Source code for WORC.tools.Transformix
#!/usr/bin/env python
# Copyright 2017-2018 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import SimpleITK as sitk
import fastr
from fastr.api import ResourceLimit
import numpy as np
import os
import WORC.addexceptions as WORCexceptions
#WIP
[docs]class Transformix(object):
[docs] def __init__(self):
self.network = self.create_network()
self.MovingImage = None
self.TransformParameterMap = None
[docs] def create_network(self):
self.network = fastr.create_network(id="transformix")
self.MovingImageSource = self.network.create_source('ITKImageFile', id='MovingImage')
self.ParameterMapSource = self.network.create_source('ElastixTransformFile', id='ParameterFile')
self.transformix_node = self.network.create_node('elastix_dev/transformix_dev:4.9-dev-wyke', tool_version='0.2', id='transformix')
self.transformix_node.inputs['image'] = self.MovingImageSource.output
self.transformix_node.inputs['transform'] = self.ParameterMapSource.output
self.outimage = self.network.create_sink('ITKImageFile', id='sink_image')
self.outimage.inputs['input'] = self.transformix_node.outputs['image']
self.network.draw(file_path='transformix.svg')
self.network.dumpf('{}.json'.format(self.network.id), indent=2)