-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: exOverlaysDCM.cxx,v $
- Language: C++
- Date: $Date: 2005/12/09 10:17:52 $
- 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 "gdcmDataEntry.h"
+#include "gdcmArgMgr.h"
#include <iostream>
-#include <stdio.h> // for fseek... FIXME
-#include <stdlib.h> // for atoi
-
- // WARNING :
- // unfinished : DO NOT to be used as is !
-
+
+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[])
-{
- gdcm::File *f;
-
- //gdcm::Debug::DebugOn();
+{
+ START_USAGE(usage)
+ " \n exReadOverlays :\n ",
+ " Extract an overlay image from a secondary capture image ",
+ " Warning : probably segfaults if no overlay ",
+ " usage: WriteOverlayImage filein=inputFileName fileout=outputFileName[debug]",
+ " debug : user wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+ // ----- Initialize Arguments Manager ------
+ gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+
+ if (argc == 1 || am->ArgMgrDefined("usage"))
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+ char *fileName = am->ArgMgrWantString("filein",usage);
+ if ( fileName == NULL )
+ {
+ delete am;
+ return 0;
+ }
- std::cout << "------------------------------------------------" << std::endl;
- std::cout << "Gets the 'Overlays' from a full gdcm-readable DCM image "
- << "uncompressed image" << std::endl;
- std::cout << "Writes them in a DicomV3 file named 'gdcmOverlay.dcm'"
- << std::endl;
- std::cout << "------------------------------------------------" << std::endl;
+ char *outputFileName = am->ArgMgrWantString("fileout",usage);
+ if ( outputFileName == NULL )
+ {
+ delete am;
+ return 0;
+ }
+ if (am->ArgMgrDefined("debug"))
+ gdcm::Debug::DebugOn();
- std::string fileName;
- if( argc > 1 )
- fileName = argv[1];
- else
- fileName = "SIEMENS_GBS_III-16-ACR_NEMA_1.acr";
+ // if unused Param we give up
+ if ( am->ArgMgrPrintUnusedLabels() )
+ {
+ am->ArgMgrUsage(usage);
+ delete am;
+ return 0;
+ }
- std::cout << fileName << std::endl;
-// ============================================================
-// Read the input image.
-// ============================================================
+ delete am; // we don't need Argument Manager any longer
- //std::cout << argv[1] << std::endl;
+ // ============================================================
+ // Read the input file.
+ // ============================================================
- f = gdcm::File::New( );
+ gdcm::File *f;
- f->SetLoadMode(gdcm::LD_ALL);
+ f = gdcm::File::New( );
+ f->SetLoadMode( gdcm::LD_ALL );
f->SetFileName( fileName );
f->AddForceLoadElement(0x6000,0x3000); // Overlay Data
- bool res = f->Load();
+ int res = f->Load();
- if( gdcm::Debug::GetDebugFlag() )
+ if ( !res )
{
- 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::cerr << "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.
-// ============================================================
+ // ============================================================
+ // Load the Overlays in memory (the first one)
+ // ============================================================
- int bitsAllocated = f->GetBitsAllocated();
-
- gdcm::DataEntry *e = f->GetDataEntry(0x6000, 0x3000);
-
+ gdcm::DataEntry *e = f->GetDataEntry(0x6000, 0x3000);
if (e == 0)
{
std::cout << " Image doesn't contain any Overlay " << std::endl;
f->Delete();
return 0;
- }
-
+ }
std::cout << " File is read! " << std::endl;
-
-// ============================================================
-// Get usefull info from FileHelper.
-// ============================================================
-
- uint32_t overlayPixelLength = e->GetLength();
-
-/*
- if ( overlayPixelLength != (size_t)nx*ny*sizeof( uint16_t) )
+ uint8_t *overlay = (uint8_t *)(e->GetBinArea());
+ if ( overlay == 0 )
{
- std::cout << "Sorry, Pixels of" << fileName << " are not "
- << "readable. expected length :" << nx*ny*sizeof( uint16_t)
- << " " << "read length : " << overlayPixelLength
- << std::endl;
+ std::cerr << "Sorry, Overlays of" << fileName <<" are not "
+ << " gdcm-readable." << std::endl;
f->Delete();
- delete pixels;
return 0;
}
- else
- {
- std::cout << "Pixels read as expected : length = " << lgt << std::endl;
- }
-*/
- uint32_t nx = f->GetXSize();
- uint32_t ny = f->GetYSize();
- uint8_t *overlayPixelArea = (uint8_t *)(e->GetBinArea());
-
- // should check overlayPixelLength == nx*ny/8 !)
