def mrinfo(image_path, field): #pylint: disable=unused-variable
from mrtrix3 import app, run #pylint: disable=import-outside-toplevel
command = [ run.exe_name(run.version_match('mrinfo')), image_path, '-' + field ]
if app.VERBOSITY > 1:
app.console('Command: \'' + ' '.join(command) + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None) #pylint: disable=consider-using-with
result = proc.communicate()[0].rstrip().decode('utf-8')
if app.VERBOSITY > 1:
app.console('Result: ' + result)
# Don't exit on error; let the calling function determine whether or not
# the absence of the key is an issue
return result
def statistics(image_path, **kwargs): #pylint: disable=unused-variable
from mrtrix3 import app, run #pylint: disable=import-outside-toplevel
mask = kwargs.pop('mask', None)
allvolumes = kwargs.pop('allvolumes', False)
ignorezero = kwargs.pop('ignorezero', False)
if kwargs:
raise TypeError(
'Unsupported keyword arguments passed to image.statistics(): ' +
str(kwargs))
command = [run.exe_name(run.version_match('mrstats')), image_path]
for stat in IMAGE_STATISTICS:
command.extend(['-output', stat])
if mask:
command.extend(['-mask', mask])
if allvolumes:
command.append('-allvolumes')
if ignorezero:
command.append('-ignorezero')
if app.VERBOSITY > 1:
app.console('Command: \'' + ' '.join(command) +
'\' (piping data to local storage)')
try:
from subprocess import DEVNULL #pylint: disable=import-outside-toplevel
except ImportError:
DEVNULL = open(os.devnull, 'wb')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=DEVNULL)
stdout = proc.communicate()[0]
if proc.returncode:
raise MRtrixError(
'Error trying to calculate statistics from image \'' + image_path +
'\'')
stdout_lines = [
line.strip() for line in stdout.decode('cp437').splitlines()
]
result = []
for line in stdout_lines:
line = line.replace('N/A', 'nan').split()
assert len(line) == len(IMAGE_STATISTICS)
result.append(
ImageStatistics(float(line[0]), float(line[1]), float(line[2]),
float(line[3]), float(line[4]), float(line[5]),
int(line[6])))
if len(result) == 1:
result = result[0]
if app.VERBOSITY > 1:
app.console('Result: ' + str(result))
return result
def __init__(self, image_path):
from mrtrix3 import app, path, run #pylint: disable=import-outside-toplevel
filename = path.name_temporary('json')
command = [
run.exe_name(run.version_match('mrinfo')), image_path, '-json_all',
filename
]
if app.VERBOSITY > 1:
app.console('Loading header for image file \'' + image_path + '\'')
app.debug(str(command))
result = subprocess.call(command, stdout=None, stderr=None)
if result:
raise MRtrixError(
'Could not access header information for image \'' +
image_path + '\'')
try:
with open(filename, 'r') as json_file:
data = json.load(json_file)
except UnicodeDecodeError:
with open(filename, 'r') as json_file:
data = json.loads(json_file.read().decode('utf-8',
errors='replace'))
os.remove(filename)
try:
#self.__dict__.update(data)
# Load the individual header elements manually, for a couple of reasons:
# - So that pylint knows that they'll be there
# - Write to private members, and give read-only access
self._name = data['name']
self._size = data['size']
self._spacing = data['spacing']
self._strides = data['strides']
self._format = data['format']
self._datatype = data['datatype']
self._intensity_offset = data['intensity_offset']
self._intensity_scale = data['intensity_scale']
self._transform = data['transform']
if not 'keyval' in data or not data['keyval']:
self._keyval = {}
else:
self._keyval = data['keyval']
except:
raise MRtrixError(
'Error in reading header information from file \'' +
image_path + '\'')
app.debug(str(vars(self)))
def statistic(image_path, stat, options=''): #pylint: disable=unused-variable
import shlex, subprocess
from mrtrix3 import app, MRtrixError, run
command = [ run.exe_name(run.version_match('mrstats')), image_path, '-output', stat ]
if options:
command.extend(shlex.split(options))
if app.VERBOSITY > 1:
app.console('Command: \'' + ' '.join(command) + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result = [ line.strip() for line in proc.communicate()[0].decode('cp437').splitlines() ]
if stat == 'count':
result = [ int(i) for i in result ]
else:
result = [ float(f) for f in result ]
if len(result) == 1:
result = result[0]
if app.VERBOSITY > 1:
app.console('Result: ' + str(result))
if proc.returncode:
raise MRtrixError('Error trying to calculate statistic \'' + stat + '\' from image \'' + image_path + '\'')
return result
