def load_DICOMseries_using_headers(self, H_REC=re.compile('^([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)$')):
'Load in one of the dicoms (prefering smaller ones) and use the information inside to construct a dicom_series_info object, which it returns'
dicomlist = os.listdir(self.path)
self.numdicoms = len(dicomlist)
dicompath = None
if self.numdicoms == 0:
return None
elif self.numdicoms == 2:
for dicom in dicomlist:
result = H_REC.match(dicom)
if result != None:
tupple = result.groups()
if tupple[1] == r'5.24.5':
dicompath = os.path.join(self.path, dicom)
break
if dicompath == None:
dicompath = os.path.join(self.path, dicomlist[0])
dicom_series = DICOMseries(subid=self.image.visit.subject.subid, visid=self.image.visit.visid, series=self.image.series, sorted_files=self.numdicoms)
try:
pydicomobject = pydicom.read_file(dicompath, stop_before_pixels=True)
dicom_series.set_from_pydicom(pydicomobject)
except Exception:
dicom_reader = dcm2txt()
series_dict = dicom_reader.make_dict(dicompath)
dicom_series.set_from_dict(series_dict)
if self.SeriesInstanceUID != dicom_series.SeriesInstanceUID:
raise Exception, "File {0} does not have same SeriesInstanceUID as folder\n{1}".format(dicompath, self.path)
if self.SeriesNumber != dicom_series.SeriesNumber:
raise Exception, "File {0} does not have same SeriesNumber as folder\n{1}".format(dicompath, self.path)
return dicom_series
def load_DICOMseries(self):
'returns a dicom_series_info object created with information from the directory structure without actually looking at the dicoms'
dicomlist = os.listdir(self.path)
self.numdicoms = len(dicomlist)
dicom_series = DICOMseries(subid=self.image.visit.subject.subid, visid=self.image.visit.visid, series=self.image.series, sorted_files=self.numdicoms)
dicom_series.SeriesInstanceUID = self.SeriesInstanceUID
dicom_series.SeriesNumber = self.SeriesNumber
return dicom_series
def load_DICOMseries(self):
'returns a dicom_series_info object created with information from the directory structure without actually looking at the dicoms'
dicomlist = os.listdir(self.path)
self.numdicoms = len(dicomlist)
dicom_series = DICOMseries(subid=self.image.visit.subject.subid,
visid=self.image.visit.visid,
series=self.image.series,
sorted_files=self.numdicoms)
dicom_series.SeriesInstanceUID = self.SeriesInstanceUID
dicom_series.SeriesNumber = self.SeriesNumber
return dicom_series
def load_DICOMseries_using_headers(
self,
H_REC=re.compile(
'^([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)$'
)):
'Load in one of the dicoms (prefering smaller ones) and use the information inside to construct a dicom_series_info object, which it returns'
dicomlist = os.listdir(self.path)
self.numdicoms = len(dicomlist)
dicompath = None
if self.numdicoms == 0:
return None
elif self.numdicoms == 2:
for dicom in dicomlist:
result = H_REC.match(dicom)
if result != None:
tupple = result.groups()
if tupple[1] == r'5.24.5':
dicompath = os.path.join(self.path, dicom)
break
if dicompath == None:
dicompath = os.path.join(self.path, dicomlist[0])
dicom_series = DICOMseries(subid=self.image.visit.subject.subid,
visid=self.image.visit.visid,
series=self.image.series,
sorted_files=self.numdicoms)
try:
pydicomobject = pydicom.read_file(dicompath,
stop_before_pixels=True)
dicom_series.set_from_pydicom(pydicomobject)
except Exception:
dicom_reader = dcm2txt()
series_dict = dicom_reader.make_dict(dicompath)
dicom_series.set_from_dict(series_dict)
if self.SeriesInstanceUID != dicom_series.SeriesInstanceUID:
raise Exception, "File {0} does not have same SeriesInstanceUID as folder\n{1}".format(
dicompath, self.path)
if self.SeriesNumber != dicom_series.SeriesNumber:
raise Exception, "File {0} does not have same SeriesNumber as folder\n{1}".format(
dicompath, self.path)
return dicom_series
def load_unsorted_series(self, H_REC=re.compile('^([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)$')):
DICOMseries_dict = defaultdict(lambda: defaultdict(dict))
dicomlist = os.listdir(self.study.config.incoming_DICOM_dir)
header_dict = {}
otherdicoms = []
dicom_reader = dcm2txt()
for dicom in dicomlist:
if dicom.find('part') != -1: #skip files in transit
continue
result = H_REC.match(dicom)
if result != None:
tupple = result.groups()
if tupple[1] == r'5.24.5':
dicompath = os.path.join(self.study.config.incoming_DICOM_dir, dicom)
try:
pydicomobject = pydicom.read_file(dicompath, stop_before_pixels=True)
dicom_series = DICOMseries.cls_from_pydicom(pydicomobject)
except NotImplementedError:
series_dict = dicom_reader.make_dict(dicompath)
dicom_series = DICOMseries.cls_from_dict(series_dict)
dicom_series.subid = self.DICOMseries2study_subid(dicom_series)
dicom_series.visid = self.DICOMseries2study_visid(dicom_series)
dicom_series.unsorted_dicom_paths.append(dicompath)
key = tupple[0] + tupple[2]
header_dict[key] = (tupple[0], tupple[1], tupple[2], dicom_series.subid, dicom_series.visid, dicom_series.SeriesInstanceUID)
if dicom_series.SeriesInstanceUID not in DICOMseries_dict[dicom_series.subid][dicom_series.visid]:
DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID] = dicom_series
