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inormalize.cc
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inormalize.cc
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/*--------------------------------------------------------------------------
@COPYRIGHT :
Copyright 1996, Alex P. Zijdenbos,
McConnell Brain Imaging Centre,
Montreal Neurological Institute, McGill University.
Permission to use, copy, modify, and distribute this
software and its documentation for any purpose and without
fee is hereby granted, provided that the above copyright
notice appear in all copies. The author and McGill University
make no representations about the suitability of this
software for any purpose. It is provided "as is" without
express or implied warranty.
----------------------------------------------------------------------------
$RCSfile: inormalize.cc,v $
$Revision: 1.4 $
$Author: claude $
$Date: 2007-10-09 21:56:35 $
$State: Exp $
--------------------------------------------------------------------------*/
/* ----------------------------- MNI Header -----------------------------------
@NAME : inormalize
@INPUT : argc, argv - command line arguments
@OUTPUT : (none)
@RETURNS : error status
@DESCRIPTION: Program for the intensity normalization of a minc volume,
following a (registered) model volume.
@METHOD : Minimization of the MSE voxel intensity difference by exhaustive
search
@GLOBALS :
@CALLS :
@CREATED : April 11, 1995 (Alex Zijdenbos)
@MODIFIED : $Log: inormalize.cc,v $
@MODIFIED : Revision 1.4 2007-10-09 21:56:35 claude
@MODIFIED : fixed inormalize for float data type
@MODIFIED :
@MODIFIED : Revision 1.3 2005/08/17 23:14:26 bert
@MODIFIED : Minor changes for some C++ warnings and issues
@MODIFIED :
@MODIFIED : Revision 1.2 2002/03/28 23:53:19 jason
@MODIFIED : switched to SimpleArray from CachedArray as there appear to be IO problems in the cached array implementation
@MODIFIED :
@MODIFIED : Revision 1.1.1.1 2002/03/27 18:36:59 jason
@MODIFIED : First import of inormalize sources. Does not work perfectly yet,
@MODIFIED : especially the median estimation appears to fail.
@MODIFIED :
@MODIFIED :
@MODIFIED : Revision 1.6 1998/04/01 18:29:49 alex
@MODIFIED : Made OpTimers quiet if -quiet was specified
@MODIFIED :
@MODIFIED : Revision 1.5 1998/02/28 20:04:34 alex
@MODIFIED : Added -range and -const options
@MODIFIED :
@MODIFIED : Revision 1.4 1997/09/11 14:26:31 alex
@MODIFIED : Various changes directed at g++ compatibility
@MODIFIED :
@MODIFIED : Revision 1.3 1996/12/19 20:47:16 alex
@MODIFIED : Various changes directed at g++ compatibility
@MODIFIED :
* Revision 1.2 1996/09/04 20:56:35 alex
* Checked Inormalize into main branch
*
* Revision 1.1.1.1 1996/08/29 19:05:04 alex
* Source for inormalize
*
@COPYRIGHT :
---------------------------------------------------------------------------- */
#include "inormalize.h"
#include <iostream>
using namespace std;
#include <time.h>
// #include "EBTKS/CachedArray.h"
#include "EBTKS/Dictionary.h"
