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
os.path.join(subject_dir, 'subject2template_warp.mif') +
' -fc ' + os.path.join(template_dir, 'fixel_mask') + ' ' +
template_fc + ' ' + subject_label + '.mif' + ' -force')
# Compute log FC
if not os.path.exists(os.path.join(template_dir, 'log_fc')):
os.mkdir(os.path.join(template_dir, 'log_fc'))
run.command('mrcalc ' +
os.path.join(template_fc, subject_label + '.mif') +
' -log ' + template_log_fc + ' -force')
if not os.path.exists(os.path.join(template_dir, 'fdc')):
os.mkdir(os.path.join(template_dir, 'fdc'))
run.command('mrcalc ' +
os.path.join(template_fd, subject_label + '.mif') + ' ' +
os.path.join(template_fc, subject_label + '.mif') +
' -mult ' + template_fdc + ' -force')
# Copy index and directions file into log FC and FDC fixel directories
run.command('cp ' + os.path.join(template_fc, 'index.mif') + ' ' +
os.path.join(template_fc, 'directions.mif') + ' ' +
os.path.join(template_dir, 'log_fc'))
run.command('cp ' + os.path.join(template_fc, 'index.mif') + ' ' +
os.path.join(template_fc, 'directions.mif') + ' ' +
os.path.join(template_dir, 'fdc'))
# Perform fixel-based statistical inference in FD, FC and FDC
elif app.args.analysis_level == "group4":
print('asdf')
app.complete()
DKI=0
if app.args.DKIparams:
DKI=1
WMTI=0
if app.args.WMTIparams:
WMTI=1
constraints=0
if app.args.fit_constraints:
constraints=app.args.fit_constraints
AKC=0
if app.args.akc:
AKC=1
KCUM=0
if app.args.kcumulants:
KCUM=1
eng.tensorfitting(path.toTemp('',True),path.fromUser(app.args.output, True),outliers,KCUM,DTI,DKI,WMTI,constraints,AKC,DKI_root,nargout=0)
eng.quit()
app.gotoTempDir()
else:
if app.args.datatype:
run.command('mrconvert -datatype ' + app.args.datatype + ' ' + path.toTemp('dwi_designer.nii',True) + ' ' + path.fromUser(app.args.output + '.nii',True))
else:
shutil.copyfile(path.toTemp('dwi_designer.nii',True),path.fromUser(app.args.output + '.nii',True))
shutil.copyfile(path.toTemp('dwi_designer.bvec',True),path.fromUser(app.args.output + '.bvec',True))
shutil.copyfile(path.toTemp('dwi_designer.bval',True),path.fromUser(app.args.output + '.bval',True))
app.complete()
def command(cmd, exitOnError=True): #pylint: disable=unused-variable
import inspect, itertools, shlex, signal, string, subprocess, sys, tempfile
from distutils.spawn import find_executable
from mrtrix3 import app
# This is the only global variable that is _modified_ within this function
global _processes
# Vectorise the command string, preserving anything encased within quotation marks
if os.sep == '/': # Cheap POSIX compliance check
cmdsplit = shlex.split(cmd)
else: # Native Windows Python
cmdsplit = [
entry.strip('\"') for entry in shlex.split(cmd, posix=False)
]
if _lastFile:
if _triggerContinue(cmdsplit):
app.debug(
'Detected last file in command \'' + cmd +
'\'; this is the last run.command() / run.function() call that will be skipped'
)
if app.verbosity:
sys.stderr.write(app.colourExec + 'Skipping command:' +
app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
return ('', '')
# This splits the command string based on the piping character '|', such that each
# individual executable (along with its arguments) appears as its own list
cmdstack = [
list(g) for k, g in itertools.groupby(cmdsplit, lambda s: s != '|')
if k
]
for line in cmdstack:
is_mrtrix_exe = line[0] in _mrtrix_exe_list
if is_mrtrix_exe:
line[0] = versionMatch(line[0])
if app.numThreads is not None:
line.extend(['-nthreads', str(app.numThreads)])
# Get MRtrix3 binaries to output additional INFO-level information if running in debug mode
if app.verbosity == 3:
line.append('-info')
elif not app.verbosity:
line.append('-quiet')
else:
line[0] = exeName(line[0])
shebang = _shebang(line[0])
if shebang:
if not is_mrtrix_exe:
