def main(configFile, filename):
#Read config
config = ConfigParser.ConfigParser()
config.read(configFile)
dcmconfig = {
'patid': config.get("DCMCONFIG", "PATID"),
'patname': config.get("DCMCONFIG", "PATNAME"),
'studydes': config.get("DCMCONFIG", "STUDYDES"),
'seriesdes': config.get("DCMCONFIG", "SERIESDES"),
'stationname': config.get("DCMCONFIG", "STATIONNAME"),
}
tag = dicom.tag.Tag(config.get("DCMCONFIG", "TAG").split(','))
dcmconfig['studydate'] = datetime.strptime(
config.get("DCMCONFIG", "STUDYDATE"), '%Y%m%d')
dcmconfig['studytime'] = datetime.strptime(
config.get("DCMCONFIG", "STUDYTIME"), '%H%M%S')
aet = config.get("SERVERCONFIG", "AET")
destip = config.get("SERVERCONFIG", "IP")
port = int(config.get("SERVERCONFIG", "PORT"))
#Get file content
with open(filename) as f:
payload = ''.join(f.readlines())
#Create DCM
tmpdicom = create_dicom.create_dicom(tag, payload, filename, dcmconfig)
#Send to PACS
if config.get("SERVERCONFIG", "IP") == "":
print("No IP specified in config.ini; saving dicom file locally")
savename = filename + '.dcm'
tmpdicom.save_as(savename)
else:
try:
storescu.StoreSCU(aet, destip, port, tmpdicom)
except:
print('Failed to send file to DCM4CHEE, check server settings?')
def main(configFile,filename):
#Read config
config = ConfigParser.ConfigParser()
config.read(configFile)
dcmconfig = {
'patid':config.get("DCMCONFIG","PATID"),
'patname':config.get("DCMCONFIG","PATNAME"),
'studydes':config.get("DCMCONFIG","STUDYDES"),
'seriesdes':config.get("DCMCONFIG","SERIESDES"),
'stationname':config.get("DCMCONFIG","STATIONNAME"),}
tag = dicom.tag.Tag(config.get("DCMCONFIG","TAG").split(','))
dcmconfig['studydate'] = datetime.strptime(config.get("DCMCONFIG","STUDYDATE"), '%Y%m%d')
dcmconfig['studytime'] = datetime.strptime(config.get("DCMCONFIG","STUDYTIME"), '%H%M%S')
aet = config.get("SERVERCONFIG","AET")
destip = config.get("SERVERCONFIG","IP")
port = int(config.get("SERVERCONFIG","PORT"))
#Get file content
with open(filename) as f:
payload = ''.join(f.readlines())
#Create DCM
tmpdicom = create_dicom.create_dicom(tag, payload, filename, dcmconfig)
#Send to PACS
if config.get("SERVERCONFIG","IP") == "":
print("No IP specified in config.ini; saving dicom file locally")
savename = filename+'.dcm'
tmpdicom.save_as(savename)
else:
try:
storescu.StoreSCU(aet, destip, port, tmpdicom)
except:
print('Failed to send file to DCM4CHEE, check server settings?')
def main(configFile):
PROCESSED_FILEPATH = "processed_files.txt"
open(PROCESSED_FILEPATH, 'a').close()
#Read config
config = ConfigParser.ConfigParser()
config.read(configFile)
sourcedir = config.get("FILECONFIG", "SRCDIR")
fileext = config.get("FILECONFIG", "EXT")
#Convert comma-separated values into list
contains = [
s.strip() for s in config.get("FILECONFIG", "CONTAINS").split(',')
]
not_contains = [
s.strip() for s in config.get("FILECONFIG", "NOT_CONTAINS").split(',')
]
dcmconfig = {
'patid': config.get("DCMCONFIG", "PATID"),
'patname': config.get("DCMCONFIG", "PATNAME"),
'studydes': config.get("DCMCONFIG", "STUDYDES"),
'seriesdes': config.get("DCMCONFIG", "SERIESDES"),
'stationname': config.get("DCMCONFIG", "STATIONNAME"),
}
tag = dicom.tag.Tag(config.get("DCMCONFIG", "TAG").split(','))
aet = config.get("SERVERCONFIG", "AET")
destip = config.get("SERVERCONFIG", "IP")
port = int(config.get("SERVERCONFIG", "PORT"))
#Processed filepaths
with open(PROCESSED_FILEPATH, 'r') as f:
processed = [f.strip() for f in f.readlines()]
#Find all files in `sourcedir` with extension `fileext`
allfiles = [fn for fn in os.listdir(sourcedir) if fn.endswith(fileext)]
#Filter allfiles
filepathlist = []
for filename in allfiles:
#Include filenames which contain all substrings in `contains`
if not all([substr in filename for substr in contains]):
continue
#Exclude filenames which contain any substring in `not_contains`
if any([substr in filename for substr in not_contains]):
continue
#Include if file hasn't been processed before
path = os.path.join(sourcedir, filename)
if path not in processed:
filepathlist.append(os.path.join(sourcedir, filename))
for path in filepathlist:
print os.path.basename(path)
