def _shebang(item):
from mrtrix3 import app, utils #pylint: disable=import-outside-toplevel
# If a complete path has been provided rather than just a file name, don't perform any additional file search
if os.sep in item:
path = item
else:
path = version_match(item)
if path == item:
path = find_executable(exe_name(item))
if not path:
app.debug('File \"' + item + '\": Could not find file to query')
return []
# Read the first 1024 bytes of the file
with open(path, 'rb') as file_in:
data = file_in.read(1024)
# Try to find the shebang line
for line in data.splitlines():
# Are there any non-text characters? If so, it's a binary file, so no need to looking for a shebang
try:
line = str(line.decode('utf-8'))
except:
app.debug('File \"' + item + '\": Not a text file')
return []
line = line.strip()
if len(line) > 2 and line[0:2] == '#!':
# Need to strip first in case there's a gap between the shebang symbol and the interpreter path
shebang = line[2:].strip().split(' ')
# On Windows, /usr/bin/env can't be easily found, and any direct interpreter path will have a similar issue.
# Instead, manually find the right interpreter to call using distutils
# Also if script is written in Python, try to execute it using the same interpreter as that currently running
if os.path.basename(shebang[0]) == 'env':
if len(shebang) < 2:
app.warn('Invalid shebang in script file \"' + item +
'\" (missing interpreter after \"env\")')
return []
if shebang[1] == 'python':
if not sys.executable:
app.warn(
'Unable to self-identify Python interpreter; file \"'
+ item +
'\" not guaranteed to execute on same version')
return []
shebang = [sys.executable] + shebang[2:]
app.debug('File \"' + item +
'\": Using current Python interpreter')
elif utils.is_windows():
shebang = [
os.path.abspath(find_executable(exe_name(shebang[1])))
] + shebang[2:]
elif utils.is_windows():
shebang = [
os.path.abspath(
find_executable(exe_name(os.path.basename(
shebang[0]))))
] + shebang[1:]
app.debug('File \"' + item + '\": string \"' + line + '\": ' +
str(shebang))
return shebang
app.debug('File \"' + item + '\": No shebang found')
return []
def from_user(filename, escape=True): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
fullpath = os.path.abspath(os.path.join(app.WORKING_DIR, filename))
if escape:
fullpath = quote(fullpath)
app.debug(filename + ' -> ' + fullpath)
return fullpath
def execute(): #pylint: disable=unused-variable
if not find_executable('N4BiasFieldCorrection'):
raise MRtrixError('Could not find ANTS program N4BiasFieldCorrection; please check installation')
for key in sorted(OPT_N4_BIAS_FIELD_CORRECTION):
if hasattr(app.ARGS, 'ants.' + key):
val = getattr(app.ARGS, 'ants.' + key)
if val is not None:
OPT_N4_BIAS_FIELD_CORRECTION[key] = (val, 'user defined')
ants_options = ' '.join(['-%s %s' %(k, v[0]) for k, v in OPT_N4_BIAS_FIELD_CORRECTION.items()])
# Generate a mean b=0 image
run.command('dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3')
# Use the brain mask as a weights image rather than a mask; means that voxels at the edge of the mask
# will have a smoothly-varying bias field correction applied, rather than multiplying by 1.0 outside the mask
run.command('mrconvert mean_bzero.mif mean_bzero.nii -strides +1,+2,+3')
run.command('mrconvert mask.mif mask.nii -strides +1,+2,+3')
init_bias_path = 'init_bias.nii'
corrected_path = 'corrected.nii'
run.command('N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [' + corrected_path + ',' + init_bias_path + '] ' + ants_options)
# N4 can introduce large differences between subjects via a global scaling of the bias field
# Estimate this scaling based on the total integral of the pre- and post-correction images within the brain mask
input_integral = float(run.command('mrcalc mean_bzero.mif mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump -').stdout)
output_integral = float(run.command('mrcalc ' + corrected_path + ' mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump -').stdout)
multiplier = output_integral / input_integral
app.debug('Integrals: Input = ' + str(input_integral) + '; Output = ' + str(output_integral) + '; resulting multiplier = ' + str(multiplier))
run.command('mrcalc ' + init_bias_path + ' ' + str(multiplier) + ' -mult bias.mif')
# Common final steps for all algorithms
run.command('mrcalc in.mif bias.mif -div result.mif')
run.command('mrconvert result.mif ' + path.from_user(app.ARGS.output), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
if app.ARGS.bias:
run.command('mrconvert bias.mif ' + path.from_user(app.ARGS.bias), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
def shared_data_path(): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
result = os.path.realpath(
os.path.abspath(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, os.pardir, 'share', 'mrtrix3')))
