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#include "BrainModelVolumeFociDensity.h"
#include "FociProjectionFile.h"
#include "VolumeFile.h"
/*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 "BrainModelVolumeFociDensity.h"
#include "FociProjectionFile.h"
#include "VolumeFile.h"
/**
* constructor.
*/
BrainModelVolumeFociDensity::BrainModelVolumeFociDensity(BrainSet* bsIn,
const FociProjectionFile* fociProjectionFileIn,
const float regionCubeSizeIn,
const DENSITY_UNITS densityUnitsIn,
VolumeFile* outputVolumeFileIn)
: BrainModelAlgorithm(bsIn),
fociProjectionFile(fociProjectionFileIn),
regionCubeSize(regionCubeSizeIn),
densityUnits(densityUnitsIn),
outputVolumeFile(outputVolumeFileIn)
{
}
/**
* destructor.
*/
BrainModelVolumeFociDensity::~BrainModelVolumeFociDensity()
{
}
/**
* execute the algorithm.
*/
void
BrainModelVolumeFociDensity::execute() throw (BrainModelAlgorithmException)
{
//
// Check dimensions
//
if (outputVolumeFile == NULL) {
throw BrainModelAlgorithmException("The volume file is invalid");
}
if (outputVolumeFile->getTotalNumberOfVoxels() <= 0) {
throw BrainModelAlgorithmException("The volume contains no voxels.");
}
if (fociProjectionFile == NULL) {
throw BrainModelAlgorithmException("The foci projection file is invalid");
}
const int numFoci = fociProjectionFile->getNumberOfCellProjections();
if (numFoci <= 0) {
throw BrainModelAlgorithmException("The foci projection file contains no foci.");
}
if (regionCubeSize <= 0.0) {
throw BrainModelAlgorithmException("Region cube size is less than or equal to zero.");
}
//
// Half the cube size
//
const float halfRegionCubeSize = regionCubeSize * 0.5;
//
// Set all voxels to zero
//
outputVolumeFile->setAllVoxels(0.0);
//
// Add units to comment
//
switch (densityUnits) {
case DENSITY_UNITS_FOCI_PER_CUBIC_CENTIMETER:
outputVolumeFile->appendToFileComment("\nUnits are number of foci per cubic centimeter.");
break;
case DENSITY_UNITS_FOCI_PER_CUBIC_MILLIMETER:
outputVolumeFile->appendToFileComment("\nUnits are number of foci per cubic millimeter.");
break;
}
//
// Create progress dialog
//
createProgressDialog("Volume Foci Density",
numFoci,
"volumeFociDensity");
//
// Loop through the foci
//
for (int n = 0; n < numFoci; n++) {
//
// Update progress dialog
//
const float pctComplete = (static_cast<float>(n)
/ numFoci) * 100.0;
const QString pctString(QString::number(pctComplete, 'f', 1)
+ "% complete.");
updateProgressDialog(pctString);
//
// Get the stereotaxic coordinate
//
float focusXYZ[3];
fociProjectionFile->getCellProjection(n)->getVolumeXYZ(focusXYZ);
if ((focusXYZ[0] != 0.0) ||
(focusXYZ[1] != 0.0) ||
(focusXYZ[2] != 0.0)) {
//
// place the ROI box at the focus and find its corners
//
const float minCornerXYZ[3] = {
focusXYZ[0] - halfRegionCubeSize,
focusXYZ[1] - halfRegionCubeSize,
focusXYZ[2] - halfRegionCubeSize
};
const float maxCornerXYZ[3] = {
focusXYZ[0] + halfRegionCubeSize,
focusXYZ[1] + halfRegionCubeSize,
focusXYZ[2] + halfRegionCubeSize
};
//
// Get voxel indices containing corners
//
int minIJK[3], maxIJK[3];
outputVolumeFile->convertCoordinatesToVoxelIJK(minCornerXYZ, minIJK);
outputVolumeFile->convertCoordinatesToVoxelIJK(maxCornerXYZ, maxIJK);
//
// Limit to valid indices
//
outputVolumeFile->clampVoxelIndex(minIJK);
outputVolumeFile->clampVoxelIndex(maxIJK);
//
// Increment the voxels
//
for (int i = minIJK[0]; i <= maxIJK[0]; i++) {
for (int j = minIJK[1]; j <= maxIJK[1]; j++) {
for (int k = minIJK[2]; k <= maxIJK[2]; k++) {
outputVolumeFile->setVoxel(i, j, k, 0,
(outputVolumeFile->getVoxel(i, j, k) + 1));
}
}
}
}
}
//
// Scale to foci per mm^3
//
int dim[3];
outputVolumeFile->getDimensions(dim);
float voxelSize[3];
outputVolumeFile->getSpacing(voxelSize);
float voxelVolume = voxelSize[0] * voxelSize[1] * voxelSize[2];
float regionCubeVolume = regionCubeSize * regionCubeSize * regionCubeSize;
switch (densityUnits) {
case DENSITY_UNITS_FOCI_PER_CUBIC_CENTIMETER:
voxelVolume = voxelSize[0]/10.0 * voxelSize[1]/10.0 * voxelSize[2]/10.0;
//regionCubeVolume = regionCubeSize/10.0 * regionCubeSize/10.0 * regionCubeSize/10.0;
break;
case DENSITY_UNITS_FOCI_PER_CUBIC_MILLIMETER:
break;
}
float mm3voxel = regionCubeVolume * voxelVolume;
for (int i = 0; i < dim[0]; i++) {
for (int j = 0; j < dim[1]; j++) {
for (int k = 0; k < dim[2]; k++) {
outputVolumeFile->setVoxel(i, j, k, 0,
(outputVolumeFile->getVoxel(i, j, k) / mm3voxel));
}
}
}
removeProgressDialog();
}
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