#Get file content
with open(path) as f:
payload = ''.join(f.readlines())
#Get date and time from filepath
match = re.findall(r'\d+', path)
print 'match', match
dcmconfig['studydate'] = datetime.strptime(''.join(match[0:3]),
'%Y%m%d')
dcmconfig['studytime'] = datetime.strptime(''.join(match[3:5]),
'%H%M%S')
#Create DCM
tmpdicom = create_dicom.create_dicom(tag, payload, path, dcmconfig)
#Send to PACS
#storescu.StoreSCU(aet, destip, port, tmpdicom)
#Add path to processed_files.txt
with open(PROCESSED_FILEPATH, 'a') as f:
f.write("\n" + path)
def main():
my_path = os.path.dirname(os.path.realpath(__file__))
#Parse command line arguments
#can be used to overrule several parameters from config.ini
parser = ArgumentParser()
parser.add_argument("-c", "--config", dest="INIFILE", default=os.path.join(my_path, 'config.ini'),
help="read configuration from FILE", metavar="FILE")
parser.add_argument("-src", "--source", dest="SRCDIR", help="read files from SRCDIR")
parser.add_argument("-p", "--processed", dest="PROCESSEDDIR", default=my_path,
help="store processed item status files in DIR", metavar="DIR")
parser.add_argument("-s", "--stationname", dest="STATIONNAME",
help="use station name NAME", metavar="NAME")
parser.add_argument("-e", "--extension", dest="EXTENSION", default='xml',
help="use file extension EXT", metavar="EXT")
parser.add_argument("-i", "--patientid", dest="PATIENTID",
help="use PatientID ID", metavar="ID")
parser.add_argument("-n", "--patientname", dest="PATIENTNAME",
help="use PatientName NAME", metavar="NAME")
parser.add_argument("-q", "--quiet", action="store_false", dest="verbose", default=True,
help="don't print status messages to stdout")
args = parser.parse_args()
configFile = args.INIFILE
#Read config
config = configparser.ConfigParser(comment_prefixes=('#',';'),inline_comment_prefixes=(';',))
config.read(configFile)
# only load some values from config if not specified on command line
sourcedir = args.SRCDIR or config.get("FILECONFIG","SRCDIR")
fileext = args.EXTENSION or config.get("FILECONFIG","EXT")
processedDir = args.PROCESSEDDIR
stationName = args.STATIONNAME or config.get("DCMCONFIG","STATIONNAME")
patientName = args.PATIENTNAME or config.get("DCMCONFIG","PATNAME")
patientID = args.PATIENTID or config.get("DCMCONFIG","PATID")
if args.verbose:
print("Reading configuration from : {}".format(configFile));
print("Storing processed status in : {}".format(processedDir));
print("Reading QA files from : {}".format(sourcedir));
#create new file if it doesn't exist
PROCESSED_FILEPATH = os.path.join(processedDir, "processed_files.txt")
open(PROCESSED_FILEPATH, 'a').close()
if args.verbose:
print("Lookup file for processed files: {0}".format(PROCESSED_FILEPATH))
with open(PROCESSED_FILEPATH, 'r') as f:
processed = [f.strip() for f in f.readlines()]
#Convert comma-separated values into list
contains = [s.strip() for s in config.get("FILECONFIG","CONTAINS").split(',')]
not_contains = [s.strip() for s in config.get("FILECONFIG","NOT_CONTAINS").split(',')]
if args.verbose:
print("Using QA file extension : {}".format(fileext));
print("Including QA files with : {}".format(contains));
print("Excluding QA files with : {}".format(not_contains));
print("Using station name : {}".format(stationName));
print("Using patient name : {}".format(patientName));
print("Using patient ID : {}".format(patientID));
dcmconfig = {
'patid': patientID,
'patname': patientName,
'studydes': config.get("DCMCONFIG","STUDYDES"),
'seriesdes': config.get("DCMCONFIG","SERIESDES"),
'stationname': stationName
}
tag = dicom.tag.Tag(config.get("DCMCONFIG","TAG").split(','))
my_aet = config.get("SERVERCONFIG","MY_AET")
remote_aet = config.get("SERVERCONFIG","REMOTE_AET")
destip = config.get("SERVERCONFIG","IP")
port = int(config.get("SERVERCONFIG","PORT"))
#Find all files in `sourcedir` with extension `fileext`
allfiles = [fn for fn in os.listdir(sourcedir) if fn.endswith(fileext)]
#Filter allfiles
filepathlist = []
for filename in allfiles:
#Include filenames which contain any substrings in `contains`
if not any([substr in filename for substr in contains]):