# If a shebang is found, and this call is therefore invoking an
# interpreter, can't rely on the interpreter finding the script
# from PATH; need to find the full path ourselves.
line[0] = find_executable(line[0])
for item in reversed(shebang):
line.insert(0, item)
app.debug('To execute: ' + str(cmdstack))
if app.verbosity:
sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' +
cmd + '\n')
sys.stderr.flush()
# Disable interrupt signal handler while threads are running
try:
signal.signal(signal.SIGINT, signal.default_int_handler)
except:
pass
# Construct temporary text files for holding stdout / stderr contents when appropriate
# (One entry per process; each is a tuple containing two entries, each of which is either a
# file-like object, or None)
tempfiles = []
# Execute all processes
assert not _processes
for index, to_execute in enumerate(cmdstack):
file_out = None
file_err = None
# If there's at least one command prior to this, need to receive the stdout from the prior command
# at the stdin of this command; otherwise, nothing to receive
if index > 0:
handle_in = _processes[index - 1].stdout
else:
handle_in = None
# If this is not the last command, then stdout needs to be piped to the next command;
# otherwise, write stdout to a temporary file so that the contents can be read later
if index < len(cmdstack) - 1:
handle_out = subprocess.PIPE
else:
file_out = tempfile.TemporaryFile()
handle_out = file_out.fileno()
# If we're in debug / info mode, the contents of stderr will be read and printed to the terminal
# as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary
# file so that the contents can be read later
if app.verbosity > 1:
handle_err = subprocess.PIPE
else:
file_err = tempfile.TemporaryFile()
handle_err = file_err.fileno()
# Set off the processes
try:
try:
process = subprocess.Popen(to_execute,
stdin=handle_in,
stdout=handle_out,
stderr=handle_err,
env=_env,
preexec_fn=os.setpgrp) # pylint: disable=bad-option-value,subprocess-popen-preexec-fn
except AttributeError:
process = subprocess.Popen(to_execute,
stdin=handle_in,
stdout=handle_out,
stderr=handle_err,
env=_env)
_processes.append(process)
tempfiles.append((file_out, file_err))
# FileNotFoundError not defined in Python 2.7
except OSError as e:
if exitOnError:
app.error('\'' + to_execute[0] + '\' not executed ("' +
str(e) + '"); script cannot proceed')
else:
app.warn('\'' + to_execute[0] + '\' not executed ("' + str(e) +
'")')
for p in _processes:
p.terminate()
_processes = []
break
return_stdout = ''
return_stderr = ''
error = False
error_text = ''
# Wait for all commands to complete
# Switch how we monitor running processes / wait for them to complete
# depending on whether or not the user has specified -info or -debug option
try:
if app.verbosity > 1:
for process in _processes:
stderrdata = b''
do_indent = True
while True:
# Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing
byte = process.stderr.read(1)
stderrdata += byte
char = byte.decode('cp1252', errors='ignore')
if not char and process.poll() is not None:
break
if do_indent and char in string.printable and char != '\r' and char != '\n':
sys.stderr.write(' ')
do_indent = False
elif char in ['\r', '\n']:
do_indent = True
sys.stderr.write(char)
sys.stderr.flush()
stderrdata = stderrdata.decode('utf-8', errors='replace')
return_stderr += stderrdata
if process.returncode:
error = True
error_text += stderrdata
else:
for process in _processes:
process.wait()
except (KeyboardInterrupt, SystemExit):
app.handler(signal.SIGINT, inspect.currentframe())
# Re-enable interrupt signal handler
try:
signal.signal(signal.SIGINT, app.handler)
except:
