def makeTempDir():
import os, random, string, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, tempDir
if args.cont:
printMessage('Skipping temporary directory creation due to use of -continue option')
return
if tempDir:
errorMessage('Script error: Cannot use multiple temporary directories')
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def initialise():
import argparse, os, random, string, sys
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, cleanup, lastFile, mrtrixNThreads, mrtrixQuiet, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
workingDir = os.getcwd()
args = parser.parse_args()
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = "-nthreads " + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = "-quiet"
if args.verbose:
verbosity = 2
mrtrixQuiet = ""
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
else:
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting("TmpFileDir")
if not dir_path:
if os.name == "posix":
dir_path = "/tmp"
else:
dir_path = "."
prefix = readMRtrixConfSetting("TmpFilePrefix")
if not prefix:
prefix = os.path.basename(sys.argv[0]) + "-tmp-"
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = "".join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage("Generated temporary directory: " + tempDir)
with open(os.path.join(tempDir, "cwd.txt"), "w") as outfile:
outfile.write(workingDir + "\n")
with open(os.path.join(tempDir, "command.txt"), "w") as outfile:
outfile.write(" ".join(sys.argv) + "\n")
use_colour = readMRtrixConfSetting("TerminalColor")
if use_colour:
use_colour = use_colour.lower() in ("yes", "true", "1")
else:
use_colour = not sys.platform.startswith("win")
if use_colour:
colourClear = "\033[0m"
colourConsole = "\033[03;34m"
colourError = "\033[01;31m"
colourPrint = "\033[03;32m"
colourWarn = "\033[00;31m"
def initialise(n):
import os, random, string, sys
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global cleanup, mrtrixQuiet, numArgs, tempDir, verbosity, workingDir
#if not numArgs:
# sys.stderr.write('Must set numArgs value before calling initialise()\n')
# exit(1)
numArgs = n
workingDir = os.getcwd()
for option in sys.argv[numArgs+1:]:
if '-verbose'.startswith(option):
verbosity = 2
mrtrixQuiet = ''
elif '-quiet'.startswith(option):
verbosity = 0
mrtrixQuiet = '-quiet'
elif '-nocleanup'.startswith(option):
cleanup = False
else:
sys.stderr.write('Unknown option: ' + option + '\n')
exit(1)
# Create the temporary directory
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
def makeTempDir():
import os, random, string, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, tempDir
if args.cont:
printMessage(
'Skipping temporary directory creation due to use of -continue option'
)
return
if tempDir:
errorMessage('Script error: Cannot use multiple temporary directories')
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def initialise():
import os, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, citationList, cleanup, externalCitations, lastFile, mrtrixNThreads, mrtrixQuiet, parser, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if not parser:
errorMessage('Script error: Command-line parser must be initialised before app')
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
if sys.argv[-1] == '__print_usage_rst__':
parser.printUsageRst()
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
# Windows now also gets coloured text terminal support, so make this the default
use_colour = True
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = ' -nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = ' -quiet'
elif args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationList:
printMessage('')
citation_warning = 'Note that this script makes use of commands / algorithms that have relevant articles for citation'
if externalCitations:
citation_warning += '; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES'
citation_warning += '. Please consult the help page (-help option) for more information.'
printMessage(citation_warning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
def initialise():
import argparse, os, random, string, sys
from lib.printMessage import printMessage
from lib.printUsageMarkdown import printUsageMarkdown
from lib.printUsageRst import printUsageRst
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, author, cleanup, lastFile, mrtrixNThreads, mrtrixQuiet, standardOptions, parser, refList, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_markdown__':
printUsageMarkdown(parser, standardOptions, refList, author)
exit(0)
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_rst__':
printUsageRst(parser, standardOptions, refList, author)
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help or len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
use_colour = not sys.platform.startswith('win')
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = '-nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = '-quiet'
if args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationWarning:
printMessage('')
printMessage(citationWarning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
else:
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def initialise():
import os, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, citationList, cleanup, externalCitations, lastFile, mrtrixNThreads, mrtrixQuiet, parser, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if not parser:
errorMessage(
'Script error: Command-line parser must be initialised before app')
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
if sys.argv[-1] == '__print_usage_rst__':
parser.printUsageRst()
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
# Windows now also gets coloured text terminal support, so make this the default
use_colour = True
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = ' -nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = ' -quiet'
elif args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationList:
printMessage('')
citation_warning = 'Note that this script makes use of commands / algorithms that have relevant articles for citation'
if externalCitations:
citation_warning += '; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES'
citation_warning += '. Please consult the help page (-help option) for more information.'
