--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exExtractOverlaysACR.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 "gdcmDocEntry.h"
+#include <iostream>
+#include <stdio.h> // for fseek... FIXME
+#include <stdlib.h> // for atoi
+
+#include "gdcmArgMgr.h"
+
+ // WARNING :
+ // unfinished : DO NOT to be used as is !
+
+ /*
+ // Example (sorry, we've got no more than this one ...)
+
+V 0028|0010[US] [Rows] [256] x(100)
+V 0028|0011[US] [Columns] [256] x(100)
+V 0028|0030[DS] [Pixel Spacing] [01.56\1.56]
+V 0028|0100[US] [Bits Allocated] [16] x(10)
+V 0028|0101[US] [Bits Stored] [12] x(c)
+V 0028|0102[US] [High Bit] [11] x(b)
+V 0028|0103[US] [Pixel Representation] [0] x(0)
+
+V 6000|0000[UL] [Group Length] [96] x(60)
+V 6000|0010[US] [Rows] [256] x(100)
+V 6000|0011[US] [Columns] [256] x(100)
+V 6000|0040[CS] [Overlay Type] [R ]
+V 6000|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
+V 6000|0100[US] [Overlay Bits Allocated] [16] x(10)
+V 6000|0102[US] [Overlay Bit Position] [12] x(c)
+...
+...
+V 6006|0000[UL] [Group Length] [96] x(60)
+V 6006|0010[US] [Rows] [256] x(100)
+V 6006|0011[US] [Columns] [256] x(100)
+V 6006|0040[CS] [Overlay Type] [R ]
+V 6006|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
+V 6006|0100[US] [Overlay Bits Allocated] [16] x(10)
+V 6006|0102[US] [Overlay Bit Position] [15] x(f)
+ */
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ " \n exExtractOverlaysACR :\n ",
+ " Extract ACR-NEMA style overlays from an image ",
+ " usage: exExtractOverlaysACR filein=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;
+ }
+
+ // "SIEMENS_GBS_III-16-ACR_NEMA_1.acr"
+
+ const char *fileName = am->ArgMgrWantString("filein", 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! ================
+
+ GDCM_NAME_SPACE::File *f;
+
+
+// ============================================================
+// Read the input image.
+// ============================================================
+
+ //std::cout << argv[1] << std::endl;
+
+ f = GDCM_NAME_SPACE::File::New( );
+
+ f->SetLoadMode(GDCM_NAME_SPACE::LD_NOSEQ | GDCM_NAME_SPACE::LD_NOSHADOW);
+ f->SetFileName( fileName );
+ bool res = f->Load();
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ {
+ std::cout << "---------------------------------------------" << std::endl;
+ f->Print();
+ std::cout << "---------------------------------------------" << std::endl;
+ }
+ if (!res) {
+ std::cout << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR File"
+ <<std::endl;
+ f->Delete();
+ return 0;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+// ============================================================
+// Check whether image contains Overlays ACR-NEMA style.
+// ============================================================
+
+ int bitsAllocated = f->GetBitsAllocated();
+ if ( bitsAllocated <= 8 )
+ {
+ std::cout << " 8 bits pixel image cannot contain Overlays " << std::endl;
+ f->Delete();
+ return 0;
+ }
+ std::string s1 = f->GetEntryString(0x6000, 0x0102);
+ if (s1 == GDCM_NAME_SPACE::GDCM_UNFOUND)
+ {
+ std::cout << " Image doesn't contain any Overlay " << std::endl;
+ f->Delete();
+ return 0;
+ }
+ std::cout << " File is read! " << std::endl;
+
+
+// ============================================================
+// Load the pixels in memory.
+// ============================================================
+
+ int nx = f->GetXSize();
+ int ny = f->GetYSize();
+
+ GDCM_NAME_SPACE::FileHelper *fh1 = GDCM_NAME_SPACE::FileHelper::New(f);
+ fh1->SetKeepOverlays(true);
+ uint16_t *pixels = (uint16_t *)fh1->GetImageDataRaw();
+ int lgt = fh1->GetImageDataRawSize();
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "Pixels read as expected : length = " << lgt << std::endl;
+
+// ============================================================
+// Prepare the stuff
+// ============================================================
+
+ uint8_t *tabPixels = new uint8_t[nx*ny]; // uint8 is enought to hold 1 bit !