#include "EBTKS/FileIO.h"
#include "EBTKS/OpTimer.h"
#include "EBTKS/amoeba.h"
#include "EBTKS/trivials.h"
class OptData {
public:
const FloatArray& modelArray;
const FloatArray& dataArray;
unsigned n;
Boolean verbose;
OptData(const FloatArray& ma, const FloatArray& da, unsigned nEl,
Boolean vb = FALSE)
: modelArray(ma),
dataArray(da)
{ n = nEl; verbose = vb; }
};
//
// Main program
//
int
main(int argc, char *argv[])
{
// Set timers
OpTimer usr(OpTimer::USR, "inormalize");
OpTimer sys(OpTimer::SYS, "inormalize");
OpTimer cpu(OpTimer::CPU, "inormalize");
// Get argument information
InormalizeArgs args(argc, argv);
if (!args.verbose) {
usr.verbose(FALSE);
sys.verbose(FALSE);
cpu.verbose(FALSE);
}
// Determine valid voxels from the mask and threshold settings
SimpleArray<Boolean> validVoxels;
unsigned nVoxels = getValidVoxels(args, validVoxels);
if (args.verbose)
cout << "Considering " << nVoxels << " voxels ("
<< 100.0*nVoxels/validVoxels.size() << "% of total)" << endl;
if (!nVoxels) {
cerr << "Error! voxel selection criterai removed all voxels. Not normalizing volume" << endl;
exit(EXIT_FAILURE);
}
if (args.verbose)
cout << "Selected normalization: " << args.methods[args.method] << endl;
// Can delete mask volume here
if (args.mask) {
delete_volume(args.mask);
args.mask = 0;
}
// Create history to append to MINC file
time_t timeVal = time(0);
MString history(ctime(&timeVal));
history.chop();
history += ">>> ";
history += args.command;
history += "; ";
// Self-normalize the input volume
if (args.zNormalize)
selfNormalizeMain(MIzspace, validVoxels, args, history);
if (args.yNormalize)
selfNormalizeMain(MIyspace, validVoxels, args, history);
if (args.xNormalize)
selfNormalizeMain(MIxspace, validVoxels, args, history);
if (args.oneConst) {
SimpleArray<float> volumeArray;
floatArrayFromVolume(volumeArray, args.volume, validVoxels, &nVoxels, args.verbose);
LinearMap iMap;
if (args.method == InormalizeArgs::RATIO_OF_MEANS)
iMap.factor(args.constants[0] / mean(volumeArray));
else if (args.method == InormalizeArgs::RATIO_OF_MEDIANS) {
iMap.factor(args.constants[0] / median(volumeArray));
cout << median(volumeArray) << endl;
cout << mean(volumeArray) << endl;
}
else {
cerr << "Invalid method " << args.methods[args.method] << endl;
exit(EXIT_FAILURE);
}
MString mapString;
appendToString(mapString, iMap);
if (args.normalize) {
history += mapString;
reMapVolume(args.volume, iMap, args.verbose);
}
}
else if (args.twoConst) {
SimpleArray<float> volumeArray;
floatArrayFromVolume(volumeArray, args.volume, validVoxels, &nVoxels, args.verbose);
FloatArray extrema(pctExtrema(volumeArray, args.rangePct, args.verbose));
LinearMap iMap(extrema[(unsigned int)0],
extrema[(unsigned int)1],
args.constants[(unsigned int)0],
args.constants[(unsigned int)1]);
MString mapString;
appendToString(mapString, iMap);
if (args.normalize) {
history += mapString;
reMapVolume(args.volume, iMap, args.verbose);
}
}
else if (args.model) {
// Make sure volume and model have compatible sizes.
