def load_single_dynamic_attr(scan, atlasobj, attrname, dynamic_conf, rootFolder = rootconfig.path.feature_root):
"""
Return a DynamicAttr (attr.data[tickIdx, timeIdx])
"""
if type(atlasobj) is str:
atlasobj = atlas.get(atlasobj)
window_length = dynamic_conf[0]
step_size = dynamic_conf[1]
# fix dynamic attr feature_name issue
if attrname.find('bc') != -1 or attrname.find('BC') != -1:
feature_name = 'BOLD.BC.inter'
elif attrname.find('ccfs') != -1 or attrname.find('CCFS') != -1:
feature_name = 'BOLD.CCFS.inter'
elif attrname.find('le') != -1 or attrname.find('LE') != -1:
feature_name = 'BOLD.LE.inter'
elif attrname.find('wd') != -1 or attrname.find('WD') != -1:
feature_name = 'BOLD.WD.inter'
else:
raise Exception('Unknown feature_name %s' % attrname)
dynamic_attr = netattr.DynamicAttr(None, atlasobj, window_length, step_size, scan = scan, feature_name = feature_name)
start = 0
dynamic_foler_path = os.path.join(rootFolder, scan, atlasobj.name, 'bold_net_attr', 'dynamic %d %d' % (step_size, window_length))
while True:
dynamic_attr_filepath = os.path.join(dynamic_foler_path, '%s-%d.%d.csv' % (attrname, start, start + window_length))
if os.path.exists(dynamic_attr_filepath):
dynamic_attr.append_one_slice(load_csvmat(dynamic_attr_filepath))
start += step_size
else:
# print('loaded %d attrs for %s' % (len(ret[scan]), scan))
break
return dynamic_attr
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_attr(self,
scan,
atlas_name,
feature,
window_length,
step_size,
comment={}):
""" Return to dynamic attr object directly """
query = dict(scan=scan, comment=comment)
col = self.getcol(atlas_name, feature, window_length, step_size)
count = self.dadb[col].find(query)
if count == 0:
raise NoRecordFoundException(scan + atlas_name + feature)
else:
records = self.dadb[col].find(query).sort([('slice',
pymongo.ASCENDING)])
atlasobj = atlas.get(atlas_name)
attr = netattr.DynamicAttr(None, atlasobj, window_length,
step_size, scan, feature)
for record in records:
attr.append_one_slice(pickle.loads(record['value']))
return attr
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))