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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 core.modules.vistrails_module import Module, ModuleError
from ITK import *
from Image import Image
class RescaleIntensityImageFilter(Module):
my_namespace = "Filter|Intensity"
def compute(self):
im = self.getInputFromPort("Input Image")
#check for input PixelType
if self.hasInputFromPort("Input PixelType"):
inPixelType = self.getInputFromPort("Input PixelType")
else:
inPixelType = im.getPixelType()
#check for output PixelType
if self.hasInputFromPort("Output PixelType"):
outPixelType = self.getInputFromPort("Output PixelType")
else:
outPixelType = inPixelType
#check for dimension
if self.hasInputFromPort("Dimension"):
dim = self.getInputFromPort("Dimension")
else:
dim = im.getDim()
#set up filter
inImgType = itk.Image[inPixelType._type, dim]
outImgType = itk.Image[outPixelType._type, dim]
minimum = self.getInputFromPort("Minimum")
maximum = self.getInputFromPort("Maximum")
self.filter_ = itk.RescaleIntensityImageFilter[inImgType, outImgType].New(im.getImg())
self.filter_.SetOutputMaximum(maximum)
self.filter_.SetOutputMinimum(minimum)
self.filter_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.filter_.GetOutput())
outIm.setPixelType(outPixelType)
outIm.setDim(dim)
#set results
self.setResult("Output Image", outIm)
self.setResult("Filter", self)
self.setResult("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Rescale Intensity Image Filter", namespace=cls.my_namespace)
reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_input_port(cls, "Minimum", (basic.Integer, 'Minimum'))
reg.add_input_port(cls, "Maximum", (basic.Integer, 'Maximum'))
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
class SigmoidImageFilter(Module):
my_namespace = "Filter|Intensity"
def compute(self):
im = self.getInputFromPort("Input Image")
#check for input PixelType
if self.hasInputFromPort("Input PixelType"):
inPixelType = self.getInputFromPort("Input PixelType")
else:
inPixelType = im.getPixelType()
#check for output PixelType
if self.hasInputFromPort("Output PixelType"):
outPixelType = self.getInputFromPort("Output PixelType")
else:
outPixelType = inPixelType
#check for dimension
if self.hasInputFromPort("Dimension"):
dim = self.getInputFromPort("Dimension")
else:
dim = im.getDim()
#set up filter
inImgType = itk.Image[inPixelType._type, dim]
outImgType = itk.Image[outPixelType._type, dim]
#default values are those that are recommended
if self.hasInputFromPort("Minimum"):
min = self.getInputFromPort("Minimum")
else:
min = 10
if self.hasInputFromPort("Maximum"):
max = self.getInputFromPort("Maximum")
else:
max = 240
if self.hasInputFromPort("Alpha"):
alpha = self.getInputFromPort("Alpha")
else:
alpha = 10
if self.hasInputFromPort("Beta"):
beta = self.getInputFromPort("Beta")
else:
beta = 170
self.filter_ = itk.SigmoidImageFilter[inImgType,outImgType].New(im.getImg())
self.filter_.SetOutputMinimum(min)
self.filter_.SetOutputMaximum(max)
self.filter_.SetAlpha(alpha)
self.filter_.SetBeta(beta)
self.filter_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.filter_.GetOutput())
outIm.setPixelType(outPixelType)
outIm.setDim(dim)
self.setResult("Output Image", outIm)
self.setResult("Filter", self)
self.setResult("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Sigmoid Image Filter", namespace=cls.my_namespace)
reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_input_port(cls, "Minimum", (basic.Integer, 'Minimum'), True)
reg.add_input_port(cls, "Maximum", (basic.Integer, 'Maximum'), True)
reg.add_input_port(cls, "Alpha", (basic.Float, 'Alpha'), True)
reg.add_input_port(cls, "Beta", (basic.Float, 'Beta'), True)
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Filter", (Filter, 'Output Filter'),True)
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
class ThresholdImageFilter(Module):
my_namespace = "Filter|Intensity"
def compute(self):
im = self.getInputFromPort("Input Image")
#check for input PixelType
if self.hasInputFromPort("Input PixelType"):
inPixelType = self.getInputFromPort("Input PixelType")
else:
inPixelType = im.getPixelType()
#check for dimension
if self.hasInputFromPort("Dimension"):
dim = self.getInputFromPort("Dimension")
else:
dim = im.getDim()
#setup filter
inImgType = itk.Image[inPixelType._type, dim]
up = self.getInputFromPort("Upper Value")
lo = self.getInputFromPort("Lower Value")
self.filter_ = itk.ThresholdImageFilter[inImgType].New(im.getImg())
self.filter_.SetUpper(up)
self.filter_.SetLower(lo)
# self.filter_.ThresholdAbove(up)
self.filter_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.filter_.GetOutput())
outIm.setPixelType(inPixelType)
outIm.setDim(dim)
self.setResult("Output Image", outIm)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Threshold Image Filter", namespace=cls.my_namespace)
reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
reg.add_input_port(cls, "Upper Value", (basic.Integer, 'Upper Value'))
reg.add_input_port(cls, "Lower Value", (basic.Integer, 'Lower Value'))
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
class ShiftScaleImageFilter(Module):
my_namespace = "Filter|Intensity"
def compute(self):
im = self.getInputFromPort("Input Image")
#check for input PixelType
if self.hasInputFromPort("Input PixelType"):
inPixelType = self.getInputFromPort("Input PixelType")
else:
inPixelType = im.getPixelType()
#check for output PixelType
if self.hasInputFromPort("Output PixelType"):
outPixelType = self.getInputFromPort("Output PixelType")
else:
outPixelType = inPixelType
#check for dimension
if self.hasInputFromPort("Dimension"):
dim = self.getInputFromPort("Dimension")
else:
dim = im.getDim()
#set up filter
inImgType = itk.Image[inPixelType._type, dim]
outImgType = itk.Image[outPixelType._type, dim]
shift_value = self.getInputFromPort("Shift Value")
scale_value = self.getInputFromPort("Scale Value")
self.filter_ = itk.ShiftScaleImageFilter[inImgType, outImgType].New(im.getImg())
self.filter_.SetShift(shift_value)
self.filter_.SetScale(scale_value)
self.filter_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.filter_.GetOutput())
outIm.setPixelType(outPixelType)
outIm.setDim(dim)
#set results
self.setResult("Output Image", outIm)
self.setResult("Filter", self)
self.setResult("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Shift Scale Image Filter", namespace=cls.my_namespace)
reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_input_port(cls, "Shift Value", (basic.Float, 'Shift Value'))
reg.add_input_port(cls, "Scale Value", (basic.Integer, 'Scale Value'))
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
class NormalizeImageFilter(Module):
my_namespace = 'Filter|Intensity'
def compute(self):
im = self.getInputFromPort("Input Image")
#check for input PixelType
if self.hasInputFromPort("Input PixelType"):
inPixelType = self.getInputFromPort("Input PixelType")
else:
inPixelType = im.getPixelType()
#check for output PixelType
if self.hasInputFromPort("Output PixelType"):
outPixelType = self.getInputFromPort("Output PixelType")
else:
outPixelType = inPixelType
#check for dimension
if self.hasInputFromPort("Dimension"):
dim = self.getInputFromPort("Dimension")
else:
dim = im.getDim()
#set up filter
inImgType = itk.Image[inPixelType._type, dim]
outImgType = itk.Image[outPixelType._type, dim]
self.filter_ = itk.NormalizeImageFilter[inImgType, outImgType].New(im.getImg())
self.filter_.Update()
#setup output image
outIm = Image()
outIm.setImg(self.filter_.GetOutput())
outIm.setPixelType(outPixelType)
outIm.setDim(dim)
#set results
self.setResult("Output Image", outIm)
self.setResult("Filter", self)
self.setResult("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Normalize Image Filter", namespace=cls.my_namespace)
reg.add_input_port(cls, "Input Image", (Image, 'Input Image'))
reg.add_input_port(cls, "Input PixelType", (PixelType, 'Input PixelType'),True)
reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
reg.add_input_port(cls, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Filter", (Filter, 'Filter'), True)
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'),True)
|