pass
# For any command stdout / stderr data that wasn't either passed to another command or
# printed to the terminal during execution, read it here.
for index in range(len(cmdstack)):
if tempfiles[index][0] is not None:
tempfiles[index][0].flush()
tempfiles[index][0].seek(0)
stdout_text = tempfiles[index][0].read().decode('utf-8',
errors='replace')
return_stdout += stdout_text
if _processes[index].returncode:
error = True
error_text += stdout_text
if tempfiles[index][1] is not None:
tempfiles[index][1].flush()
tempfiles[index][1].seek(0)
stderr_text = tempfiles[index][1].read().decode('utf-8',
errors='replace')
return_stderr += stderr_text
if _processes[index].returncode:
error = True
error_text += stderr_text
_processes = []
if error:
if exitOnError:
app.cleanup = False
caller = inspect.getframeinfo(inspect.stack()[1][0])
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] Command failed: ' + cmd +
app.colourClear + app.colourDebug + ' (' +
os.path.basename(filename) + ':' + str(lineno) +
')' + app.colourClear + '\n')
sys.stderr.write(script_name + ': ' + app.colourConsole +
'Output of failed command:' + 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(cmd + '\n\n' + error_text + '\n')
app.complete()
sys.exit(1)
else:
app.warn('Command failed: ' + cmd)
# Only now do we append to the script log, since the command has completed successfully
# Note: Writing the command as it was formed as the input to run.command():
# other flags may potentially change if this file is eventually used to resume the script
if app.tempDir:
with open(os.path.join(app.tempDir, 'log.txt'), 'a') as outfile:
outfile.write(cmd + '\n')
return (return_stdout, return_stderr)
def command(cmd, exitOnError=True):
import inspect, itertools, os, shlex, subprocess, sys, tempfile
from distutils.spawn import find_executable
from mrtrix3 import app
# This is the only global variable that is _modified_ within this function
global _processes
# Vectorise the command string, preserving anything encased within quotation marks
cmdsplit = shlex.split(cmd)
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 cmdsplit:
if entry.startswith('--') and '=' in entry:
cmdtotest = entry.split('=')[1]
else:
cmdtotest = entry
filetotest = [ app._lastFile, os.path.splitext(app._lastFile)[0] ]
if cmdtotest in filetotest:
app.debug('Detected last file \'' + app._lastFile + '\' in command \'' + cmd + '\'; 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 command:' + app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
return
# This splits the command string based on the piping character '|', such that each
# individual executable (along with its arguments) appears as its own list
# Note that for Python2 support, it is necessary to convert groupby() output from
# a generator to a list before it is passed to filter()
cmdstack = [ list(g) for k, g in filter(lambda t : t[0], ((k, list(g)) for k, g in itertools.groupby(cmdsplit, lambda s : s is not '|') ) ) ]
for line in cmdstack:
is_mrtrix_exe = line[0] in _mrtrix_exe_list
if is_mrtrix_exe:
line[0] = versionMatch(line[0])
if app._nthreads is not None:
line.extend( [ '-nthreads', str(app._nthreads) ] )
# Get MRtrix3 binaries to output additional INFO-level information if running in debug mode
if app._verbosity == 3:
line.append('-info')
elif not app._verbosity:
line.append('-quiet')
else:
line[0] = exeName(line[0])
shebang = _shebang(line[0])
if len(shebang):
if not is_mrtrix_exe:
