void LabelsVolumeGenerator::postProcessTargetITK()
{
typedef unsigned char PixelType;
typedef Image<PixelType, 3> ImageType;
// create a new image from the target data
ImageType::Pointer input = ImageType::New();
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
for (int i = 0; i < 3; ++i) size[i] = m_targetVolume->dimensions[i];
ImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
input->SetRegions(region);
input->SetSpacing(m_targetVolume->spacing.data());
input->Allocate();
memcpy(input->GetBufferPointer(), m_targetVolume->data, m_bufferSize);
// create a grayscale dilation filter and a structuring element
typedef BinaryBallStructuringElement<PixelType, 3> StructureType;
typedef GrayscaleDilateImageFilter<ImageType, ImageType, StructureType> DilateFilterType;
DilateFilterType::Pointer filter = DilateFilterType::New();
StructureType structure;
structure.SetRadius(1);
filter->SetKernel(structure);
// set up progress reporting
if (m_progressReporter)
{
CStyleCommand::Pointer command = CStyleCommand::New();
command->SetClientData(m_progressReporter);
command->SetCallback(ProgressCallback);
filter->AddObserver(ProgressEvent(), command);
m_progressReporter->start("Post-Processing Label volume",
"Dilating label field...");
}
// hook up the filters and run
filter->SetInput(input);
filter->Update();
if (m_progressReporter)
m_progressReporter->finish();
// copy back into the target volume data
memcpy(m_targetVolume->data, filter->GetOutput()->GetBufferPointer(), m_bufferSize);
// threshold and gaussian blur to put a smooth version into the alpha channel
typedef BinaryThresholdImageFilter<ImageType, ImageType> ThresholderType;
// typedef DiscreteGaussianImageFilter<ImageType, ImageType> SmoothFilterType;
typedef SmoothingRecursiveGaussianImageFilter<ImageType, ImageType> SmoothFilterType;
ThresholderType::Pointer thresholder = ThresholderType::New();
thresholder->SetLowerThreshold(1);
thresholder->SetUpperThreshold(255);
thresholder->SetInsideValue(255);
thresholder->SetOutsideValue(0);
SmoothFilterType::Pointer smoother = SmoothFilterType::New();
// smoother->SetVariance(0.05); // in physical units
// smoother->SetMaximumKernelWidth(5);
smoother->SetSigma(0.2);
// set up progress reporting (again)
if (m_progressReporter)
{
CStyleCommand::Pointer command = CStyleCommand::New();
command->SetClientData(m_progressReporter);
command->SetCallback(ProgressCallback);
smoother->AddObserver(ProgressEvent(), command);
m_progressReporter->start("Post-Processing Label volume",
"Smoothing alpha mask...");
}
// hook up the filters and run
thresholder->SetInput(input);
smoother->SetInput(thresholder->GetOutput());
smoother->Update();
// copy back into the target volume data
memcpy(m_targetMask->data, smoother->GetOutput()->GetBufferPointer(), m_bufferSize);
if (m_progressReporter)
m_progressReporter->finish();
}
void
DistanceMapFilter::applyDistanceMapFilter(QString flnm,
QList<Vec> clipPos,
QList<Vec> clipNormal,
QList<CropObject> crops,
QList<PathObject> paths,
uchar *lut,
int chan)
{
int bpv = 1;
if (m_voxelType > 0) bpv = 2;
int nbytes = bpv*m_nY*m_nZ;
bool trim = (qRound(m_dataSize.x) < m_height ||
qRound(m_dataSize.y) < m_width ||
qRound(m_dataSize.z) < m_depth);