printMessage(citation_warning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
def print_help(self):
import subprocess, textwrap
import lib.app
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global author, citationList, copyright
def bold(text):
return ''.join( c + chr(0x08) + c for c in text)
def underline(text):
return ''.join( '_' + chr(0x08) + c for c in text)
w = textwrap.TextWrapper(width=80, initial_indent=' ', subsequent_indent=' ')
w_arg = textwrap.TextWrapper(width=80, initial_indent='', subsequent_indent=' ')
s = ' ' + bold(self.prog) + ': Script using the MRtrix3 Python libraries\n'
s += '\n'
s += bold('SYNOPSIS') + '\n'
s += '\n'
synopsis = self.prog + ' [ options ]'
# Compulsory sub-parser algorithm selection (if present)
if self._subparsers:
synopsis += ' ' + self._subparsers._group_actions[0].dest + ' ...'
# Find compulsory input arguments
for arg in self._positionals._group_actions:
if arg.metavar:
synopsis += ' ' + arg.metavar
else:
synopsis += ' ' + arg.dest
# Unfortunately this can line wrap early because textwrap is counting each
# underlined character as 3 characters when calculating when to wrap
# Fix by underlining after the fact
s += w.fill(synopsis).replace(self.prog, underline(self.prog), 1) + '\n'
s += '\n'
if self._subparsers:
s += ' ' + w_arg.fill(self._subparsers._group_actions[0].dest + ' '*(max(13-len(self._subparsers._group_actions[0].dest), 1)) + self._subparsers._group_actions[0].help).replace (self._subparsers._group_actions[0].dest, underline(self._subparsers._group_actions[0].dest), 1) + '\n'
s += '\n'
for arg in self._positionals._group_actions:
line = ' '
if arg.metavar:
name = arg.metavar
else:
name = arg.dest
line += name + ' '*(max(13-len(name), 1)) + arg.help
s += w_arg.fill(line).replace(name, underline(name), 1) + '\n'
s += '\n'
s += bold('DESCRIPTION') + '\n'
s += '\n'
s += w.fill(self.description) + '\n'
s += '\n'
# Option groups
for group in reversed(self._action_groups):
# * Don't display empty groups
# * Don't display the subparser option; that's dealt with in the synopsis
# * Don't re-display any compulsory positional arguments; they're also dealt with in the synopsis
if group._group_actions and not (len(group._group_actions) == 1 and isinstance(group._group_actions[0], argparse._SubParsersAction)) and not group == self._positionals:
s += bold(group.title) + '\n'
s += '\n'
for option in group._group_actions:
s += ' ' + underline('/'.join(option.option_strings))
if option.metavar:
s += ' '
if isinstance(option.metavar, tuple):
s += ' '.join(option.metavar)
else:
s += option.metavar
elif option.nargs:
s += (' ' + option.dest.upper())*option.nargs
elif option.type is not None:
s += ' ' + option.type.__name__.upper()
elif option.default is None:
s += ' ' + option.dest.upper()
# Any options that haven't tripped one of the conditions above should be a store_true or store_false, and
# therefore there's nothing to be appended to the option instruction
s += '\n'
s += w.fill(option.help) + '\n'
s += '\n'
s += bold('AUTHOR') + '\n'
s += w.fill(lib.app.author) + '\n'
s += '\n'
s += bold('COPYRIGHT') + '\n'
s += w.fill(lib.app.copyright) + '\n'
if lib.app.citationList:
s += '\n'
s += bold('REFERENCES') + '\n'
s += '\n'
for entry in lib.app.citationList:
if entry[0]:
s += w.fill('* ' + entry[0] + ':') + '\n'
s += w.fill(entry[1]) + '\n'
s += '\n'
command = readMRtrixConfSetting('HelpCommand')
if not command:
command = 'less -X'
if command:
try:
process = subprocess.Popen(command.split(' '), stdin=subprocess.PIPE)
process.communicate(s.encode())
except:
print (s)
else:
print (s)
def print_help(self):
import subprocess, textwrap
import lib.app
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global author, citationList, copyright
def bold(text):
return ''.join(c + chr(0x08) + c for c in text)
def underline(text):
return ''.join('_' + chr(0x08) + c for c in text)
w = textwrap.TextWrapper(width=80,
initial_indent=' ',
subsequent_indent=' ')
w_arg = textwrap.TextWrapper(width=80,
initial_indent='',
subsequent_indent=' ')
s = ' ' + bold(
self.prog) + ': Script using the MRtrix3 Python libraries\n'
s += '\n'
s += bold('SYNOPSIS') + '\n'
s += '\n'
synopsis = self.prog + ' [ options ]'
# Compulsory sub-parser algorithm selection (if present)
if self._subparsers:
synopsis += ' ' + self._subparsers._group_actions[0].dest + ' ...'
