예제 #1
0
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;
}
예제 #2
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;
}
예제 #3
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;
}
예제 #4
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;
}
예제 #5
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;
}