# If a shebang is found, and this call is therefore invoking an
# interpreter, can't rely on the interpreter finding the script
# from PATH; need to find the full path ourselves.
line[0] = find_executable(line[0])
for item in reversed(shebang):
line.insert(0, item)
if app._verbosity:
sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
app.debug('To execute: ' + str(cmdstack))
# Construct temporary text files for holding stdout / stderr contents when appropriate
# (One entry per process; each is a tuple containing two entries, each of which is either a
# file-like object, or None)
tempfiles = [ ]
# Execute all processes
_processes = [ ]
for index, command in enumerate(cmdstack):
file_out = None
file_err = None
# If there's at least one command prior to this, need to receive the stdout from the prior command
# at the stdin of this command; otherwise, nothing to receive
if index > 0:
handle_in = _processes[index-1].stdout
else:
handle_in = None
# If this is not the last command, then stdout needs to be piped to the next command;
# otherwise, write stdout to a temporary file so that the contents can be read later
if index < len(cmdstack)-1:
handle_out = subprocess.PIPE
else:
file_out = tempfile.TemporaryFile()
handle_out = file_out.fileno()
# If we're in debug / info mode, the contents of stderr will be read and printed to the terminal
# as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary
# file so that the contents can be read later
if app._verbosity > 1:
handle_err = subprocess.PIPE
else:
file_err = tempfile.TemporaryFile()
handle_err = file_err.fileno()
# Set off the processes
try:
process = subprocess.Popen (command, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env)
_processes.append(process)
tempfiles.append( ( file_out, file_err ) )
# FileNotFoundError not defined in Python 2.7
except OSError as e:
if exitOnError:
app.error('\'' + command[0] + '\' not executed ("' + str(e) + '"); script cannot proceed')
else:
app.warn('\'' + command[0] + '\' not executed ("' + str(e) + '")')
for p in _processes:
p.terminate()
_processes = [ ]
break
except (KeyboardInterrupt, SystemExit):
import inspect, signal
app._handler(signal.SIGINT, inspect.currentframe())
return_stdout = ''
return_stderr = ''
error = False
error_text = ''
# Wait for all commands to complete
try:
# Switch how we monitor running processes / wait for them to complete
# depending on whether or not the user has specified -verbose or -debug option
if app._verbosity > 1:
for process in _processes:
stderrdata = ''
while True:
# Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing
line = process.stderr.read(1).decode('utf-8')
sys.stderr.write(line)
sys.stderr.flush()
stderrdata += line
if not line and process.poll() is not None:
break
return_stderr += stderrdata
if process.returncode:
error = True
error_text += stderrdata
else:
for process in _processes:
process.wait()
except (KeyboardInterrupt, SystemExit):
import inspect, signal
app._handler(signal.SIGINT, inspect.currentframe())
# For any command stdout / stderr data that wasn't either passed to another command or
# printed to the terminal during execution, read it here.
for index in range(len(cmdstack)):
if tempfiles[index][0] is not None:
tempfiles[index][0].flush()
tempfiles[index][0].seek(0)
stdout_text = tempfiles[index][0].read().decode('utf-8')
return_stdout += stdout_text
if _processes[index].returncode:
error = True
error_text += stdout_text
if tempfiles[index][1] is not None:
tempfiles[index][1].flush()
tempfiles[index][1].seek(0)
stderr_text = tempfiles[index][1].read().decode('utf-8')
return_stderr += stderr_text
if _processes[index].returncode:
error = True
error_text += stderr_text
_processes = [ ]
if (error):
app._cleanup = False
if exitOnError:
caller = inspect.getframeinfo(inspect.stack()[1][0])
app.console('')
sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourError + '[ERROR] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')' + app.colourClear + '\n')
sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourConsole + 'Output of failed command:' + app.colourClear + '\n')
sys.stderr.write(error_text)
sys.stderr.flush()
if app._tempDir:
with open(os.path.join(app._tempDir, 'error.txt'), 'w') as outfile:
outfile.write(cmd + '\n\n' + error_text + '\n')
app.complete()
sys.exit(1)
else:
app.warn('Command failed: ' + cmd)
# Only now do we append to the script log, since the command has completed successfully
# Note: Writing the command as it was formed as the input to run.command():
# other flags may potentially change if this file is eventually used to resume the script
if app._tempDir:
with open(os.path.join(app._tempDir, 'log.txt'), 'a') as outfile:
outfile.write(cmd + '\n')
return (return_stdout, return_stderr)
def command(cmd, exitOnError=True): #pylint: disable=unused-variable
import inspect, itertools, shlex, signal, string, subprocess, sys, tempfile
from distutils.spawn import find_executable
from mrtrix3 import app
# This is the only global variable that is _modified_ within this function
global _processes
# Vectorise the command string, preserving anything encased within quotation marks
if os.sep == '/': # Cheap POSIX compliance check
cmdsplit = shlex.split(cmd)
else: # Native Windows Python
cmdsplit = [ entry.strip('\"') for entry in shlex.split(cmd, posix=False) ]
if _lastFile:
if _triggerContinue(cmdsplit):
app.debug('Detected last file in command \'' + cmd + '\'; this is the last run.command() / run.function() call that will be skipped')
if app.verbosity:
sys.stderr.write(app.colourExec + 'Skipping command:' + app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
return ('', '')
# This splits the command string based on the piping character '|', such that each
# individual executable (along with its arguments) appears as its own list
cmdstack = [ list(g) for k, g in itertools.groupby(cmdsplit, lambda s : s != '|') if k ]
for line in cmdstack:
is_mrtrix_exe = line[0] in _mrtrix_exe_list
if is_mrtrix_exe:
line[0] = versionMatch(line[0])
if app.numThreads is not None:
line.extend( [ '-nthreads', str(app.numThreads) ] )
# Get MRtrix3 binaries to output additional INFO-level information if running in debug mode
if app.verbosity == 3:
line.append('-info')
elif not app.verbosity:
line.append('-quiet')
else:
line[0] = exeName(line[0])
shebang = _shebang(line[0])
if shebang:
if not is_mrtrix_exe:
