X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Example%2FWriteDicomAsJPEG.cxx;h=b8d52fbc2371ec7142346c44624329428eb244cd;hb=e7a642c06e4cdcfdbaf024090754283ccc564408;hp=e848a915ea8d652c044761ae0dcead9db0b830f9;hpb=6087138eeaa97704ed3d20831922183ee160b796;p=gdcm.git diff --git a/Example/WriteDicomAsJPEG.cxx b/Example/WriteDicomAsJPEG.cxx index e848a915..b8d52fbc 100644 --- a/Example/WriteDicomAsJPEG.cxx +++ b/Example/WriteDicomAsJPEG.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: WriteDicomAsJPEG.cxx,v $ Language: C++ - Date: $Date: 2005/10/19 22:19:20 $ - Version: $Revision: 1.8 $ + Date: $Date: 2007/08/29 08:13:40 $ + Version: $Revision: 1.20 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -19,330 +19,17 @@ #include "gdcmFile.h" #include "gdcmFileHelper.h" #include "gdcmUtil.h" - -#include -#include - -#include -extern "C" { -#include "gdcmjpeg/8/jconfig.h" -#include "gdcmjpeg/8/jpeglib.h" -#include "gdcmjpeg/8/jinclude.h" -#include "gdcmjpeg/8/jerror.h" -} - -#include "gdcmJPEGFragment.h" -#include -#include - -#include "jdatasrc.cxx" -#include "jdatadst.cxx" - -typedef std::pair JpegPair; //offset, jpeg size -typedef std::vector JpegVector; - -void WriteDICOMItems(std::ostream *fp, JpegVector &v) -{ - // Item tag: - uint16_t group = 0xfffe; - uint16_t elem = 0xe000; - gdcm::binary_write(*fp, group); - gdcm::binary_write(*fp, elem); - // Item Length - uint32_t dummy = 0x12345678; - size_t offset = fp->tellp(); - JpegPair jp; - jp.first = offset; - v.push_back(jp); - gdcm::binary_write(*fp, dummy); -} - -// PS 3.5, page 66 -void EncodeWithoutBasicOffsetTable(std::ostream *fp, int numFrag)// JpegVector& v) //, uint32_t length) -{ - assert( numFrag == 1); - - // Item tag: - uint16_t group = 0xfffe; - uint16_t elem = 0xe000; - gdcm::binary_write(*fp, group); - gdcm::binary_write(*fp, elem); - // Item Length - uint32_t item_length = 0x0000; - gdcm::binary_write(*fp, item_length); - -} - -// PS 3.5, page 67 -void EncodeWithBasicOffsetTable(std::ostream *fp, int numFrag, size_t &start) -{ - // Item tag: - uint16_t group = 0xfffe; - uint16_t elem = 0xe000; - gdcm::binary_write(*fp, group); - gdcm::binary_write(*fp, elem); - // Item Length - uint32_t item_length = numFrag*4; // sizeof(uint32_t) - gdcm::binary_write(*fp, item_length); - - // Just prepare the space - start = fp->tellp(); //to be able to rewind - for(int i=0; iseekp( pos ); - const JpegPair &first = v[0]; - for(i=v.begin(); i!=v.end(); ++i) - { - const JpegPair &jp = *i; - if(i == v.begin() ){ assert( jp.first - first.first == 0); } - gdcm::binary_write(*fp, jp.first - first.first); - std::cerr << "Updating Table:" << jp.first - first.first << std::endl; - } -} - -void UpdateJpegFragmentSize(std::ostream *fp, JpegVector const &v) -{ - JpegVector::const_iterator i; - for(i= v.begin(); i!=v.end(); ++i) - { - const JpegPair &jp = *i; - fp->seekp( jp.first ); - gdcm::binary_write(*fp, jp.second ); - std::cerr << "Updating:" << jp.first << "," << jp.second << std::endl; - } -} - -void CloseJpeg(std::ostream *fp, JpegVector &v) -{ - // sequence terminator - uint16_t group = 0xfffe; - uint16_t elem = 0xe000; - gdcm::binary_write(*fp, group); - gdcm::binary_write(*fp, elem); - - uint32_t length = 0x0; - gdcm::binary_write(*fp, length); - - // Jpeg is done, now update the frag length - UpdateJpegFragmentSize(fp, v); -} - -bool InitializeJpeg(std::ostream *fp, int fragment_size, int image_width, int image_height, - int sample_pixel, int quality, struct jpeg_compress_struct &cinfo, int &row_stride) -{ - - /* This struct contains the JPEG compression parameters and pointers to - * working space (which is allocated as needed by the JPEG library). - * It is possible to have several such structures, representing