bool clipPresent = (clipPos.count() > 0);
m_cropPresent = false;
m_tearPresent = false;
m_blendPresent = false;
for(int ci=0; ci<m_crops.count(); ci++)
{
if (crops[ci].cropType() < CropObject::Tear_Tear)
m_cropPresent = true;
else if (crops[ci].cropType() < CropObject::View_Tear)
m_tearPresent = true;
else if (m_crops[ci].cropType() > CropObject::Displace_Displace &&
m_crops[ci].cropType() < CropObject::Glow_Ball)
m_blendPresent = true;
}
m_pathCropPresent = false;
m_pathBlendPresent = false;
for (int i=0; i<m_paths.count(); i++)
{
if (m_paths[i].blend()) m_pathBlendPresent = true;
if (m_paths[i].crop()) m_pathCropPresent = true;
}
m_meshLog->moveCursor(QTextCursor::End);
int d0 = 0;
int d1 = m_nX-1;
int d0z = d0 + qRound(m_dataMin.z);
int d1z = d1 + qRound(m_dataMin.z);
uchar *opacityVol = new uchar[m_nX*m_nY*m_nZ];
uchar *cropped = new uchar[nbytes];
uchar *tmp = new uchar[nbytes];
int i0 = 0;
for(int i=d0z; i<=d1z; i++)
{
m_meshProgress->setValue((int)(100.0*(float)i0/(float)m_nX));
qApp->processEvents();
int iv = qBound(0, i, m_depth-1);
uchar *vslice = m_vfm->getSlice(iv);
memset(cropped, 0, nbytes);
if (!trim)
memcpy(tmp, vslice, nbytes);
else
{
int wmin = qRound(m_dataMin.y);
int hmin = qRound(m_dataMin.x);
if (m_voxelType == 0)
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
tmp[w*m_nZ + h] = vslice[(wmin+w)*m_height + (hmin+h)];
}
else
{
for(int w=0; w<m_nY; w++)
for(int h=0; h<m_nZ; h++)
((ushort*)tmp)[w*m_nZ + h] = ((ushort*)vslice)[(wmin+w)*m_height + (hmin+h)];
}
}
int jk = 0;
for(int j=0; j<m_nY; j++)
for(int k=0; k<m_nZ; k++)
{
Vec po = Vec(m_dataMin.x+k, m_dataMin.y+j, iv);
bool ok = true;
// we don't want to scale before pruning
int mop = 0;
{
Vec pp = po - m_dataMin;
int ppi = pp.x/m_pruneLod;
int ppj = pp.y/m_pruneLod;
int ppk = pp.z/m_pruneLod;
ppi = qBound(0, ppi, m_pruneX-1);
ppj = qBound(0, ppj, m_pruneY-1);
ppk = qBound(0, ppk, m_pruneZ-1);
int mopidx = ppk*m_pruneY*m_pruneX + ppj*m_pruneX + ppi;
mop = m_pruneData[3*mopidx + chan];
ok = (mop > 0);
}
po *= m_samplingLevel;
if (ok && clipPresent)
ok = StaticFunctions::getClip(po, clipPos, clipNormal);
if (ok && m_cropPresent)
ok = checkCrop(po);
if (ok && m_pathCropPresent)
ok = checkPathCrop(po);
if (ok && m_blendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkBlend(po, v, lut);
}
if (ok && m_pathBlendPresent)
{
ushort v;
if (m_voxelType == 0)
v = tmp[j*m_nZ + k];
else
v = ((ushort*)tmp)[j*m_nZ + k];
ok = checkPathBlend(po, v, lut);
}
if (ok)
cropped[jk] = mop;
else
cropped[jk] = 0;
jk ++;
}
if (m_voxelType == 0)
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
tmp[j] = 0;
}
}
else
{
for(int j=0; j<m_nY*m_nZ; j++)
{
if (cropped[j] == 0)
((ushort*)tmp)[j] = 0;
}
}
applyOpacity(iv, cropped, lut, tmp);
memcpy(opacityVol + i0*m_nY*m_nZ, tmp, m_nY*m_nZ);
i0++;
}
delete [] tmp;
delete [] cropped;
m_meshProgress->setValue(100);
qApp->processEvents();
//------------
if (m_tearPresent)
{
uchar *data0 = new uchar[m_nX*m_nY*m_nZ];
memcpy(data0, opacityVol, m_nX*m_nY*m_nZ);
applyTear(d0, d1, 0,
data0, opacityVol, false);
delete [] data0;
}
typedef uchar PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::IndexType start;
start.Fill(0);
ImageType::SizeType size;
size[0] = m_nZ;
