excluding 4D imageswhich brake nnUNet
This commit is contained in:
parent
18df7a2d4f
commit
29b3965c5a
4 changed files with 301 additions and 70 deletions
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@ -1,3 +1,6 @@
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from pathlib import Path
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import base64
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import collections
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import datetime
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@ -9,6 +12,9 @@ import shelve
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import shutil
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import tempfile
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from lmdbm import Lmdb
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from tqdm import tqdm
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import dicom2nifti
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import pydicom
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@ -23,6 +29,7 @@ INCLUDED_HASH = [
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LAST_DAY = datetime.datetime.strptime("2025-11-01", "%Y-%m-%d")
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MAX_PATIENT = 10//3
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MAX_PATIENT = 1000
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SRC_ROOT = "/mnt/t24/Public/kimo/TSHA"
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RAW_DIR = "/mnt/t24/Public/kimo/raw/"
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@ -31,7 +38,7 @@ DST_ROOT = os.path.join(RAW_DIR, "DICOM")
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imagesTs_DIR = os.path.join(RAW_DIR, "Dataset2602_BraTS-CK/imagesTs/")
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NII_JSON_PATH = os.path.join(RAW_DIR, 'nii.json')
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if os.path.exists(NII_JSON_PATH):
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if os.path.isfile(NII_JSON_PATH):
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with open(NII_JSON_PATH, 'r') as f:
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NII_DICT = json.load(f)
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else:
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@ -46,57 +53,147 @@ else:
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BodyPartExamined = collections.Counter()
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BodyPartIncluded = set([
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'BRAIN',
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'BRAIN_CE',
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'CIRCLEOFWILLIS',
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'HEAD',
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'IAC',
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# 'ORBIT',
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])
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def is_axial(o):
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return o[1]==0 and o[2]==0 and o[3]==0 and o[5]==0
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STUDY_DB_PATH = 'study.db'
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class JsonLmdb(Lmdb):
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def _pre_key(self, value):
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return value.encode("utf-8")
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def _post_key(self, value):
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return value.decode("utf-8")
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def _pre_value(self, value):
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def default(o):
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if isinstance(o, (pydicom.dataset.FileDataset, pydicom.Dataset)):
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return json.loads(o.to_json(suppress_invalid_tags=True))
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raise TypeError(f"Object of type {o.__class__.__name__} is not JSON serializable")
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return json.dumps(value, default=default).encode("utf-8")
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def _post_value(self, value):
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data = json.loads(value.decode("utf-8"))
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if isinstance(data, dict):
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for k, v in data.items():
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if isinstance(v, dict) and 'FileDataset' in v:
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if isinstance(v['FileDataset'], dict) or isinstance(v['FileDataset'], str):
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v['FileDataset'] = pydicom.Dataset.from_json(v['FileDataset'])
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return data
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# study_db = shelve.open(STUDY_DB_PATH, 'c')
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study_db = JsonLmdb.open(STUDY_DB_PATH, "c")
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def is_axial(s):
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o = s.split(' ')
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return o[1]=='0' and o[2]=='0' and o[3]=='0' and o[5]=='0'
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def int_orientation(o):
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orientation = [str(round(f)) for f in o]
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return ' '.join(orientation)
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def check_4d_series(ds_list):
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# path = Path(directory_path)
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# Dictionary to group slices by their 3D coordinates (x, y, z)
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spatial_groups = collections.defaultdict(list)
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for ds in ds_list:
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try:
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# ds = pydicom.dcmread(dcm_file, stop_before_pixels=True)
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# Use ImagePositionPatient (0020, 0032) to identify unique 3D locations
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if "ImagePositionPatient" in ds:
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pos = tuple(ds.ImagePositionPatient)
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# Store relevant temporal tags for inspection
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time_info = {
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"AcquisitionTime": getattr(ds, "AcquisitionTime", "N/A"),
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"ContentTime": getattr(ds, "ContentTime", "N/A"),
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"InstanceNumber": getattr(ds, "InstanceNumber", "N/A")
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}
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spatial_groups[pos].append(time_info)
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except Exception as e:
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logging.error(f"Error reading {dcm_file.name}: {e}")
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# Analyze findings
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is_4d = False
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for pos, slices in spatial_groups.items():
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if len(slices) > 1:
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is_4d = True
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logging.warning(f"{ds.SeriesDescription} Detected 4D: Position {pos} has {len(slices)} temporal frames.")