int volume_sizes[3], model_sizes[3];
get_volume_sizes(args.volume, volume_sizes);
get_volume_sizes(args.model, model_sizes);
if( ( model_sizes[0] != volume_sizes[0] ) ||
( model_sizes[1] != volume_sizes[1] ) ||
( model_sizes[2] != volume_sizes[2] ) ) {
cerr << "Volume and model dimensions do not match!" << endl;
exit(EXIT_FAILURE);
}
// Convert entire volume to float arrays (cached to conserve memory)
SimpleArray<float> volumeArray;
SimpleArray<float> modelArray;
floatArrayFromVolume(volumeArray, args.volume, validVoxels, &nVoxels, args.verbose);
floatArrayFromVolume(modelArray, args.model, validVoxels, &nVoxels, args.verbose);
// Can delete model volume here
delete_volume(args.model);
args.model = 0;
#ifdef HAVE_MATLAB
if (args.matlabOutputString) {
SimpleArray<float> samples = SimpleArray<float>(volumeArray.sample(10000));
samples.saveMatlab(args.matlabOutputString, "volume");
samples = SimpleArray<float>(modelArray.sample(10000));
samples.saveMatlab(args.matlabOutputString, "model");
}
#endif
history += "global:";
for (unsigned method = 0; method < args.nMethods; method++)
if ((method == args.method) || args.printValues) {
if (args.printValues)
cout << " " << args.methods[method] << ":" << flush;
LinearMap iMap = determineMap(modelArray, volumeArray, args, method);
MString mapString;
appendToString(mapString, iMap);
if (args.printValues)
cout << mapString << endl;
#ifdef HAVE_MATLAB
if (args.matlabOutputString) {
SimpleArray<float> mapArray(2);
LinearMap tempMap(iMap);
tempMap.inv();
mapArray[0] = tempMap.factor();
mapArray[1] = tempMap.offset();
mapArray.saveMatlab(args.matlabOutputString, args.methods[method]);
}
#endif
if (args.normalize && (args.method == method)) {
history += mapString;
reMapVolume(args.volume, iMap, args.verbose);
}
}
}
if (args.normalize) {
history += "\n";
if (!saveVolume(args.volume, args.outputPath, args.inputPath, history,
args.compress, args.verbose))
exit(EXIT_FAILURE);
}
return(EXIT_SUCCESS);
}
//
//
//
void
scanVoxelRange(const Volume volume, double *voxelMin, double *voxelMax)
{
int sizes[3];
get_volume_sizes(volume, sizes);
unsigned D1 = sizes[0];
unsigned D2 = sizes[1];
unsigned D3 = sizes[2];
Real minVal = get_volume_voxel_value(volume, 0, 0, 0, 0, 0);
Real maxVal = minVal;
for (unsigned d1 = 0; d1 < D1; d1++)
for (unsigned d2 = 0; d2 < D2; d2++)
for (unsigned d3 = 0; d3 < D3; d3++) {
Real value = get_volume_voxel_value(volume, d1, d2, d3, 0, 0);
if (value < minVal)
minVal = value;
else if (value > maxVal)
maxVal = value;
}
*voxelMin = minVal;
*voxelMax = maxVal;
}
//
//
//
unsigned
getValidVoxels(const InormalizeArgs& args, BoolArray& validVoxels)
{
int sizes[3];
get_volume_sizes(args.volume, sizes);
unsigned D1 = sizes[0];
unsigned D2 = sizes[1];
unsigned D3 = sizes[2];
unsigned nVoxels = D1*D2*D3;
validVoxels.newSize(nVoxels);
double minT = args.thresholds[0];
double maxT = args.thresholds[1];
Boolean useThreshold =
((maxT >= minT) && ((minT > -MAXDOUBLE) || (maxT < MAXDOUBLE)));
