--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exReadPapyrus.cxx,v $
+ Language: C++
+ Date: $Date: 2005/02/03 15:44:50 $
+ 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"
+#include "gdcmSQItem.h"
+#include "gdcmDebug.h"
+#include "gdcmUtil.h"
+
+//#include <fstream>
+
+#ifndef _WIN32
+#include <unistd.h> //for access, unlink
+#else
+#include <io.h> //for _access
+#endif
+
+// return true if the file exists
+bool FileExists(const char *filename)
+{
+#ifdef _MSC_VER
+# define access _access
+#endif
+#ifndef R_OK
+# define R_OK 04
+#endif
+ if ( access(filename, R_OK) != 0 )
+ {
+ return false;
+ }
+ else
+ {
+ return true;
+ }
+}
+
+bool RemoveFile(const char *source)
+{
+#ifdef _MSC_VER
+#define _unlink unlink
+#endif
+ return unlink(source) != 0 ? false : true;
+}
+
+// ----------------------------------------------------------------------
+// Here we load a supposed to be Papyrus File (gdcm::File compliant)
+// and then try to get the pixels, using low-level SeqEntry accessors.
+// Since it's not a general purpose Papyrus related program
+// (just a light example) we suppose *everything* is clean
+// and we don't perform any integrity check
+// ----------------------------------------------------------------------
+
+int main(int argc, char *argv[])
+{
+ if (argc < 3)
+ {
+ std::cerr << "Usage :" << std::endl <<
+ argv[0] << " input_papyrus output_dicom verbose" << std::endl;
+ return 1;
+ }
+
+ std::string filename = argv[1];
+ std::string output = argv[2];
+
+ if (argc > 3)
+ gdcm::Debug::DebugOn();
+
+ if( FileExists( output.c_str() ) )
+ {
+ if( !RemoveFile( output.c_str() ) )
+ {
+ std::cerr << "Ouch, the file exist, but I cannot remove it" << std::endl;
+ return 1;
+ }
+ }
+ gdcm::FileHelper *original = new gdcm::FileHelper( filename );
+ gdcm::File *h = original->GetFile();
+
+ // Look for private Papyrus Sequence
+ gdcm::SeqEntry *seqPapyrus= h->GetSeqEntry(0x0041, 0x1050);
+ if (!seqPapyrus)
+ {
+ std::cout << "NOT a Papyrus File" << std::endl;
+ delete h;
+ return 1;
+ }
+
+ gdcm::SQItem *sqi = seqPapyrus->GetFirstSQItem();
+ if (sqi == 0)
+ {
+ std::cout << "NO SQItem found within private Papyrus Sequence"
+ << std::endl;
+ delete h;
+ return 1;
+ }
+
+ std::string TransferSyntax;
+ std::string StudyDate;
+ std::string StudyTime;
+ std::string Modality;
+ std::string PatientName;
+ std::string MediaStSOPinstUID;
+
+// Get informations on the file :
+// Modality, Transfer Syntax, Study Date, Study Time
+// Patient Name, Media Storage SOP Instance UID, etc
+
+ MediaStSOPinstUID = h->GetEntryValue(0x0002,0x0002);
+ TransferSyntax = h->GetEntryValue(0x0002,0x0010);
+ StudyDate = sqi->GetEntryValue(0x0008,0x0020);
+ StudyTime = sqi->GetEntryValue(0x0008,0x0030);
+ Modality = sqi->GetEntryValue(0x0008,0x0060);
+ PatientName = sqi->GetEntryValue(0x0010,0x0010);
+
+ std::cout << "TransferSyntax " << TransferSyntax << std::endl;
+
+ std::string Rows;
+ std::string Columns;
+ std::string SamplesPerPixel;
+ std::string BitsAllocated;
+ std::string BitsStored;
+ std::string HighBit;
+ std::string PixelRepresentation;
+
+
+ // we brutally suppose all the images within a Papyrus file
+ // have the same caracteristics.