size[1] = m_nY;
size[2] = m_nX;
ImageType::RegionType region(start, size);
ImageType::Pointer image = ImageType::New();
image->SetRegions(region);
image->Allocate();
image->FillBuffer(0);
uchar *iptr = (uchar*)image->GetBufferPointer();
memcpy(iptr, opacityVol, m_nX*m_nY*m_nZ);
typedef itk::Image< float, 3 > OutputImageType;
typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, OutputImageType> DistanceMapFilter;
DistanceMapFilter::Pointer filter = DistanceMapFilter::New();
filter->SetInput( image );
filter->SetSquaredDistance(0);
filter->SetUseImageSpacing(0);
filter->SetInsideIsPositive(1);
filter->Update();
QFile fp;
fp.setFileName(flnm);
fp.open(QFile::WriteOnly);
uchar vt = 8;
fp.write((char*)&vt, 1);
fp.write((char*)&m_nX, 4);
fp.write((char*)&m_nY, 4);
fp.write((char*)&m_nZ, 4);
OutputImageType *dimg = filter->GetOutput();
char *tdata = (char*)(dimg->GetBufferPointer());
fp.write(tdata, 4*m_nX*m_nY*m_nZ);
fp.close();
m_meshLog->moveCursor(QTextCursor::End);
m_meshLog->insertPlainText("Signed Distance Map data saved in "+flnm);
QMessageBox::information(0, "", QString("Signed Distance Map saved in "+flnm));
}
int main(int argc, char**argv)
{
int nx, ny, nz, nbytes, direction, nx8, ny8, nz8, k;
// int n, x, y, z, dx, dy;
long long width, height, depth, xysize;
char *dataFile, *tiffFile;
bool use_compression = true, data2tiff, compressdata = true;
FILE *fpdata;
if (argc != 4) {
printf("Usage: maketiff dataFile tiffFile direction\n");
printf(" direction = 0 (tiff to data) = 1 (data to tiff)\n");
return 1;
}
dataFile = argv[1];
tiffFile = argv[2];
sscanf(argv[3],"%d",&direction);
if (direction == 0) {
data2tiff = false;
printf("Output data file: %s\n",dataFile);
} else {
data2tiff = true;
printf("Output image file: %s\n",tiffFile);
}
if (data2tiff) { // create tiff file
fpdata = fopen(dataFile,"rb");
if (fpdata == NULL) {
return 2;
}
fread(&nx,4,1,fpdata);
fread(&ny,4,1,fpdata);
fread(&nz,4,1,fpdata);
// fread(&nbytes,4,1,fpdata);
//if (nbytes != nx*ny*nz) {
// printf("Error: this is a compressed data file\n");
// return 10;
//}
width = nx;
height = ny;
depth = nz;
xysize = width*height;
printf("Desired image dimensions: width, height, depth: %d %d %d\n",width,height,depth);
ImageType::Pointer im = ImageType::New();
ImageType::SizeType imsize;
imsize[0] = width;
imsize[1] = height;
imsize[2] = depth;
ImageType::IndexType imstart;
imstart[0] = 0;
imstart[1] = 0;
imstart[2] = 0;
ImageType::RegionType imregion;
imregion.SetSize(imsize);
imregion.SetIndex(imstart);
im->SetRegions(imregion);
im->Allocate();
p = (unsigned char *)(im->GetBufferPointer());
nbytes = nx*ny*nz;
fread(p,nbytes,1,fpdata);
typedef itk::ImageFileWriter<ImageType> FileWriterType;
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(tiffFile);
writer->SetInput(im);
if (use_compression) {
writer->UseCompressionOn();
}
try
{
writer->Update();
}
catch (itk::ExceptionObject &e)
{
std::cout << e << std::endl;
return 3;
}
if (use_compression) {
printf("Created compressed image file: %s\n",tiffFile);
} else {
printf("Created uncompressed image file: %s\n",tiffFile);
}
} else { // create data file
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(tiffFile);
try
{
reader->Update();
}