multiple - * compression/decompression processes, in existence at once. We refer - * to any one struct (and its associated working data) as a "JPEG object". - */ - //struct jpeg_compress_struct cinfo; - /* This struct represents a JPEG error handler. It is declared separately - * because applications often want to supply a specialized error handler - * (see the second half of this file for an example). But here we just - * take the easy way out and use the standard error handler, which will - * print a message on stderr and call exit() if compression fails. - * Note that this struct must live as long as the main JPEG parameter - * struct, to avoid dangling-pointer problems. - */ - struct jpeg_error_mgr jerr; - /* More stuff */ - - /* Step 1: allocate and initialize JPEG compression object */ - - /* We have to set up the error handler first, in case the initialization - * step fails. (Unlikely, but it could happen if you are out of memory.) - * This routine fills in the contents of struct jerr, and returns jerr's - * address which we place into the link field in cinfo. - */ - cinfo.err = jpeg_std_error(&jerr); - /* Now we can initialize the JPEG compression object. */ - jpeg_create_compress(&cinfo); - - /* Step 2: specify data destination (eg, a file) */ - /* Note: steps 2 and 3 can be done in either order. */ - - jpeg_stdio_dest(&cinfo, fp, fragment_size, 1); - - /* Step 3: set parameters for compression */ - - /* First we supply a description of the input image. - * Four fields of the cinfo struct must be filled in: - */ - cinfo.image_width = image_width;/* image width and height, in pixels */ - cinfo.image_height = image_height; - if ( sample_pixel == 3 ) - { - cinfo.input_components = 3; /* # of color components per pixel */ - cinfo.in_color_space = JCS_RGB; /* colorspace of input image */ - } - else - { - cinfo.input_components = 1; /* # of color components per pixel */ - cinfo.in_color_space = JCS_GRAYSCALE; /* colorspace of input image */ - } - /* Now use the library's routine to set default compression parameters. - * (You must set at least cinfo.in_color_space before calling this, - * since the defaults depend on the source color space.) - */ - jpeg_set_defaults(&cinfo); - /* - * http://www.koders.com/c/fid80DBBF1D49D004EF71CE7C493C34610C4F17D3D3.aspx - * http://studio.imagemagick.org/pipermail/magick-users/2002-September/004685.html - * You need to set -quality 101 or greater. If quality is 100 or less you - * get regular JPEG output. This is not explained in the documentation, only - * in the comments in coder/jpeg.c. When you have configured libjpeg with - * lossless support, then - * - * quality=predictor*100 + point_transform - * - * If you don't know what these values should be, just use 101. - * They only affect the compression ratio, not the image appearance, - * which is lossless. - */ - jpeg_simple_lossless (&cinfo, 1, 1); - /* Now you can set any non-default parameters you wish to. - * Here we just illustrate the use of quality (quantization table) scaling: - */ - jpeg_set_quality(&cinfo, quality, TRUE /* limit to baseline-JPEG values */); - - /* Step 4: Start compressor */ - - /* TRUE ensures that we will write a complete interchange-JPEG file. - * Pass TRUE unless you are very sure of what you're doing. - */ - jpeg_start_compress(&cinfo, TRUE); - - /* Step 5: while (scan lines remain to be written) */ - /* jpeg_write_scanlines(...); */ - - /* Here we use the library's state variable cinfo.next_scanline as the - * loop counter, so that we don't have to keep track ourselves. - * To keep things simple, we pass one scanline per call; you can pass - * more if you wish, though. - */ - if (sample_pixel == 3) - { - row_stride = image_width * 