# If a shebang is found, and this call is therefore invoking an
# interpreter, can't rely on the interpreter finding the script
# from PATH; need to find the full path ourselves.
line[0] = find_executable(line[0])
for item in reversed(shebang):
line.insert(0, item)
app.debug('To execute: ' + str(cmdstack))
if app.verbosity:
sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
# Disable interrupt signal handler while threads are running
try:
signal.signal(signal.SIGINT, signal.default_int_handler)
except:
pass
# Construct temporary text files for holding stdout / stderr contents when appropriate
# (One entry per process; each is a tuple containing two entries, each of which is either a
# file-like object, or None)
tempfiles = [ ]
# Execute all processes
assert not _processes
for index, to_execute in enumerate(cmdstack):
file_out = None
file_err = None
# If there's at least one command prior to this, need to receive the stdout from the prior command
# at the stdin of this command; otherwise, nothing to receive
if index > 0:
handle_in = _processes[index-1].stdout
else:
handle_in = None
# If this is not the last command, then stdout needs to be piped to the next command;
# otherwise, write stdout to a temporary file so that the contents can be read later
if index < len(cmdstack)-1:
handle_out = subprocess.PIPE
else:
file_out = tempfile.TemporaryFile()
handle_out = file_out.fileno()
# If we're in debug / info mode, the contents of stderr will be read and printed to the terminal
# as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary
# file so that the contents can be read later
if app.verbosity > 1:
handle_err = subprocess.PIPE
else:
file_err = tempfile.TemporaryFile()
handle_err = file_err.fileno()
# Set off the processes
try:
try:
process = subprocess.Popen (to_execute, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env, preexec_fn=os.setpgrp) # pylint: disable=bad-option-value,subprocess-popen-preexec-fn
except AttributeError:
process = subprocess.Popen (to_execute, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env)
_processes.append(process)
tempfiles.append( ( file_out, file_err ) )
# FileNotFoundError not defined in Python 2.7
except OSError as e:
if exitOnError:
app.error('\'' + to_execute[0] + '\' not executed ("' + str(e) + '"); script cannot proceed')
else:
app.warn('\'' + to_execute[0] + '\' not executed ("' + str(e) + '")')
for p in _processes:
p.terminate()
_processes = [ ]
break
return_stdout = ''
return_stderr = ''
error = False
error_text = ''
# Wait for all commands to complete
# Switch how we monitor running processes / wait for them to complete
# depending on whether or not the user has specified -info or -debug option
try:
if app.verbosity > 1:
for process in _processes:
stderrdata = b''
do_indent = True
while True:
# Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing
byte = process.stderr.read(1)
stderrdata += byte
char = byte.decode('cp1252', errors='ignore')
if not char and process.poll() is not None:
break
if do_indent and char in string.printable and char != '\r' and char != '\n':
sys.stderr.write(' ')
do_indent = False
elif char in [ '\r', '\n' ]:
do_indent = True
sys.stderr.write(char)
sys.stderr.flush()
stderrdata = stderrdata.decode('utf-8', errors='replace')
return_stderr += stderrdata
if process.returncode:
error = True
error_text += stderrdata
else:
for process in _processes:
process.wait()
except (KeyboardInterrupt, SystemExit):
app.handler(signal.SIGINT, inspect.currentframe())
# Re-enable interrupt signal handler
try:
signal.signal(signal.SIGINT, app.handler)
except:
pass
# For any command stdout / stderr data that wasn't either passed to another command or
# printed to the terminal during execution, read it here.
for index in range(len(cmdstack)):
if tempfiles[index][0] is not None:
tempfiles[index][0].flush()
tempfiles[index][0].seek(0)
stdout_text = tempfiles[index][0].read().decode('utf-8', errors='replace')
return_stdout += stdout_text
if _processes[index].returncode:
error = True
error_text += stdout_text
if tempfiles[index][1] is not None:
tempfiles[index][1].flush()
tempfiles[index][1].seek(0)
stderr_text = tempfiles[index][1].read().decode('utf-8', errors='replace')
return_stderr += stderr_text
if _processes[index].returncode:
error = True
error_text += stderr_text
_processes = [ ]
if error:
if exitOnError:
app.cleanup = False
caller = inspect.getframeinfo(inspect.stack()[1][0])
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] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(filename) + ':' + str(lineno) + ')' + app.colourClear + '\n')
sys.stderr.write(script_name + ': ' + app.colourConsole + 'Output of failed command:' + 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(cmd + '\n\n' + error_text + '\n')
app.complete()
sys.exit(1)
else:
app.warn('Command failed: ' + cmd)
# Only now do we append to the script log, since the command has completed successfully
# Note: Writing the command as it was formed as the input to run.command():
# other flags may potentially change if this file is eventually used to resume the script
if app.tempDir:
with open(os.path.join(app.tempDir, 'log.txt'), 'a') as outfile:
outfile.write(cmd + '\n')
return (return_stdout, return_stderr)
def command(cmd, exitOnError=True):
import inspect, itertools, os, shlex, subprocess, sys, tempfile
from distutils.spawn import find_executable
from mrtrix3 import app
global _mrtrix_exe_list
# Vectorise the command string, preserving anything encased within quotation marks
cmdsplit = shlex.split(cmd)
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 cmdsplit:
if entry.startswith('--') and '=' in entry:
cmdtotest = entry.split('=')[1]
else:
cmdtotest = entry
filetotest = [ app._lastFile, os.path.splitext(app._lastFile)[0] ]
if cmdtotest in filetotest:
app.debug('Detected last file \'' + app._lastFile + '\' in command \'' + cmd + '\'; 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 command:' + app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
return
# This splits the command string based on the piping character '|', such that each
# individual executable (along with its arguments) appears as its own list
# Note that for Python2 support, it is necessary to convert groupby() output from
# a generator to a list before it is passed to filter()
cmdstack = [ list(g) for k, g in filter(lambda t : t[0], ((k, list(g)) for k, g in itertools.groupby(cmdsplit, lambda s : s is not '|') ) ) ]
for line in cmdstack:
is_mrtrix_exe = line[0] in _mrtrix_exe_list
if is_mrtrix_exe:
line[0] = versionMatch(line[0])
if app._nthreads is not None:
line.extend( [ '-nthreads', str(app._nthreads) ] )
# Get MRtrix3 binaries to output additional INFO-level information if running in debug mode
if app._verbosity == 3:
line.append('-info')
elif not app._verbosity:
line.append('-quiet')
else:
line[0] = exeName(line[0])
shebang = _shebang(line[0])
if len(shebang):
if not is_mrtrix_exe:
