exReadPapyrus
exReadWriteFile
exAnonymize
-
+ exAnonymizeNoLoad
+ exColorToRGB
+ exGC
+ exImageLighten
+
#the following are utilities
PrintDicomDir
PrintDocument
--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exColorToRGB.cxx,v $
+ Language: C++
+ Date: $Date: 2005/02/09 14:39:48 $
+ 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 "gdcmDocument.h"
+#include "gdcmValEntry.h"
+#include "gdcmBinEntry.h"
+#include "gdcmSeqEntry.h"
+
+
+int main(int argc, char *argv[])
+{
+
+ std::cout << "------------------------------------------------" << std::endl;
+ std::cout << "Tranforms a full gdcm-readable 'color' Dicom image "
+ << " (e.g Palette Color, YBR, 3-Planes RGB) "
+ << " into an 'RGB_Pixels' Dicom Image "
+ << " " << std::endl;
+
+ if (argc < 3)
+ {
+ std::cerr << "Usage :" << std::endl <<
+ argv[0] << " input_dicom output_dicom" << std::endl;
+ return 1;
+ }
+
+ std::string fileName = argv[1];
+ std::string output = argv[2];
+
+
+// ============================================================
+// Read the input image.
+// ============================================================
+ // a gdcm::File contains all the Dicom Field but the Pixels Element
+
+ gdcm::File *f1= new gdcm::File( fileName );
+
+
+ std::cout << argv[1] << std::endl;
+
+ f1 = new gdcm::File( fileName );
+ if (!f1->IsReadable()) {
+ std::cerr << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR File"
+ <<std::endl;
+ return 0;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+/*
+ if (!f1->IsMonochrome()) {
+ std::cerr << "Sorry, " << fileName <<" not a 'color' File "
+ << " "
+ <<std::endl;
+ return 0;
+ }
+*/
+
+// ============================================================
+// Load the pixels in memory.
+// ============================================================
+
+ // We need a gdcm::FileHelper, since we want to load the pixels
+ gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1);
+
+ // (unit8_t DOESN'T mean it's mandatory for the image to be a 8 bits one)
+
+ uint8_t *imageData = fh1->GetImageData();
+
+ if ( imageData == 0 )
+ {
+ std::cerr << "Sorry, Pixels of" << fileName <<" are not "
+ << " gdcm-readable." << std::endl;
+ return 0;
+ }
+
+
+
+
+ // ------ User wants write a new image without shadow groups -------------
+ // ------ without Sequences -------------
+
+
+ gdcm::FileHelper *copy = new gdcm::FileHelper( output );
+
+ gdcm::DocEntry *d = f1->GetFirstEntry();
+ while(d)
+ {
+ // We skip SeqEntries, since user cannot do much with them
+ if ( !(dynamic_cast<gdcm::SeqEntry*>(d))
+ // We skip Shadow Groups, since nobody knows what they mean
+ && !( d->GetGroup()%2 ) )
+ {
+
+ if ( gdcm::BinEntry *b = dynamic_cast<gdcm::BinEntry*>(d) )
+ {
+ copy->GetFile()->InsertBinEntry( b->GetBinArea(),b->GetLength(),
+ b->GetGroup(),b->GetElement(),
+ b->GetVR() );
+ }
+ else if ( gdcm::ValEntry *v = dynamic_cast<gdcm::ValEntry*>(d) )
+ {
+ copy->GetFile()->InsertValEntry( v->GetValue(),
+ v->GetGroup(),v->GetElement(),
+ v->GetVR() );
+ }
+ else
+ {
+ // We skip gdcm::SeqEntries
+ }
+ }
+ d = f1->GetNextEntry();
+ }
+
+ // User knows the image is a 'color' one -RGB, YBR, Palette Color-
+ // and wants to write it as RGB
+ copy->SetImageData(imageData, fh1->GetImageDataSize());
+ copy->SetWriteModeToRGB();
+
+ copy->WriteDcmExplVR( output );
+
+
+ delete f1;
+ delete fh1;
+ delete copy;
+
+ exit (0);
+}
+
--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exGC.cxx,v $
+ Language: C++
+ Date: $Date: 2005/02/09 14:39:48 $
+ 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 "gdcmDocument.h"
+#include "gdcmValEntry.h"
+#include "gdcmBinEntry.h"
+#include "gdcmSeqEntry.h"
+
+typedef struct // Maybe we should add it to gdcm ?
+{
+ uint8_t r;
+ uint8_t g;
+ uint8_t b;
+} rgb8_t;
+
+
+// This small application, for a given Creatis user (G.C.)