app.debug(result)
return result
def to_scratch(filename, escape=True): #pylint: disable=unused-variable
import os
from mrtrix3 import app
fullpath = os.path.abspath(os.path.join(app.SCRATCH_DIR, filename))
if escape:
fullpath = quote(fullpath)
app.debug(filename + ' -> ' + fullpath)
return fullpath
def function(fn, *args, **kwargs): #pylint: disable=unused-variable
import inspect, sys
from mrtrix3 import app
fnstring = fn.__module__ + '.' + fn.__name__ + \
'(' + ', '.join(['\'' + str(a) + '\'' if isinstance(a, str) else str(a) for a in args]) + \
(', ' if (args and kwargs) else '') + \
', '.join([key+'='+str(value) for key, value in kwargs.items()]) + ')'
if _lastFile:
if _triggerContinue(args) or _triggerContinue(kwargs.values()):
app.debug('Detected last file in function \'' + fnstring + '\'; this is the last run.command() / run.function() call that will be skipped')
if app.verbosity:
sys.stderr.write(app.colourExec + 'Skipping function:' + app.colourClear + ' ' + fnstring + '\n')
sys.stderr.flush()
return None
if app.verbosity:
sys.stderr.write(app.colourExec + 'Function:' + app.colourClear + ' ' + fnstring + '\n')
sys.stderr.flush()
# Now we need to actually execute the requested function
try:
if kwargs:
result = fn(*args, **kwargs)
else:
result = fn(*args)
except Exception as e: # pylint: disable=broad-except
app.cleanup = False
caller = inspect.getframeinfo(inspect.stack()[1][0])
error_text = str(type(e).__name__) + ': ' + str(e)
script_name = os.path.basename(sys.argv[0])
app.console('')
try:
filename = caller.filename
lineno = caller.lineno
except AttributeError:
filename = caller[1]
lineno = caller[2]
sys.stderr.write(script_name + ': ' + app.colourError + '[ERROR] Function failed: ' + fnstring + app.colourClear + app.colourDebug + ' (' + os.path.basename(filename) + ':' + str(lineno) + ')' + app.colourClear + '\n')
sys.stderr.write(script_name + ': ' + app.colourConsole + 'Information from failed function:' + app.colourClear + '\n')
for line in error_text.splitlines():
sys.stderr.write(' ' * (len(script_name)+2) + line + '\n')
app.console('')
sys.stderr.flush()
if app.tempDir:
with open(os.path.join(app.tempDir, 'error.txt'), 'w') as outfile:
outfile.write(fnstring + '\n\n' + error_text + '\n')
app.complete()
sys.exit(1)
# Only now do we append to the script log, since the function has completed successfully
if app.tempDir:
with open(os.path.join(app.tempDir, 'log.txt'), 'a') as outfile:
outfile.write(fnstring + '\n')
return result
def sharedDataPath(): #pylint: disable=unused-variable
import os
from mrtrix3 import app
result = os.path.realpath(
os.path.abspath(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.pardir, os.pardir, 'share', 'mrtrix3')))
app.debug(result)
return result
def fromUser(filename, is_command): #pylint: disable=unused-variable
import os
from mrtrix3 import app
wrapper=''
if is_command and (filename.count(' ') or app.workingDir.count(' ')):
wrapper='\"'
path = wrapper + os.path.abspath(os.path.join(app.workingDir, filename)) + wrapper
app.debug(filename + ' -> ' + path)
return path
def toTemp(filename, is_command):
import os
from mrtrix3 import app
wrapper=''
if is_command and filename.count(' '):
wrapper='\"'
path = wrapper + os.path.abspath(os.path.join(app._tempDir, filename)) + wrapper
app.debug(filename + ' -> ' + path)
return path
def fromUser(filename, is_command):
import os
from mrtrix3 import app
wrapper=''
if is_command and (filename.count(' ') or app._workingDir.count(' ')):
wrapper='\"'
path = wrapper + os.path.abspath(os.path.join(app._workingDir, filename)) + wrapper
app.debug(filename + ' -> ' + path)
return path
def make_dir(path): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
try:
os.makedirs(path)
app.debug('Created directory ' + path)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
app.debug('Directory \'' + path + '\' already exists')
def makeDir(path):
import errno, os
from mrtrix3 import app
try:
os.makedirs(path)
app.debug('Created directory ' + path)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
app.debug('Directory ' + path + ' already exists')
def makeDir(path): #pylint: disable=unused-variable
import errno, os
from mrtrix3 import app
try:
os.makedirs(path)
app.debug('Created directory ' + path)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
app.debug('Directory \'' + path + '\' already exists')
def makeDir(path):
import errno, os
from mrtrix3 import app
try:
os.makedirs(path)
app.debug('Created directory ' + path)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
app.debug('Directory ' + path + ' already exists')
def get_list(): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
algorithm_list = [ ]
for filename in os.listdir(_algorithms_path()):
filename = filename.split('.')
