--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exExtractOverlaysDCM.cxx,v $
+ Language: C++
+ Date: $Date: 2007/09/12 10:43:47 $
+ Version: $Revision: 1.1 $
+
+ 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.
+
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cerr << "Deal with [" << it->c_str()
+ << "] File" <<std::endl;
+
+ 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);
+ f->AddForceLoadElement(0x6010,0x3000);
+ f->AddForceLoadElement(0x6012,0x3000);
+ f->AddForceLoadElement(0x6014,0x3000);
+ f->AddForceLoadElement(0x6016,0x3000);
+ f->AddForceLoadElement(0x6018,0x3000);
+ f->AddForceLoadElement(0x601a,0x3000);
+ f->AddForceLoadElement(0x601c,0x3000);
+ f->AddForceLoadElement(0x601e,0x3000); // Hope it's enought : Dicom says 60xx ...
+
+ int res = f->Load();
+
+ if ( !res )
+ {
+ std::cerr << "Sorry, " << it->c_str() <<" not a gdcm-readable "
+ << "DICOM / ACR File" <<std::endl;
+ f->Delete();
+ continue;
+ }
+
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " ... is readable " << std::endl;
+
+ // ============================================================
+ // Load Overlay info in memory
+ // ============================================================
+
+/// \todo : deal with *each* overlay Data Element (not only the first one!)
+
+ uint16_t ovlyGroup = 0x6000;
+
+ for (int k=0; k<32; k+=2)
+ {
+
+ GDCM_NAME_SPACE::DataEntry *e10 = f->GetDataEntry(ovlyGroup+k, 0x0010); // nb Row Ovly
+ if (e10 == 0)
+ {
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " Image doesn't contain Overlay on " <<std::hex
+ << ovlyGroup+k << std::endl;
+ continue;
+ }
+
+ // ============================================================
+ // Image data preparation
+ // ============================================================
+
+ unsigned int dimX= f->GetXSize();
+ unsigned int dimY= f->GetYSize();
+ unsigned int dimXY=dimX*dimY;
+
+ unsigned char *outputData = new unsigned char[dimXY];
+
+
+ GDCM_NAME_SPACE::DataEntry *e = f->GetDataEntry(ovlyGroup+k, 0x3000);
+ if (e == 0)
+ {
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " Image doesn't contain DICOM Overlay Data " <<std::hex
+ << ovlyGroup+k << std::endl;
+
+ // ============================================================
+ // DICOM Overlay Image data generation
+ // ============================================================
+
+ GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
+ uint8_t *pixelData= fh->GetImageDataRaw();
+
+ if (pixelData == 0)
+ {
+ std::cerr << "Sorry, Pixel Data of [" << it->c_str() <<"] are not "
+ << " gdcm-readable." << std::endl;
+ continue;
+ }
+
+ }
+ else
+ {
+ uint8_t *overlay = (uint8_t *)(e->GetBinArea());
+ if ( overlay == 0 )
+ {
+ std::cerr << "Sorry, Overlays of [" << it->c_str() <<"] are not "
+ << " gdcm-readable." << std::endl;
+ continue;
+ }
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " Overlay on group [" << std::hex << ovlyGroup+k << "] is read! " << std::endl;
+
+ // ============================================================
+ // DICOM Overlay Image data generation
+ // ============================================================
+
+
+ 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( );
+ GDCM_NAME_SPACE::FileHelper *fh2 = GDCM_NAME_SPACE::FileHelper::New(f2);
+
+ 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");
+
+ // feel free to add any field (Dicom Data Entry) you like, here.
+ // ...
+
+ sprintf(outputFileName, "../%s.ovly.%04x.dcm",it->c_str(), ovlyGroup+k);
+
+ fh2->SetImageData(outputData,dimXY);
+ fh2->WriteDcmExplVR(outputFileName);
+
+ std::cout <<"File written successfully [" << outputFileName << "]" <<std::endl;
+
+ delete outputData;
+ f2->Delete();
+ fh2->Delete();
+
+ } // end on loop on 60xx
+
+ f->Delete();
+
+
+} // end of loop on files ( DirListType::iterator )
+
+ return 0;
+}
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff