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############################################################################
##
## Copyright (C) 2006-2007 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundation
## and appearing in the file LICENSE.GPL included in the packaging of
## this file. Please review the following to ensure GNU General Public
## Licensing requirements will be met:
## http://www.opensource.org/licenses/gpl-license.php
##
## If you are unsure which license is appropriate for your use (for
## instance, you are interested in developing a commercial derivative
## of VisTrails), please contact us at contact@vistrails.org.
##
## This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
## WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
##
############################################################################
import itk
import core.modules
from ITK import *
from Image import Image
class ImageReader(Module):
my_namespace = "ImageReader"
def compute(self):
dim = self.getInputFromPort("Dimension")
outPixelType = self.getInputFromPort("Pixel Type")
fn = self.getInputFromPort("Filename")
self.reader = itk.ImageFileReader[itk.Image[outPixelType._type, dim]].New()
self.reader.SetFileName(fn)
self.reader.Update()
#setup output image
outIm = Image()
outIm.setImg(self.reader.GetOutput())
outIm.setPixelType(outPixelType)
outIm.setDim(dim)
self.setResult("Image", outIm)
self.setResult("Reader", self)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="ImageReader", namespace=cls.my_namespace)
reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'))
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
reg.add_output_port(cls, "Image", (Image, 'Image'))
reg.add_output_port(cls, "Reader", (ImageReader, 'Reader'))
class ImageToFile(Module):
my_namespace = "ImageReader"
def compute(self):
im = self.getInputFromPort("Image")
#check for input PixelType
if self.hasInputFromPort("Input PixelType"):
inPixelType = self.getInputFromPort("Input PixelType")._type
else:
inPixelType = im.getPixelType()
#check for dimension
if self.hasInputFromPort("Dimension"):
dim = self.getInputFromPort("Dimension")
else:
dim = im.getDim()
suf = self.getInputFromPort("Suffix")
f = self.createOutputFile(suf)
writeType = itk.Image[inPixelType._type, dim]
writer = itk.ImageFileWriter[writeType].New(im.getImg(), FileName=f.name)
writer.Update()
self.setResult("File", f)
def createOutputFile(self, s):
return self.interpreter.filePool.create_file(suffix=s)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="ImageToFile", namespace=cls.my_namespace)
reg.add_input_port(cls, "Suffix", (basic.String, 'Suffix'))
reg.add_input_port(cls, "Pixel Type", (PixelType, 'Pixel Type'),True)
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_input_port(cls, "Image", (Image, 'Image'))
reg.add_output_port(cls, "File", (basic.File, 'File'))
class GDCMReader(Module):
my_namespace = "ImageReader"
def compute(self):
dir = self.getInputFromPort("Directory")
dim = self.getInputFromPort("Dimension")
self.dicomNames_ = itk.GDCMSeriesFileNames.New()
self.dicomNames_.SetDirectory(dir)
self.dicomNames_.SetUseSeriesDetails(True)
self.dicomNames_.SetRecursive(True)
self.dicomNames_.LoadSequencesOn()
self.iType_ = itk.Image[itk.US,dim]
self.reader_ = itk.ImageSeriesReader[self.iType_].New()
self.reader_.SetFileNames(self.dicomNames_.GetInputFileNames())
self.io_ = itk.GDCMImageIO.New()
self.reader_.SetImageIO(self.io_.GetPointer())
self.reader_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.reader_.GetOutput())
outIm.setPixelType(itk.US)
outIm.setDim(dim)
self.setResult("Image Series", outIm)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="GDCMReader", namespace=cls.my_namespace)
reg.add_input_port(cls, "Directory", (basic.String, 'Directory'))
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
reg.add_output_port(cls, "Image Series", (Image, 'Image Series'))
class DICOMReader(Module):
my_namespace = "ImageReader"
def compute(self):
dir = self.getInputFromPort("Directory")
dim = self.getInputFromPort("Dimension")
self.dicomNames_ = itk.DICOMSeriesFileNames.New()
self.dicomNames_.SetFileNameSortingOrderToSortByImagePositionPatient()
self.dicomNames_.SetDirectory(dir)
self.iType_ = itk.Image[itk.US,dim]
self.reader_ = itk.ImageSeriesReader[self.iType_].New()
self.reader_.SetFileNames(self.dicomNames_.GetFileNames(False))
self.reader_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.reader_.GetOutput())
outIm.setPixelType(itk.US)
outIm.setDim(dim)
self.setResult("Image Series", outIm)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="DICOMReader", namespace=cls.my_namespace)
reg.add_input_port(cls, "Directory", (basic.String, 'Directory'))
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'))
reg.add_output_port(cls, "Image Series", (Image, 'Image Series'))
class ITKImageToVTKData(Module):
my_namespace = "ImageReader"
def compute(self):
dim = self.getInputFromPort("Dimension")
pType = self.getInputFromPort("Input PixelType")
iType = itk.Image[itk.pType,dim]
self.vtkExport_ = itk.VTKImageExport[iType].New()
im = self.getInputFromPort("Input Image")
self.vtkExport_.SetInput(im)
self.vtkExport_.Update()
self.setResult("VTK Output", self.vtkExport_.GetOutput())
#TODO add register method
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