+// may be taken as an example
+
+int main(int argc, char *argv[])
+{
+
+ // we need a user friendly way for passign parameters on the command line !
+
+ std::cout << "------------------------------------------------" << std::endl;
+ std::cout << "Transforms a full gdcm-readable 'color' Dicom image "
+ << " (e.g Palette Color, YBR, 3-Planes RGB) "
+ << " into an 'RGB_Pixels' Dicom Image " << std::endl
+ << " Blacks out any 'grey' pixel (r=g=b) "
+ << " Blacks out any 'dark' pixel (r,g,b < threshold) "
+ << " " << std::endl;
+ std::cout << "------------------------------------------------" << std::endl;
+
+ if (argc < 3)
+ {
+ std::cerr << "Usage :" << std::endl <<
+ argv[0] << " input_dicom output_dicom threshold background" << std::endl;
+ return 1;
+ }
+
+ std::string fileName = argv[1];
+ std::string output = argv[2];
+
+ int threshold = 0;
+ if (argc > 3)
+ threshold = atoi( argv[3] );
+
+ int background = 0;
+ if (argc > 4)
+ background = atoi( argv[4] );
+
+// ============================================================
+// Read the input image.
+// ============================================================
+ // a gdcm::File contains all the Dicom Field but the Pixels Element
+
+ gdcm::File *f1= new gdcm::File( fileName );
+
+
+ std::cout << argv[1] << std::endl;
+
+ f1 = new gdcm::File( fileName );
+ if (!f1->IsReadable()) {
+ std::cerr << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR File"
+ <<std::endl;
+ return 0;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+/*
+ if (!f1->IsMonochrome()) {
+ std::cerr << "Sorry, " << fileName <<" not a 'color' File "
+ << " "
+ <<std::endl;
+ return 0;
+ }
+*/
+
+// ============================================================
+// Load the pixels in memory.
+// ============================================================
+
+ // We need a gdcm::FileHelper, since we want to load the pixels
+ gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1);
+
+ // (unit8_t DOESN'T mean it's mandatory for the image to be a 8 bits one)
+
+ uint8_t *imageData = fh1->GetImageData();
+
+ if ( imageData == 0 )
+ {
+ std::cerr << "Sorry, Pixels of" << fileName <<" are not "
+ << " gdcm-readable." << std::endl;
+ return 0;
+ }
+
+ // ------ User wants write a new image without shadow groups -------------
+ // ------ without Sequences -------------
+
+
+ gdcm::FileHelper *copy = new gdcm::FileHelper( output );
+
+ gdcm::DocEntry *d = f1->GetFirstEntry();
+ while(d)
+ {
+ // We skip SeqEntries, since user cannot do much with them
+ if ( !(dynamic_cast<gdcm::SeqEntry*>(d))
+ // We skip Shadow Groups, since nobody knows what they mean
+ && !( d->GetGroup()%2 ) )
+ {
+
+ if ( gdcm::BinEntry *b = dynamic_cast<gdcm::BinEntry*>(d) )
+ {
+ copy->GetFile()->InsertBinEntry( b->GetBinArea(),b->GetLength(),
+ b->GetGroup(),b->GetElement(),
+ b->GetVR() );
+ }
+ else if ( gdcm::ValEntry *v = dynamic_cast<gdcm::ValEntry*>(d) )
+ {
+ copy->GetFile()->InsertValEntry( v->GetValue(),
+ v->GetGroup(),v->GetElement(),
+ v->GetVR() );
+ }
+ else
+ {
+ // We skip gdcm::SeqEntries
+ }
+ }
+ d = f1->GetNextEntry();
+ }
+
+ int imageSize = fh1->GetImageDataSize();
+// Black up all 'grey' pixels
+ int n = 0;
+ for (int i = 0; i<imageSize/3; i++)
+ {
+ if ( ((rgb8_t *)imageData)[i].r == ((rgb8_t *)imageData)[i].g
+ &&
+ ((rgb8_t *)imageData)[i].r == ((rgb8_t *)imageData)[i].b )
+ {
+ n++;
+ ((rgb8_t *)imageData)[i].r = background;
+ ((rgb8_t *)imageData)[i].g = background;
+ ((rgb8_t *)imageData)[i].b = background;
+ }
+ }
+
+ std::cout << n << " points put to black (within "
+ << imageSize/3 << ")" << std::endl;
+
+ n = 0;
+ for (int i = 0; i<imageSize/3; i++)
+ {
+ if ( ((rgb8_t *)imageData)[i].r < threshold
+ &&
+ ((rgb8_t *)imageData)[i].g < threshold
+ &&
+ ((rgb8_t *)imageData)[i].b < threshold )
+ {
+ n++;
+ ((rgb8_t *)imageData)[i].r = background;
+ ((rgb8_t *)imageData)[i].g = background;
+ ((rgb8_t *)imageData)[i].b = background;
+ }
+ }
+
+ std::cout << n << " points put to black (within "