# Find compulsory input arguments
for arg in self._positionals._group_actions:
if arg.metavar:
synopsis += ' ' + arg.metavar
else:
synopsis += ' ' + arg.dest
# Unfortunately this can line wrap early because textwrap is counting each
# underlined character as 3 characters when calculating when to wrap
# Fix by underlining after the fact
s += w.fill(synopsis).replace(self.prog, underline(self.prog),
1) + '\n'
s += '\n'
if self._subparsers:
s += ' ' + w_arg.fill(
self._subparsers._group_actions[0].dest + ' ' *
(max(13 - len(self._subparsers._group_actions[0].dest), 1)) +
self._subparsers._group_actions[0].help).replace(
self._subparsers._group_actions[0].dest,
underline(self._subparsers._group_actions[0].dest),
1) + '\n'
s += '\n'
for arg in self._positionals._group_actions:
line = ' '
if arg.metavar:
name = arg.metavar
else:
name = arg.dest
line += name + ' ' * (max(13 - len(name), 1)) + arg.help
s += w_arg.fill(line).replace(name, underline(name), 1) + '\n'
s += '\n'
s += bold('DESCRIPTION') + '\n'
s += '\n'
s += w.fill(self.description) + '\n'
s += '\n'
# Option groups
for group in reversed(self._action_groups):
# * Don't display empty groups
# * Don't display the subparser option; that's dealt with in the synopsis
# * Don't re-display any compulsory positional arguments; they're also dealt with in the synopsis
if group._group_actions and not (
len(group._group_actions) == 1 and isinstance(
group._group_actions[0], argparse._SubParsersAction)
) and not group == self._positionals:
s += bold(group.title) + '\n'
s += '\n'
for option in group._group_actions:
s += ' ' + underline('/'.join(option.option_strings))
if option.metavar:
s += ' '
if isinstance(option.metavar, tuple):
s += ' '.join(option.metavar)
else:
s += option.metavar
elif option.nargs:
s += (' ' + option.dest.upper()) * option.nargs
elif option.type is not None:
s += ' ' + option.type.__name__.upper()
elif option.default is None:
s += ' ' + option.dest.upper()
# Any options that haven't tripped one of the conditions above should be a store_true or store_false, and
# therefore there's nothing to be appended to the option instruction
s += '\n'
s += w.fill(option.help) + '\n'
s += '\n'
s += bold('AUTHOR') + '\n'
s += w.fill(lib.app.author) + '\n'
s += '\n'
s += bold('COPYRIGHT') + '\n'
s += w.fill(lib.app.copyright) + '\n'
if lib.app.citationList:
s += '\n'
s += bold('REFERENCES') + '\n'
s += '\n'
for entry in lib.app.citationList:
if entry[0]:
s += w.fill('* ' + entry[0] + ':') + '\n'
s += w.fill(entry[1]) + '\n'
s += '\n'
command = readMRtrixConfSetting('HelpCommand')
if not command:
command = 'less -X'
if command:
try:
process = subprocess.Popen(command.split(' '),
stdin=subprocess.PIPE)
process.communicate(s.encode())
except:
print(s)
else:
print(s)
def initialise():
import argparse, os, random, string, sys
from lib.printMessage import printMessage
from lib.printUsageMarkdown import printUsageMarkdown
from lib.printUsageRst import printUsageRst
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, author, cleanup, lastFile, mrtrixNThreads, mrtrixQuiet, standardOptions, parser, refList, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_markdown__':
printUsageMarkdown(parser, standardOptions, refList, author)
exit(0)
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_rst__':
printUsageRst(parser, standardOptions, refList, author)
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help or len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
use_colour = not sys.platform.startswith('win')
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = ' -nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = ' -quiet'
if args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationWarning:
printMessage('')
printMessage(citationWarning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
else:
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