# If a shebang is found, and this call is therefore invoking an
# interpreter, can't rely on the interpreter finding the script
# from PATH; need to find the full path ourselves.
line[0] = find_executable(line[0])
for item in reversed(shebang):
line.insert(0, item)
if app._verbosity:
sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n')
sys.stderr.flush()
app.debug('To execute: ' + str(cmdstack))
# Construct temporary text files for holding stdout / stderr contents when appropriate
# (One entry per process; each is a tuple containing two entries, each of which is either a
# file-like object, or None)
tempfiles = [ ]
# Execute all processes
_processes = [ ]
for index, command in enumerate(cmdstack):
file_out = None
file_err = None
# If there's at least one command prior to this, need to receive the stdout from the prior command
# at the stdin of this command; otherwise, nothing to receive
if index > 0:
handle_in = _processes[index-1].stdout
else:
handle_in = None
# If this is not the last command, then stdout needs to be piped to the next command;
# otherwise, write stdout to a temporary file so that the contents can be read later
if index < len(cmdstack)-1:
handle_out = subprocess.PIPE
else:
file_out = tempfile.TemporaryFile()
handle_out = file_out.fileno()
# If we're in debug / info mode, the contents of stderr will be read and printed to the terminal
# as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary
# file so that the contents can be read later
if app._verbosity > 1:
handle_err = subprocess.PIPE
else:
file_err = tempfile.TemporaryFile()
handle_err = file_err.fileno()
# Set off the processes
try:
process = subprocess.Popen (command, stdin=handle_in, stdout=handle_out, stderr=handle_err)
_processes.append(process)
tempfiles.append( ( file_out, file_err ) )
# FileNotFoundError not defined in Python 2.7
except OSError as e:
if exitOnError:
app.error('\'' + command[0] + '\' not executed ("' + str(e) + '"); script cannot proceed')
else:
app.warn('\'' + command[0] + '\' not executed ("' + str(e) + '")')
for p in _processes:
p.terminate()
_processes = [ ]
break
except (KeyboardInterrupt, SystemExit):
import inspect, signal
app._handler(signal.SIGINT, inspect.currentframe())
return_stdout = ''
return_stderr = ''
error = False
error_text = ''
# Wait for all commands to complete
try:
# Switch how we monitor running processes / wait for them to complete
# depending on whether or not the user has specified -verbose or -debug option
if app._verbosity > 1:
for process in _processes:
stderrdata = ''
while True:
# Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing
line = process.stderr.read(1).decode('utf-8')
sys.stderr.write(line)
sys.stderr.flush()
stderrdata += line
if not line and process.poll() is not None:
break
return_stderr += stderrdata
if process.returncode:
error = True
error_text += stderrdata
else:
for process in _processes:
process.wait()
except (KeyboardInterrupt, SystemExit):
import inspect, signal
app._handler(signal.SIGINT, inspect.currentframe())
# For any command stdout / stderr data that wasn't either passed to another command or
# printed to the terminal during execution, read it here.
for index in range(len(cmdstack)):
if tempfiles[index][0] is not None:
tempfiles[index][0].flush()
tempfiles[index][0].seek(0)
stdout_text = tempfiles[index][0].read().decode('utf-8')
return_stdout += stdout_text
if _processes[index].returncode:
error = True
error_text += stdout_text
if tempfiles[index][1] is not None:
tempfiles[index][1].flush()
tempfiles[index][1].seek(0)
stderr_text = tempfiles[index][1].read().decode('utf-8')
return_stderr += stderr_text
if _processes[index].returncode:
error = True
error_text += stderr_text
_processes = [ ]
if (error):
app._cleanup = False
if exitOnError:
caller = inspect.getframeinfo(inspect.stack()[1][0])
app.console('')
sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourError + '[ERROR] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')' + app.colourClear + '\n')
sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourConsole + 'Output of failed command:' + app.colourClear + '\n')
sys.stderr.write(error_text)
sys.stderr.flush()
if app._tempDir:
with open(os.path.join(app._tempDir, 'error.txt'), 'w') as outfile:
outfile.write(cmd + '\n\n' + error_text + '\n')
app.complete()
sys.exit(1)
else:
app.warn('Command failed: ' + cmd)
# Only now do we append to the script log, since the command has completed successfully
# Note: Writing the command as it was formed as the input to run.command():
# other flags may potentially change if this file is eventually used to resume the script
if app._tempDir:
with open(os.path.join(app._tempDir, 'log.txt'), 'a') as outfile:
outfile.write(cmd + '\n')
return (return_stdout, return_stderr)