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break
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# if not is_4d:
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# logging.warning(f"{ds.SeriesDescription} Series appears to be standard 3D (one slice per position).")
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return is_4d
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def check_study(study_dir):
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SeriesDescription = set()
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series = {}
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for root, dirs, files in os.walk(study_dir):
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for file in sorted(files, key=lambda x: int(x.split("_")[-1].split(".")[0])):
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if file.endswith(".dcm"):
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dcm_file = os.path.join(root, file)
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ds = pydicom.dcmread(dcm_file, force=True, stop_before_pixels=True)
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key = '_'.join(Path(study_dir).parts[-2:])
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if 'BodyPartExamined' in ds:
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BodyPartExamined[ds.BodyPartExamined] += 1
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if 'StudyDescription' in ds:
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StudyDescription = ds.StudyDescription
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# with JsonLmdb.open(STUDY_DB_PATH, "c") as db:
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study = study_db.get(key, None)
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if 'ImageOrientationPatient' not in ds:
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continue
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if study:
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logging.warning(f"use cached series for {study_dir}")
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else:
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logging.warning(f"scan series for {study_dir}")
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# print(f"{dcm_file}")
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series_instance_uid = ds.SeriesInstanceUID
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SeriesDescription.add(ds.SeriesDescription)
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# print(body_part_examined, series_description)
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SeriesDescription = set()
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study = {}
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if series_instance_uid not in series:
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series[series_instance_uid] = {
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'FileDataset': ds,
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DCMS = []
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SERIES_DS = {}
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'1st_file': dcm_file,
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for root, dirs, files in os.walk(study_dir):
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for file in sorted(files, key=lambda x: int(x.split("_")[-1].split(".")[0])):
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if file.endswith(".dcm"):
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DCMS.append(os.path.join(root, file))
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'orientations': [],
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'files': [],
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}
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for dcm_file in tqdm(DCMS):
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ds = pydicom.dcmread(dcm_file, force=True, stop_before_pixels=True)
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series[series_instance_uid]['files'].append(dcm_file)
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series[series_instance_uid]['orientations'].append(tuple(ds.ImageOrientationPatient))
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# print(ds.ImageOrientationPatient)
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# exit()
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if 'BodyPartExamined' in ds:
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BodyPartExamined[ds.BodyPartExamined] += 1
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if 'ImageOrientationPatient' not in ds:
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continue
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# print(f"{dcm_file}")
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series_instance_uid = ds.SeriesInstanceUID
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SeriesDescription.add(ds.SeriesDescription)
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# print(body_part_examined, series_description)
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if series_instance_uid not in study:
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study[series_instance_uid] = {
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'FileDataset': ds,
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'1st_file': dcm_file,
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'orientations': [],
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'files': [],
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}
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SERIES_DS[series_instance_uid] = []
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study[series_instance_uid]['files'].append(os.path.relpath(dcm_file, study_dir))
