--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exOverlaysACR.cxx,v $
+ Language: C++
+ Date: $Date: 2005/04/20 11:22:28 $
+ 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>
+
+ // 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::File *f1;
+
+ //gdcm::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;
+
+ f1 = new gdcm::File( );
+
+ f1->SetLoadMode(NO_SEQ | NO_SHADOW);
+ f1->Load( fileName );
+
+ if( gdcm::Debug::GetDebugFlag() )
+ {
+ std::cout << "---------------------------------------------" << std::endl;
+ f1->Print();
+ std::cout << "---------------------------------------------" << std::endl;
+ }
+ if (!f1->IsReadable()) {
+ std::cout << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR File"
+ <<std::endl;
+ delete f1;
+ return 0;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+// ============================================================
+// Check whether image contains Overlays ACR-NEMA style.
+// ============================================================
+
+ int bitsAllocated = f1->GetBitsAllocated();
+ if ( bitsAllocated <= 8 )
+ {
+ std::cout << " 8 bits pixel image cannot contain Overlays " << std::endl;
+ delete f1;
+ return 0;
+ }
+ std::string s1 = f1->GetEntryValue(0x6000, 0x0102);
+ if (s1 == gdcm::GDCM_UNFOUND)
+ {
+ std::cout << " Image doesn't contain any Overlay " << std::endl;
+ delete f1;
+ return 0;
+ }
+ std::cout << " File is read! " << std::endl;
+
+
+// ============================================================
+// Load the pixels in memory.
+// ============================================================
+
+ // We don't use a gdcm::FileHelper, since it rubs out
+ // the 'non image' bits of the pixels...
+
+ int nx = f1->GetXSize();
+ int ny = f1->GetYSize();
+
+ std::cout << "Dimensions " << ny << " " <<ny << std::endl;
+
+ gdcm::DocEntry *p = f1->GetDocEntry(f1->GetGrPixel(), f1->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;
+ delete f1;
+ 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;
+ delete f1;
+ 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::File *fileToBuild;
+ gdcm::FileHelper *fh;
+
+
+
+while ( (strOvlBitPosition = f1->GetEntryValue(currentOvlGroup, 0x0102))
+ != gdcm::GDCM_UNFOUND )
+{
+
+ strOverlayLocation = f1->GetEntryValue(currentOvlGroup, 0x0200);
+ if ( strOverlayLocation != gdcm::GDCM_UNFOUND )
+ {
+ overlayLocation = atoi(strOverlayLocation.c_str());
+ if ( overlayLocation != f1->GetGrPixel() )
+ {
+ std::cout << "Big Trouble : Overlays are NOT in the Pixels Group "
+ << std::hex << "(" << overlayLocation << " vs "
+ << f1->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::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::Debug::GetDebugFlag() )
+ std::cout << "About to built empty file" << std::endl;
+
+ fileToBuild = new gdcm::File();
+
+ if( gdcm::Debug::GetDebugFlag() )
+ std::cout << "Finish to built empty file" << std::endl;
+
+ str.str("");
+ str << nx;
+ fileToBuild->InsertValEntry(str.str(),0x0028,0x0011); // Columns
+ str.str("");
+ str << ny;
+ fileToBuild->InsertValEntry(str.str(),0x0028,0x0010); // Rows
+
+ fileToBuild->InsertValEntry("8",0x0028,0x0100); // Bits Allocated
+ fileToBuild->InsertValEntry("8",0x0028,0x0101); // Bits Stored
+ fileToBuild->InsertValEntry("7",0x0028,0x0102); // High Bit
+ fileToBuild->InsertValEntry("0",0x0028,0x0103); // Pixel Representation
+ fileToBuild->InsertValEntry("1",0x0028,0x0002); // Samples per Pixel
+
+ fileToBuild->InsertValEntry("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;
+
+ fh = new gdcm::FileHelper(fileToBuild);
+
+ if( gdcm::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";
+ delete fh;
+ delete fileToBuild;
+ delete pixels;
+ delete tabPixels;
+ return 0;
+ }
+ else
+ {
+ std::cout << "File written successfully" << std::endl;
+ }
+ currentOvlGroup += 2;
+ i++;
+ }
+
+ delete f1;
+ delete fh;
+ delete fileToBuild;
+ delete pixels;
+ delete tabPixels;
+ return 0;
+}
+
projects / gdcm.git / commitdiff