def trans_dynamic_netattr(self, subject_scan, atlas_name, feature_name, window_length, step_size, value): if value.ndim == 2: # 这里要改一下 arr = netattr.DynamicAttr(value.swapaxes(0,1), atlas.get(atlas_name), window_length, step_size, subject_scan, feature_name) return arr else: net = netattr.DynamicNet(value.swapaxes(0,2).swapaxes(0,1), atlas.get(atlas_name), window_length, step_size, subject_scan, feature_name) return net
def get_dynamic_net(self,
scan,
atlas_name,
window_length,
step_size,
comment={}):
""" Return to dynamic attr object directly """
query = dict(scan=scan, comment=comment)
col = self.getcol(atlas_name, 'BOLD.net', window_length, step_size)
if self.dndb[col].find_one(query) == None:
raise NoRecordFoundException((scan, atlas, 'BOLD.net'))
else:
records = self.dndb[col].find(query).sort([('slice',
pymongo.ASCENDING)])
atlasobj = atlas.get(atlas_name)
net = netattr.DynamicNet(None, atlasobj, window_length, step_size,
scan, 'BOLD.net')
for record in records:
net.append_one_slice(pickle.loads(record['value']))
return net
def load_single_dynamic_network(scan, atlasobj, dynamic_conf, rootFolder = rootconfig.path.feature_root): """ Return a DynamicNet (net.data[timeIdx, tickIdx, tickIdx]) """ if type(atlasobj) is str: atlasobj = atlas.get(atlasobj) window_length = dynamic_conf[0] step_size = dynamic_conf[1] start = 0 dynamic_foler_path = os.path.join(rootFolder, scan, atlasobj.name, 'bold_net', 'dynamic %d %d' % (step_size, window_length)) time_slice_count = len(list(os.listdir(dynamic_foler_path))) - 1 # get rid of timeseries.csv dynamic_net = netattr.DynamicNet(np.zeros((atlasobj.count, atlasobj.count, time_slice_count)), atlasobj, window_length, step_size, scan = scan, feature_name = 'BOLD.net') timeIdx = 0 while True: dynamic_net_filepath = os.path.join(dynamic_foler_path, 'corrcoef-%d.%d.csv' % (start, start+window_length)) if os.path.exists(dynamic_net_filepath): time_slice_net = load_csvmat(dynamic_net_filepath) dynamic_net.data[:, :, timeIdx] = time_slice_net timeIdx += 1 start += step_size else: break return dynamic_net
def run_feature(self, feature_name, feature_config):
"""
Override super run_feature.
Stores csv files to MongoDB directly
"""
if feature_config['file_type'] != '.csv':
# only supports csv features
return
in_file_list, out_file_list = self.get_feature_file_path(feature_config)
if self.is_dynamic and feature_config['modal'] == 'BOLD':
if len(in_file_list) < 1:
print('==Not Exist:', self.mriscan, self.atlasname, feature_name)
return
if feature_name.find('net') != -1:
feature = netattr.DynamicNet(None, self.atlasname, self.dataconfig['dynamic']['window_length'], self.dataconfig['dynamic']['step_size'], scan = self.mriscan, feature_name = feature_name)
for file in in_file_list:
feature.append_one_slice(load_csvmat(file))
try:
self.mdb.save_dynamic_network(feature)
except mongodb_database.MultipleRecordException:
if self.force:
# delete and overwrite
self.mdb.remove_dynamic_network(self.mriscan, self.dataconfig['dynamic']['window_length'], self.dataconfig['dynamic']['step_size'], self.atlasname)
self.mdb.save_dynamic_network(feature)
else:
print('!!!Already Exist: %s %s %s. Skipped' % (self.mriscan, self.atlasname, feature_name))
else:
feature = netattr.DynamicAttr(None, self.atlasname, self.dataconfig['dynamic']['window_length'], self.dataconfig['dynamic']['step_size'], scan = self.mriscan, feature_name = feature_name)
for file in in_file_list:
feature.append_one_slice(load_csvmat(file))
try:
self.mdb.save_dynamic_attr(feature)
except mongodb_database.MultipleRecordException:
if self.force:
# delete and overwrite
self.mdb.remove_dynamic_attr(self.mriscan, feature_name, self.dataconfig['dynamic']['window_length'], self.dataconfig['dynamic']['step_size'], self.atlasname)
self.mdb.save_dynamic_attr(feature)
else:
print('!!!Already Exist: %s %s %s. Skipped' % (self.mriscan, self.atlasname, feature_name))
elif self.is_dynamic:
# dynamic but not BOLD feature
return
else:
# not dynamic
for file in in_file_list:
if not os.path.isfile(file):
print('==Not Exist:', self.mriscan, self.atlasname, feature_name)
continue
if feature_name.find('net') != -1:
feature = netattr.Net(load_csvmat(file), self.atlasname, self.mriscan, feature_name)
else:
feature = netattr.Attr(load_csvmat(file), self.atlasname, self.mriscan, feature_name)
try:
self.mdb.save_static_feature(feature)
except mongodb_database.MultipleRecordException:
if self.force:
# delete and overwrite
self.mdb.remove_static_feature(self.mriscan, self.atlasname, feature_name)
self.mdb.save_static_feature(feature)
else:
print('!!!Already Exist: %s %s %s. Skipped' % (self.mriscan, self.atlasname, feature_name))