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study[series_instance_uid]['orientations'].append(int_orientation(ds.ImageOrientationPatient))
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SERIES_DS[series_instance_uid].append(ds)
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for uid, ds_list in SERIES_DS.items():
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study[uid]['is_4d'] = check_4d_series(ds_list)
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# with JsonLmdb.open(STUDY_DB_PATH, "c") as db:
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# with shelve.open(STUDY_DB_PATH) as db:
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study_db[key] = study
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brain_list = []
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body_parts = set()
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for uid, s in series.items():
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# logging.info(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].BodyPartExamined} {s['FileDataset'].SeriesDescription} {len(s['files'])} {s['1st_file']}")
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s = None
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for uid, s in study.items():
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# logging.warning(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].BodyPartExamined} {s['FileDataset'].SeriesDescription} {len(s['files'])} {s['1st_file']}")
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if 'BodyPartExamined' in s['FileDataset']:
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if s['FileDataset'].BodyPartExamined in BodyPartIncluded:
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brain_list.append(s)
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@ -105,41 +202,52 @@ def check_study(study_dir):
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if not brain_list:
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if body_parts:
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logging.info(f"no brain, BodyPartExamined: {body_parts}")
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logging.warning(f"no brain, BodyPartExamined: {body_parts}")
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return None
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else:
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logging.info(f"BodyPartExamined is empty")
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if 'brain' in StudyDescription.lower():
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logging.info(f"brain in {StudyDescription}, adding all series")
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brain_list = list(series.values())
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# print(series)
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# print(brain_list)
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# exit()
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if not s:
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logging.warning(f"no series found")
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return None
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logging.warning(f"BodyPartExamined is empty")
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if 'brain' in s['FileDataset'].StudyDescription.lower():
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logging.warning(f"brain in {s['FileDataset'].StudyDescription}, adding all series")
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brain_list = list(study.values())
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else:
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logging.info(f"no brain in {StudyDescription}")
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logging.warning(f"no brain in {s['FileDataset'].StudyDescription}")
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return None
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t1c = []
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for s in brain_list:
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sd = s['FileDataset'].SeriesDescription.lower()
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if not ('+' in sd or 'gd' in sd):
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continue
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if s['is_4d']:
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logging.warning(f"4D series found: {s['FileDataset'].SeriesDescription}")
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continue
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if 't1' not in sd and (
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'flair' in sd or
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't2' in sd or
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'perf' in sd # perfusion series (ep2d_perf)
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'tof' in sd or
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'dwi' in sd or
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'ep2d' in sd or
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'perf' in sd # perfusion series
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):
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continue
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t1c.append(s)
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if not t1c:
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logging.info(f"no t1c in {StudyDescription}")
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logging.warning(f"no t1c in {s['FileDataset'].StudyDescription}")
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for s in brain_list:
