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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 IsolatedWatershedImageFilter(Module):
my_namespace="Filter|Segmentation"
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.IsolatedWatershedImageFilter[inImgType, outImgType].New(im.getImg())
if self.hasInputFromPort("Seed1"):
self.filter_.SetSeed1(self.getInputFromPort("Seed1").ind_)
if self.hasInputFromPort("Seed2"):
self.filter_.SetSeed2(self.getInputFromPort("Seed2").ind_)
if self.hasInputFromPort("ReplaceValue1"):
self.filter_.SetReplaceValue1(self.getInputFromPort("ReplaceValue1"))
if self.hasInputFromPort("ReplaceValue2"):
self.filter_.SetReplaceValue2(self.getInputFromPort("ReplaceValue2"))
if self.hasInputFromPort("Threshold"):
self.filter_.SetThreshold(self.getInputFromPort("Threshold"))
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("Output PixelType", outPixelType)
self.setResult("Filter", self)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Isolated Watershed 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, "Dimension", (basic.Integer, 'Dimension'),True)
reg.add_input_port(cls, "Seed1", (Index2D, 'Seed 1 Location'))
reg.add_input_port(cls, "Output PixelType", (PixelType, 'Output PixelType'), True)
reg.add_input_port(cls, "Threshold", (basic.Float, 'Threshold'), True)
reg.add_input_port(cls, "Seed2", (Index2D, 'Seed 2 Location'))
reg.add_input_port(cls, "ReplaceValue1", (basic.Float, 'Replacement Value 1'), True);
reg.add_input_port(cls, "ReplaceValue2", (basic.Float, 'Replacement Value 2'), True);
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
class ConnectedThresholdImageFilter(Module):
my_namespace="Filter|Segmentation"
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()
if self.hasInputFromPort("Seed2D"):
seed = self.getInputFromPort("Seed2D")
else:
seed = self.getInputFromPort("Seed3D")
replace = self.getInputFromPort("Replace Value")
t_lower = self.getInputFromPort("Lower Value")
t_upper = self.getInputFromPort("Upper Value")
#setup filter
inImgType = itk.Image[inPixelType._type, dim]
outImgType = itk.Image[outPixelType._type, dim]
self.filter_ = itk.ConnectedThresholdImageFilter[inImgType,outImgType].New(im.getImg())
self.filter_.SetSeed(seed.ind_)
self.filter_.SetReplaceValue(replace)
self.filter_.SetLower(t_lower)
self.filter_.SetUpper(t_upper)
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("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Connected Threshold 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, "Seed2D", (Index2D, 'Seed Point'))
reg.add_input_port(cls, "Seed3D", (Index3D, 'Seed Point'))
reg.add_input_port(cls, "Replace Value", (basic.Float, 'Replacement Value'))
reg.add_input_port(cls, "Upper Value", (basic.Float, 'Upper Threshold Value'))
reg.add_input_port(cls, "Lower Value", (basic.Float, 'Lower Threshold Value'))
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
class ConfidenceConnectedImageFilter(Module):
my_namespace="Filter|Segmentation"
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()
if self.hasInputFromPort("Seed2D"):
seed = self.getInputFromPort("Seed2D")
else:
seed = self.getInputFromPort("Seed3D")
replace = self.getInputFromPort("Replace Value")
multiplier = self.getInputFromPort("Multiplier")
iterations = self.getInputFromPort("Iterations")
radius = self.getInputFromPort("Neighborhood Radius")
#setup filter
inImgType = itk.Image[inPixelType._type,dim]
outImgType = itk.Image[outPixelType._type,dim]
self.filter_ = itk.ConfidenceConnectedImageFilter[inImgType,outImgType].New(im.getImg())
self.filter_.SetReplaceValue(replace)
self.filter_.SetMultiplier(multiplier)
self.filter_.SetNumberOfIterations(iterations)
self.filter_.SetInitialNeighborhoodRadius(radius)
self.filter_.SetSeed(seed.ind_)
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("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Confidence Connected 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, "Seed2D", (Index2D, 'Seed Point'))
reg.add_input_port(cls, "Seed3D", (Index3D, 'Seed Point'))
reg.add_input_port(cls, "Replace Value", (basic.Float, 'Replacement Value'))
reg.add_input_port(cls, "Multiplier", (basic.Float, 'Multiplier'))
reg.add_input_port(cls, "Iterations", (basic.Float, 'Iterations'))
reg.add_input_port(cls, "Neighborhood Radius", (basic.Float, 'Neighborhood Radius'))
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
class IsolatedConnectedImageFilter(Module):
my_namespace="Filter|Segmentation"
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()
seed1 = self.getInputFromPort("Seed1")
seed2 = self.getInputFromPort("Seed2")
replace = self.getInputFromPort("Replace Value")
t_lower = self.getInputFromPort("Lower Value")
t_upper = self.getInputFromPort("Upper Value")
inImgType = itk.Image[inPixelType._type,dim]
outImgType = itk.Image[outPixelType._type,dim]
self.filter_ = itk.IsolatedConnectedImageFilter[inImgType,outImgType].New(im.getImg())
self.filter_.SetReplaceValue(replace)
self.filter_.SetLower(t_lower)
self.filter_.SetUpperValueLimit(t_upper)
self.filter_.SetSeed1(seed1.ind_)
self.filter_.SetSeed2(seed2.ind_)
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("Output PixelType", outPixelType)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="Isolated Connected 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, "Seed1", (Index2D, 'Seed Point'))
reg.add_input_port(cls, "Seed2", (Index2D, 'Seed Point'))
reg.add_input_port(cls, "Replace Value", (basic.Integer, 'Replacement Value'))
reg.add_input_port(cls, "Upper Value", (basic.Integer, 'Upper Threshold Value'))
reg.add_input_port(cls, "Lower Value", (basic.Integer, 'Lower Threshold Value'))
reg.add_output_port(cls, "Output Image", (Image, 'Output Image'))
reg.add_output_port(cls, "Output PixelType", (PixelType, 'Output PixelType'))
|