3;/* JSAMPLEs per row in image_buffer */ - } - else - { - row_stride = image_width * 1;/* JSAMPLEs per row in image_buffer */ - } - - /* everything was ok */ - return true; -} - -bool FinalizeJpeg(struct jpeg_compress_struct &cinfo) -{ - /* Step 6: Finish compression */ - - jpeg_finish_compress(&cinfo); - - /* Step 7: release JPEG compression object */ - - /* This is an important step since it will release a good deal of memory. */ - jpeg_destroy_compress(&cinfo); - - /* And we're done! */ - return true; -} - -// If false then suspension return -bool WriteScanlines(struct jpeg_compress_struct &cinfo, void *input_buffer, int row_stride) -{ - JSAMPLE *image_buffer = (JSAMPLE*) input_buffer; - JSAMPROW row_pointer[1]; /* pointer to JSAMPLE row[s] */ - row_pointer[0] = image_buffer; - - while (cinfo.next_scanline < cinfo.image_height) { - /* jpeg_write_scanlines expects an array of pointers to scanlines. - * Here the array is only one element long, but you could pass - * more than one scanline at a time if that's more convenient. - */ - //row_pointer[0] = & image_buffer[cinfo.next_scanline * row_stride]; - - if( jpeg_write_scanlines(&cinfo, row_pointer, 1) != 1) - { - //entering suspension mode, basically we wrote the whole jpeg fragment - // technically we could enforce that by checkig the value of row_pointer to - // actually be at the end of the image...TODO - return false; - } - row_pointer[0] += row_stride; - } - - // Well looks like we are done writting the scanlines - return true; -} - -// input_buffer is ONE image -// fragment_size is the size of this image (fragment) -bool CreateOneFrame (std::ostream *fp, void *input_buffer, int fragment_size, - int image_width, int image_height, int numZ, int sample_pixel, int quality, JpegVector &v) -{ - struct jpeg_compress_struct cinfo; - int row_stride; /* physical row width in image buffer */ - size_t beg = fp->tellp(); - bool r = InitializeJpeg(fp, fragment_size, image_width, image_height, - sample_pixel, quality, cinfo, row_stride); - assert( r ); - (void)numZ; - - uint8_t *pbuffer = (uint8_t*)input_buffer; - //int i; - //for(i=0; itellp(); -// std::cerr << "DIFF: " << end-beg << std::endl; - -// JpegPair &jp = v[i]; -// jp.second = end-beg; - //beg = end; // - // } - - r = FinalizeJpeg(cinfo); - assert( r ); - size_t end = fp->tellp(); - static int i = 0; - JpegPair &jp = v[i]; - jp.second = end-beg; - std::cerr << "DIFF: " << i <<" -> " << end-beg << std::endl; - ++i; - - //JpegPair &jp = v[0]; - //jp.second = 15328; - - return true; -} - -//bool CreateMultipleFrames (std::ostream *fp, void *input_buffer, int fragment_size, -// int image_width, int image_height, int sample_pixel, int quality, JpegVector &v) -//{ -//} - -#define WITHOFFSETTABLE 1 +#include "gdcmDebug.h" // Open a dicom file and compress it as JPEG stream int main(int argc, char *argv[]) { if( argc < 2) + { + std::cerr << argv[0] << " inputfilename.dcm [ outputfilename.dcm" + << " quality debug]\n"; return 1; + } std::string filename = argv[1]; std::string outfilename = "/tmp/bla.dcm"; @@ -350,162 +37,134 @@ int main(int argc, char *argv[]) outfilename = argv[2]; int quality = 100; if( argc >= 4 ) - quality = atoi(argv[2]); + quality = atoi(argv[3]); std::cerr << "Using quality: " << quality << std::endl; - -// Step 1 : Create the header of the image - gdcm::File *f = new gdcm::File(); - f->SetLoadMode ( gdcm::LD_ALL ); // Load everything + + if (argc > 4) + GDCM_NAME_SPACE::Debug::DebugOn(); + +// Step 1 : Read the image + GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New(); + f->SetLoadMode ( GDCM_NAME_SPACE::LD_ALL ); // Load everything f->SetFileName( filename ); f->Load(); - gdcm::FileHelper *tested = new gdcm::FileHelper( f ); + GDCM_NAME_SPACE::FileHelper *tested = GDCM_NAME_SPACE::FileHelper::New( f ); std::string PixelType = tested->GetFile()->GetPixelType(); int xsize = f->GetXSize(); int ysize = f->GetYSize(); int zsize = f->GetZSize(); + //tested->Print( std::cout ); int samplesPerPixel = f->GetSamplesPerPixel(); - size_t testedDataSize = tested->GetImageDataSize(); - std::cerr << "testedDataSize:" << testedDataSize << std::endl; - uint8_t *testedImageData = tested->GetImageData(); - - //std::ofstream *of = new std::ofstream("/tmp/jpeg.jpg"); - std::ostringstream *of = new std::ostringstream(); - std::cout << "X: " << xsize << std::endl; - std::cout << "Y: " << ysize << std::endl; - std::cout << "Sample: " << samplesPerPixel << std::endl; - int fragment_size = xsize*ysize*samplesPerPixel; - - JpegVector JpegFragmentSize; -#if WITHOFFSETTABLE - size_t bots; //basic offset table start - EncodeWithBasicOffsetTable(of, zsize, bots); -#else - EncodeWithoutBasicOffsetTable(of, 1); -#endif - uint8_t *pImageData = testedImageData; - for(int i=0; iIsReadable() ) - { - std::cerr << "-------------------------------\n" - << "Error while creating the file\n" - << "This file is considered to be not readable\n"; - - return 1; + size_t testedDataSize = tested->GetImageDataRawSize(); // Raw : Don't convert gray pixels+LUT to RBG pixels + uint8_t *testedImageData = tested->GetImageDataRaw(); + + if( GDCM_NAME_SPACE::Debug::GetDebugFlag() ) { + tested->Print( std::cout ); + std::cout << "-------------------------------------------------------------------------------" << std::endl; } - std::streambuf* sb = of->rdbuf(); - (void)sb; - - // Let save the file as jpeg standalone - { - std::ofstream *jof = new std::ofstream( "/tmp/test.jpg" ); - CreateOneFrame(jof, testedImageData, fragment_size, xsize, ysize, zsize, - samplesPerPixel, 70, JpegFragmentSize); - jof->close(); - delete jof; - } - - - - - -// Step 1 : Create the header of the image - - gdcm::File *fileToBuild = new gdcm::File(); +// Step 1 : Create the header of the new file + GDCM_NAME_SPACE::File *fileToBuild = GDCM_NAME_SPACE::File::New(); std::ostringstream str; // Set the image size str.str(""); str << xsize; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0011); // Columns + fileToBuild->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns str.str(""); str << ysize; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0010); // Rows + fileToBuild->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows if(zsize>1) { str.str(""); str << zsize; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0008); // Number of Frames + fileToBuild->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames } + int bitsallocated = f->GetBitsAllocated(); + int bitsstored = f->GetBitsStored(); + int highbit = f->GetHighBitPosition(); + //std::string pixtype = f->GetPixelType(); + int sign = f->IsSignedPixelData(); + // Set the pixel type str.str(""); - str << 8; //img.componentSize; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0100); // Bits Allocated - + str << bitsallocated; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0100,"US");// Bits Allocated str.str(""); - str << 8; //img.componentUse; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0101); // Bits Stored + str << bitsstored; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored str.str(""); - str << 7; //( img.componentSize - 1 ); - fileToBuild->InsertEntryString(str.str(),0x0028,0x0102); // High Bit + str << highbit; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit // Set the pixel representation str.str(""); - str << 0; //img.sign; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0103); // Pixel Representation + str << sign; + fileToBuild->InsertEntryString(str.str(),0x0028,0x0103,"US"); // Pixel