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logging.info(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].SeriesDescription} {len(s['files'])}")
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logging.warning(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].SeriesDescription} {len(s['files'])}")
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return None
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t1c_axial = []
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@ -147,23 +255,20 @@ def check_study(study_dir):
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for s in t1c:
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c = collections.Counter(s['orientations'])
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orientation_str = c.most_common(1)[0][0]
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orientation_float = tuple(float(f) for f in orientation_str)
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orientation = tuple(round(f) for f in orientation_float)
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s['Orientation'] = orientation
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if is_axial(orientation):
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logging.info(f"--- {s['FileDataset'].SeriesNumber} {s['FileDataset'].SeriesDescription} {s['Orientation']} {len(s['files'])}")
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if is_axial(orientation_str):
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logging.warning(f"--- {s['FileDataset'].SeriesNumber} {s['FileDataset'].SeriesDescription} {orientation_str} {len(s['files'])}")
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t1c_axial.append(s)
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if not t1c_axial:
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logging.info(f"no axial t1c in {study_dir}")
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logging.warning(f"no axial t1c in {study_dir}")
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for s in t1c:
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logging.info(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].SeriesDescription} {s['Orientation']} {len(s['files'])} {StudyDescription}")
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logging.warning(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].SeriesDescription} {orientation_str} {len(s['files'])} {s['FileDataset'].StudyDescription}")
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return None
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best_series = max(t1c_axial, key=lambda x: (len(x['files']), -x['FileDataset'].SeriesNumber))
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# best_series = min(t1c_axial, key=lambda x: len(x['files'], x['FileDataset'].SeriesNumber)))
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logging.info(f"{best_series['FileDataset'].SeriesNumber} {best_series['FileDataset'].SeriesDescription} {best_series['Orientation']} {len(best_series['files'])}")
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logging.warning(f"{best_series['FileDataset'].SeriesNumber} {best_series['FileDataset'].SeriesDescription} {orientation_str} {len(best_series['files'])}")
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return best_series
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@ -176,10 +281,10 @@ def hashptid(mrn, hosp='NTUH'):
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hash = base64.b32encode(hash_in_bytes.digest())[:8].decode()
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return md5, hash
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def anonymize_series_to_nifti(series_files, dst_dir):
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def anonymize_series_to_nifti(study_dir, series_files, dst_dir):
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os.makedirs(dst_dir, exist_ok=True)
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for f in series_files:
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ds = pydicom.dcmread(f)
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ds = pydicom.dcmread(os.path.join(study_dir, f))
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md5, hash = hashptid(ds.PatientID)
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for elem in ds:
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if elem.tag.group == 0x0010:
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@ -195,7 +300,7 @@ def anonymize_series_to_nifti(series_files, dst_dir):
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if e.is_file() and e.name.endswith(".nii.gz"):
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stem = f"{hash}-{ds.StudyDate}"
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dst_file = os.path.join(imagesTs_DIR, f"{stem}_0000.nii.gz")
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logging.info(f"copying to {dst_file}")
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logging.warning(f"copying to {dst_file}")
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shutil.copyfile(e.path, dst_file)
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NII_DICT[stem] = os.path.relpath(dst_dir, DST_ROOT)
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@ -203,7 +308,7 @@ def main():
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FORMAT = '%(asctime)s [%(filename)s:%(lineno)d] %(message)s'
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logging.basicConfig(
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level=logging.INFO,
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level=logging.WARNING,
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format=FORMAT,
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handlers=[