if (args.mask || useThreshold) {
validVoxels.clear(FALSE);
unsigned maskD1, maskD2, maskD3;
if (args.mask) {
if (args.verbose)
cout << "Scanning mask" << flush;
int maskSizes[3];
get_volume_sizes(args.mask, maskSizes);
maskD1 = maskSizes[0];
maskD2 = maskSizes[1];
maskD3 = maskSizes[2];
if (!args.useWorldCoord && ((maskD1 != D1) || (maskD2 != D2) || (maskD3 != D3))) {
cerr << "Volume and mask dimensions do not match!" << endl;
exit(EXIT_FAILURE);
}
}
nVoxels = 0;
unsigned i = 0;
for (unsigned d1 = 0; d1 < D1; d1++) {
for (unsigned d2 = 0; d2 < D2; d2++) {
for (unsigned d3 = 0; d3 < D3; d3++) {
Boolean valid = TRUE;
if (useThreshold) {
Real value = get_volume_real_value(args.volume, d1, d2, d3, 0, 0);
if ((value < minT) || (value > maxT))
valid = FALSE;
}
if (valid && args.mask) {
Real maskValue = 0;
if (args.useWorldCoord) {
Real xWorld, yWorld, zWorld;
convert_3D_voxel_to_world(args.volume, d1, d2, d3,
&xWorld, &yWorld, &zWorld);
Real voxel1, voxel2, voxel3;
convert_3D_world_to_voxel(args.mask, xWorld, yWorld, zWorld,
&voxel1, &voxel2, &voxel3);
int v1 = ROUND(voxel1);
int v2 = ROUND(voxel2);
int v3 = ROUND(voxel3);
if ((v1 >= 0) && (v2 >= 0) && (v3 >= 0) &&
(v1 < maskD1) && (v2 < maskD2) && (v3 < maskD3))
maskValue = get_volume_real_value(args.mask, v1, v2, v3, 0, 0);
}
else
maskValue = get_volume_real_value(args.mask, d1, d2, d3, 0, 0);
if (!maskValue)
valid = FALSE;
}
if (validVoxels[i++] = valid)
nVoxels++;
}
}
if (args.verbose)
cout << "." << flush;
}
if (args.verbose)
cout << "Done" << endl;
}
else
validVoxels.clear(TRUE);
return nVoxels;
}
//
//
//
void
floatArrayFromVolume(FloatArray& array, const Volume volume,
const BoolArray& validVoxels, unsigned *N,
int verbose)
{
unsigned nVoxels = (N && *N) ? *N : validVoxels.occurrencesOf(TRUE);
if (N && !*N)
*N = nVoxels;
if (verbose)
cout << "Converting volume" << flush;
array.newSize(nVoxels);
int sizes[3];
get_volume_sizes(volume, sizes);
unsigned D1 = sizes[0];
unsigned D2 = sizes[1];
unsigned D3 = sizes[2];
unsigned voxelCtr = 0;
unsigned valueCtr = 0;
for (unsigned d1 = 0; d1 < D1; d1++) {
for (unsigned d2 = 0; d2 < D2; d2++) {
for (unsigned d3 = 0; d3 < D3; d3++)
if (validVoxels[voxelCtr++])
array[valueCtr++] = (float) get_volume_real_value(volume, d1, d2, d3, 0, 0);
}
if (verbose)
cout << "." << flush;
}
if (verbose)
cout << "Done" << endl;
}
//
//
//
void
floatArraysFromSlices(const Volume volume, const BoolArray& validVoxels,
unsigned axis, unsigned slice1, unsigned slice2,
FloatArray& array1, FloatArray& array2)
{
int sizes[3];
get_volume_sizes(volume, sizes);
unsigned D1 = sizes[0];
unsigned D2 = sizes[1];
unsigned D3 = sizes[2];
switch(axis) {
case 0: {
unsigned N = D2*D3;
array1.newSize(N);
array1.newSize(0); // Allocated but empty
array2.newSize(N);
array2.newSize(0); // Allocated but empty
unsigned valid1 = slice1*N;
unsigned valid2 = slice2*N;
// const Boolean *valid1 = validVoxels.contents() + slice1*N;
