+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: ExtractOverlays.cxx,v $
- Language: C++
- Date: $Date: 2007/05/23 14:18:04 $
- Version: $Revision: 1.3 $
-
- Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
- l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the above copyright notices for more information.
-
-=========================================================================*/
-
-
-#include "gdcmFile.h"
-#include "gdcmFileHelper.h"
-#include "gdcmCommon.h"
-#include "gdcmDebug.h"
-#include "gdcmDataEntry.h"
-#include "gdcmDirList.h"
-
-#include "gdcmArgMgr.h"
-#include <iostream>
-
-// Each BIT of Overlay Data (0x6000,0x3000) corresponds
-// to a BYTE of overlay image.
-void explodeByte(unsigned char byte, unsigned char* result)
-{
- unsigned char mask = 1;
- for (int i=0;i<8;i++)
- {
- if ((byte & mask)==0)
- result[i]=0;
- else
- result[i]=1;
- mask<<=1;
- }
- return;
-}
-
-
-int main(int argc, char *argv[])
-{
- START_USAGE(usage)
- " \n ExtractOverlays :\n ",
- " Extract overlay images from all DICOM image within a directory ",
- " Warning : probably segfaults if no overlay ",
- " usage: ExtractOverlays dirin=inputDirectoryName [debug] ",
- " debug : developper wants to run the program in 'debug mode' ",
- FINISH_USAGE
-
- // ----- Initialize Arguments Manager ------
-
- GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
-
- if (argc == 1 || am->ArgMgrDefined("usage"))
- {
- am->ArgMgrUsage(usage); // Display 'usage'
- delete am;
- return 0;
- }
-
- const char *dirIn = am->ArgMgrWantString("dirin", usage);
-
- if (am->ArgMgrDefined("debug"))
- GDCM_NAME_SPACE::Debug::DebugOn();
-
- if (am->ArgMgrDefined("warning"))
- GDCM_NAME_SPACE::Debug::WarningOn();
-
- // if unused Param we give up
- if ( am->ArgMgrPrintUnusedLabels() )
- {
- am->ArgMgrUsage(usage);
- delete am;
- return 0;
- }
-
- delete am; // we don't need Argument Manager any longer
-
-
- // ========================== Now, we can do the job! ================
-
-
- // ======================== more checking on the params ==============
-
- if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirIn) )
- {
- std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl;
- return 0;
-
- }
-
- char outputFileName[1024]; // Hope it's enough for a file name!
-
- GDCM_NAME_SPACE::File *f;
-
- GDCM_NAME_SPACE::DirList dirList(dirIn,true); // gets (recursively) the file list
- GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames();
- for( GDCM_NAME_SPACE::DirListType::iterator it = fileList.begin();
- it != fileList.end();
- ++it )
- {
- // Just to see *all* the file names:
- // std::cout << "file [" << it->c_str() << "]" << std::endl;
-
- // Read the input file.
-
- f = GDCM_NAME_SPACE::File::New( );
- f->SetLoadMode( GDCM_NAME_SPACE::LD_ALL );
- f->SetFileName( it->c_str() );
-
- f->AddForceLoadElement(0x6000,0x3000); // Overlay Data
- f->AddForceLoadElement(0x6002,0x3000);
- f->AddForceLoadElement(0x6004,0x3000);
- f->AddForceLoadElement(0x6006,0x3000);
- f->AddForceLoadElement(0x6008,0x3000);
- f->AddForceLoadElement(0x600a,0x3000);
- f->AddForceLoadElement(0x600c,0x3000);
- f->AddForceLoadElement(0x600e,0x3000);
-
- int res = f->Load();
-
- if ( !res )
- {
- std::cerr << "Sorry, " << it->c_str() <<" not a gdcm-readable "
- << "DICOM / ACR File" <<std::endl;
- f->Delete();
- continue;
- }
- std::cout << " ... is readable " << std::endl;
-
- // ============================================================
- // Load the Overlays in memory (the first one)
- // ============================================================
-
-/// \todo : deal with *each* overlay Data Element (not only the first one!)
-
- uint16_t ovlyGroup = 0x6000;
-
- GDCM_NAME_SPACE::DataEntry *e = f->GetDataEntry(ovlyGroup, 0x3000);
- if (e == 0)
- {
- std::cout << " Image doesn't contain any Overlay " << std::endl;
- f->Delete();
- continue;
- }
- std::cout << " File is read! " << std::endl;
-
- uint8_t *overlay = (uint8_t *)(e->GetBinArea());
- if ( overlay == 0 )
- {
- std::cerr << "Sorry, Overlays of" << it->c_str() <<" are not "
- << " gdcm-readable." << std::endl;
- f->Delete();
- continue;
- }
-
- // ============================================================
- // Image data generation.
- // ============================================================
-
- unsigned int dimX= f->GetXSize();
- unsigned int dimY= f->GetYSize();
-
- unsigned int dimXY=dimX*dimY;
- std::cout << "DimX : "<< dimX <<" DimY : " << dimY
- << " DimXY : " <<dimXY << std::endl;
- unsigned char *outputData = new unsigned char[dimXY];
-
- unsigned char *result=outputData;
- for (unsigned int i=0;i<(dimXY/8);i++)
- {
- explodeByte(overlay[i], result);
- result+=8;
- }
-
- // ============================================================
- // Write a new file
- // ============================================================
- GDCM_NAME_SPACE::File *f2;
- f2 = GDCM_NAME_SPACE::File::New( );
-
- char temp[256];
-
- sprintf(temp,"%d ",dimX);
- f2->InsertEntryString(temp,0x0028,0x0011, "US"); // Columns
- sprintf(temp,"%d ",dimY);
- f2->InsertEntryString(temp,0x0028,0x0010, "US"); // Rows
-
- f2->InsertEntryString("8",0x0028,0x0100, "US"); // Bits Allocated
- f2->InsertEntryString("8",0x0028,0x0101, "US"); // Bits Stored
- f2->InsertEntryString("7",0x0028,0x0102, "US"); // High Bit
- f2->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
- f2->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
- f2->InsertEntryString("MONOCHROME2 ",0x0028,0x0004, "LO");
-
- sprintf(outputFileName, "%s.ovly.dcm",it->c_str() );
-
- // feel free to add any field (Dicom Data Entry) you like, here.
- // ...
- GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f2);
-
- fh->SetImageData(outputData,dimXY);
- fh->WriteDcmExplVR(outputFileName);
- std::cout <<"End WriteOverlayImage" << std::endl;
-
- delete outputData;
- f->Delete();
- f2->Delete();
- fh->Delete();
-
-} // end of loop on files
-
- return 0;
-}
-
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