def run(self):
opts, args = self.parse_args()
if args:
vrange = parseVolRangeOption(opts.vol_range, self)
try:
image = readImage(args[0], vrange=vrange)
except:
image = None
print 'Could not find image %s, try loading manually' % args[0]
else:
image = None
recon_gui(image=image, logfile=opts.log_file)
def run(self):
opts, args = self.parse_args()
if args:
vrange = parseVolRangeOption(opts.vol_range, self)
try:
image = readImage(args[0], vrange=vrange)
except:
image = None
print 'Could not find image %s, try loading manually'%args[0]
else:
image = None
recon_gui(image=image, logfile=opts.log_file)
def getOptions(self):
"""
Bundle command-line arguments and options into a single options
object, including a resolved list of callable data operations.
Uses OptionParser to fill in the options list from command line input;
appends volume range specifications, and input/output directories as
options; asks for an index of requested operations from
configureOperations()
"""
options, args = self.parse_args()
options.vrange = parseVolRangeOption(options.vol_range, self)
# Two usages are special cases:
# oplist example will be handled after an oplist is found..
# operation help doesn't require arguments, so handle it here
if options.ophelp is not None:
self._printOpHelp(options.ophelp)
sys.exit(0)
if options.opsexample:
if not args:
self.error("You must provide a fid-directory to get an example oplist")
# just append a false output file name to be safe
args.append("foo")
# Recon can be run with these combos defined:
# (_, _) (first logic stage, try to find fid files in pwd)
# (args, _) (2nd logic stage, try to find default oplist)
# (_, oplist) (3rd logic stage, try a couple things here)
# (args,oplist) (last stage, not ambiguous)
if not options.oplist and len(args) != 2:
try:
args = self._argsFromPWD()
except:
self.print_help()
sys.exit(0)
if not options.oplist:
options.oplist = self._findOplist(args[0])
options.operations = self.configureOperations(open(options.oplist,'r'))
if len(args) != 2:
# only care if we need to set up ReadImage and WriteImage later
if not (self._running('ReadImage', options.operations) and \
self._running('WriteImage', options.operations)):
args = self._argsFromPWD()
if not self._running('ReadImage', options.operations):
# append ReadImage op to BEGINNING of list
op_args = {'filename': os.path.abspath(args[0]),
'vrange': options.vrange}
opclass = self._opmanager.getOperation('ReadImage')
options.operations.insert(0,(opclass, op_args))
if not self._running('WriteImage', options.operations):
op_args = {'filename': os.path.abspath(args[1]),
'suffix': options.suffix,
'filedim': options.filedim,
'format': options.file_format,
'datatype': options.output_datatype}
opclass = self._opmanager.getOperation('WriteImage')
options.operations.append((opclass, op_args))
# run some checks on the operations sequence
self.confirmOps(options.operations)
if options.fastArray:
global _FAST_ARRAY
_FAST_ARRAY = True
return options