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)
# Rembrandt Bakker, December 2014
import argparse, sys, os
import os.path as op
import re, json
import numpy
import jsonrpc2
report = jsonrpc2.report_class()
def argument_parser():
""" Define the argument parser and return the parser object. """
parser = argparse.ArgumentParser(
description='description',
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('-m','--moving', type=str, help="Moving (nifti) volume", required=True)
parser.add_argument('-f','--fixed', type=str, help="Fixed (nifti) volume", required=True)
parser.add_argument('-v','--via', type=str, default=None, help="Via intermediate (nifti) volume", required=False)
parser.add_argument('-o','--outdir', type=str, help="Output directory", required=True)
parser.add_argument('-p','--program', type=str, default="elastix", help="Name of registration software package (default: elastix)", required=False)
parser.add_argument('-par','--paramfile', type=str, help="Parameter file", required=True)
parser.add_argument('--jsonrpc2', action='store_true', help="return output as json-rpc 2.0", required=False)
return parser
def parse_arguments(raw=None):
global report
try:
""" Apply the argument parser. """
args = argument_parser().parse_args(raw)
if args.jsonrpc2:
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)