def gen_dicom_list(DicomDir, refSeries):
from pydicom.filereader import read_dicomdir
basedir = os.path.dirname(DicomDir) + '/DICOM'
lstFilesDCM = [] # create an empty list
dicom_dir = read_dicomdir(DicomDir)
for patient_record in dicom_dir.patient_records:
if (hasattr(patient_record, 'PatientID')
and hasattr(patient_record, 'PatientName')):
studies = patient_record.children
for study in studies:
all_series = study.children
for series in all_series:
if (int(series.SeriesNumber) == int(refSeries)):
data = series.children
for img in data:
fileID = img.ReferencedFileID
imgtype = img.DirectoryRecordType
if (fileID[0] == 'DICOM' and imgtype == 'IMAGE'):
if (len(fileID) == 3):
filename = basedir + '/' + fileID[
1] + '/' + fileID[2]
else:
filename = basedir + '/' + fileID[1]
lstFilesDCM.append(filename)
return lstFilesDCM
def sortsessions(session: str, subjectid: str='', sessionid: str='', rename: bool=False, ext: str='', nosort: bool=False, pattern: str='.*\.(IMA|dcm)$') -> None:
"""
:param session: The root folder containing the source [sub/][ses/]dicomfiles or the DICOMDIR file
:param subjectid: The prefix of the sub folders in session
:param sessionid: The prefix of the ses folders in sub folder
:param rename: Boolean to rename the DICOM files to a PatientName_SeriesNumber_SeriesDescription_AcquisitionNumber_InstanceNumber scheme
:param ext: The file extension after sorting (empty value keeps original file extension)
:param nosort: Boolean to skip sorting of DICOM files into SeriesNumber-SeriesDescription directories (useful in combination with -r for renaming only)
:param pattern: The regular expression pattern used in re.match() to select the dicom files
:return: Nothing
"""
# Input checking
session = os.path.abspath(os.path.expanduser(session))
# Define the sessionfolder, collect all DICOM files and run sortsession()
if subjectid: # Do a recursive search, assuming session is a foldername, not a DICOMDIR file
for subfolder in bids.lsdirs(session, subjectid + '*'):
if sessionid:
sessionfolders = bids.lsdirs(subfolder, sessionid + '*')
else:
sessionfolders = [subfolder]
for sessionfolder in sessionfolders:
dicomfiles = [os.path.join(sessionfolder, dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)]
sortsession(sessionfolder, dicomfiles, rename, ext, nosort)
else:
if os.path.basename(session) == 'DICOMDIR':
from pydicom.filereader import read_dicomdir
dicomdir = read_dicomdir(session)
sessionfolder = os.path.dirname(session)
sessionfolder_ = sessionfolder
for patient in dicomdir.patient_records:
if len(dicomdir.patient_records) > 1:
sessionfolder = os.path.join(sessionfolder_, f'sub-{cleanup(str(patient.PatientName))}')
for n, study in enumerate(patient.children, 1): # TODO: Check order
if len(patient.children) > 1:
sessionfolder = os.path.join(sessionfolder_, f'ses-{n:02}{cleanup(str(study.StudyDescription))}') # TODO: Leave out StudyDescrtiption?
