Program: gdcm
Module: $RCSfile: WriteDicomAsJPEG.cxx,v $
Language: C++
- Date: $Date: 2007/05/23 14:18:04 $
- Version: $Revision: 1.14 $
+ Date: $Date: 2007/08/21 15:10:04 $
+ Version: $Revision: 1.15 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmFile.h"
#include "gdcmFileHelper.h"
#include "gdcmUtil.h"
-
-#include <iostream>
-#include <sstream>
-
-#include <stdio.h>
-extern "C" {
-#include "gdcmjpeg/8/jconfig.h"
-#include "gdcmjpeg/8/jpeglib.h"
-#include "gdcmjpeg/8/jinclude.h"
-#include "gdcmjpeg/8/jerror.h"
-}
-
-#if defined(__BORLANDC__)
- #include <mem.h> // for memcpy
-#endif
-
-#include "gdcmJPEGFragment.h"
-#include <setjmp.h>
-#include <fstream>
-
-#include "jdatasrc.cxx"
-#include "jdatadst.cxx"
-
-typedef std::pair<size_t, uint32_t> JpegPair; //offset, jpeg size
-typedef std::vector<JpegPair> JpegVector;
-
-void WriteDICOMItems(std::ostream *fp, JpegVector &v)
-{
- // Item tag:
- uint16_t group = 0xfffe;
- uint16_t elem = 0xe000;
- GDCM_NAME_SPACE::binary_write(*fp, group);
- GDCM_NAME_SPACE::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_NAME_SPACE::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_NAME_SPACE::binary_write(*fp, group);
- GDCM_NAME_SPACE::binary_write(*fp, elem);
- // Item Length
- uint32_t item_length = 0x0000;
- GDCM_NAME_SPACE::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_NAME_SPACE::binary_write(*fp, group);
- GDCM_NAME_SPACE::binary_write(*fp, elem);
- // Item Length
- uint32_t item_length = numFrag*4; // sizeof(uint32_t)
- GDCM_NAME_SPACE::binary_write(*fp, item_length);
-
- // Just prepare the space
- start = fp->tellp(); //to be able to rewind
- for(int i=0; i<numFrag;++i)
- {
- uint32_t dummy = 0x0000;
- GDCM_NAME_SPACE::binary_write(*fp, dummy);
- }
-}
-
-void UpdateBasicOffsetTable(std::ostream *fp, JpegVector const &v, size_t pos)
-{
- JpegVector::const_iterator i;
- fp->seekp( 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); }
- uint32_t offset = jp.first - first.first;
- GDCM_NAME_SPACE::binary_write(*fp, offset);
- //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 );
- uint32_t length = jp.second;
- GDCM_NAME_SPACE::binary_write(*fp, length );
- //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_NAME_SPACE::binary_write(*fp, group);
- GDCM_NAME_SPACE::binary_write(*fp, elem);
-
- uint32_t length = 0x0;
- GDCM_NAME_SPACE::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)
- {
- assert( sample_pixel == 1 );
- 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; i<numZ; ++i)
-// {
- r = WriteScanlines(cinfo, pbuffer, row_stride);
- assert( r );
-// pbuffer+=fragment_size; //shift to next image
-
- //Upodate frag size
-// size_t end = fp->tellp();
-// 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;
-
- if( ((end-beg) % 2) )
- {
- fp->put( '\0' );
- jp.second += 1;
- }
- assert( !(jp.second % 2) );
- std::cerr << "DIFF: " << i <<" -> " << jp.second << 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
// 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\n";
return 1;
+ }
std::string filename = argv[1];
std::string outfilename = "/tmp/bla.dcm";
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
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; i<zsize;i++)
- {
- WriteDICOMItems(of, JpegFragmentSize);
- CreateOneFrame(of, pImageData, fragment_size, xsize, ysize, zsize,
- samplesPerPixel, quality, JpegFragmentSize);
- assert( !(fragment_size % 2) );
- pImageData += fragment_size;
- }
- CloseJpeg(of, JpegFragmentSize);
-#if WITHOFFSETTABLE
- UpdateBasicOffsetTable(of, JpegFragmentSize, bots);
-#endif
-
- if( !f->IsReadable() )
- {
- std::cerr << "-------------------------------\n"
- << "Error while creating the file\n"
- << "This file is considered to be not readable\n";
-
- return 1;
- }
- 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_NAME_SPACE::File *fileToBuild = GDCM_NAME_SPACE::File::New();
str.str("");
str << ysize;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
+
if(zsize>1)
{
str << zsize;
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,"US"); // 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,"US"); // Bits Stored
+ str << bitsstored;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
str.str("");
- str << 7; //( img.componentSize - 1 );
+ str << highbit;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0102,"US"); // High Bit
// Set the pixel representation
str.str("");
- str << 0; //img.sign;
+ str << sign;
fileToBuild->InsertEntryString(str.str(),0x0028,0x0103,"US"); // Pixel Representation
// Set the samples per pixel
fileToBuild->InsertEntryString(str.str(),0x0028,0x0002,"US"); // Samples per Pixel
// 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_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New(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();
fileH->SetWriteTypeToJPEG( );
+ fileH->SetImageData(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;
f->Delete();
tested->Delete();
fileToBuild->Delete();
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