catch (itk::ExceptionObject &e)
{
std::cout << e << std::endl;
printf("Read error on input file\n");
return 2; // Read error on input tiff file
}
im = reader->GetOutput();
width = im->GetLargestPossibleRegion().GetSize()[0];
height = im->GetLargestPossibleRegion().GetSize()[1];
depth = im->GetLargestPossibleRegion().GetSize()[2];
printf("Image dimensions: width, height, depth: %d %d %d\n",width,height,depth);
p = (unsigned char *)(im->GetBufferPointer());
fpdata = fopen(dataFile,"wb");
if (fpdata == NULL) {
return 2;
}
nx = width;
ny = height;
nz = depth;
if (compressdata) {
// create compressed buffer pc from p using (0,1)
// First round up nx, ny, nz to a multiple of 8
k = nx%8;
if (k == 0)
nx8 = nx;
else
nx8 = nx + 8-k;
k = ny%8;
if (k == 0)
ny8 = ny;
else
ny8 = ny + 8-k;
k = nx%8;
if (k == 0)
nz8 = nz;
else
nz8 = nz + 8-k;
nbytes = nx8*ny8*nz8/8;
pc = (unsigned char *)malloc(nbytes*sizeof(unsigned char));
int kbit = 0;
int kbyte = 0;
k = 0;
unsigned char pcbyte = 0;
for (int iz=0; iz<nz8; iz++) {
bool zok = (iz<nz);
for (int iy=0; iy<ny8; iy++) {
bool yok = (iy<ny);
for (int ix=0; ix<nx8; ix++) {
bool xok = (ix<nx);
if (xok && yok && zok) {
// set bit kbit of pcbyte to (0,1) based on p[k]
if (p[k] == 1 || p[k] == 255) {
pcbyte |= 1 << kbit;
}
if (kbyte < 4) printf("ix,iy,iz k p[k] pcbyte: %d %d %d %d %d %d\n", ix,iy,iz,k,p[k],pcbyte);
k++;
}
kbit++;
if (kbit == 8) {
pc[kbyte] = pcbyte;
if (kbyte == 0) {
printf("byte:%d %d\n",kbyte,pc[kbyte]);
}
kbyte++;
pcbyte = 0;
kbit = 0;
}
}
}
}
}
fwrite(&nx,4,1,fpdata);
fwrite(&ny,4,1,fpdata);
fwrite(&nz,4,1,fpdata);
fwrite(&nx8,4,1,fpdata);
fwrite(&ny8,4,1,fpdata);
fwrite(&nz8,4,1,fpdata);
fwrite(&nbytes,4,1,fpdata);
printf("nx,ny,nz nx8,ny8,nz8: %d %d %d %d %d %d\n",nx,ny,nz,nx8,ny8,nz8);
width = nx;
height = ny;
depth = nz;
xysize = width*height;
// write(nfdata) nx,ny,nz,(((imagedata(ix,iy,iz),ix=1,nx),iy=1,ny),iz=1,nz)
// try this...
if (compressdata) {
fwrite(pc,1,nbytes,fpdata);
} else {
fwrite(p,1,nx*ny*nz,fpdata);
}
fclose(fpdata);
}
return 0;
}
mitk::Image::Pointer PartialVolumeAnalysisClusteringCalculator::CaculateAngularErrorImage(
mitk::Image::Pointer comp1, mitk::Image::Pointer comp2, mitk::Image::Pointer probImg) const
{
// cast input images to itk
typedef itk::Image<float, 3> ImageType;
typedef mitk::ImageToItk<ImageType> CastType;
CastType::Pointer caster = CastType::New();
caster->SetInput(comp1);
caster->Update();
ImageType::Pointer comp1Image = caster->GetOutput();
caster = CastType::New();
caster->SetInput(comp2);
caster->Update();
ImageType::Pointer comp2Image = caster->GetOutput();
caster = CastType::New();
caster->SetInput(probImg);
caster->Update();
ImageType::Pointer probImage = caster->GetOutput();
// figure out maximum probability for fiber class
float maxProb = 0;
itk::ImageRegionConstIterator<ImageType>
itprob(probImage, probImage->GetLargestPossibleRegion());
itprob.GoToBegin();
while( !itprob.IsAtEnd() )
{
maxProb = itprob.Get() > maxProb ? itprob.Get() : maxProb;
++itprob;
}
// generate a list sample of angles at positions
// where the fiber-prob is higher than .2*maxprob
typedef float MeasurementType;
const unsigned int MeasurementVectorLength = 2;
typedef itk::Vector< MeasurementType , MeasurementVectorLength >