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logging.StreamHandler(),
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@ -212,7 +317,7 @@ def main():
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]
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)
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shutil.rmtree(imagesTs_DIR, ignore_errors=True)
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# shutil.rmtree(imagesTs_DIR, ignore_errors=True)
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os.makedirs(imagesTs_DIR, exist_ok=True)
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for patho in sorted(os.listdir(SRC_ROOT)):
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@ -234,8 +339,12 @@ def main():
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if not os.path.isdir(patient_dir):
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continue
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if not os.path.isfile(patient_dir+'.complete'):
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continue
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if not os.path.isfile(os.path.join(patho_dir, f"{patient}.complete")):
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logging.info(f"skip {patient_dir}")
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logging.warning(f"skip {patient_dir}")
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continue
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md5, hash = hashptid(patient)
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@ -244,7 +353,7 @@ def main():
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complete_file = os.path.join(DST_ROOT, patho, f'{hash}.complete')
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if os.path.exists(complete_file):
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logging.info(f"skip {patient_dir}")
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logging.warning(f"skip {patient_dir}")
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continue
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num_study = 0
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@ -252,20 +361,20 @@ def main():
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for study in sorted(os.listdir(patient_dir), reverse=True):
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study_date = study.split('_')[0]
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if datetime.datetime.strptime(study_date, "%Y%m%d") > LAST_DAY:
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logging.info(f"skip {study_date}")
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logging.warning(f"skip {study_date}")
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continue
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study_dir = os.path.join(patient_dir, study)
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if not os.path.isdir(study_dir):
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continue
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logging.info(study_dir)
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# logging.warning(study_dir)
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best_series = check_study(study_dir)
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if not best_series:
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continue
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dst_dir = os.path.join(dst_patient_dir, study)
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anonymize_series_to_nifti(best_series['files'], dst_dir)
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anonymize_series_to_nifti(study_dir, best_series['files'], dst_dir)
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num_study += 1
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if num_study > 0:
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@ -275,11 +384,79 @@ def main():
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if num_patient >= MAX_PATIENT:
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break
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# break
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print(NII_DICT)
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logging.info(f"BodyPartExamined: {BodyPartExamined}")
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logging.warning(f"BodyPartExamined: {BodyPartExamined}")
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with open(NII_JSON_PATH, 'w') as f:
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json.dump(NII_DICT, f, indent=1)
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def list_4d():
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PLUS_3D = set()
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PLUS_4D = set()
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for study_id, study in study_db.items():
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brain_list = []
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body_parts = set()
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s = None
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for uid, s in study.items():
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# logging.warning(f"{s['FileDataset'].SeriesNumber} {s['FileDataset'].BodyPartExamined} {s['FileDataset'].SeriesDescription} {len(s['files'])} {s['1st_file']}")
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if 'BodyPartExamined' in s['FileDataset']:
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if s['FileDataset'].BodyPartExamined in BodyPartIncluded:
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brain_list.append(s)
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else:
|
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body_parts.add(s['FileDataset'].BodyPartExamined)