print(f'WARNING: the session index-number "{n:02}" is not necessarily meaningful: {sessionfolder}')
dicomfiles = []
for series in study.children:
dicomfiles.extend([os.path.join(sessionfolder_, *image.ReferencedFileID) for image in series.children])
sortsession(sessionfolder, dicomfiles, rename, ext, nosort)
else:
sessionfolder = session
dicomfiles = [os.path.join(sessionfolder,dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)]
sortsession(sessionfolder, dicomfiles, rename, ext, nosort)
def run(self):
if self.dicomdir.endswith('DICOMDIR'):
dicomDir = read_dicomdir(self.dicomdir)
self.parserDICOMDIR(dicomDir,os.path.dirname(self.dicomdir))
logging.info('DICOMFileDirectory: Parsing of DICOMDIR completed')
else:
if not os.path.isdir(self.dicomdir):
raise DicomException('%s is not a directory!' % self.dicomdir)
else:
self.loadFilesDirectory()
logging.info('DICOMFileDirectory: Parsing of dicom directory completed')
def run(self):
if self.dicomdir.endswith('DICOMDIR'):
dicomDir = read_dicomdir(self.dicomdir)
self.parserDICOMDIR(dicomDir, os.path.dirname(self.dicomdir))
logging.info('DICOMFileDirectory: Parsing of DICOMDIR completed')
else:
if not os.path.isdir(self.dicomdir):
raise DicomException('%s is not a directory!' % self.dicomdir)
else:
self.loadFilesDirectory()
logging.info(
'DICOMFileDirectory: Parsing of dicom directory completed')
def __init__(self, source='', destination=''):
self.inputPath = Path(source).expanduser()
self.outputPath = Path(destination).expanduser()
# self.dcmDirFilePath = self.inputPath
self.dcmDirFilePath = self.inputPath / "DICOMDIR" # 測試用路徑, 自動加上DICOMDIR
"""讀取DICOMDIR檔案,下一行是讀取 DICOMDIR 檔案的物件"""
self.DICOMDIRFILE = read_dicomdir(self.dcmDirFilePath)
self.pathL1 = ''
self.pathL2 = ''
self.pathL3 = ''
DcmDIRlDict = {}
def setPatientView(self):
self.patientModel.clear()
dialog = FileDialog()
self.filepath = dialog.openFileNameDialog(title="Open DICOMDIR",
typeFile=CS_DICOMDIR)
if self.filepath:
self.base_dir = dirname(self.filepath)
self.dicom_dir = read_dicomdir(self.filepath)
for patient in range(len(self.dicom_dir.patient_records)):
ID = self.dicom_dir.patient_records[patient].PatientID
NAME = str(self.dicom_dir.patient_records[patient].PatientName
).replace('^', ' ')
it = QtGui.QStandardItem("%s\t%s" % (ID, NAME))
self.patientModel.appendRow(it)
def get_series_info(DicomDir):
# adapted from plot_read_dicom_directory at
# https://pydicom.github.io/pydicom/stable/auto_examples/input_output/plot_read_dicom_directory.html
from pydicom.filereader import read_dicomdir
info = {}
series_num = []
protocols = [] #create an empty list
# find all Series in the folder
dicom_dir = read_dicomdir(DicomDir)
for patient_record in dicom_dir.patient_records:
if (hasattr(patient_record, 'PatientID')
and hasattr(patient_record, 'PatientName')):
studies = patient_record.children
for study in studies:
all_series = study.children
for series in all_series:
if (hasattr(series, 'SeriesNumber')
and hasattr(series, 'ProtocolName')):
if int(series.SeriesNumber) > 0:
series_num.append(series.SeriesNumber)
protocols.append(series.ProtocolName)
info['series'] = series_num
info['protocol'] = protocols
return info
import pydicom
from pydicom.filereader import read_dicomdir
# pydicom.debug()
if __name__ == "__main__":
print("------------------------------------------------------------")
print("Example program showing DICOMDIR contents, assuming standard")
print("Patient -> Study -> Series -> Images hierarchy")
print("------------------------------------------------------------")
print()
if len(sys.argv) > 1:
filepath = sys.argv[1]
if os.path.isdir(filepath): # only gave directory, add standard name
filepath = os.path.join(filepath, "DICOMDIR")
dcmdir = read_dicomdir(filepath)
base_dir = os.path.dirname(filepath)
else:
# Read standard "DICOMDIR" filename from current directory
dcmdir = pydicom.read_dicomdir()
base_dir = "."
