def set_host_items(self):
if self.selected_db_type == 'sqlite':
db_files = [basename(f) for f in get_file_paths(DATA_DIR, extension='.db') if is_file_sqlite_db(f)]
db_files.sort()
self.input['host'].SetItems(db_files)
else:
self.input['host'].SetItems(self.ip_history)
def get_queue(self):
file_paths = get_file_paths(self.start_path, search_subfolders=self.search_subfolders)
file_count = len(file_paths)
queue = Queue()
for file_index, file_path in enumerate(file_paths):
msg = {'label': "File Name: %s" % os.path.basename(file_path),
'gauge': file_index / file_count}
queue.put((file_path, msg))
return queue
def run(self):
"""
Begin the thread to parse directory. Returns plan_file_sets and dicom_file_paths through pubsub
"""
file_paths = get_file_paths(self.start_path,
search_subfolders=self.search_subfolders)
file_count = len(file_paths)
other_dicom_files = {}
for file_index, file_path in enumerate(file_paths):
msg = {
'label': "File Name: %s" % os.path.basename(file_path),
'gauge': file_index / file_count
}
wx.CallAfter(pub.sendMessage,
"dicom_directory_parser_update",
msg=msg)
try:
ds = dicom.read_file(file_path,
stop_before_pixels=True,
force=True)
except InvalidDicomError:
ds = None
if ds is not None:
if not self.is_data_set_valid(ds):
print('Cannot parse %s\nOne of these tags is missing: %s' %
(file_path, ', '.join(self.req_tags)))
else:
modality = ds.Modality.lower()
timestamp = os.path.getmtime(file_path)
self.dicom_tag_values[file_path] = {
'timestamp': timestamp,
'study_instance_uid': ds.StudyInstanceUID,
'sop_instance_uid': ds.SOPInstanceUID,
'patient_name': ds.PatientName,
'mrn': ds.PatientID
}
if modality not in self.file_types:
if ds.StudyInstanceUID not in other_dicom_files.keys():
other_dicom_files[ds.StudyInstanceUID] = []
other_dicom_files[ds.StudyInstanceUID].append(
file_path) # Store these to move after import
else:
self.dicom_files[modality].append(file_path)
# All RT Plan files need to be found first
if modality == 'rtplan':
uid = ds.ReferencedStructureSetSequence[
0].ReferencedSOPInstanceUID
mrn = self.dicom_tag_values[file_path]['mrn']
self.uid_to_mrn[uid] = ds.PatientID
self.dicom_tag_values[file_path][
'ref_sop_instance'] = {
'type': 'struct',
'uid': uid
}
study_uid = ds.StudyInstanceUID
plan_uid = ds.SOPInstanceUID
if mrn not in list(self.plan_file_sets):
self.plan_file_sets[mrn] = {}
if study_uid not in list(self.plan_file_sets[mrn]):
self.plan_file_sets[mrn][study_uid] = {}
self.plan_file_sets[mrn][study_uid][plan_uid] = {
'rtplan': {
'file_path': file_path,
'sop_instance_uid': plan_uid
},
'rtstruct': {
'file_path': None,
'sop_instance_uid': None
},
'rtdose': {
'file_path': None,
'sop_instance_uid': None
}
}
if plan_uid not in self.dicom_file_paths.keys():
self.dicom_file_paths[plan_uid] = {
key: []
for key in self.file_types + ['other']
}
self.dicom_file_paths[plan_uid]['rtplan'] = [
file_path
]
elif modality == 'rtdose':
uid = ds.ReferencedRTPlanSequence[
0].ReferencedSOPInstanceUID
self.dicom_tag_values[file_path][
'ref_sop_instance'] = {
'type': 'plan',
'uid': uid
}
else:
self.dicom_tag_values[file_path][
'ref_sop_instance'] = {
'type': None,
'uid': None
}
# associate appropriate rtdose files to plans
for file_index, dose_file in enumerate(self.dicom_files['rtdose']):
dose_tag_values = self.dicom_tag_values[dose_file]
ref_plan_uid = dose_tag_values['ref_sop_instance']['uid']
study_uid = dose_tag_values['study_instance_uid']
mrn = dose_tag_values['mrn']
for plan_file_set in self.plan_file_sets[mrn][study_uid].values():
plan_uid = plan_file_set['rtplan']['sop_instance_uid']
if plan_uid == ref_plan_uid:
plan_file_set['rtdose'] = {
'file_path': dose_file,
'sop_instance_uid': dose_tag_values['sop_instance_uid']
}
if 'rtdose' in self.dicom_file_paths[plan_uid].keys():
self.dicom_file_paths[plan_uid]['rtdose'].append(
dose_file)
else:
self.dicom_file_paths[plan_uid]['rtdose'] = [dose_file]
# associate appropriate rtstruct files to plans
for mrn_index, mrn in enumerate(list(self.plan_file_sets)):
for study_uid in list(self.plan_file_sets[mrn]):
for plan_uid, plan_file_set in self.plan_file_sets[mrn][
study_uid].items():
plan_file = plan_file_set['rtplan']['file_path']
ref_struct_uid = self.dicom_tag_values[plan_file][
'ref_sop_instance']['uid']
for struct_file in self.dicom_files['rtstruct']:
struct_uid = self.dicom_tag_values[struct_file][
'sop_instance_uid']
if struct_uid == ref_struct_uid:
plan_file_set['rtstruct'] = {
'file_path': struct_file,
'sop_instance_uid': struct_uid
}
if 'rtstruct' in self.dicom_file_paths[
plan_uid].keys():
self.dicom_file_paths[plan_uid][
'rtstruct'].append(struct_file)
else:
self.dicom_file_paths[plan_uid]['rtstruct'] = [
struct_file
]
wx.CallAfter(pub.sendMessage,
'dicom_directory_parser_set_file_tree',
tree=self.plan_file_sets,
file_paths=self.dicom_file_paths,
other_dicom_files=other_dicom_files)