+ // if you're aware they have not, just move the GetEntryValue
+ // inside the loop
+
+ // Get caracteristics of the first image
+ SamplesPerPixel = sqi->GetEntryValue(0x0028,0x0002);
+ Rows = sqi->GetEntryValue(0x0028,0x0010);
+ Columns = sqi->GetEntryValue(0x0028,0x0011);
+ BitsAllocated = sqi->GetEntryValue(0x0028,0x0100);
+ BitsStored = sqi->GetEntryValue(0x0028,0x0101);
+ HighBit = sqi->GetEntryValue(0x0028,0x0102);
+ PixelRepresentation = sqi->GetEntryValue(0x0028,0x0102);
+
+ // just convert those needed to compute PixelArea length
+ int iRows = (uint32_t) atoi( Rows.c_str() );
+ int iColumns = (uint32_t) atoi( Columns.c_str() );
+ int iSamplesPerPixel = (uint32_t) atoi( SamplesPerPixel.c_str() );
+ int iBitsAllocated = (uint32_t) atoi( BitsAllocated.c_str() );
+
+ int lgrImage = iRows*iColumns * iSamplesPerPixel * (iBitsAllocated/8);
+
+ // compute number of images
+ int nbImages = seqPapyrus->GetNumberOfSQItems();
+ std::cout <<"Number of frames :" << nbImages << std::endl;
+
+ // allocate enough room to get the pixels of all images.
+ uint8_t *PixelArea = new uint8_t[lgrImage*nbImages];
+ uint8_t *currentPosition = PixelArea;
+ gdcm::BinEntry *pixels;
+
+ // declare and open the file
+ std::ifstream *Fp;
+ Fp = new std::ifstream(filename.c_str(), std::ios::in | std::ios::binary);
+ if( ! *Fp )
+ {
+ std::cout << "Cannot open file: " << filename << std::endl;
+ //gdcmDebugMacro( "Cannot open file: " << filename.c_str() );
+ delete Fp;
+ Fp = 0;
+ return 0;
+ }
+ // to be sure to be at the beginning
+ Fp->seekg(0, std::ios::end);
+
+ uint32_t offset;
+ std::string previousRows = Rows;
+ sqi = seqPapyrus->GetFirstSQItem();
+ while (sqi)
+ {
+ std::cout << "One more image read. Keep waiting" << std::endl;
+ Rows = sqi->GetEntryValue(0x0028,0x0010);
+ // minimum integrity check
+ if (Rows != previousRows)
+ {
+ std::cout << "Consistency check failed " << std::endl;
+ return 1;
+ }
+ // get the images pixels
+ pixels = sqi->GetBinEntry(0x7fe0,0x0010);
+ offset = pixels->GetOffset();
+ // perform a fseek, on offset length on the 'right' length
+ Fp->seekg(offset, std::ios::beg);
+ // perform a fread into the right place
+ Fp->read((char *)currentPosition, (size_t)lgrImage);
+ currentPosition +=lgrImage;
+
+ std::string previousRowNb = Rows;
+
+ sqi = seqPapyrus->GetNextSQItem();
+ }
+
+ // build up a new File, with file info + images info + global pixel area.
+
+ std::string NumberOfFrames = gdcm::Util::Format("%d", nbImages);
+
+ gdcm::File *n = new gdcm::File();
+
+ n->InsertValEntry(MediaStSOPinstUID, 0x0002,0x0002);
+ // Whe keep default gdcm Transfer Syntax (Explicit VR Little Endian)
+ // since using Papyrus one (Implicit VR Little Endian) is a mess
+ //n->InsertValEntry(TransferSyntax, 0x0002,0x0010);
+ n->InsertValEntry(StudyDate, 0x0008,0x0020);
+ n->InsertValEntry(StudyTime, 0x0008,0x0030);
+ n->InsertValEntry(Modality, 0x0008,0x0060);
+ n->InsertValEntry(PatientName, 0x0010,0x0010);
+
+ n->InsertValEntry(SamplesPerPixel, 0x0028,0x0002);
+ n->InsertValEntry(NumberOfFrames, 0x0028,0x0008);
+ n->InsertValEntry(Rows, 0x0028,0x0010);
+ n->InsertValEntry(Columns, 0x0028,0x0011);
+ n->InsertValEntry(BitsAllocated, 0x0028,0x0100);
+ n->InsertValEntry(BitsStored, 0x0028,0x0101);
+ n->InsertValEntry(HighBit, 0x0028,0x0102);
+ n->InsertValEntry(PixelRepresentation,0x0028,0x0102);
+
+ // create the file
+ gdcm::FileHelper *file = new gdcm::FileHelper(n);
+
+ file->SetImageData(PixelArea,lgrImage*nbImages);
+ file->SetWriteTypeToDcmExplVR();
+
+ //file->SetPrintLevel(2);
+ file->Print();
+
+ // Write the file
+ file->Write(argv[2]);
+ if (!file)
+ {
+ std::cout <<"Fail to open (write) file:[" << argv[2]<< "]" << std::endl;;
+ return 1;
+ }
+ return 0;
+}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff