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/*=========================================================================
Program: ITK-SNAP
Module: $RCSfile: MultiLabelMeshPipeline.h,v $
Language: C++
Date: $Date: 2009/01/23 20:09:38 $
Version: $Revision: 1.3 $
Copyright (c) 2007 Paul A. Yushkevich
This file is part of ITK-SNAP
ITK-SNAP is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
-----
Copyright (c) 2003 Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __MultiLabelMeshPipeline_h_
#define __MultiLabelMeshPipeline_h_
#include "SNAPCommon.h"
#include "itkImageRegion.h"
#include "itkSmartPointer.h"
#include "vtkSmartPointer.h"
#include "itksys/MD5.h"
#include "itkObjectFactory.h"
#include "ImageWrapperTraits.h"
#include "RLERegionOfInterestImageFilter.h"
#include "RLEImageScanlineIterator.h"
// Forward reference to itk classes
namespace itk {
template <class TPixel,unsigned int VDimension> class Image;
template <class TInputImage, class TOutputImage> class BinaryThresholdImageFilter;
template <class TImage> class ImageLinearConstIteratorWithIndex;
}
// Forward references
class MeshOptions;
class VTKMeshPipeline;
class vtkPolyData;
class AllPurposeProgressAccumulator;
/**
* \class MultiLabelMeshPipeline
* \brief A small pipeline used to convert a multi-label segmentation image to
* a collection of VTK meshes.
*
* For each label, the pipeline uses the checksum mechanism to keep track of
* whether it has been updated relative to the corresponding mesh. This makes
* it possible for selective mesh recomputation, leading to fast mesh computation
* even for big segmentations.
*/
class MultiLabelMeshPipeline : public itk::Object
{
public:
// Cached information about a VTK mesh
struct MeshInfo
{
// The pointer to the mesh
vtkSmartPointer<vtkPolyData> Mesh;
// The checksum for the mesh
unsigned long CheckSum;
// The extents of the bounding box
Vector3i BoundingBox[2];
// The number of voxels
unsigned long Count;
MeshInfo();
~MeshInfo();
};
// Collection of mesh data for labels present in the image
typedef std::map<LabelType, MeshInfo> MeshInfoMap;
irisITKObjectMacro(MultiLabelMeshPipeline, itk::Object)
/** Input image type */
typedef LabelImageWrapperTraits::ImageType InputImageType;
typedef itk::SmartPointer<InputImageType> InputImagePointer;
/** Set the input segmentation image */
void SetImage(InputImageType *input);
/** Compute the bounding boxes for different regions. Prerequisite for
* calling ComputeMesh(). Returns the total number of voxels in all boxes */
unsigned long ComputeBoundingBoxes();
unsigned long GetVoxelsInBoundingBox(LabelType label) const;
const MeshInfoMap& GetMeshInfo() { return m_MeshInfo; }
/** Set the mesh options for this filter */
void SetMeshOptions(const MeshOptions *options);
/** Can we compute a mesh for this label? */
bool CanComputeMesh(LabelType label)
{
return m_Histogram[label] > 0l;
}
/** Compute a mesh for a particular color label. Returns true if
* the color label is not present in the image */
bool ComputeMesh(LabelType label, vtkPolyData *outData);
/** Update the meshes */
void UpdateMeshes(itk::Command *progressCommand);
/** Get the collection of computed meshes */
std::map<LabelType, vtkSmartPointer<vtkPolyData> > GetMeshCollection();
/** Get the progress accumulator from the VTK mesh pipeline */
AllPurposeProgressAccumulator *GetProgressAccumulator();
protected:
/** Constructor, which builds the pipeline */
MultiLabelMeshPipeline();
/** Deallocate the pipeline filters */
~MultiLabelMeshPipeline();
private:
// Type definitions for the various filters used by this object
typedef itk::Image<float,3> InternalImageType;
typedef itk::SmartPointer<InternalImageType> InternalImagePointer;
typedef itk::RegionOfInterestImageFilter<
InputImageType,InputImageType> ROIFilter;
typedef itk::SmartPointer<ROIFilter> ROIFilterPointer;
typedef itk::BinaryThresholdImageFilter<
InputImageType,InternalImageType> ThresholdFilter;
typedef itk::SmartPointer<ThresholdFilter> ThresholdFilterPointer;
// Current set of mesh options
SmartPtr<MeshOptions> m_MeshOptions;
// The input image
InputImagePointer m_InputImage;
// The ROI extraction filter used for constructing a bounding box
ROIFilterPointer m_ROIFilter;
// The thresholding filter used to map intensity in the bounding box to
// standardized range
ThresholdFilterPointer m_ThrehsoldFilter;
MeshInfoMap m_MeshInfo;
// Set of bounding boxes
itk::ImageRegion<3> m_BoundingBox[MAX_COLOR_LABELS];
// Histogram of the image
long m_Histogram[MAX_COLOR_LABELS];
// The VTK pipeline
VTKMeshPipeline * m_VTKPipeline;
// Helper routine for the update command
void UpdateMeshInfoHelper(
MeshInfo *current_meshinfo,
const itk::Index<3> &run_start,
itk::ImageRegionConstIteratorWithIndex<InputImageType> &it,
unsigned long pos);
};
#endif
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