From b551d44903972c0bc729caa3df97a2ce484851a7 Mon Sep 17 00:00:00 2001 From: jpr Date: Wed, 20 Apr 2005 11:22:28 +0000 Subject: [PATCH 1/1] Add a 'heavy documented' example on the way to extract 'overlays' when they are stored in the 'ACR fashion' (that's NOT to say in ACR-NEMA images; it still works an DICOM V3 images) --- Example/exOverlaysACR.cxx | 298 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 298 insertions(+) create mode 100644 Example/exOverlaysACR.cxx diff --git a/Example/exOverlaysACR.cxx b/Example/exOverlaysACR.cxx new file mode 100644 index 00000000..9bd48c54 --- /dev/null +++ b/Example/exOverlaysACR.cxx @@ -0,0 +1,298 @@ +/*========================================================================= + + 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 + #include + + // 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" + <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 << " " <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 :[" <= 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-"<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; +} + -- 2.45.1