if len(filename) == 2 and filename[1] == 'py' and filename[0] != '__init__':
algorithm_list.append(filename[0])
algorithm_list = sorted(algorithm_list)
app.debug('Found algorithms: ' + str(algorithm_list))
return algorithm_list
def toTemp(filename, is_command): #pylint: disable=unused-variable
import os
from mrtrix3 import app
wrapper = ''
if is_command and (filename.count(' ') or app.tempDir.count(' ')):
wrapper = '\"'
path = wrapper + os.path.abspath(os.path.join(app.tempDir,
filename)) + wrapper
app.debug(filename + ' -> ' + path)
return path
def initialise(): #pylint: disable=unused-variable
import importlib, pkgutil
from mrtrix3 import app, path
initlist = [ ]
base_parser = app.Parser(description='Base parser for construction of subparsers', parents=[app.cmdline])
subparsers = app.cmdline.add_subparsers(title='Algorithm choices', help='Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ' + ', '.join(getList()), dest='algorithm')
for dummy_importer, package_name, dummy_ispkg in pkgutil.iter_modules( [ _algorithmsPath() ] ):
module = importlib.import_module('mrtrix3.' + path.scriptSubDirName() + '.' + package_name)
module.initialise(base_parser, subparsers)
initlist.extend(package_name)
app.debug('Initialised algorithms: ' + str(initlist))
def delTempFile(path):
import os
from mrtrix3 import app
if not app._cleanup:
return
if app._verbosity > 2:
app.console('Deleting temporary file: ' + path)
try:
os.remove(path)
except OSError:
app.debug('Unable to delete temporary file ' + path)
def exe_name(name): #pylint: disable=unused-variable
from mrtrix3 import app, MRtrixError
from distutils.spawn import find_executable
if find_executable(name):
output = name
elif find_executable('fsl5.0-' + name):
output = 'fsl5.0-' + name
else:
raise MRtrixError('Could not find FSL program \"' + name + '\"; please verify FSL install')
app.debug(output)
return output
def delTempFolder(path):
import shutil
from mrtrix3 import app
if not app._cleanup:
return
if app._verbosity > 2:
app.console('Deleting temporary folder: ' + path)
try:
shutil.rmtree(path)
except OSError:
app.debug('Unable to delete temprary folder ' + path)
def waitFor(path):
import os, time
from mrtrix3 import app
def inUse(path):
import subprocess
from distutils.spawn import find_executable
if app.isWindows():
if not os.access(path, os.W_OK):
return None
try:
with open(path, 'rb+') as f:
pass
return False
except:
return True
if not find_executable('fuser'):
return None
# fuser returns zero if there IS at least one process accessing the file
# A fatal error will result in a non-zero code -> inUse() = False, so waitFor() can return
return not subprocess.call(['fuser', '-s', path],
shell=False,
stdin=None,
stdout=None,
stderr=None)
if not os.path.exists(path):
delay = 1.0 / 1024.0
app.console('Waiting for creation of new file \"' + path + '\"')
while not os.path.exists(path):
time.sleep(delay)
delay = max(60.0, delay * 2.0)
app.debug('File \"' + path + '\" appears to have been created')
if not os.path.isfile(path):
app.debug('Path \"' + path +
'\" is not a file; not testing for finalization')
return
init_test = inUse(path)
if init_test is None:
app.debug('Unable to test for finalization of new file \"' + path +
'\"')
return
if not init_test:
app.debug('File \"' + path + '\" immediately ready')
return
app.console('Waiting for finalization of new file \"' + path + '\"')
delay = 1.0 / 1024.0
while True:
if inUse(path):
time.sleep(delay)
delay = max(60.0, delay * 2.0)
else:
app.debug('File \"' + path + '\" appears to have been finalized')
return
def check3DNonunity(image_in): #pylint: disable=unused-variable
from mrtrix3 import app
if not isinstance(image_in, Header):
if not isinstance(image_in, str):
app.error('Error trying to test \'' + str(image_in) + '\': Not an image header or file path')
image_in = Header(image_in)
if len(image_in.size()) < 3:
app.error('Image \'' + image_in.name() + '\' does not contain 3 spatial dimensions')
if min(image_in.size()[:3]) == 1:
app.error('Image \'' + image_in.name() + '\' does not contain 3D spatial information (has axis with size 1)')
app.debug('Image \'' + image_in.name() + '\' is >= 3D, and does not contain a unity spatial dimension')
def name_temporary(suffix): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
dir_path = CONFIG['TmpFileDir'] if 'TmpFileDir' in CONFIG else (app.SCRATCH_DIR if app.SCRATCH_DIR else os.getcwd())
prefix = CONFIG['TmpFilePrefix'] if 'TmpFilePrefix' in CONFIG else 'mrtrix-tmp-'
full_path = dir_path
suffix = suffix.lstrip('.')
