def _run_interface(self, runtime):
if not isdefined(self.inputs.out_file):
fname = os.path.splitext(os.path.basename(self.inputs.in_file))[0]
dname = os.getcwd() #os.path.dirname(self.inputs.nativeT1)
self.inputs.out_file = dname + os.sep + fname + self._suffix
try:
os.remove(self.inputs.out_file)
except OSError:
pass
class InfoOptions:
def __init__(self, command, variable, attribute, type_):
self.command = command
self.variable = variable
self.attribute = attribute
self.type_ = type_
temp_out_file = os.getcwd() + os.sep + "temp.json"
try:
img = pyezminc.Image(self.inputs.in_file, metadata_only=True)
hd = img.get_MINC_header()
for key in hd.keys():
self._params[key] = {}
for subkey in hd[key].keys():
self._params[key][subkey] = {}
data_in = hd[key][subkey]
var = str(key)
attr = str(subkey)
#Populate dictionary with some useful image parameters (e.g., world coordinate start values of dimensions)
self._params[key][subkey] = data_in
update_minchd_json(temp_out_file, data_in, var, attr)
except RuntimeError:
print("Warning: Could not read header file from",
self.inputs.in_file)
header = json.load(open(temp_out_file, "r+"))
minc_input = True
if not isdefined(self.inputs.json_header):
print("Error: could not find json file", self.inputs.json_header)
exit(1)
json_header = json.load(open(self.inputs.json_header, "r+"))
header.update(json_header)
minc_input = False
header = set_frame_duration(header, minc_input)
header = set_isotope_halflife(header, self.inputs.halflife, 'halflife')
fp = open(self.inputs.out_file, "w+")
fp.seek(0)
json.dump(header, fp, sort_keys=True, indent=4)
fp.close()
self._params = header
return runtime
def _run_interface(self, runtime):
if not isdefined(self.inputs.out_file):
fname, ext = os.path.splitext(self.inputs.in_file)
self.inputs.out_file = fname + self._suffix
# if os.path.exists(self.inputs.out_file):
# os.remove(self.inputs.out_file)
try:
os.remove(self.inputs.out_file)
except OSError:
pass
class InfoOptions:
def __init__(self, command, variable, attribute, type_):
self.command = command
self.variable = variable
self.attribute = attribute
self.type_ = type_
options = [
InfoOptions('-dimnames', 'time', 'dimnames', 'string'),
InfoOptions('-varvalue time', 'time', 'frames-time', 'integer'),
InfoOptions('-varvalue time-width', 'time', 'frames-length',
'integer')
]
for opt in options:
run_mincinfo = InfoCommand()
run_mincinfo.inputs.in_file = self.inputs.in_file
run_mincinfo.inputs.out_file = self.inputs.out_file
run_mincinfo.inputs.opt_string = opt.command
run_mincinfo.inputs.json_var = opt.variable
run_mincinfo.inputs.json_attr = opt.attribute
run_mincinfo.inputs.json_type = opt.type_
run_mincinfo.inputs.error = 'unknown'
if self.inputs.verbose:
print run_mincinfo.cmdline
if self.inputs.run:
run_mincinfo.run()
img = minc.Image(self.inputs.in_file, metadata_only=True)
hd = img.get_MINC_header()
for key in hd.keys():
for subkey in hd[key].keys():
data_in = hd[key][subkey]
var = str(key)
attr = str(subkey)
print key, subkey, var, attr
update_minchd_json(self.inputs.out_file, data_in, var, attr)
return runtime
def aggregate_outputs(self, runtime=None, needed_outputs=None):
outputs = self._outputs()
if runtime is None:
try:
out_info = load_json(self.inputs.out_file)[
self.inputs.json_attr][self.inputs.json_var]
except IOError:
return self.run().outputs
else:
out_info = []
for line in runtime.stdout.split('\n'):
if line:
values = line.split()
if self.inputs.json_type == 'float':