+ << imageSize/3 << ")" << std::endl;
+ // User knows the image is a 'color' one -RGB, YBR, Palette Color-
+ // and wants to write it as RGB
+ copy->SetImageData(imageData, imageSize);
+ copy->SetWriteModeToRGB();
+
+ copy->WriteDcmExplVR( output );
+
+ delete f1;
+ delete fh1;
+ delete copy;
+
+ exit (0);
+}
--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exImageLighten.cxx,v $
+ Language: C++
+ Date: $Date: 2005/02/09 14:39:49 $
+ 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 "gdcmDocument.h"
+#include "gdcmValEntry.h"
+#include "gdcmBinEntry.h"
+#include "gdcmSeqEntry.h"
+
+int main(int argc, char *argv[])
+{
+ gdcm::File *f1;
+
+ std::cout << "-----------------------------------------------" << std::endl;
+ std::cout << "Removes from a full gdcm-readable Dicom image" << std::endl;
+ std::cout << " all the 'Shadow groups' and the 'Sequence' entries"
+ << " Warning : 'Compressed images' are uncompressed"
+ << std::endl
+ << " : 'YBR images' are converted into 'RGB images'"
+ << std::endl
+ << " : 'RGB planes' are converted into 'RGB pixels'"
+ << std::endl
+ << " : 'Palette Color images' are kept 'as is'"
+ << std::endl;
+ std::cout << "-----------------------------------------------" << std::endl;
+
+ if( argc < 3 )
+ {
+ std::cerr << "Usage " << argv[0] << " Source image.dcm "
+ << " Output image.dcm " << std::endl;
+ return 1;
+ }
+
+ std::string fileName = argv[1];
+ std::string output = argv[2];
+
+// ============================================================
+// Read the input image.
+// ============================================================
+
+ std::cout << argv[1] << std::endl;
+
+ f1 = new gdcm::File( fileName );
+ if (!f1->IsReadable()) {
+ std::cerr << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR File"
+ <<std::endl;
+ return 0;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+// ============================================================
+// Read the Pixels
+//
+// ============================================================
+
+ // Pixel Reading must be done here, to be sure
+ // to load the Palettes Color (if any)
+
+ // First, create a gdcm::FileHelper
+ gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1);
+
+ // Load the pixels, DO NOT transform LUT (if any) into RGB Pixels
+ uint8_t *imageDataRaw = fh1->GetImageDataRaw();
+ // Get the image data size
+ size_t dataRawSize = fh1->GetImageDataRawSize();
+
+// ============================================================
+// Create a new gdcm::Filehelper, to hold new image.
+// ============================================================
+
+ gdcm::FileHelper *copy = new gdcm::FileHelper( output );
+
+// ============================================================
+// Selective copy of the entries (including Pixel Element).
+// ============================================================
+
+ gdcm::DocEntry *d = f1->GetFirstEntry();
+
+ d = f1->GetFirstEntry();
+ while(d)
+ {
+ // We skip SeqEntries, since user cannot do much with them
+ if ( !(dynamic_cast<gdcm::SeqEntry*>(d))
+ // We skip Shadow Groups, since nobody knows what they mean
+ && !( d->GetGroup()%2 ) )
+ {
+
+ if ( gdcm::BinEntry *b = dynamic_cast<gdcm::BinEntry*>(d) )
+ {
+ copy->GetFile()->InsertBinEntry( b->GetBinArea(),b->GetLength(),
+ b->GetGroup(),b->GetElement(),
+ b->GetVR() );
+ }
+ else if ( gdcm::ValEntry *v = dynamic_cast<gdcm::ValEntry*>(d) )
+ {
+ copy->GetFile()->InsertValEntry( v->GetValue(),
+ v->GetGroup(),v->GetElement(),
+ v->GetVR() );
+ }
+ else
+ {
+ // We skip gdcm::SeqEntries
+ }
+ }
+ d = f1->GetNextEntry();
+ }
+
+ // User wants to keep the Palette Color -if any-
+ // and write the image as it was
+ copy->SetImageData(imageDataRaw, dataRawSize);
+ copy->SetWriteModeToRaw();
+ copy->WriteDcmExplVR( output );
+
+ std::cout << std::endl
+ << "------------------------------------------------------------"
+ << std::endl;
+ delete f1;
+ delete fh1;
+ delete copy;
+
+ exit (0);
+}
+
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff