int main()
{
std::string votesfilename = "../../half_vessel_votes2.txt";
std::string outputfilename = "half_vessel_votes2.tif";
FILE * fp = fopen(votesfilename.c_str(), "r");
int x,y,z,v;
int maxx = -1,maxy = -1, maxz = -1;
while(fscanf(fp,"%d %d %d %d",&x,&y,&z,&v)>0)
{
maxx = MAX(maxx, x);
maxy = MAX(maxy, y);
maxz = MAX(maxz, z);
}
printf("maxx = %d maxy = %d maxz = %d\n",maxx,maxy,maxz);
fclose(fp);
fp = fopen(votesfilename.c_str(), "r");
ImageType::Pointer im = ImageType::New();
ImageType::SizeType size;
ImageType::IndexType index;
ImageType::RegionType region;
size[0] = maxx+1;
size[1] = maxy+1;
size[2] = maxz+1;
index[0] = index[1] = index[2] = 0;
region.SetIndex(index);
region.SetSize(size);
im->SetRegions(region);
im->Allocate();
while(fscanf(fp,"%d %d %d %d",&x,&y,&z,&v)>0)
{
index[0] = x;
index[1] = y;
index[2] = z;
im->SetPixel(index,v);
}
// scanf("%*d");
fclose(fp);
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(outputfilename.c_str());
writer->SetInput(im);
writer->Update();
return 0;
}
int MainWindow::createTiff(const char *tifffile, unsigned char *buffer, int width, int height, int depth)
{
bool use_compression = true;
unsigned char *p_u8_new;
typedef itk::Image<unsigned char,3> ImageType_u8;
// ImageType_u8::Pointer im_u8;
typedef itk::ImageFileReader<ImageType_u8> FileReaderType_u8;
ImageType_u8::Pointer im_u8_new = ImageType_u8::New();
ImageType_u8::SizeType imsize;
ImageType_u8::IndexType imstart;
ImageType_u8::RegionType imregion;
imsize[0] = width;
imsize[1] = height;
imsize[2] = depth;
imstart[0] = 0;
imstart[1] = 0;
imstart[2] = 0;
imregion.SetSize(imsize);
imregion.SetIndex(imstart);
im_u8_new->SetRegions(imregion);
im_u8_new->Allocate();
p_u8_new = (unsigned char *)(im_u8_new->GetBufferPointer());
// copy buffer to p_u8
memcpy(p_u8_new,buffer,(size_t)(width*height*depth));
// for (x=0; x<width; x++) {
// for (y=0; y<height; y++) {
// for (z=0; z<depth; z++) {
// if (issigned)
// V_u8(x,y,z) = V_s16(x,y,z)/256;
// else
// V_u8(x,y,z) = V_u16(x,y,z)/256;
// }
// }
// }
// printf("Writing 8-bit file: %s dimensions: width, height, depth: %d %d %d\n",argv[2],width,height,depth);
typedef itk::ImageFileWriter<ImageType_u8> FileWriterType;
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(tifffile);
writer->SetInput(im_u8_new);
if (use_compression) {
writer->UseCompressionOn();
}
try
{
writer->Update();
}
catch (itk::ExceptionObject &e)
{
std::cout << e << std::endl;
return 1;
}
printf("Wrote tiff file\n");
return 0;
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
int ImWriter(ImageType::Pointer im, char *filename)
{
typedef itk::ImageFileWriter<ImageType> FileWriterType;
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(filename);
writer->SetInput(im);
writer->UseCompressionOn();
try
{
writer->Update();
}
catch (itk::ExceptionObject &e)
{
std::cout << e << std::endl;
return 1;
}
return 0;
}
int main(int argc, char **argv)
{
std::cout << "nrrd2vtk. Version 1.3. Works bboth ways."<< std::endl;
if(argc<4)
{
std::cout << "nrrd2vtk input.nrrd output.vtk uint|short|uchar"<< std::endl;
return 0;
}
const char* inp = argv[1];
const char* outp = argv[2];
const char* type = argv[3];
if(strcmp(type, "uint")==0)
{
typedef itk::Image< unsigned int, 3 > ImageType;
typedef ImageType::Pointer ImageTypePointer;
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(inp);
reader->Update();
typedef itk::ImageFileWriter<ImageType> FileWriterType;
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(outp);
writer->SetInput( reader->GetOutput() );
writer->Update();
}
else if(strcmp(type, "short")==0)
{
typedef itk::Image< short, 3 > ImageType;
typedef ImageType::Pointer ImageTypePointer;
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(inp);
reader->Update();
typedef itk::ImageFileWriter<ImageType> FileWriterType;
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(outp);
writer->SetInput( reader->GetOutput() );
writer->Update();
}
else if(strcmp(type, "uchar")==0)
{
typedef itk::Image< unsigned char, 3 > ImageType;
typedef ImageType::Pointer ImageTypePointer;
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetFileName(inp);
reader->Update();
typedef itk::ImageFileWriter<ImageType> FileWriterType;
FileWriterType::Pointer writer = FileWriterType::New();
writer->SetFileName(outp);
writer->SetInput( reader->GetOutput() );
writer->Update();
}
/* ConnectorType::Pointer connector = ConnectorType::New();
connector->SetInput(reader->GetOutput());
connector->Update();
CommonTools::SaveImage( connector->GetOutput(), outp );
*/
return 0;
}
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;
}