while os.path.exists(full_path):
random_string = ''.join(random.choice(string.ascii_uppercase + string.ascii_lowercase + string.digits) for x in range(6))
full_path = os.path.join(dir_path, prefix + random_string + '.' + suffix)
app.debug(full_path)
return full_path
def check_3d_nonunity(image_in): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
if not isinstance(image_in, Header):
if not isinstance(image_in, STRING_TYPES):
raise MRtrixError('Error trying to test \'' + str(image_in) + '\': Not an image header or file path')
image_in = Header(image_in)
if len(image_in.size()) < 3:
raise MRtrixError('Image \'' + image_in.name() + '\' does not contain 3 spatial dimensions')
if min(image_in.size()[:3]) == 1:
raise MRtrixError('Image \'' + image_in.name() + '\' does not contain 3D spatial information (has axis with size 1)')
app.debug('Image \'' + image_in.name() + '\' is >= 3D, and does not contain a unity spatial dimension')
def initialise():
import importlib, pkgutil
from mrtrix3 import app, path
initlist = [ ]
base_parser = app.Parser(description='Base parser for construction of subparsers', parents=[app.cmdline])
subparsers = app.cmdline.add_subparsers(title='Algorithm choices', help='Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ' + ', '.join(getList()), dest='algorithm')
for importer, package_name, ispkg in pkgutil.iter_modules( [ _algorithmsPath() ] ):
module = importlib.import_module('mrtrix3.' + path.scriptSubDirName() + '.' + package_name)
module.initialise(base_parser, subparsers)
initlist.extend(package_name)
app.debug('Initialised algorithms: ' + str(initlist))
def delTempFile(path):
import os
from mrtrix3 import app
if not app._cleanup:
return
if app._verbosity > 2:
app.console('Deleting temporary file: ' + path)
try:
os.remove(path)
except OSError:
app.debug('Unable to delete temporary file ' + path)
def check3DNonunity(image_in): #pylint: disable=unused-variable
from mrtrix3 import app
if not isinstance(image_in, Header):
if not isinstance(image_in, str):
app.error('Error trying to test \'' + str(image_in) + '\': Not an image header or file path')
image_in = Header(image_in)
if len(image_in.size()) < 3:
app.error('Image \'' + image_in.name() + '\' does not contain 3 spatial dimensions')
if min(image_in.size()[:3]) == 1:
app.error('Image \'' + image_in.name() + '\' does not contain 3D spatial information (has axis with size 1)')
app.debug('Image \'' + image_in.name() + '\' is >= 3D, and does not contain a unity spatial dimension')
def exeName(name): #pylint: disable=unused-variable
from mrtrix3 import app
from distutils.spawn import find_executable
if find_executable('fsl5.0-' + name):
output = 'fsl5.0-' + name
elif find_executable(name):
output = name
else:
app.error('Could not find FSL program \"' + name + '\"; please verify FSL install')
app.debug(output)
return output
def delTempFolder(path):
import shutil
from mrtrix3 import app
if not app._cleanup:
return
if app._verbosity > 2:
app.console('Deleting temporary folder: ' + path)
try:
shutil.rmtree(path)
except OSError:
app.debug('Unable to delete temprary folder ' + path)
def getList(): #pylint: disable=unused-variable
import os
from mrtrix3 import app
algorithm_list = [ ]
src_file_list = os.listdir(_algorithmsPath())
for filename in src_file_list:
filename = filename.split('.')
if len(filename) == 2 and filename[1] == 'py' and not filename[0] == '__init__':
algorithm_list.append(filename[0])
algorithm_list = sorted(algorithm_list)
app.debug('Found algorithms: ' + str(algorithm_list))
return algorithm_list
def find_image(name): #pylint: disable=unused-variable
import os
from mrtrix3 import app, MRtrixError
prefix = os.path.join(os.path.dirname(name), os.path.basename(name).split('.')[0])
if os.path.isfile(prefix + suffix()):
app.debug('Image at expected location: \"' + prefix + suffix() + '\"')
return prefix + suffix()
for suf in ['.nii', '.nii.gz', '.img']:
if os.path.isfile(prefix + suf):
app.debug('Expected image at \"' + prefix + suffix() + '\", but found at \"' + prefix + suf + '\"')
return prefix + suf
raise MRtrixError('Unable to find FSL output file for path \"' + name + '\"')
def findImage(name):
import os
from mrtrix3 import app
basename = name.split('.')[0]
if os.path.isfile(basename + suffix()):
app.debug('Image at expected location: \"' + basename + suffix() + '\"')
return basename + suffix()
for suf in ['.nii', '.nii.gz', '.img']:
if os.path.isfile(basename + suf):
app.debug('Expected image at \"' + basename + suffix() + '\", but found at \"' + basename + suf + '\"')
return basename + suf
