+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: exOverlaysACR.cxx,v $
- Language: C++
- Date: $Date: 2007/05/23 14:18:05 $
- Version: $Revision: 1.11 $
-
- 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
-
- // 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[])
-{
- GDCM_NAME_SPACE::File *f;
-
- //GDCM_NAME_SPACE::Debug::DebugOn();
-
- std::cout << "------------------------------------------------" << std::endl;
- std::cout << "Gets the 'Overlays' from a full gdcm-readable ACR-NEMA "
- << "uncompressed image" << std::endl;
- std::cout << "Writes them in DicomV3 files named 'gdcmOverlay-xxx.dcm'"
- << std::endl;
- std::cout << "(Note : we just have ONE image : "
- << "SIEMENS_GBS_III-16-ACR_NEMA_1.acr)"
- << std::endl;
- std::cout << "------------------------------------------------" << std::endl;
-
- std::string fileName;
- if( argc > 1 )
- fileName = argv[1];
- else
- fileName = "SIEMENS_GBS_III-16-ACR_NEMA_1.acr";
-
- std::cout << fileName << std::endl;
-// ============================================================
-// 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.
-// ============================================================
-
- // We don't use a GDCM_NAME_SPACE::FileHelper, since it rubs out
- // the 'non image' bits of the pixels...
-
- /// \todo : Previous remark doesn't work if pixels are compressed !
-
- int nx = f->GetXSize();
- int ny = f->GetYSize();
-
- std::cout << "Dimensions " << ny << " " <<ny << std::endl;
-
- GDCM_NAME_SPACE::DocEntry *p = f->GetDocEntry(f->GetGrPixel(), f->GetNumPixel());
- if (p == 0)
- std::cout << "Pixels element not found" << std::endl;
- else
- std::cout << "Pixels element FOUND" << std::endl;
-
- int offset = (int)(p->GetOffset());
-
- std::cout << "Offset " << offset << std::endl;
-
- FILE *fp = fopen(fileName.c_str(), "r");
-
- if (fp == 0)
- {
- std::cout << "Unable to open File" << std::endl;
- f->Delete();
- return 0;
- }
- else
- std::cout << "File open successfully" << std::endl;
-
- fseek(fp, (long) offset,SEEK_SET);
- uint16_t *pixels = new uint16_t[nx*ny];
- size_t lgt = fread(pixels, 1, nx*ny*sizeof( uint16_t) , fp );
-
- if ( lgt != (size_t)nx*ny*sizeof( uint16_t) )
- {
- std::cout << "Sorry, Pixels of" << fileName << " are not "
- << "readable. expected length :" << nx*ny
- << " " << "read length : " << lgt
- << std::endl;
- f->Delete();
- delete pixels;
- return 0;
- }
- else
- {
- std::cout << "Pixels read as expected : length = " << lgt << std::endl;
- }
-
-
-// ============================================================
-// Get each overlay Bit into an image
-// ============================================================
-
- 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;
-
-
- while ( (strOvlBitPosition = f->GetEntryString(currentOvlGroup, 0x0102))
- != GDCM_NAME_SPACE::GDCM_UNFOUND )
- {
-
- 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;
- 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();
-
- str.str("");
- str<<"gdcmOverlay-"<<i << ".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 pixels;
- delete tabPixels;
- return 0;
- }
- else
- {
- std::cout << "File written successfully" << std::endl;
- }
- currentOvlGroup += 2;
- i++;
- }
-
- if (f)
- fh->Delete();
- if (fileToBuild)
- fileToBuild->Delete();
- f->Delete();
- delete pixels;
- delete tabPixels;
-
- return 0;
-}
-
+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: exOverlaysDCM.cxx,v $
- Language: C++
- Date: $Date: 2007/09/04 13:04:18 $
- Version: $Revision: 1.11 $
-
- 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 "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 exOverlaysDCM :\n ",
- " Extract an overlay image from a DICOM image ",
- " Warning : probably segfaults if no overlay ",
- " usage: exOverlaysDCM filein=inputFileName fileout=outputFileName [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;
- }
-
-/*
- char *fileName = am->ArgMgrWantString("filein",usage);
- if ( fileName == NULL )
- {
- delete am;
- return 0;
- }
-*/
-
-
- const char *fileName = am->ArgMgrGetString("filein");
- const char *dirName = am->ArgMgrGetString("dirin");
-
- if ( (fileName == 0 && dirName == 0) ||
- (fileName != 0 && dirName != 0) )
- {
- std::cerr << std::endl
- << "Either 'filein=' or 'dirin=' must be present;"
- << std::endl << "Not both" << std::endl;
- am->ArgMgrUsage(usage); // Display 'usage'
- delete am;
- return 1;
- }
-
-
- char *outputFileName = am->ArgMgrWantString("fileout",usage);
- if ( outputFileName == NULL )
- {
- delete am;
- return 0;
- }
- 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
-
- // ============================================================
- // Read the input file.
- // ============================================================
-
- GDCM_NAME_SPACE::File *f;
-
- f = GDCM_NAME_SPACE::File::New( );
- f->SetLoadMode( GDCM_NAME_SPACE::LD_ALL );
- f->SetFileName( fileName );
- f->AddForceLoadElement(0x6000,0x3000); // Overlay Data
- int res = f->Load();
-
- if ( !res )
- {
- std::cerr << "Sorry, " << fileName <<" not a gdcm-readable "
- << "DICOM / ACR File" <<std::endl;
- f->Delete();
- return 0;
- }
- std::cout << " ... is readable " << std::endl;
-
- // ============================================================
- // Load the Overlays in memory (the first one)
- // ============================================================
-
- GDCM_NAME_SPACE::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;
-
- uint8_t *overlay = (uint8_t *)(e->GetBinArea());
- if ( overlay == 0 )
- {
- std::cerr << "Sorry, Overlays of" << fileName <<" are not "
- << " gdcm-readable." << std::endl;
- f->Delete();
- return 0;
- }
-
- // ============================================================
- // 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");
-
-
- // 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();
-
- return 0;
-}
-
projects / gdcm.git / commitdiff