// const Boolean *valid2 = validVoxels.contents() + slice2*N;
for (unsigned d2 = 0; d2 < D2; d2++)
for (unsigned d3 = 0; d3 < D3; d3++, valid1++, valid2++)
if (validVoxels[valid1] && validVoxels[valid2]) {
Real value1 = get_volume_real_value(volume, slice1, d2, d3, 0, 0);
Real value2 = get_volume_real_value(volume, slice2, d2, d3, 0, 0);
if (value1 && value2) {
array1.append(value1);
array2.append(value2);
}
}
break;
}
case 1: {
unsigned N = D1*D3;
array1.newSize(N);
array1.newSize(0); // Allocated but empty
array2.newSize(N);
array2.newSize(0); // Allocated but empty
// const Boolean *validBase = validVoxels.contents();
for (unsigned d1 = 0; d1 < D1; d1++) {
unsigned valid1 = (d1*D2 + slice1)*D3;
unsigned valid2 = (d1*D2 + slice2)*D3;
// const Boolean *valid1 = validBase + (d1*D2 + slice1)*D3;
// const Boolean *valid2 = validBase + (d1*D2 + slice2)*D3;
for (unsigned d3 = 0; d3 < D3; d3++, valid1++, valid2++)
if (validVoxels[valid1] && validVoxels[valid2]) {
Real value1 = get_volume_real_value(volume, d1, slice1, d3, 0, 0);
Real value2 = get_volume_real_value(volume, d1, slice2, d3, 0, 0);
if (value1 && value2) {
array1.append(value1);
array2.append(value2);
}
}
}
break;
}
case 2: {
unsigned N = D1*D2;
array1.newSize(N);
array1.newSize(0); // Allocated but empty
array2.newSize(N);
array2.newSize(0); // Allocated but empty
// const Boolean *validBase = validVoxels.contents();
for (unsigned d1 = 0; d1 < D1; d1++) {
// const Boolean *valid1 = validBase + d1*D2*D3 + slice1;
// const Boolean *valid2 = validBase + d1*D2*D3 + slice2;
unsigned valid1 = d1*D2*D3 + slice1;
unsigned valid2 = d1*D2*D3 + slice2;
for (unsigned d2 = 0; d2 < D2; d2++) {
if (validVoxels[valid1] && validVoxels[valid2]) {
Real value1 = get_volume_real_value(volume, d1, d2, slice1, 0, 0);
Real value2 = get_volume_real_value(volume, d1, d2, slice2, 0, 0);
if (value1 && value2) {
array1.append(value1);
array2.append(value2);
}
}
valid1 += D3;
valid2 += D3;
}
}
break;
}
}
}
//
//
//
void
selfNormalizeMain(char *dimension, const BoolArray& validVoxels,
const InormalizeArgs& args, MString& history)
{
for (unsigned method = 0; method < args.nMethods; method++)
if ((method == args.method) || args.printValues) {
Array<LinearMap> iMaps(selfNormalize(args.volume, validVoxels, dimension,
args, method));
MString mapString(dimension);
mapString += ":";
appendToString(mapString, iMaps);
if (args.method == method)
history += mapString;
if (args.printValues)
cout << " " << args.methods[method] << ":" << mapString << endl;
}
}
//
//
//
Array<LinearMap>
selfNormalize(Volume volume, const BoolArray& validVoxels, char *dimension,
const InormalizeArgs& args, int method)
{
if (method < -1)
method = args.method;
int sizes[3];
get_volume_sizes(volume, sizes);
int axis;
if (!convert_dim_name_to_spatial_axis(dimension, &axis)) {
cerr << "inormalize: couldn't convert dim_name " << dimension
<< " to axis" << endl;
exit(EXIT_FAILURE);
}
axis = 2 - axis; // ??? Why is this necessary?
