def headerKeyValue(image_path, key):
import subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('mrinfo')), image_path, '-property', key ]
if app._verbosity > 1:
app.console('Command: \'' + ' '.join(command) + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if app._verbosity > 1:
app.console('Result: ' + result)
return result
def mrinfo(image_path, field): #pylint: disable=unused-variable
import subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('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)
result, dummy_err = proc.communicate()
result = result.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 mrinfo(image_path, field): #pylint: disable=unused-variable
import subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('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)
result, dummy_err = proc.communicate()
result = result.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 statistic(image_path, statistic, mask_path = ''):
import subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('mrstats')), image_path, '-output', statistic ]
if mask_path:
command.extend([ '-mask', mask_path ])
if app._verbosity > 1:
app.console('Command: \'' + ' '.join(command) + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if app._verbosity > 1:
app.console('Result: ' + result)
return result
def statistic(image_path, stat, options=''): #pylint: disable=unused-variable
import shlex, subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('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, dummy_err = proc.communicate()
result = result.rstrip().decode('utf-8')
if app.verbosity > 1:
app.console('Result: ' + result)
if proc.returncode:
app.error('Error trying to calculate statistic \'' + stat + '\' from image \'' + image_path + '\'')
return result
def statistic(image_path, stat, options=''): #pylint: disable=unused-variable
import shlex, subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('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, dummy_err = proc.communicate()
result = result.rstrip().decode('utf-8')
if app.verbosity > 1:
app.console('Result: ' + result)
if proc.returncode:
app.error('Error trying to calculate statistic \'' + stat + '\' from image \'' + image_path + '\'')
return result
def headerField(image_path, field):
import subprocess
from mrtrix3 import app, run
command = [ run.exeName(run.versionMatch('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)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if app._verbosity > 1:
if '\n' in result:
app.console('Result: (' + str(result.count('\n')+1) + ' lines)')
app.debug(result)
else:
app.console('Result: ' + result)
return result
def getScheme(image_path):
import subprocess
from mrtrix3 import app, run
command = [ run.versionMatch('mrinfo'), image_path, '-petable' ]
if app._verbosity > 1:
app.console('Command: \'' + ' '.join(command) + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if result:
result = [ [ float(f) for f in line.split() ] for line in result.split('\n') ]
if app._verbosity > 1:
if not result:
app.console('Result: No phase encoding table found')
else:
app.console('Result: ' + str(len(result)) + ' x ' + str(len(result[0])) + ' table')
app.debug(str(result))
return result
def __init__(self, image_path):
import json, os, subprocess
from mrtrix3 import app, path, run
filename = path.newTemporary('json')
command = [
run.exeName(run.versionMatch('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:
app.error('Could not access header information for image \'' +
image_path + '\'')
try:
with open(filename, 'r') as f:
data = json.load(f)
except UnicodeDecodeError:
with open(filename, 'r') as f:
data = json.loads(f.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:
app.error('Error in reading header information from file \'' +
image_path + '\'')
app.debug(str(vars(self)))
def __init__(self, image_path):
import json, os, subprocess
from mrtrix3 import app, path, run
filename = path.newTemporary('json')
command = [ run.exeName(run.versionMatch('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:
app.error('Could not access header information for image \'' + image_path + '\'')
try:
with open(filename, 'r') as f:
data = json.load(f)
except UnicodeDecodeError:
with open(filename, 'r') as f:
data = json.loads(f.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:
app.error('Error in reading header information from file \'' + image_path + '\'')
app.debug(str(vars(self)))