for patrec in dcmdir.patient_records:
if hasattr(patrec, 'PatientID') and hasattr(patrec, 'PatientsName'):
print("Patient: {0.PatientID}: {0.PatientsName}".format(patrec))
studies = patrec.children
for study in studies:
print(" Study {0.StudyID}: {0.StudyDate}:"
" {0.StudyDescription}".format(study))
all_series = study.children
for series in all_series:
dicompath = '/home/seolen/disk/CTav/DICOMDIR'
import pydicom
from pydicom.filereader import read_dicomdir
from os.path import dirname, join
dicom_dir = read_dicomdir(dicompath)
base_dir = dirname(dicompath)
# patients.txt
log_filename = './patients2.txt'
open(log_filename, 'w+').close
log = open(log_filename, 'a+')
for patient_record in dicom_dir.patient_records:
if (hasattr(patient_record, 'PatientID') and
hasattr(patient_record, 'PatientName')):
print("Patient: {}: {}".format(patient_record.PatientID,
patient_record.PatientName))
studies = patient_record.children
# got through each serie
for study in studies:
print(" " * 4 + "Study {}: {}: {}".format(study.StudyID,
study.StudyDate,
study.StudyDescription))
all_series = study.children
# go through each serie
for series in all_series:
image_count = len(series.children)
# Write basic series info and image count
# fetch the path to the test data
flesh_threshold = -200
bone_threshold = 220
correctedHeight = 550
zoom_scaling = .125
SAVEPATH = "/path/to/save/"
LOADPATH = "/path/to/load/"
DICOMDIRS_PATHS = [] # Complete with DICOM directories
# Read the DICOM directories
dicom_dirs = []
for path in DICOMDIRS_PATHS:
dicom_dirs.append({
"dicom": read_dicomdir(LOADPATH + path + "/DICOMDIR"),
"path": LOADPATH + path
})
# find the maximum height in the scans
maxHeight = 0
scans = []
for d in dicom_dirs:
for patient_record in d["dicom"].patient_records:
for study in patient_record.children:
for series in study.children:
if len(series.children) > 10:
maxHeight = max(maxHeight, len(series.children))
scans.append({'path': d['path'], 'series': series})
def write_message(self, line):
self.handler.writelines(line)
def close(self):
self.handler.close()
if __name__ == "__main__":
args = argparse.ArgumentParser(description="anonymization program")
args.add_argument("--dicomdir_path", help="full path to DICOMDIR"
) #"/raid/seanyu/check_hemmo/Image/0709_dicom-dir/"
args = args.parse_args()
print(args)
dicomdir_file = read_dicomdir(os.path.join(args.dicomdir_path, "DICOMDIR"))
file_object = Filehandler(
filename=os.path.join(args.dicomdir_path, "anonymous_mapping.csv"))
file_object.write_message(
"select,subject_id,dir_order,date,time,series_num,series_modality,series_description,n_images,origin_file_start,origin_file_end\n"
)
for patient in dicomdir_file.patient_records:
these_studies, this_pid, *_ = parse_patient_record(patient)
print("Processing Subject: %s" % (this_pid))
subj_path = os.path.join(args.dicomdir_path, "anonymous", this_pid)
try:
os.makedirs(subj_path)
except:
pass
# authors : Guillaume Lemaitre <*****@*****.**>
# license : MIT
from os.path import dirname, join
from pprint import pprint
import pydicom
from pydicom.data import get_testdata_files
from pydicom.filereader import read_dicomdir
# fetch the path to the test data
filepath = get_testdata_files('DICOMDIR')[0]
print('Path to the DICOM directory: {}'.format(filepath))
# load the data
dicom_dir = read_dicomdir(filepath)
base_dir = dirname(filepath)
# go through the patient record and print information
for patient_record in dicom_dir.patient_records:
if (hasattr(patient_record, 'PatientID') and