app.error('Unable to find FSL output file for path \"' + name + '\"')
def findImage(name):
import os
from mrtrix3 import app
basename = name.split('.')[0]
if os.path.isfile(basename + suffix()):
app.debug('Image at expected location: \"' + basename + suffix() + '\"')
return basename + suffix()
for suf in ['.nii', '.nii.gz', '.img']:
if os.path.isfile(basename + suf):
app.debug('Expected image at \"' + basename + suffix() + '\", but found at \"' + basename + suf + '\"')
return basename + suf
app.error('Unable to find FSL output file for path \"' + name + '\"')
def exe_name(name): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
if find_executable(name):
output = name
elif find_executable('fsl5.0-' + name):
output = 'fsl5.0-' + name
app.warn('Using FSL binary \"' + output + '\" rather than \"' + name +
'\"; suggest checking FSL installation')
else:
raise MRtrixError('Could not find FSL program \"' + name +
'\"; please verify FSL install')
app.debug(output)
return output
def findImage(name): #pylint: disable=unused-variable
import os
from mrtrix3 import app
prefix = os.path.join(os.path.dirname(name), os.path.basename(name).split('.')[0])
if os.path.isfile(prefix + suffix()):
app.debug('Image at expected location: \"' + prefix + suffix() + '\"')
return prefix + suffix()
for suf in ['.nii', '.nii.gz', '.img']:
if os.path.isfile(prefix + suf):
app.debug('Expected image at \"' + prefix + suffix() + '\", but found at \"' + prefix + suf + '\"')
return prefix + suf
app.error('Unable to find FSL output file for path \"' + name + '\"')
return ''
def script_subdir_name(): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
frameinfo = inspect.stack()[-1]
try:
frame = frameinfo.frame
except: # Prior to Version 3.5
frame = frameinfo[0]
# If the script has been run through a softlink, we need the name of the original
# script in order to locate the additional data
name = os.path.basename(os.path.realpath(inspect.getfile(frame)))
if not name[0].isalpha():
name = '_' + name
app.debug(name)
return name
def match(image_one, image_two):
import math
from mrtrix3 import app
debug_prefix = '\'' + image_one + '\' \'' + image_two + '\''
# Image dimensions
one_dim = [ int(i) for i in headerField(image_one, 'size').split() ]
two_dim = [ int(i) for i in headerField(image_two, 'size').split() ]
if not one_dim == two_dim:
app.debug(debug_prefix + ' dimension mismatch (' + str(one_dim) + ' ' + str(two_dim) + ')')
return False
# Voxel size
one_spacing = [ float(f) for f in headerField(image_one, 'vox').split() ]
two_spacing = [ float(f) for f in headerField(image_two, 'vox').split() ]
for one, two in zip(one_spacing, two_spacing):
if one and two and not math.isnan(one) and not math.isnan(two):
if (abs(two-one) / (0.5*(one+two))) > 1e-04:
app.debug(debug_prefix + ' voxel size mismatch (' + str(one_spacing) + ' ' + str(two_spacing) + ')')
return False
# Image transform
one_transform = [ float(f) for f in headerField(image_one, 'transform').replace('\n', ' ').replace(',', ' ').split() ]
two_transform = [ float(f) for f in headerField(image_two, 'transform').replace('\n', ' ').replace(',', ' ').split() ]
for one, two in zip(one_transform, two_transform):
if abs(one-two) > 1e-4:
app.debug(debug_prefix + ' transform mismatch (' + str(one_transform) + ' ' + str(two_transform) + ')')
return False
# Everything matches!
app.debug(debug_prefix + ' image match')
return True
def usage(cmdline): #pylint: disable=unused-variable
from mrtrix3 import app, path #pylint: disable=import-outside-toplevel
sys.path.insert(0, os.path.realpath(os.path.join(_algorithms_path(), os.pardir)))
initlist = [ ]
# Don't let Python 3 try to read incompatible .pyc files generated by Python 2 for no-longer-existent .py files
pylist = get_list()
base_parser = app.Parser(description='Base parser for construction of subparsers', parents=[cmdline])
subparsers = cmdline.add_subparsers(title='Algorithm choices', help='Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ' + ', '.join(get_list()), dest='algorithm')
for dummy_importer, package_name, dummy_ispkg in pkgutil.iter_modules( [ _algorithms_path() ] ):
if package_name in pylist:
module = importlib.import_module(path.script_subdir_name() + '.' + package_name)
module.usage(base_parser, subparsers)
initlist.extend(package_name)
app.debug('Initialised algorithms: ' + str(initlist))
def function(fn_to_execute, *args, **kwargs): #pylint: disable=unused-variable
import os, sys
from mrtrix3 import ANSI, app
if not fn_to_execute:
raise TypeError('Invalid input to run.function()')
show = kwargs.pop('show', True)
