def parse_arguments(raw=None):
global report
try:
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
report = jsonrpc2.rpc_report_class()
""" Basic argument checking """
if not op.exists(args.nifti_src):
raise Exception('Nifti file "{}" not found.'.format(
args.nifti_src))
if args.slicedir.isdigit():
args.dim = args.slicedir
if args.slicedir < 0 or args.slicedir > 3:
raise Exception('Invalid slice dimension "{}".'.format(
args.slicedir))
else:
dir2dim = {'x': 0, 'y': 1, 'z': 2}
if args.slicedir in dir2dim:
args.dim = dir2dim[args.slicedir]
else:
raise Exception('Invalid slice direction "{}".'.format(
args.slicedir))
return args
except:
report.fail(__file__)
def parse_arguments(raw=None):
global report
try:
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
report = jsonrpc2.rpc_report_class()
try:
fromto = map(int, args.range.split(','))
except:
try:
fromto = json.loads(args.range)
except:
report.error('Cannot parse range "' + args.range + '"')
if len(fromto) <= 2:
fromto.append(1)
args.input_range = range(fromto[0], fromto[1] + 1, fromto[2])
""" Basic argument checking """
for r in args.input_range:
fname = args.inp % (r)
if not op.exists(fname):
raise Exception('Image file "{}" not found.'.format(fname))
return args
except:
report.fail(__file__)
def parse_arguments(raw=None):
global report
try:
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
report = jsonrpc2.rpc_report_class()
""" Basic argument checking """
if not op.exists(args.nifti_in):
raise Exception('Nifti file "{}" not found.'.format(args.nifti_in))
try:
args.filter = json.loads(args.filter)
if len(args.filter)%2 != 1:
report.error('invalid filter {}; length must be odd.'.format(args.filter))
report.fail(__file__)
except ValueError:
tmp = re.split('[, ]+',args.filter)
args.filter = [float(s) for s in tmp]
try:
args.ignore = json.loads(args.bg)
except:
raise
return args
except:
report.fail(__file__)
def parse_arguments(raw=None):
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
global report
report = jsonrpc2.rpc_report_class()
""" Basic argument checking """
if not op.exists(args.png_src):
report.error('PNG folder "{}" not found.'.format(args.png_src))
report.fail(__file__)
return args
def parse_arguments(raw=None):
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
global report
report = jsonrpc2.rpc_report_class()
""" Basic argument checking """
args.useFilePattern = False
if not op.exists(args.png_src):
print 'PNG folder or pattern "{}" not found.'.format(args.png_src)
exit(1)
return args
def parse_arguments(raw=None):
global report
try:
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
report = jsonrpc2.rpc_report_class()
""" Basic argument checking """
if not op.exists(args.inp):
raise Exception('Nifti file "{}" not found.'.format(args.inp))
return args
except:
report.fail(__file__)
def parse_arguments(raw=None):
global report
try:
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
report = jsonrpc2.rpc_report_class()
""" Basic argument checking """
if not op.exists(args.inp):
raise Exception('Nifti file "{}" not found.'.format(args.inp))
if not args.out:
args.out = re.sub('\.nii($)|\.nii(\.gz$)', '_downsampled.nii.gz',
args.inp)
return args
except:
report.fail(__file__)
deformedFacesFile = '{}/meshes/{}'.format(spacesFolder,meshConfig['faces'])
if deformedVerticesFile != verticesFile:
V = LoadVertices.fromParent(self).setInput(deformedVerticesFile).requestOutput('vertices')
if deformedFacesFile != facesFile:
F = LoadFaces.fromParent(self).setInput(deformedFacesFile).requestOutput('faces')
if labelnames:
with open(labelnames) as fp:
labelnames = json.load(fp)
generateX3D = GenerateX3D.fromParent(self).setInput(
vertices = V,
faces = F,
facelabels = faceLabels,
label2rgb = label2rgb,
label2name = labelnames,
label2value = label2value,
colormap = colormap
)
return FancyDict(
x3dfile = generateX3D.requestOutput('x3dfile'),
x3dviewer = generateX3D.requestOutput('x3dviewer'),
x3d_files = generateX3D.requestOutput('x3dviewer_files')
)
#endclass
if __name__ == '__main__':
report = JR2.rpc_report_class() if '--jsonrpc2' in sys.argv else JR2.report_class()
mainTask = RenderSurface.fromCommandLine()
ans = mainTask.run()
report.success(mainTask.myOutput.kwargs)
deformedVerticesFile).requestOutput('vertices')
if deformedFacesFile != facesFile:
F = LoadFaces.fromParent(self).setInput(
deformedFacesFile).requestOutput('faces')
if labelnames:
with open(labelnames) as fp:
labelnames = json.load(fp)
generateX3D = GenerateX3D.fromParent(self).setInput(
vertices=V,
faces=F,
facelabels=faceLabels,
label2rgb=label2rgb,
label2name=labelnames,
label2value=label2value,
colormap=colormap)
return FancyDict(
x3dfile=generateX3D.requestOutput('x3dfile'),
x3dviewer=generateX3D.requestOutput('x3dviewer'),
x3d_files=generateX3D.requestOutput('x3dviewer_files'))
#endclass
if __name__ == '__main__':
report = JR2.rpc_report_class(
) if '--jsonrpc2' in sys.argv else JR2.report_class()
mainTask = RenderSurface.fromCommandLine()
ans = mainTask.run()
report.success(mainTask.myOutput.kwargs)