elif dicom_series.is_same_series(DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID]):
DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID].unsorted_dicom_paths.append(dicompath)
else:
raise FindUnsortedSeriesError(dicom_series, DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID])
continue
otherdicoms.append(dicom)
numloading = 0
for dicom in otherdicoms:
numloading = numloading + 1
if numloading % 200 == 0:
print "\t\tnumloading: {}".format(numloading)
dicompath = os.path.join(self.study.config.incoming_DICOM_dir, dicom)
result = H_REC.match(dicom)
if result != None:
tupple = result.groups()
key = tupple[0] + tupple[2]
if (key) in header_dict:
tupple = header_dict[key]
DICOMseries_dict[tupple[3]][tupple[4]][tupple[5]].unsorted_dicom_paths.append(dicompath)
continue
try:
pydicomobject = pydicom.read_file(dicompath, stop_before_pixels=True)
dicom_series = DICOMseries.cls_from_pydicom(pydicomobject)
except Exception:
series_dict = dicom_reader.make_dict(dicompath)
dicom_series = DICOMseries.cls_from_dict(series_dict)
dicom_series.subid = self.DICOMseries2study_subid(dicom_series)
dicom_series.visid = self.DICOMseries2study_visid(dicom_series)
dicom_series.unsorted_dicom_paths.append(dicompath)
if dicom_series.SeriesInstanceUID not in DICOMseries_dict[dicom_series.subid][dicom_series.visid]:
DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID] = dicom_series
elif dicom_series.is_same_series(DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID]):
DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID].unsorted_dicom_paths.append(dicompath)
else:
raise FindUnsortedSeriesError(dicom_series, DICOMseries_dict[dicom_series.subid][dicom_series.visid][dicom_series.SeriesInstanceUID])
return DICOMseries_dict
def load_unsorted_series(
self,
H_REC=re.compile(
'^([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)\.([0-9]+\.[0-9]+\.[0-9]+)$'
)):
DICOMseries_dict = defaultdict(lambda: defaultdict(dict))
dicomlist = os.listdir(self.study.config.incoming_DICOM_dir)
header_dict = {}
otherdicoms = []
dicom_reader = dcm2txt()
for dicom in dicomlist:
if dicom.find('part') != -1: #skip files in transit
continue
result = H_REC.match(dicom)
if result != None:
tupple = result.groups()
if tupple[1] == r'5.24.5':
dicompath = os.path.join(
self.study.config.incoming_DICOM_dir, dicom)
try:
pydicomobject = pydicom.read_file(
dicompath, stop_before_pixels=True)
dicom_series = DICOMseries.cls_from_pydicom(
pydicomobject)
except NotImplementedError:
series_dict = dicom_reader.make_dict(dicompath)
dicom_series = DICOMseries.cls_from_dict(series_dict)
dicom_series.subid = self.DICOMseries2study_subid(
dicom_series)
dicom_series.visid = self.DICOMseries2study_visid(
dicom_series)
dicom_series.unsorted_dicom_paths.append(dicompath)
key = tupple[0] + tupple[2]
header_dict[key] = (tupple[0], tupple[1], tupple[2],
dicom_series.subid, dicom_series.visid,
dicom_series.SeriesInstanceUID)
if dicom_series.SeriesInstanceUID not in DICOMseries_dict[
dicom_series.subid][dicom_series.visid]:
DICOMseries_dict[dicom_series.subid][
dicom_series.visid][
dicom_series.SeriesInstanceUID] = dicom_series
elif dicom_series.is_same_series(
DICOMseries_dict[dicom_series.subid]
[dicom_series.visid][dicom_series.SeriesInstanceUID]):
DICOMseries_dict[dicom_series.subid][
dicom_series.visid][
dicom_series.
SeriesInstanceUID].unsorted_dicom_paths.append(
dicompath)
else:
raise FindUnsortedSeriesError(
dicom_series, DICOMseries_dict[dicom_series.subid][
dicom_series.visid][
dicom_series.SeriesInstanceUID])
continue
otherdicoms.append(dicom)
numloading = 0
for dicom in otherdicoms:
numloading = numloading + 1
if numloading % 200 == 0:
print "\t\tnumloading: {}".format(numloading)
dicompath = os.path.join(self.study.config.incoming_DICOM_dir,
dicom)
result = H_REC.match(dicom)
if result != None:
tupple = result.groups()
key = tupple[0] + tupple[2]
if (key) in header_dict:
tupple = header_dict[key]
DICOMseries_dict[tupple[3]][tupple[4]][
tupple[5]].unsorted_dicom_paths.append(dicompath)
continue
try:
pydicomobject = pydicom.read_file(dicompath,
stop_before_pixels=True)
dicom_series = DICOMseries.cls_from_pydicom(pydicomobject)
except Exception:
series_dict = dicom_reader.make_dict(dicompath)
dicom_series = DICOMseries.cls_from_dict(series_dict)
dicom_series.subid = self.DICOMseries2study_subid(dicom_series)
dicom_series.visid = self.DICOMseries2study_visid(dicom_series)
dicom_series.unsorted_dicom_paths.append(dicompath)
if dicom_series.SeriesInstanceUID not in DICOMseries_dict[
dicom_series.subid][dicom_series.visid]:
DICOMseries_dict[dicom_series.subid][dicom_series.visid][
dicom_series.SeriesInstanceUID] = dicom_series
elif dicom_series.is_same_series(
DICOMseries_dict[dicom_series.subid][dicom_series.visid][
dicom_series.SeriesInstanceUID]):
DICOMseries_dict[dicom_series.subid][dicom_series.visid][
dicom_series.
SeriesInstanceUID].unsorted_dicom_paths.append(dicompath)
else:
raise FindUnsortedSeriesError(
dicom_series, DICOMseries_dict[dicom_series.subid][
dicom_series.visid][dicom_series.SeriesInstanceUID])
return DICOMseries_dict