MeasurementVectorType;
typedef itk::Statistics::ListSample< MeasurementVectorType > ListSampleType;
ListSampleType::Pointer listSample = ListSampleType::New();
listSample->SetMeasurementVectorSize( MeasurementVectorLength );
itk::ImageRegionIterator<ImageType>
it1(comp1Image, comp1Image->GetLargestPossibleRegion());
itk::ImageRegionIterator<ImageType>
it2(comp2Image, comp2Image->GetLargestPossibleRegion());
it1.GoToBegin();
it2.GoToBegin();
itprob.GoToBegin();
while( !itprob.IsAtEnd() )
{
if(itprob.Get() > 0.2 * maxProb)
{
MeasurementVectorType mv;
mv[0] = ( MeasurementType ) it1.Get();
mv[1] = ( MeasurementType ) it2.Get();
listSample->PushBack(mv);
}
++it1;
++it2;
++itprob;
}
// generate a histogram from the list sample
typedef float HistogramMeasurementType;
typedef itk::Statistics::Histogram< HistogramMeasurementType, itk::Statistics::DenseFrequencyContainer2 > HistogramType;
typedef itk::Statistics::SampleToHistogramFilter< ListSampleType, HistogramType > GeneratorType;
GeneratorType::Pointer generator = GeneratorType::New();
GeneratorType::HistogramType::SizeType size(2);
size.Fill(30);
generator->SetHistogramSize( size );
generator->SetInput( listSample );
generator->SetMarginalScale( 10.0 );
generator->Update();
// look for frequency mode in the histogram
GeneratorType::HistogramType::ConstPointer histogram = generator->GetOutput();
GeneratorType::HistogramType::ConstIterator iter = histogram->Begin();
float maxFreq = 0;
MeasurementVectorType maxValue;
maxValue.Fill(0);
while ( iter != histogram->End() )
{
if(iter.GetFrequency() > maxFreq)
{
maxFreq = iter.GetFrequency();
maxValue[0] = iter.GetMeasurementVector()[0];
maxValue[1] = iter.GetMeasurementVector()[1];
}
++iter;
}
// generate return image that contains the angular
// error of the voxels to the histogram max measurement
ImageType::Pointer returnImage = ImageType::New();
returnImage->SetSpacing( comp1Image->GetSpacing() ); // Set the image spacing
returnImage->SetOrigin( comp1Image->GetOrigin() ); // Set the image origin
returnImage->SetDirection( comp1Image->GetDirection() ); // Set the image direction
returnImage->SetRegions( comp1Image->GetLargestPossibleRegion() );
returnImage->Allocate();
itk::ImageRegionConstIterator<ImageType>
cit1(comp1Image, comp1Image->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ImageType>
cit2(comp2Image, comp2Image->GetLargestPossibleRegion());
itk::ImageRegionIterator<ImageType>
itout(returnImage, returnImage->GetLargestPossibleRegion());
cit1.GoToBegin();
cit2.GoToBegin();
itout.GoToBegin();
vnl_vector<float> v(3);
v[0] = cos( maxValue[0] ) * sin( maxValue[1] );
v[1] = sin( maxValue[0] ) * sin( maxValue[1] );
v[2] = cos( maxValue[1] );
// MITK_INFO << "max vector: " << v;
while( !cit1.IsAtEnd() )
{
vnl_vector<float> v1(3);
v1[0] = cos( cit1.Get() ) * sin( cit2.Get() );
v1[1] = sin( cit1.Get() ) * sin( cit2.Get() );
v1[2] = cos( cit2.Get() );
itout.Set(fabs(angle(v,v1)));
// MITK_INFO << "ang_error " << v1 << ": " << fabs(angle(v,v1));
++cit1;
++cit2;
++itout;
}
mitk::Image::Pointer retval = mitk::Image::New();
retval->InitializeByItk(returnImage.GetPointer());
retval->SetVolume(returnImage->GetBufferPointer());
return retval;
}