unsigned sliceDim = sizes[axis];
Array<LinearMap> iMaps(sliceDim);
if (sliceDim < 2)
return iMaps;
unsigned centerSlice = sliceDim/2;
unsigned int slice;
FloatArray refArray, array;
for (slice = centerSlice; slice < sliceDim - 1; slice++) {
floatArraysFromSlices(volume, validVoxels, axis, slice, slice+1, refArray, array);
LinearMap sliceMap(determineMap(refArray, array, args, method));
iMaps[slice + 1] = iMaps[slice];
iMaps[slice + 1].concat(sliceMap);
}
for (slice = centerSlice; slice > 0; slice--) {
floatArraysFromSlices(volume, validVoxels, axis, slice, slice-1, refArray, array);
LinearMap sliceMap(determineMap(refArray, array, args, method));
iMaps[slice - 1] = iMaps[slice];
iMaps[slice - 1].concat(sliceMap);
}
for (slice = 0; slice < sliceDim; slice++)
cout << slice << ": " << iMaps[slice].factor() << endl;
reMapVolume(volume, axis, iMaps, args.verbose);
return iMaps;
}
//
//
//
void
reMapVolume(Volume volume, const LinearMap& iMap, int verbose)
{
// Scan voxel range, just in case the volume attributes are messed up
double voxelMin, voxelMax;
scanVoxelRange(volume, &voxelMin, &voxelMax);
// Get real extrema
double realMin = CONVERT_VOXEL_TO_VALUE(volume, voxelMin);
double realMax = CONVERT_VOXEL_TO_VALUE(volume, voxelMax);
// cout << "(" << voxelMin << ", " << voxelMax << ") -> ("
// << realMin << ", " << realMax << ")" << endl;
if (verbose)
cout << "Normalizing (" << iMap.factor() << ", " << iMap.offset() << ")" << endl;
// Concatenate original and derived mapping
realMin = iMap(realMin);
realMax = iMap(realMax);
//LinearMap fullMap(voxelMin, voxelMax, realMin, realMax);
//cout << "FullMap: " << fullMap << endl;
// cout << "(" << voxelMin << ", " << voxelMax << ") -> ("
// << realMin << ", " << realMax << ")" << endl;
// Scale the voxel values if not working with ranges (for FLOAT and DOUBLE).
if( !volume->real_range_set ) {
cout << "Fixing voxel values for real data type..." << endl;
int sizes[3];
get_volume_sizes(volume, sizes);
for (unsigned d1 = 0; d1 < sizes[0]; d1++) {
for (unsigned d2 = 0; d2 < sizes[1]; d2++) {
for (unsigned d3 = 0; d3 < sizes[2]; d3++) {
Real value = get_volume_voxel_value(volume, d1, d2, d3, 0, 0);
set_volume_voxel_value(volume, d1, d2, d3, 0, 0,
clamp(iMap(value), realMin, realMax));
}
}
}
} else {
// Reset the voxel range and set the desired real range
set_volume_voxel_range(volume, voxelMin, voxelMax);
}
set_volume_real_range(volume, realMin, realMax);
}
//
//
//
void
reMapVolume(Volume volume, int axis, const Array<LinearMap>& iMaps, int verbose)
{
int sizes[3];
get_volume_sizes(volume, sizes);
unsigned D1 = sizes[0];
unsigned D2 = sizes[1];
unsigned D3 = sizes[2];
// Scan voxel range, just in case the volume attributes are messed up
double voxelMin = MAXDOUBLE;
double voxelMax = -MAXDOUBLE;
double mappedRealMin = MAXDOUBLE;
double mappedRealMax = -MAXDOUBLE;
// Traverse volume to find new global min and max
LinearMap iMap;
unsigned d1;
for (d1 = 0; d1 < D1; d1++) {
if (!axis)
iMap = iMaps[d1];
for (unsigned d2 = 0; d2 < D2; d2++) {
if (axis == 1)
iMap = iMaps[d2];
for (unsigned d3 = 0; d3 < D3; d3++) {
if (axis == 2)
iMap = iMaps[d3];
Real value = get_volume_voxel_value(volume, d1, d2, d3, 0, 0);
if (value < voxelMin)
voxelMin = value;
if (value > voxelMax)
voxelMax = value;
value = iMap(CONVERT_VOXEL_TO_VALUE(volume, value));