hasattr(patient_record, 'PatientName')):
print("Patient: {}: {}".format(patient_record.PatientID,
patient_record.PatientName))
studies = patient_record.children
# got through each serie
for study in studies:
print(" " * 4 + "Study {}: {}: {}".format(study.StudyID,
study.StudyDate,
study.StudyDescription))
all_series = study.children
def load_dicom_dir_file(self):
# plt.imshow(dcm_dataset.pixel_array, cmap=plt.cm.bone)
# plt.show()
# fetch the path to the test data
# filepath = get_testdata_files('DICOMDIR')[0]
# filepath = 'D:/Projects/C++/Qt/5/BodySnitches/Builds/BodySnitches/!DicomDatasets/FantasticNine/09-Kydryavcev/2011.12.09/DICOMDIR'
filepath = 'd:/Projects/BodySnitches/Builds/BodySnitches/DicomDatasets/FantasticNine/09-Kydryavcev/2011.12.09/DICOMDIR'
print('Path to the DICOM directory: {}'.format(filepath))
# load the data
dicom_dir = read_dicomdir(filepath)
print('dicom_dir', dicom_dir)
base_dir = dirname(filepath)
print('base_dir', base_dir)
# go through the patient record and print information
print('patient_records type', type(dicom_dir.patient_records))
for patient_record in dicom_dir.patient_records:
print('rrr:', type(patient_record))
if (hasattr(patient_record, 'PatientID') and
hasattr(patient_record, 'PatientName')):
print("Patient: {}: {}".format(patient_record.PatientID,
patient_record.PatientName))
studies = patient_record.children
# got through each serie
for study in studies:
print('sss:', type(study))
print(" " * 4 + "Study {}: {}: {}".format(study.StudyID,
study.StudyDate,
study.StudyDescription))
all_series = study.children
# go through each serie
for series in all_series:
image_count = len(series.children)
plural = ('', 's')[image_count > 1]
# Write basic series info and image count
# Put N/A in if no Series Description
if 'SeriesDescription' not in series:
series.SeriesDescription = "N/A"
print(" " * 8 + "Series {}: {}: {} ({} image{})".format(
series.SeriesNumber, series.Modality, series.SeriesDescription,
image_count, plural))
# Open and read something from each image, for demonstration
# purposes. For file quick overview of DICOMDIR, leave the
# following out
print(" " * 12 + "Reading images...")
image_records = series.children
image_filenames = [join(base_dir, *image_rec.ReferencedFileID)
for image_rec in image_records]
datasets = [pydicom.dcmread(image_filename)
for image_filename in image_filenames]
patient_names = set(ds.PatientName for ds in datasets)
patient_IDs = set(ds.PatientID for ds in datasets)
# List the image filenames
print("\n" + " " * 12 + "Image filenames:")
print(" " * 12, end=' ')
pprint(image_filenames, indent=12)
# Expect all images to have same patient name, id
# Show the set of all names, IDs found (should each have one)
print(" " * 12 + "Patient Names in images..: {}".format(
patient_names))
print(" " * 12 + "Patient IDs in images..: {}".format(
patient_IDs))
import matplotlib.pyplot as plt
import pydicom
import os
from pydicom.filereader import dcmread, read_dicomdir
from glob import glob
import cv2
import numpy as np
import shutil
filepath = r"E:\BTSynchSGH\datasets\necklysis\input\mr\DICOMDIR"
ds = read_dicomdir(filepath)
base_dir = os.path.dirname(filepath)
fps = []
for record in ds.DirectoryRecordSequence:
if record.DirectoryRecordType == "IMAGE":
# Extract the relative path to the DICOM file
fps.append(os.path.join(base_dir, *record.ReferencedFileID))
num_images = len(fps)
key = ''
counter = 0
current_window_name = ''
while counter < num_images:
image = dcmread(fps[counter]).pixel_array
