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/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET 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 2 of the License, or
* (at your option) any later version.
*
* CARET 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 CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "BrainModelVolumeROISmoothing.h"
#include "VolumeFile.h"
#include <cmath>
#include <omp.h>
#include <iostream>
using namespace std;
BrainModelVolumeROISmoothing::BrainModelVolumeROISmoothing(BrainSet* bs,
VolumeFile* valuesIn,
VolumeFile* regionIn,
std::vector <VolumeFile *> * smoothVolVecIn,
float sigmaIn)
: BrainModelAlgorithm(bs)
{
values = valuesIn;
region = regionIn;
smoothVolVec = smoothVolVecIn;
sigma = sigmaIn;
}
BrainModelVolumeROISmoothing::~BrainModelVolumeROISmoothing()
{
}
void BrainModelVolumeROISmoothing::execute() throw (BrainModelAlgorithmException)
{
int i, j, k, ki, kj, kk, dim[3], dim2[3];
float spacing[3], spacing2[3], origin[3], origin2[3];
float inputVal, smoothVal, weightVal;
if (!values || !region || !smoothVolVec)
{
throw BrainModelAlgorithmException("Invalid volume.");
}
values->getSpacing(spacing);
values->getOrigin(origin);
values->getDimensions(dim);
bool match = true;
region->getSpacing(spacing2);
region->getOrigin(origin2);
region->getDimensions(dim2);
for (i = 0; i < 3; ++i)
{
if (abs(spacing[i] - spacing2[i]) > 0.0001f)
{
match = false;
}
if (abs(origin[i] - origin2[i]) > 0.0001f)
{
match = false;
}
if (dim[i] != dim2[i])
{
match = false;
}
}
if (!match)
{
throw BrainModelAlgorithmException("Input volumes do not match.");
}
VolumeFile::ORIENTATION myorient[3];// = {VolumeFile::ORIENTATION_LEFT_TO_RIGHT,
// VolumeFile::ORIENTATION_POSTERIOR_TO_ANTERIOR,
// VolumeFile::ORIENTATION_INFERIOR_TO_SUPERIOR};
values->getOrientation(myorient);
float frange = sigma * 6.0f;
int irange[3];
irange[0] = (int)floor(frange / fabs(spacing[0]));
irange[1] = (int)floor(frange / fabs(spacing[1]));
irange[2] = (int)floor(frange / fabs(spacing[2]));
if (!irange[0] || !irange[1] || !irange[2])
{
throw BrainModelAlgorithmException("Kernel too small.");
}
float*** weights = new float**[2 * irange[0] + 1];//precompute sigma weights
float tempf, tempf2;
for (i = 0; i < 2 * irange[0] + 1; ++i)
{
weights[i] = new float*[2 * irange[1] + 1];
for (j = 0; j < 2 * irange[1] + 1; ++j)
{
weights[i][j] = new float[2 * irange[2] + 1];
for (k = 0; k < 2 * irange[2] + 1; ++k)
{
tempf = (i - irange[0]) * spacing[0];
tempf *= tempf;
tempf2 = (j - irange[1]) * spacing[1];
tempf2 *= tempf2;
tempf += tempf2;
tempf2 = (k - irange[2]) * spacing[2];
tempf2 *= tempf2;
tempf += tempf2;//square of euclidean distance
tempf /= sigma * sigma;
weights[i][j][k] = exp(-tempf / 2.0f);
}
}
}
int numSubVolumes = values->getNumberOfSubVolumes();
smoothVolVec->resize(numSubVolumes);
for( int s = 0;s<numSubVolumes;s++)
{
std::cout << "volume: " << s <<std::endl;
//set up our output sub volume
VolumeFile * smoothSubVol = new VolumeFile;
smoothSubVol->initialize(VolumeFile::VOXEL_DATA_TYPE_FLOAT, dim, myorient, origin, spacing);//because setDimensions doesn't allocate...
(*smoothVolVec)[s] = smoothSubVol;
//get our input sub volume
VolumeFile subVol;
try {
subVol.readFile(values->getFileName(), s);
}
catch(FileException e)
{
exit(1);
// std::cout << "Exception caught while reading volume " << i << " of nifti file, " << values->getFileName() << std::endl;
// std::cout << e.whatQString() << std::endl;
throw BrainModelAlgorithmException("Error while reading Nifti Sub Volume.");
}
for (i = 0; i < dim[0]; ++i)
{//all voxels
for (j = 0; j < dim[1]; ++j)
{
for (k = 0; k < dim[2]; ++k)
{
if (region->getVoxel(i, j, k) > 0.0f)
{//if selected
float weightSum = 0.0f;
smoothVal = 0.0f;
for (ki = -irange[0]; ki <= irange[0]; ++ki)
{//loop through kernel
if (i + ki < 0 || i + ki >= dim[0])
{
continue;//makes the indentation a bit less daunting
}
for (kj = -irange[1]; kj <= irange[1]; ++kj)
{
if (j + kj < 0 || j + kj >= dim[1])
{
continue;
}
for (kk = -irange[2]; kk <= irange[2]; ++kk)
{
if (k + kk < 0 || k + kk >= dim[2])// || (ki == 0 && kj == 0 && kk == 0))
{//dont skip center point?
continue;
}
if (region->getVoxel(i + ki, j + kj, k + kk) > 0.0f)
{
inputVal = subVol.getVoxel(i + ki, j + kj , k + kk);
weightVal = weights[ki + irange[0]][kj + irange[1]][kk + irange[2]];
smoothVal += inputVal * weightVal;
weightSum += weightVal;
}
}
}
}
if (smoothVal != smoothVal)
{
smoothVal = 0.0f;//set NaNs to zero
}
else
{
smoothVal /= weightSum;
}
smoothSubVol->setVoxel(i, j, k, 0, smoothVal);
} else {
smoothSubVol->setVoxel(i, j, k, 0, 0.0f);
}
}
}
}
}
}
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