|
||||
|
||||
if not brain_list:
|
||||
if body_parts:
|
||||
logging.warning(f"no brain, BodyPartExamined: {body_parts}")
|
||||
continue
|
||||
else:
|
||||
if not s:
|
||||
logging.warning(f"no series found")
|
||||
continue
|
||||
logging.warning(f"BodyPartExamined is empty")
|
||||
if 'brain' in s['FileDataset'].StudyDescription.lower():
|
||||
logging.warning(f"brain in {s['FileDataset'].StudyDescription}, adding all series")
|
||||
brain_list = list(study.values())
|
||||
else:
|
||||
logging.warning(f"no brain in {s['FileDataset'].StudyDescription}")
|
||||
continue
|
||||
|
||||
|
||||
for s in brain_list:
|
||||
sd = s['FileDataset'].SeriesDescription.lower()
|
||||
if not ('+' in sd or 'gd' in sd):
|
||||
continue
|
||||
|
||||
if 't1' in sd:
|
||||
continue
|
||||
if 't2' in sd:
|
||||
continue
|
||||
if 'flair' in sd:
|
||||
continue
|
||||
|
||||
c = collections.Counter(s['orientations'])
|
||||
orientation_str = c.most_common(1)[0][0]
|
||||
if not is_axial(orientation_str):
|
||||
continue
|
||||
|
||||
if s['is_4d']:
|
||||
logging.warning(f"4D series found: {s['FileDataset'].SeriesDescription}")
|
||||
PLUS_4D.add(s['FileDataset'].SeriesDescription)
|
||||
else:
|
||||
PLUS_3D.add(s['FileDataset'].SeriesDescription)
|
||||
|
||||
with open("plus_4d.json", 'w') as f:
|
||||
json.dump(sorted(PLUS_4D), f, indent=1)
|
||||
|
||||
with open("plus_3d.json", 'w') as f:
|
||||
json.dump(sorted(PLUS_3D), f, indent=1)
|
||||
|
||||
exit()
|
||||
|
||||
if __name__ == '__main__':
|
||||
# list_4d()
|
||||
main()
|
||||
|
|
|
|||
|
|
@ -38,14 +38,33 @@ def main():
|
|||
config = yaml.safe_load(f)
|
||||
|
||||
PREPROCESSED_DIR = config["nnunet_preprocessed"]
|
||||
RAW_DIR = config["nnunet_raw"]
|
||||
RESULTS_DIR = config["nnunet_results"]
|
||||
|
||||
|
||||
IMAGES_TS = os.path.join(RAW_DIR, DATASET, "imagesTs")
|
||||
IMAGES_TS_DONE = os.path.join(RAW_DIR, DATASET, "imagesTs_done")
|
||||
|
||||
POSTPROCESSED_DIR = os.path.join(RESULTS_DIR, DATASET, "ensemble_predictions_postprocessed")
|
||||
|
||||
os.makedirs(IMAGES_TS_DONE, exist_ok=True)
|
||||
if os.path.exists(POSTPROCESSED_DIR):
|
||||
processed_files = [f for f in os.listdir(POSTPROCESSED_DIR) if f.endswith('.nii.gz')]
|
||||
processed_ids = [f.replace('.nii.gz', '') for f in processed_files]
|
||||
for pid in processed_ids:
|
||||
for mod in range(10): # support up to 10 modalities
|
||||
mod_file = f"{pid}_{mod:04d}.nii.gz"
|
||||
src_path = os.path.join(IMAGES_TS, mod_file)
|
||||
dst_path = os.path.join(IMAGES_TS_DONE, mod_file)
|
||||
if os.path.exists(src_path):
|
||||
shutil.move(src_path, dst_path)
|
||||
|
||||
# clean up
|
||||
shutil.rmtree(f'{RESULTS_DIR}/{DATASET}/pred_2d', ignore_errors=True)
|
||||
shutil.rmtree(f'{RESULTS_DIR}/{DATASET}/pred_3d_fullres', ignore_errors=True)
|
||||
shutil.rmtree(f'{RESULTS_DIR}/{DATASET}/pred_3d_lowres', ignore_errors=True)
|
||||
shutil.rmtree(f'{RESULTS_DIR}/{DATASET}/ensemble_predictions', ignore_errors=True)
|
||||
shutil.rmtree(f'{RESULTS_DIR}/{DATASET}/ensemble_predictions_postprocessed', ignore_errors=True)
|
||||
# shutil.rmtree(f'{RESULTS_DIR}/{DATASET}/ensemble_predictions_postprocessed', ignore_errors=True)
|
||||
|
||||
runner = nnUNetV2Runner(YAML)
|
||||
try:
|
||||
|
|
|
|||
|
|
@ -187,15 +187,38 @@ def main():
|
|||
]
|
||||
)
|
||||
|
||||
with open(NII_JSON_PATH, 'r') as f:
|
||||
NII_DICT = json.load(f)
|
||||
NII_DICT = {}
|
||||
|
||||
for pathology in sorted(os.listdir(DICOM_ROOT)):
|
||||
pathology_path = os.path.join(DICOM_ROOT, pathology)
|
||||
if not os.path.isdir(pathology_path):
|
||||
continue
|
||||
pathology_name = pathology
|
||||
|
||||
for patient in sorted(os.listdir(pathology_path)):
|
||||
patient_path = os.path.join(pathology_path, patient)
|
||||
if not os.path.isdir(patient_path):
|
||||
continue
|
||||
patient_name = patient
|
||||
|
||||
for study in sorted(os.listdir(patient_path)):
|
||||
study_path = os.path.join(patient_path, study)
|
||||
if not os.path.isdir(study_path):
|
||||
continue
|
||||
study_name = study
|
||||
|
||||
key = f"{patient_name}-{study_name.split('_')[0]}"
|
||||
NII_DICT[key] = os.path.relpath(study_path, DICOM_ROOT)
|
||||
# print(NII_DICT)
|
||||
# exit()
|
||||
|
||||
for stem, dicomdir in sorted(NII_DICT.items()):
|
||||
logging.info(f"{stem} {dicomdir}")
|
||||
hash, date = stem.split("-")
|
||||
if hash in CASE_SET:
|
||||
logging.info(f"skip {stem} {dicomdir}")
|
||||
continue
|
||||
|
||||
logging.info(f"{stem} {dicomdir}")
|
||||
category = dicomdir.split("/")[0]
|
||||
|
||||
image_nii = f"{imagesTs_DIR}/{stem}_0000.nii.gz"
|
||||
|
|
@ -207,8 +230,10 @@ def main():
|
|||
dest_dir = f"{category_dir}/{stem}"
|
||||
|
||||
if not os.path.exists(image_nii):
|
||||
logging.info(f"{image_nii} not exists")
|
||||
continue
|
||||
if not os.path.exists(label_nii):
|
||||
logging.info(f"{label_nii} not exists")
|
||||
continue
|
||||
|
||||
con_ov = contour_overlay(image_nii, label_nii)
|
||||
|
|
@ -222,7 +247,7 @@ def main():
|
|||
|
||||
shutil.copyfile(image_nii, f"{dest_dir}/image.nii.gz")
|
||||
shutil.copyfile(label_nii, f"{dest_dir}/label.nii.gz")
|
||||
# copytree(dicomdir, f"{dest_dir}/DICOM")
|
||||
copytree(dicomdir, f"{dest_dir}/DICOM")
|
||||
|
||||
CASE_SET.add(hash)
|
||||
# exit()
|
||||
|
|
|
|||
10
test_dicom_json.py
Normal file
10
test_dicom_json.py
Normal file
|
|
@ -0,0 +1,10 @@
|
|||
import pydicom
|
||||
import json
|
||||
ds = pydicom.dataset.Dataset()
|
||||
ds.PatientName = "Test"
|
||||
json_str = ds.to_json()
|
||||
print("to_json:", json_str)
|
||||
dict_obj = json.loads(json_str)
|
||||
|
||||
print("type of dict_obj:", type(dict_obj))
|
||||
print("dict_obj keys:", dict_obj.keys())
|
||||
Loading…
Reference in a new issue