image = np.stack([image] * 3, axis=-1) # stack for bgr/rgb
image = cv2.normalize(image,
dst=None,
alpha=0,
def sortsessions(session: Path,
subprefix: str = '',
sesprefix: str = '',
dicomfield: str = 'SeriesDescription',
rename: bool = False,
ext: str = '',
nosort: bool = False,
pattern: str = '.*\.(IMA|dcm)$',
dryrun: bool = False) -> None:
"""
:param session: The root folder containing the source [sub/][ses/]dicomfiles or the DICOMDIR file
:param subprefix: The prefix for searching the sub folders in session
:param sesprefix: The prefix for searching the ses folders in sub folder
:param dicomfield: The dicomfield that is used to construct the series folder name (e.g. SeriesDescription or ProtocolName, which are both used as fallback)
:param rename: Boolean to rename the DICOM files to a PatientName_SeriesNumber_SeriesDescription_AcquisitionNumber_InstanceNumber scheme
:param ext: The file extension after sorting (empty value keeps original file extension)
:param nosort: Boolean to skip sorting of DICOM files into SeriesNumber-SeriesDescription directories (useful in combination with -r for renaming only)
:param pattern: The regular expression pattern used in re.match() to select the dicom files
:param dryrun: Boolean to just display the action
:return: Nothing
"""
# Input checking
session = Path(session)
# Start logging
bids.setup_logging()
# Do a recursive call if subprefix is given
if subprefix:
for subfolder in bids.lsdirs(session, subprefix + '*'):
if sesprefix:
sessionfolders = bids.lsdirs(subfolder, sesprefix + '*')
else:
sessionfolders = [subfolder]
for sessionfolder in sessionfolders:
sortsessions(session=sessionfolder,
dicomfield=dicomfield,
rename=rename,
ext=ext,
nosort=nosort,
pattern=pattern,
dryrun=dryrun)
# Use the DICOMDIR file if it is there
if (session / 'DICOMDIR').is_file():
dicomdir = read_dicomdir(str(session / 'DICOMDIR'))
sessionfolder = session
for patient in dicomdir.patient_records:
if len(dicomdir.patient_records) > 1:
sessionfolder = session / f"sub-{cleanup(patient.PatientName)}"
for n, study in enumerate(patient.children,
1): # TODO: Check order
if len(patient.children) > 1:
sessionfolder = session / f"ses-{n:02}{cleanup(study.StudyDescription)}" # TODO: Leave out StudyDescrtiption? Include PatientName/StudiesDescription?
LOGGER.warning(
f"The session index-number '{n:02}' is not necessarily meaningful: {sessionfolder}"
)
dicomfiles = [
session.joinpath(*image.ReferencedFileID)
for series in study.children for image in series.children
]
sortsession(sessionfolder, dicomfiles, dicomfield, rename, ext,
nosort, dryrun)
else:
dicomfiles = [
dcmfile for dcmfile in session.iterdir()
if dcmfile.is_file() and re.match(pattern, str(dcmfile))
]
sortsession(session, dicomfiles, dicomfield, rename, ext, nosort,
dryrun)
import pydicom
from pydicom.filereader import read_dicomdir
# pydicom.debug()
if __name__ == "__main__":
print("------------------------------------------------------------")
print("Example program showing DICOMDIR contents, assuming standard")
print("Patient -> Study -> Series -> Images hierarchy")
print("------------------------------------------------------------")
print()
if len(sys.argv) > 1:
filepath = sys.argv[1]
if os.path.isdir(filepath): # only gave directory, add standard name
filepath = os.path.join(filepath, "DICOMDIR")
dcmdir = read_dicomdir(filepath)
base_dir = os.path.dirname(filepath)
else:
# Read standard "DICOMDIR" filename from current directory
dcmdir = read_dicomdir()
base_dir = "."