+
+ uint16_t currentOvlGroup = 0x6000;
+ std::string strOvlBitPosition;
+ int ovlBitPosition;
+ uint16_t mask;
+ int i = 0;
+ uint16_t overlayLocation;
+ std::ostringstream str;
+
+ std::string strOverlayLocation;
+
+ GDCM_NAME_SPACE::File *fileToBuild = 0;
+ GDCM_NAME_SPACE::FileHelper *fh = 0;
+
+// ============================================================
+// Get each overlay Bit into an image
+// ============================================================
+ for(i=0, currentOvlGroup=0x6000; i<32; i+=2 ,currentOvlGroup+=2)
+ {
+ if ( (strOvlBitPosition = f->GetEntryString(currentOvlGroup, 0x0102))
+ == GDCM_NAME_SPACE::GDCM_UNFOUND )
+ continue;
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "Current Overlay Group " << std::hex << currentOvlGroup
+ << " OvlBitPosition " << strOvlBitPosition << std::endl;
+
+ strOverlayLocation = f->GetEntryString(currentOvlGroup, 0x0200);
+ if ( strOverlayLocation != GDCM_NAME_SPACE::GDCM_UNFOUND )
+ {
+ overlayLocation = atoi(strOverlayLocation.c_str());
+ if ( overlayLocation != f->GetGrPixel() )
+ {
+ std::cout << "Big Trouble : Overlays are NOT in the Pixels Group "
+ << std::hex << "(" << overlayLocation << " vs "
+ << f->GetGrPixel() << std::endl;
+ // Actually, here, we should (try to) read the overlay location
+ // and go on the job.
+ continue;
+ }
+ }
+ ovlBitPosition = atoi(strOvlBitPosition.c_str());
+ mask = 1 << ovlBitPosition;
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "Mask :[" <<std::hex << mask << "]" << std::endl;
+ for (int j=0; j<nx*ny ; j++)
+ {
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ if (pixels[j] >= 0x1000)// if it contains at least one overlay bit
+ printf("%d : %04x\n",j, pixels[j]);
+
+ if ( (pixels[j] & mask) == 0 )
+ tabPixels[j] = 0;
+ else
+ tabPixels[j] = 128;
+ }
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "About to built empty file" << std::endl;
+
+ fileToBuild = GDCM_NAME_SPACE::File::New();
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "Finish to built empty file" << std::endl;
+
+ str.str("");
+ str << nx;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0011); // Columns
+ str.str("");
+ str << ny;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0010); // Rows
+
+ fileToBuild->InsertEntryString("8",0x0028,0x0100); // Bits Allocated
+ fileToBuild->InsertEntryString("8",0x0028,0x0101); // Bits Stored
+ fileToBuild->InsertEntryString("7",0x0028,0x0102); // High Bit
+ fileToBuild->InsertEntryString("0",0x0028,0x0103); // Pixel Representation
+ fileToBuild->InsertEntryString("1",0x0028,0x0002); // Samples per Pixel
+
+ fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004);
+ // Other mandatory fields will be set automatically,
+ // just before Write(), by FileHelper::CheckMandatoryElements()
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "-------------About to built FileHelper" << std::endl;
+
+ fh = GDCM_NAME_SPACE::FileHelper::New(fileToBuild);
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "-------------Finish to built FileHelper" << std::endl;
+
+ fh->SetImageData(tabPixels,nx*ny);
+ fh->SetWriteTypeToDcmExplVR();
+
+std::ostringstream tmp;
+tmp <<std::hex;
+tmp <<currentOvlGroup;
+
+ str.str("");
+// -> Why doesn't it work ?!?
+ //str << fileName << std::hex << currentOvlGroup << ".dcm" << std::ends;
+
+str << fileName << ".ovly." << tmp.str() << ".dcm" << std::ends;
+
+ // Write the current 'overlay' file
+
+ if( !fh->Write(str.str()) )
+ {
+ std::cout << "Failed\n"
+ << "File [" << str.str() << "] is unwrittable" << std::endl;
+ /*
+ fh->Delete();
+ if (fileToBuild)
+ fileToBuild->Delete();
+ delete pixels;
+ delete tabPixels;
+ return 0;
+ */
+ }
+ else
+ {
+ std::cout << "File written successfully [" << str.str() << "]" << std::endl;
+ }
+ }
+
+ if (f)
+ fh->Delete();
+ if (fileToBuild)
+ fileToBuild->Delete();
+ f->Delete();
+ delete pixels;
+ delete tabPixels;
+
+ return 0;
+}
+
--- /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;
+}
+
projects / gdcm.git / commitdiff