group_path: str,
): ):
"""fetch or create a gitlab group""" """fetch or create a gitlab group"""
group_list = group.split("/") group_list = group_path.split("/")
found = False found = False
for keep_groups in reversed(range(len(group_list) + 1)): for keep_groups in reversed(range(len(group_list) + 1)):
tmp_repo_path = "/".join(group_list[0:keep_groups]) tmp_repo_path = "/".join(group_list[0:keep_groups])
@ -426,7 +429,7 @@ def get_or_create_gitlab_project(gl: gitlab.Gitlab, project_path: str):
if curr_p.path_with_namespace == project_path: if curr_p.path_with_namespace == project_path:
return curr_p return curr_p
g = get_or_create_gitlab_group(gl, project_name[:-1]) g = get_or_create_gitlab_group(gl, '/'.join(project_name[:-1]))
p = gl.projects.create({"name": project_name[-1], "namespace_id": g.id}) p = gl.projects.create({"name": project_name[-1], "namespace_id": g.id})
return p return p