if (value < mappedRealMin)
mappedRealMin = value;
if (value > mappedRealMax)
mappedRealMax = value;
}
}
}
// Get real extrema
double realMin = CONVERT_VOXEL_TO_VALUE(volume, voxelMin);
double realMax = CONVERT_VOXEL_TO_VALUE(volume, voxelMax);
// Retrieve original voxel->real mapping
LinearMap voxelToRealMap(voxelMin, voxelMax, CONVERT_VOXEL_TO_VALUE(volume, voxelMin),
CONVERT_VOXEL_TO_VALUE(volume, voxelMax));
// Reset the voxel range to the full range of the data type
// And set the desired real range
set_volume_voxel_range(volume, voxelMin, voxelMax);
set_volume_real_range(volume, mappedRealMin, mappedRealMax);
// Retrieve range of data type
// get_volume_voxel_range(volume, &voxelMin, &voxelMax);
// Determine final real->voxel map
LinearMap realToVoxelMap(mappedRealMin, mappedRealMax, voxelMin, voxelMax);
/*
cout << "Axis: " << axis << endl
<< "voxelMin: " << voxelMin << " voxelMax: " << voxelMax << endl
<< "Voxel->real map: " << voxelToRealMap << endl
<< "Real->voxel map: " << realToVoxelMap << endl;
*/
// Remap volume
if (verbose)
cout << "Remapping slices" << flush;
for (d1 = 0; d1 < D1; d1++) {
if (!axis) {
iMap = voxelToRealMap;
iMap.concat(iMaps[d1]);
iMap.concat(realToVoxelMap);
// iMap = realToVoxelMap(iMaps[d1](voxelToRealMap));
}
for (unsigned d2 = 0; d2 < D2; d2++) {
if (axis == 1) {
iMap = realToVoxelMap;
iMap.concat(iMaps[d2]);
iMap.concat(voxelToRealMap);
// iMap = realToVoxelMap(iMaps[d2](voxelToRealMap));
}
for (unsigned d3 = 0; d3 < D3; d3++) {
if (axis == 2) {
iMap = realToVoxelMap;
iMap.concat(iMaps[d3]);
iMap.concat(voxelToRealMap);
// iMap = realToVoxelMap(iMaps[d3](voxelToRealMap));
}
Real value = get_volume_voxel_value(volume, d1, d2, d3, 0, 0);
set_volume_voxel_value(volume, d1, d2, d3, 0, 0,
clamp(iMap(value), voxelMin, voxelMax));
}
}
if (verbose)
cout << "." << flush;
}
if (verbose)
cout << "Done" << endl;
}
//
//
//
LinearMap
determineMap(const FloatArray& modelArray, const FloatArray& dataArray,
const InormalizeArgs& args, int method)
{
unsigned nVoxels = size(modelArray);
if (size(dataArray) != nVoxels) {
cerr << "determineMap: sizes of data- and modelarray are not equal!" << endl;
exit(EXIT_FAILURE);
}
if (method < 0)
method = args.method;
LinearMap map;
if (nVoxels < args.minVoxels)
return map;
if (method == InormalizeArgs::RMS) {
OptData optData(modelArray, dataArray, nVoxels, args.verbose);
FloatArray temp(modelArray);
double f = temp.medianVolatile();
temp = dataArray;
f /= temp.medianVolatile();
double fStep = 0.1;
amoeba_struct amoeba;
initialize_amoeba(&amoeba, 1, &f, &fStep, evaluateRMS, (void *) &optData, 1e-6);
unsigned iter = 0;
while ((iter < 100) && perform_amoeba(&amoeba))
iter++;
double minRMS = get_amoeba_parameters(&amoeba, &f);
terminate_amoeba(&amoeba);
map.factor() = f;
}
else if (method == InormalizeArgs::VR) {
OptData optData(modelArray, dataArray, nVoxels, args.verbose);
FloatArray temp(modelArray);
double f = temp.medianVolatile();
temp = dataArray;
f /= temp.medianVolatile();
double fStep = 0.1;
amoeba_struct amoeba;
initialize_amoeba(&amoeba, 1, &f, &fStep, evaluateVR, (void *)&optData, 1e-6);
unsigned iter = 0;
while ((iter < 100) && perform_amoeba(&amoeba))
iter++;
double minVR = get_amoeba_parameters(&amoeba, &f);
terminate_amoeba(&amoeba);
map.factor() = f;
}
else if (method == InormalizeArgs::RATIO_OF_MEANS)