fnstring = fn_to_execute.__module__ + '.' + fn_to_execute.__name__ + \
'(' + ', '.join(['\'' + str(a) + '\'' if isinstance(a, str) else str(a) for a in args]) + \
(', ' if (args and kwargs) else '') + \
', '.join([key+'='+str(value) for key, value in kwargs.items()]) + ')'
if shared.get_continue():
if shared.trigger_continue(args) or shared.trigger_continue(
kwargs.values()):
app.debug(
'Detected last file in function \'' + fnstring +
'\'; this is the last run.command() / run.function() call that will be skipped'
)
if shared.verbosity:
sys.stderr.write(ANSI.execute + 'Skipping function:' + ANSI.clear +
' ' + fnstring + '\n')
sys.stderr.flush()
return None
if (shared.verbosity and show) or shared.verbosity > 1:
sys.stderr.write(ANSI.execute + 'Function:' + ANSI.clear + ' ' +
fnstring + '\n')
sys.stderr.flush()
# Now we need to actually execute the requested function
try:
if kwargs:
result = fn_to_execute(*args, **kwargs)
else:
result = fn_to_execute(*args)
except Exception as exception: # pylint: disable=broad-except
raise MRtrixFnError(fnstring, str(exception))
# Only now do we append to the script log, since the function has completed successfully
if shared.get_scratch_dir():
with shared.lock:
with open(os.path.join(shared.get_scratch_dir(), 'log.txt'),
'a') as outfile:
outfile.write(fnstring + '\n')
return result
def scriptSubDirName(): #pylint: disable=unused-variable
import inspect, os
from mrtrix3 import app
frameinfo = inspect.stack()[-1]
try:
frame = frameinfo.frame
except: # Prior to Version 3.5
frame = frameinfo[0]
# If the script has been run through a softlink, we need the name of the original
# script in order to locate the additional data
name = os.path.basename(os.path.realpath(inspect.getfile(frame)))
if not name[0].isalpha():
name = '_' + name
app.debug(name)
return name
def make_temporary(suffix): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=import-outside-toplevel
is_directory = suffix in '\\/' and len(suffix) == 1
while True:
temp_path = name_temporary(suffix)
try:
if is_directory:
os.makedirs(temp_path)
else:
open(temp_path, 'a').close()
app.debug(temp_path)
return temp_path
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
def commonPostfix(inputFiles): #pylint: disable=unused-variable
from mrtrix3 import app
first = inputFiles[0]
cursor = 0
found = False
common = ''
for dummy_i in reversed(first):
if not found:
for j in inputFiles:
if j[len(j)-cursor-1] != first[len(first)-cursor-1]:
found = True
break
if not found:
common = first[len(first)-cursor-1] + common
cursor += 1
app.debug('Common postfix of ' + str(len(inputFiles)) + ' is \'' + common + '\'')
return common
def commonPostfix(inputFiles):
from mrtrix3 import app
first = inputFiles[0];
cursor = 0
found = False;
common = ''
for i in reversed(first):
if found == False:
for j in inputFiles:
if j[len(j)-cursor-1] != first[len(first)-cursor-1]:
found = True
break
if found == False:
common = first[len(first)-cursor-1] + common
cursor += 1
app.debug('Common postfix of ' + str(len(inputFiles)) + ' is \'' + common + '\'')
return common
def axis2dir(string): #pylint: disable=unused-variable
from mrtrix3 import app
if string == 'i':
direction = [1,0,0]
elif string == 'i-':
direction = [-1,0,0]
elif string == 'j':
direction = [0,1,0]
elif string == 'j-':
direction = [0,-1,0]
elif string == 'k':
direction = [0,0,1]
elif string == 'k-':
direction = [0,0,-1]
else:
app.error('Unrecognized NIfTI axis & direction specifier: ' + string)
app.debug(string + ' -> ' + str(direction))
return direction
def getScheme(arg): #pylint: disable=unused-variable
from mrtrix3 import app, image
if not isinstance(arg, image.Header):
if not isinstance(arg, str):
app.error('Error trying to derive phase-encoding scheme from \'' + str(arg) + '\': Not an image header or file path')
arg = image.Header(arg)
if 'pe_scheme' in arg.keyval():
app.debug(str(arg.keyval()['pe_scheme']))
return arg.keyval()['pe_scheme']
if 'PhaseEncodingDirection' not in arg.keyval():
return None
line = direction(arg.keyval()['PhaseEncodingDirection'])
if 'TotalReadoutTime' in arg.keyval():
line = [ float(value) for value in line ]
line.append(float(arg.keyval()['TotalReadoutTime']))
num_volumes = 1 if len(arg.size()) < 4 else arg.size()[3]
app.debug(str(line) + ' x ' + str(num_volumes) + ' rows')
return [ line ] * num_volumes
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 newTempFile(suffix):
import os, random, string, sys
from mrtrix3 import app
if 'TmpFileDir' in app.config:
dir_path = app.config['TmpFileDir']
else:
dir_path = app._tempDir