print("{} contains".format(filename))
continue
#Exclude filenames which contain any substring in `not_contains`
if any([substr in filename for substr in not_contains]):
print("{} not contains".format(filename))
continue
print("{} filtered out".format(filename))
#Include file if it fits the matching/exclusion criteria
#and hasn't been processed before
path = os.path.join(sourcedir, filename)
if path not in processed:
filepathlist.append(os.path.join(sourcedir, filename))
for path in filepathlist:
#dicom encapsulate scan and send to wad server
print("preparing wadqc dicom object for: {0}".format(os.path.basename(path)))
#Get file content
with open(path) as f:
payload = bytes(''.join(f.readlines()), 'utf-8')
#Get date and time from filepath
match = re.findall(r'\d+', path)
studydate = match[-2]
studytime = match[-1]
dcmconfig['studydate'] = datetime.strptime(studydate, '%d%m%Y')
dcmconfig['studytime'] = datetime.strptime(studytime, '%H%M%S')
dcmconfig['seriestime'] = datetime.strptime(studytime, '%H%M%S')
filename_noext = os.path.splitext(os.path.basename(path))[0]
dcmconfig['seriesdes'] = filename_noext
dcmconfig['studyuid']=dicom.uid.generate_uid(entropy_srcs=[filename_noext,studydate,studytime,'study'])
dcmconfig['seriesuid']=dicom.uid.generate_uid(entropy_srcs=[filename_noext,studydate,studytime,'series'])
dcmconfig['instanceuid']=dicom.uid.generate_uid(entropy_srcs=[filename_noext,studydate,studytime,'instance'])
#Create DCM
tmpdicom = create_dicom.create_dicom(tag, payload, path, dcmconfig, verbose=args.verbose)
#Send to PACS
print("sending to wadqc dicom node: {0}@{1}:{2}".format(remote_aet,destip,port))
status=storescu.StoreSCU(remotehost=destip, remoteport=port, dicomobject=tmpdicom, aec=remote_aet, aet=my_aet, verbose=args.verbose)
if status:
#Add path to processed_files.txt
with open(PROCESSED_FILEPATH, 'a') as f:
f.write(path+"\n")
def main(configFile):
PROCESSED_FILEPATH = "processed_files.txt"
open(PROCESSED_FILEPATH, "a").close()
# Read config
config = ConfigParser.ConfigParser()
config.read(configFile)
sourcedir = config.get("FILECONFIG", "SRCDIR")
fileext = config.get("FILECONFIG", "EXT")
# Convert comma-separated values into list
contains = [s.strip() for s in config.get("FILECONFIG", "CONTAINS").split(",")]
not_contains = [s.strip() for s in config.get("FILECONFIG", "NOT_CONTAINS").split(",")]
dcmconfig = {
"patid": config.get("DCMCONFIG", "PATID"),
"patname": config.get("DCMCONFIG", "PATNAME"),
"studydes": config.get("DCMCONFIG", "STUDYDES"),
"seriesdes": config.get("DCMCONFIG", "SERIESDES"),
"stationname": config.get("DCMCONFIG", "STATIONNAME"),
}
tag = dicom.tag.Tag(config.get("DCMCONFIG", "TAG").split(","))
aet = config.get("SERVERCONFIG", "AET")
destip = config.get("SERVERCONFIG", "IP")
port = int(config.get("SERVERCONFIG", "PORT"))
# Processed filepaths
with open(PROCESSED_FILEPATH, "r") as f:
processed = [f.strip() for f in f.readlines()]
# Find all files in `sourcedir` with extension `fileext`
allfiles = [fn for fn in os.listdir(sourcedir) if fn.endswith(fileext)]
# Filter allfiles
filepathlist = []
for filename in allfiles:
# Include filenames which contain all substrings in `contains`
if not all([substr in filename for substr in contains]):
continue
# Exclude filenames which contain any substring in `not_contains`
if any([substr in filename for substr in not_contains]):
continue
# Include if file hasn't been processed before
path = os.path.join(sourcedir, filename)
if path not in processed:
filepathlist.append(os.path.join(sourcedir, filename))
for path in filepathlist:
print os.path.basename(path)
# Get file content
with open(path) as f:
payload = "".join(f.readlines())
# Get date and time from filepath
match = re.findall(r"\d+", path)
dcmconfig["studydate"] = datetime.strptime(match[-2], "%d%m%Y")
dcmconfig["studytime"] = datetime.strptime(match[-1], "%H%M%S")
# Create DCM
tmpdicom = create_dicom.create_dicom(tag, payload, path, dcmconfig)
# Send to PACS
storescu.StoreSCU(aet, destip, port, tmpdicom)
# Add path to processed_files.txt
with open(PROCESSED_FILEPATH, "a") as f:
f.write("\n" + path)