if len(values) > 1:
#out_info.append([float(val) for val in values])
out_info.append([val for val in values])
else:
#out_info.extend([float(val) for val in values])
out_info.extend([val for val in values])
elif self.inputs.json_type == 'integer':
if len(values) > 1:
#out_info.append([int(val) for val in values])
out_info.append([val for val in values])
else:
#out_info.extend([int(val) for val in values])
out_info.extend([val for val in values])
else:
if len(values) > 1:
out_info.append([val for val in values])
else:
out_info.extend([val for val in values])
if len(out_info) == 1:
out_info = out_info[0]
if os.path.exists(self.inputs.out_file):
update_minchd_json(self.inputs.out_file, out_info,
self.inputs.json_var, self.inputs.json_attr)
else:
save_json(
self.inputs.out_file,
dict(((self.inputs.json_var,
dict(((self.inputs.json_attr, out_info), ))), )))
outputs.out_file = out_info
return outputs
def _run_interface(self, runtime):
if not isdefined(self.inputs.out_file):
fname = os.path.splitext(os.path.basename(self.inputs.in_file))[0]
dname = os.getcwd() #os.path.dirname(self.inputs.nativeT1)
self.inputs.out_file = dname + os.sep + fname + self._suffix
try:
os.remove(self.inputs.out_file)
except OSError:
pass
#pettot1_4d_header_fixed = pe.Node(interface=FixHeaderCommand(), name="pettot1_4d_header_fixed")
#pettot1_4d_header_fixed.inputs.time_only=True
#pettot1_4d_header_fixed.inputs.in_file = fixIrregular.inputs.out_file
#pettot1_4d_header_fixed.inputs.header = self.inputs.header
class InfoOptions:
def __init__(self, command, variable, attribute, type_):
self.command = command
self.variable = variable
self.attribute = attribute
self.type_ = type_
#options = [ InfoOptions('-dimnames','time','dimnames','string'),
# InfoOptions('-varvalue time','time','frames-time','integer'),
# InfoOptions('-varvalue time-width','time','frames-length','integer') ]
temp_out_file = os.getcwd() + os.sep + "temp.json"
#for opt in options:
# run_mincinfo=InfoCommand()
# run_mincinfo.inputs.in_file = self.inputs.in_file
# run_mincinfo.inputs.out_file = temp_out_file
# run_mincinfo.inputs.opt_string = opt.command
# run_mincinfo.inputs.json_var = opt.variable
# run_mincinfo.inputs.json_attr = opt.attribute
# run_mincinfo.inputs.json_type = opt.type_
# run_mincinfo.inputs.error = 'unknown'
# print run_mincinfo.cmdline
# if self.inputs.run:
# run_mincinfo.run()
img = pyezminc.Image(self.inputs.in_file, metadata_only=True)
hd = img.get_MINC_header()
for key in hd.keys():
self._params[key] = {}
for subkey in hd[key].keys():
self._params[key][subkey] = {}
data_in = hd[key][subkey]
var = str(key)
attr = str(subkey)
#Populate dictionary with some useful image parameters (e.g., world coordinate start values of dimensions)
self._params[key][subkey] = data_in
update_minchd_json(temp_out_file, data_in, var, attr)
header = json.load(open(temp_out_file, "r"))
#fp.close()
minc_input = True
if not isdefined(self.inputs.json_header):
print("Error: could not find json file", self.inputs.json_header)
exit(1)
print("\n\nMINC INPUT =", minc_input, self.inputs.json_header)
json_header = json.load(open(self.inputs.json_header, "r+"))
header.update(json_header)
minc_input = False
header = set_frame_duration(header, minc_input)
header = set_isotope_halflife(header, self.inputs.halflife, 'halflife')
fp = open(self.inputs.out_file, "w+")
fp.seek(0)
json.dump(header, fp, sort_keys=True, indent=4)
fp.close()
self._params = header
return runtime