map.factor() = mean(modelArray)/mean(dataArray);
else if (method == InormalizeArgs::RATIO_OF_MEDIANS) {
FloatArray temp(modelArray);
map.factor() = temp.medianVolatile();
temp = dataArray;
map.factor() /= temp.medianVolatile();
}
else if (method == InormalizeArgs::MEAN_OF_RATIOS) {
FloatArray temp(modelArray);
temp /= dataArray;
prune(temp);
if (args.constrained) {
float ceil = pow(10, 0.1);
float floor = pow(10, -0.1);
temp.removeAllNotIn(floor, ceil);
}
if (size(temp) >= args.minVoxels) {
map.factor() = mean(temp);
if (args.constrained && args.verbose)
cout << "+";
}
}
else if (method == InormalizeArgs::MEAN_OF_LOG_RATIOS) {
FloatArray temp(modelArray);
temp /= dataArray;
temp = log(temp);
prune(temp);
if (args.constrained) {
float ceil = 0.1;
float floor = -0.1;
temp.removeAllNotIn(floor, ceil);
}
if (size(temp) >= args.minVoxels) {
map.factor() = pow(10, mean(temp));
if (args.constrained && args.verbose)
cout << "+";
}
}
else if (method == InormalizeArgs::MEDIAN_OF_RATIOS) {
FloatArray temp(modelArray);
temp /= dataArray;
prune(temp);
if (args.constrained) {
float ceil = pow(10, 0.1);
float floor = pow(10, -0.1);
temp.removeAllNotIn(floor, ceil);
}
if (size(temp) >= args.minVoxels) {
map.factor() = temp.medianVolatile();
if (args.constrained && args.verbose)
cout << "+";
}
}
else if (method == InormalizeArgs::RANGE) {
FloatArray dataExtrema(pctExtrema(dataArray, args.rangePct, args.verbose));
FloatArray modelExtrema(pctExtrema(modelArray, args.rangePct, args.verbose));
map(dataExtrema[(unsigned int)0],
dataExtrema[(unsigned int)1],
modelExtrema[(unsigned int)0],
modelExtrema[(unsigned int)1]);
}
else {
cerr << "Unknown method " << method << " encountered" << endl;
exit(EXIT_FAILURE);
}
return map;
}
//
//
//
Boolean
saveVolume(const Volume volume, const Path& path, const Path& mincModel,
const MString& history, int compress, int verbose)
{
char *mincModelString = 0;
if (!mincModel.isEmpty())
mincModelString = (char *) mincModel.string();
char *historyString = 0;
if (!history.isEmpty())
historyString = (char *) history.string();
Path outputPath(path.expanded());
outputPath.removeCompressedExtension();
if (output_modified_volume(outputPath, NC_UNSPECIFIED, FALSE, 0.0, 0.0,
volume, mincModelString, historyString,
(minc_output_options *) NULL) != OK) {
cerr << "Couldn't save " << outputPath << endl;
return FALSE;
}
if (compress) {
if (verbose)
cout << "Compressing " << outputPath << "..." << flush;
MString zipCommand("gzip -f " + outputPath);
system(zipCommand);
if (verbose)
cout << "Done" << endl;
}
return TRUE;
}
//
//
//
MString&
appendToString(MString& string, const LinearMap& iMap)
{
string += " (";
string += iMap.factor();
string += ", ";
string += iMap.offset();
string += ")";
return string;
}
//
//
//
MString&
appendToString(MString& string, const Array<LinearMap>& iMaps)
{
unsigned n = iMaps.size();
if (n)
for (unsigned i = 0; i < n; i++) {
string += " (";
string += iMaps[i].factor();
string += ", ";
string += iMaps[i].offset();
string += ")";
}
return string;
}
double
evaluateRMS(void *data, float *f)
{
OptData& optData = *(OptData *) data;
double RMS = 0;
optData.modelArray.resetIterator();
optData.dataArray.resetIterator();
for (unsigned i = optData.n; i; i--) {
double value = optData.modelArray++ - (optData.dataArray++) * (*f);
RMS += value*value;