for patrec in dcmdir.patient_records:
if hasattr(patrec, 'PatientID') and hasattr(patrec, 'PatientsName'):
print("Patient: {0.PatientID}: {0.PatientsName}".format(patrec))
studies = patrec.children
for study in studies:
print(" Study {0.StudyID}: {0.StudyDate}:"
" {0.StudyDescription}".format(study))
all_series = study.children
for series in all_series:
print(t, loss.item())
optimizer.zero_grad()
loss.backward()
optimizer.step()
import pathlib
file = pathlib.Path.cwd().parent.parent/'PAVES Challenge'
file=file.rglob('')
for i in file: print(i)
imgs = [i for i in file]
print(i)
import pydicom
from pydicom.data import get_testdata_files
from pydicom.filereader import read_dicomdir
dicom_dir = read_dicomdir(file.absolute())
#ds = pydicom.dcmread("C:\Users\animeshs\OneDrive - NTNU\PAVES Challenge\Case 9")
import cv2
import matplotlib.pylab as plt
%matplotlib inline
cvimg = cv2.imread(i,1)
plt.imshow(i)
import numpy as np
Xrays256 = np.array([cv2.resize(cv2.imread(img,0), (256, 256), interpolation = cv2.INTER_AREA)/255 for img in imgs[:]])
print(Xrays256.shape)
import pandas as pd
validation = pd.read_table(dataP+'labels/val_list.txt.sel', sep=' ', header=None, index_col=0)
train = pd.read_table(dataP+"labels/train_list.txt.sel", sep=' ',index_col=0,header=None)
import SimpleITK as sitk
import numpy as np
import cv2
import pydicom
from os.path import dirname, join
from pprint import pprint
from pydicom.filereader import read_dicomdir
case_path = r'D:\文件\毕设\DICOMDIR '
dicom_dir = read_dicomdir(case_path)
base_dir = dirname(case_path)
dirnames = ""
for patient_record in dicom_dir.patient_records:
if (hasattr(patient_record, 'PatientID') and
hasattr(patient_record, 'PatientsName')):
print("Patient: {}: {}".format(patient_record.PatientID,
patient_record.PatientsName))
studies = patient_record.children
# got through each serie
for study in studies:
print(" " * 4 + "Study {}: {}: {}".format(study.StudyID,
study.StudyDate,
study.StudyDescription))
all_series = study.children
# go through each serie
for series in all_series:
image_count = len(series.children)
plural = ('', 's')[image_count > 1]
def _getstudies(filepath):
filepath = filepath
dicom_dir = read_dicomdir(filepath)
base_dir = dirname(filepath)
allstudies = {}
# go through the patient record and print information
for patient_record in dicom_dir.patient_records:
#if (hasattr(patient_record, 'PatientID') and hasattr(patient_record, 'PatientName')):
#print("Patient: {}: {}".format(patient_record.PatientID,
# patient_record.PatientName))
studies = patient_record.children
# got through each serie
for study in studies:
#print(" " * 4 + "Study {}: {}: {}".format(study.StudyID,
# study.StudyDate,
# study.StudyDescription))
allstudies[study.StudyID] = []
all_series = study.children
# go through each serie
tmpseries = {}
for series in all_series:
image_count = len(series.children)
plural = ('', 's')[image_count > 1]
# Write basic series info and image count
# Put N/A in if no Series Description
if 'SeriesDescription' not in series:
series.SeriesDescription = "N/A"
#print(" " * 8 + "Series {}: {}: {} ({} image{})".format(
# series.SeriesNumber, series.Modality, series.SeriesDescription,
# image_count, plural))
# Open and read something from each image, for demonstration
# purposes. For simple quick overview of DICOMDIR, leave the
# following out
#print(" " * 12 + "Reading images...")
image_records = series.children
image_filenames = [
join(base_dir, *image_rec.ReferencedFileID)
for image_rec in image_records
]
datasets = [
pydicom.dcmread(image_filename)
for image_filename in image_filenames
]
patient_names = set(ds.PatientName for ds in datasets)
patient_IDs = set(ds.PatientID for ds in datasets)
# List the image filenames
#print("\n" + " " * 12 + "Image filenames:")
#print(" " * 12, end=' ')
#pprint(image_filenames, indent=12)
# Expect all images to have same patient name, id
# Show the set of all names, IDs found (should each have one)
#print(" " * 12 + "Patient Names in images..: {}".format(
# patient_names))
#print(" " * 12 + "Patient IDs in images..: {}".format(
# patient_IDs))
tmpseries[int(series.SeriesNumber)] = datasets
allstudies[study.StudyID].append(tmpseries)
return allstudies