Representation // Set the samples per pixel str.str(""); str << samplesPerPixel; //img.components; - fileToBuild->InsertEntryString(str.str(),0x0028,0x0002); // Samples per Pixel - + fileToBuild->InsertEntryString(str.str(),0x0028,0x0002,"US"); // Samples per Pixel + +// The image may be displayed uncorectly if these fields are missing + + // Set the Pixel Aspect Ratio, if any + std::string par = f->GetEntryString(0x0028,0x0034); + std::cerr <<"Pixel Aspect Ratio [" << par << "]" << std::endl; + if ( par != GDCM_NAME_SPACE::GDCM_UNFOUND ) + fileToBuild->InsertEntryString(par,0x0028,0x0034,"IS"); // Pixel Aspect Ratio + + // Set the Modality, if any + std::string modality = f->GetEntryString(0x0008,0x0060); + std::cerr <<"Modality [" << modality << "]" << std::endl; + if ( modality != GDCM_NAME_SPACE::GDCM_UNFOUND ) + fileToBuild->InsertEntryString(modality,0x0008,0x0060,"CS"); // Modality + + // Set the Media Storage SOP Class UID, if any + std::string mssop = f->GetEntryString(0x0002,0x0002); + std::cerr <<"Media Storage SOP Class UID [" << mssop << "]" << std::endl; + if ( mssop != GDCM_NAME_SPACE::GDCM_UNFOUND ) + fileToBuild->InsertEntryString(mssop,0x0002,0x0002,"UI"); // Media Storage SOP Class UID + + // This one is mandatory to deal with Pixel Aspect Ratio, in ultrasound images ! + // Set the SOP Class UID, if any + std::string sop = f->GetEntryString(0x0008,0x0016); + std::cerr <<"SOP Class UID [" << sop << "]" << std::endl; + if ( sop != GDCM_NAME_SPACE::GDCM_UNFOUND ) + fileToBuild->InsertEntryString(sop,0x0008,0x0016,"UI"); // SOP Class UID + // Step 2 : Create the output image -// std::cout << "2..."; -// if( img.componentSize%8 > 0 ) -// { -// img.componentSize += 8-img.componentSize%8; -// } size_t size = xsize * ysize * zsize - * samplesPerPixel /* * img.componentSize / 8*/; + * samplesPerPixel * bitsallocated / 8; - uint8_t *imageData = new uint8_t[size]; - gdcm::FileHelper *fileH = new gdcm::FileHelper(fileToBuild); - //fileH->SetImageData(imageData,size); - assert( size == testedDataSize ); - size = of->str().size(); - //size = sb->in_avail(); - std::cerr << "Size JPEG:" << size << std::endl; - //fileH->SetImageData((uint8_t*)of->str().c_str(), size); - memcpy(imageData, of->str().c_str(), size); - fileH->SetImageData(imageData, size); - //str::string *s = of->str(); - //fileH->SetWriteTypeToDcmExplVR(); + GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New(fileToBuild); + + // Consider that pixels are unmodified + fileH->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE); + std::cerr << "xsize " << xsize << " ysize " << ysize << " zsize " << zsize << " samplesPerPixel " << samplesPerPixel + << " bitsallocated " << bitsallocated << std::endl; + std::cerr << "size " << size << " testedDataSize " << testedDataSize << + std::endl; + assert(abs (size-testedDataSize) <= 1 ); fileH->SetWriteTypeToJPEG( ); + //fileH->SetImageData(testedImageData, testedDataSize); + + // SetUserData will ensure the compression + fileH->SetUserData(testedImageData, testedDataSize); if( !fileH->Write(outfilename) ) { - std::cerr << "Badddd" << std::endl; + std::cerr << "write fails" << std::endl; } - //of->close(); - std::ofstream out("/tmp/jpeg2.jpg"); - //out.write( of->str(), of - //out << of->str(); //rdbuf is faster than going through str() - //out.write( (char*)imageData, size); - out.write( of->str().c_str(), size); - //std::cerr << "JPEG marker is: " << imageData[6] << imageData[7] << - // imageData[8] << imageData[9] << std::endl; - //out.rdbuf( *sb ); - out.close(); - - delete of; - delete f; - delete tested; - delete fileToBuild; - delete fileH; + + f->Delete(); + tested->Delete(); + fileToBuild->Delete(); + fileH->Delete(); return 0; }