if 'TmpFilePrefix' in app.config:
prefix = app.config['TmpFilePrefix']
else:
prefix = 'mrtrix-tmp-'
full_path = dir_path
if not suffix:
suffix = 'mif'
while os.path.exists(full_path):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
full_path = os.path.join(dir_path, prefix + random_string + '.' + suffix)
app.debug(full_path)
return full_path
def direction(string): #pylint: disable=unused-variable
from mrtrix3 import app
pe_dir = ''
try:
PE_axis = abs(int(string))
if PE_axis > 2:
app.error('When specified as a number, phase encode axis must be either 0, 1 or 2 (positive or negative)')
reverse = (string.contains('-')) # Allow -0
pe_dir = [0,0,0]
if reverse:
pe_dir[PE_axis] = -1
else:
pe_dir[PE_axis] = 1
except:
string = string.lower()
if string == 'lr':
pe_dir = [1,0,0]
elif string == 'rl':
pe_dir = [-1,0,0]
elif string == 'pa':
pe_dir = [0,1,0]
elif string == 'ap':
pe_dir = [0,-1,0]
elif string == 'is':
pe_dir = [0,0,1]
elif string == 'si':
pe_dir = [0,0,-1]
elif string == 'i':
pe_dir = [1,0,0]
elif string == 'i-':
pe_dir = [-1,0,0]
elif string == 'j':
pe_dir = [0,1,0]
elif string == 'j-':
pe_dir = [0,-1,0]
elif string == 'k':
pe_dir = [0,0,1]
elif string == 'k-':
pe_dir = [0,0,-1]
else:
app.error('Unrecognized phase encode direction specifier: ' + string)
app.debug(string + ' -> ' + str(pe_dir))
return pe_dir
def newTemporary(suffix): #pylint: disable=unused-variable
import os.path, random, string
from mrtrix3 import app
if 'TmpFileDir' in app.config:
dir_path = app.config['TmpFileDir']
elif app.tempDir:
dir_path = app.tempDir
else:
dir_path = os.getcwd()
if 'TmpFilePrefix' in app.config:
prefix = app.config['TmpFilePrefix']
else:
prefix = 'mrtrix-tmp-'
full_path = dir_path
suffix = suffix.lstrip('.')
while os.path.exists(full_path):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
full_path = os.path.join(dir_path, prefix + random_string + '.' + suffix)
app.debug(full_path)
return full_path
def delTemporary(path): #pylint: disable=unused-variable
import shutil, os
from mrtrix3 import app
if not app.cleanup:
return
if os.path.isfile(path):
temporary_type = 'file'
func = os.remove
elif os.path.isdir(path):
temporary_type = 'directory'
func = shutil.rmtree
else:
app.debug('Unknown target \'' + path + '\'')
return
if app.verbosity > 2:
app.console('Deleting temporary ' + temporary_type + ': \'' + path + '\'')
try:
func(path)
except OSError:
app.debug('Unable to delete temporary ' + temporary_type + ': \'' + path + '\'')
def eddyBinary(cuda):
import os
from mrtrix3 import app
from distutils.spawn import find_executable
if cuda:
if find_executable('eddy_cuda'):
app.debug('Selecting CUDA version of eddy')
return 'eddy_cuda'
else:
app.warn('CUDA version of eddy not found; running standard version')
if find_executable('eddy_openmp'):
path = 'eddy_openmp'
elif find_executable('eddy'):
path = 'eddy'
elif find_executable('fsl5.0-eddy'):
path = 'fsl5.0-eddy'
else:
app.error('Could not find FSL program eddy; please verify FSL install')
app.debug(path)
return path
def function(fn, *args):
import os, sys
from mrtrix3 import app
fnstring = fn.__module__ + '.' + fn.__name__ + '(' + ', '.join(args) + ')'
if app._lastFile:
# Check to see if the last file produced in the previous script execution is
# intended to be produced by this command; if it is, this will be the last
# command that gets skipped by the -continue option
# It's possible that the file might be defined in a '--option=XXX' style argument
# It's also possible that the filename in the command string has the file extension omitted
for entry in args:
if entry.startswith('--') and '=' in entry:
totest = entry.split('=')[1]
else:
totest = entry
filetotest = [ app._lastFile, os.path.splitext(app._lastFile)[0] ]
if totest in filetotest:
app.debug('Detected last file \'' + app._lastFile + '\' in function \'' + fnstring + '\'; this is the last run.command() / run.function() call that will be skipped')
app._lastFile = ''
break
if app._verbosity:
sys.stderr.write(app.colourExec + 'Skipping function:' + app.colourClear + ' ' + fnstring + '\n')
sys.stderr.flush()
return
if app._verbosity:
sys.stderr.write(app.colourExec + 'Function:' + app.colourClear + ' ' + fnstring + '\n')
sys.stderr.flush()
# Now we need to actually execute the requested function
result = fn(*args)
# Only now do we append to the script log, since the function has completed successfully
if app._tempDir:
with open(os.path.join(app._tempDir, 'log.txt'), 'a') as outfile:
outfile.write(fnstring + '\n')
return result
def exeName(item):
from distutils.spawn import find_executable