-
- uint8_t *overlayPixelImage = new uint8_t[nx*ny];// uint8 is enough to hold 1 bit !
-
- uint16_t m;
- for (unsigned int j=0; j<overlayPixelLength; j++)
+ // ============================================================
+ // 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[dimXY];
+
+ unsigned char *result=outputData;
+ for (int i=0;i<(dimXY/8);i++)
{
- if (overlayPixelArea[j] != 0)
- {
- std::cout << "j : " << std::dec << j << " Ox(" << std::hex <<(int)overlayPixelArea[j]
- << ")" << std::endl;
- for (unsigned int k=0; k<8; k++)
- {
- m = overlayPixelArea[j]<<k;
- //printf("m : %04x ", m);
- m = m & 0x00ff;
- //printf(" : %04x \n", m);
- overlayPixelImage[j*8 +k] = ( m > 127)?255:0;
-
- printf("%04x ", overlayPixelImage[j*8 +k]);
- }
- std::cout << std::endl;
- }
+ explodeByte(overlay[i], result);
+ result+=8;
}
- if( gdcm::Debug::GetDebugFlag() )
- std::cout << "About to built empty file" << std::endl;
-
- gdcm::File *fileToBuild = gdcm::File::New();
-
- if( gdcm::Debug::GetDebugFlag() )
- std::cout << "Finish to built empty file" << std::endl;
-
- std::ostringstream str;
- 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::Debug::GetDebugFlag() )
- std::cout << "-------------About to built FileHelper" << std::endl;
-
- gdcm::FileHelper *fh = gdcm::FileHelper::New(fileToBuild);
-
- if( gdcm::Debug::GetDebugFlag() )
- std::cout << "-------------Finish to built FileHelper" << std::endl;
-
- fh->SetImageData(overlayPixelImage,nx*ny);
- fh->SetWriteTypeToDcmExplVR();
-
- str.str("");
- str<<"gdcmOverlay" << ".dcm";
- // Write the current 'overlay' file
-
- if( !fh->Write(str.str()) )
- {
- std::cout << "Failed\n"
- << "File in unwrittable\n";
- fh->Delete();
- if (fileToBuild)
- fileToBuild->Delete();
- delete overlayPixelImage;
-
- return 0;
- }
- else
- {
- std::cout << "File written successfully" << std::endl;
- }
-
- if (f)
- fh->Delete();
- if (fileToBuild)
- fileToBuild->Delete();
- f->Delete();
- delete overlayPixelImage;
-
+ // ============================================================
+ // Write a new file
+ // ============================================================
+ char temp[256];
+
+ sprintf(temp,"%d\0",dimX);
+ f->InsertEntryString(temp,0x0028,0x0011); // Columns
+ sprintf(temp,"%d\0",dimY);
+ f->InsertEntryString(temp,0x0028,0x0010); // Rows
+
+ f->InsertEntryString("8",0x0028,0x0100); // Bits Allocated
+ f->InsertEntryString("8",0x0028,0x0101); // Bits Stored
+ f->InsertEntryString("7",0x0028,0x0102); // High Bit
+ f->InsertEntryString("0",0x0028,0x0103); // Pixel Representation
+ f->InsertEntryString("1",0x0028,0x0002); // Samples per Pixel
+ f->InsertEntryString("MONOCHROME2 ",0x0028,0x0004);
+
+ // We need a gdcm::FileHelper, since we want to load the pixels
+ gdcm::FileHelper *fh = gdcm::FileHelper::New(f);
+
+ fh->SetImageData(outputData,dimXY);
+ fh->WriteDcmExplVR(outputFileName);
+ std::cout <<"End WriteOverlayImage" << std::endl;
+
+ f->Delete();
+ fh->Delete();
return 0;
}
projects / gdcm.git / commitdiff