from mrtrix3 import app
global _mrtrix_bin_path
if not app.isWindows():
path = item
elif item.endswith('.exe'):
path = item
elif os.path.isfile(os.path.join(_mrtrix_bin_path, item)):
path = item
elif os.path.isfile(os.path.join(_mrtrix_bin_path, item + '.exe')):
path = item + '.exe'
elif find_executable(item) is not None:
path = item
elif find_executable(item + '.exe') is not None:
path = item + '.exe'
# If it can't be found, return the item as-is; find_executable() fails to identify Python scripts
else:
path = item
app.debug(item + ' -> ' + path)
return path
def eddyBinary(cuda): #pylint: disable=unused-variable
import os
from mrtrix3 import app
from distutils.spawn import find_executable
if cuda:
if find_executable('eddy_cuda'):
app.debug('Selected soft-linked CUDA version (\'eddy_cuda\')')
return 'eddy_cuda'
# Cuda versions are now provided with a CUDA trailing version number
# Users may not necessarily create a softlink to one of these and
# call it "eddy_cuda"
# Therefore, hunt through PATH looking for them; if more than one,
# select the one with the highest version number
binaries = [ ]
for directory in os.environ['PATH'].split(os.pathsep):
if os.path.isdir(directory):
for entry in os.listdir(directory):
if entry.startswith('eddy_cuda'):
binaries.append(entry)
max_version = 0.0
exe_path = ''
for entry in binaries:
try:
version = float(entry.lstrip('eddy_cuda'))
if version > max_version:
max_version = version
exe_path = entry
except:
pass
if exe_path:
app.debug('CUDA version ' + str(max_version) + ': ' + exe_path)
return exe_path
app.debug('No CUDA version of eddy found')
return ''
for candidate in [ 'eddy_openmp', 'eddy_cpu', 'eddy', 'fsl5.0-eddy' ]:
if find_executable(candidate):
app.debug(candidate)
return candidate
app.debug('No CPU version of eddy found')
return ''
def suffix(): #pylint: disable=unused-variable
import os
from mrtrix3 import app
global _suffix
if _suffix:
return _suffix
fsl_output_type = os.environ.get('FSLOUTPUTTYPE', '')
if fsl_output_type == 'NIFTI':
app.debug('NIFTI -> .nii')
_suffix = '.nii'
elif fsl_output_type == 'NIFTI_GZ':
app.debug('NIFTI_GZ -> .nii.gz')
_suffix = '.nii.gz'
elif fsl_output_type == 'NIFTI_PAIR':
app.debug('NIFTI_PAIR -> .img')
_suffix = '.img'
elif fsl_output_type == 'NIFTI_PAIR_GZ':
app.error('MRtrix3 does not support compressed NIFTI pairs; please change FSLOUTPUTTYPE environment variable')
elif fsl_output_type:
app.warn('Unrecognised value for environment variable FSLOUTPUTTYPE (\"' + fsl_output_type + '\"): Expecting compressed NIfTIs, but FSL commands may fail')
_suffix = '.nii.gz'
else:
app.warn('Environment variable FSLOUTPUTTYPE not set; FSL commands may fail, or script may fail to locate FSL command outputs')
_suffix = '.nii.gz'
return _suffix
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 _shebang(item):
import os
from mrtrix3 import app
from distutils.spawn import find_executable
# If a complete path has been provided rather than just a file name, don't perform any additional file search
if os.sep in item:
path = item
else:
path = versionMatch(item)
if path == item:
path = find_executable(exeName(item))
if not path:
app.debug('File \"' + item + '\": Could not find file to query')
return []
# Read the first 1024 bytes of the file
with open(path, 'rb') as f:
data = f.read(1024)
# Try to find the shebang line
for line in data.splitlines():
# Are there any non-text characters? If so, it's a binary file, so no need to looking for a shebang
try :
line = str(line.decode('utf-8'))
except:
app.debug('File \"' + item + '\": Not a text file')
return []
line = line.strip()
if len(line) > 2 and line[0:2] == '#!':
# Need to strip first in case there's a gap between the shebang symbol and the interpreter path
shebang = line[2:].strip().split(' ')
if app.isWindows():
# On Windows, /usr/bin/env can't be easily found, and any direct interpreter path will have a similar issue.
# Instead, manually find the right interpreter to call using distutils
if os.path.basename(shebang[0]) == 'env':
new_shebang = [ os.path.abspath(find_executable(exeName(shebang[1]))) ]
new_shebang.extend(shebang[2:])
shebang = new_shebang
else:
new_shebang = [ os.path.abspath(find_executable(exeName(os.path.basename(shebang[0])))) ]
new_shebang.extend(shebang[1:])
shebang = new_shebang
if not shebang or not shebang[0]:
app.error('Malformed shebang in file \"' + item + '\": \"' + line + '\"')
app.debug('File \"' + item + '\": string \"' + line + '\": ' + str(shebang))
return shebang
app.debug('File \"' + item + '\": No shebang found')
return []