--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: PcpdenseToDicom.cxx,v $
+ Language: C++
+ Date: $Date: 2008/09/04 14:10:44 $
+ 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 <fstream>
+#include <iostream>
+//#include <values.h>
+
+#if defined(__BORLANDC__)
+#include <ctype.h>
+#endif
+
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+#include "gdcmArgMgr.h"
+
+/**
+ * \brief
+ * Converts the "pcpdense" ".txt" (2008 version) files into 16 bits Dicom Files,
+ * Hope they don't change soon!
+ */
+
+void MakeDicomImage(unsigned short int *tabVal, int X, int Y, std::string dcmImageName,
+ const char * patientname, int nbFrames, std::string studyUID, std::string serieUID, std::string studyUID, int imgNum,bool m );
+
+void LoadImage(std::ifstream &from, unsigned short int * );
+
+void LoadImageX2(std::ifstream &from, unsigned short int * );
+bool verbose;
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ " \n pcpdenseToDicom :\n ",
+ " Converts the '.txt' files into 16 bits Dicom Files, ",
+ " usage: ",
+ " pcpdenseToDicom rootfilename=... ",
+ " (e.g.. : meas_MID380_DENSE_stacked_slices_aif_FID81637)",
+ " numberOfSlices = (default : 3) ",
+ " X2 : multiply x 2 image size ",
+ " m :create multiframe files instead of image stacks ",
+ " [patientname = Patient's name] ",
+ " [verbose] [debug] ",
+ " ",
+ " verbose : user wants to run the program in 'verbose mode' ",
+ " debug : *developer* 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;
+ }
+ // Seems that ArgMgrWantString doesn't work on MacOS
+ if(!am->ArgMgrDefined("rootfilename"))
+ {
+ std::cout << "'rootfilename' is mandatory" << std::endl;
+ exit(0);
+ }
+
+ const char *rootfilename = am->ArgMgrWantString("rootfilename",usage);
+ int numberOfSlices = am->ArgMgrGetInt("numberOfSlices",3);
+ const char *patientName = am->ArgMgrGetString("patientname", "Patient^Name");
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ verbose = ( 0 != am->ArgMgrDefined("verbose") );
+ bool X2 = ( 0 != am->ArgMgrDefined("X2") );
+ bool multiframe = ( 0 != am->ArgMgrDefined("m") );
+
+ // 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
+
+ // ----- Begin Processing -----
+
+ std::ostringstream Ecc;
+ std::ostringstream perf;
+ std::ostringstream WashoutTc;
+
+ std::string strSerieUID;
+ std::string strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ std::string dcmImageName, textFileName, patientname,/* studyUID, serieUID, */ serieDescr ;
+ std::string deb(rootfilename);
+
+ unsigned short int *image;
+
+ int NX, NY;
+
+ // Get some info
+ // -------------
+
+ {
+ Ecc.str(rootfilename);
+ Ecc << Ecc.str() << "_s0" << "_Ecc.txt";
+
+ std::ifstream fromEcc( Ecc.str().c_str() );
+ if ( !fromEcc )
+ {
+ std::cout << "Can't open file [" << Ecc.str() << "]" << std::endl;
+ exit(0);
+ }
+ std::string str1;
+
+ fromEcc >> str1;
+ fromEcc >> str1;
+
+ fromEcc >> NX;
+ fromEcc >> NY;
+ std::cout << "NX, NY : " << NX << ", " << NY << std::endl;
+ }
+
+ int mult;
+ if (X2)
+ mult=4;
+ else
+ mult=1;
+
+ if (multiframe)
+ image = new unsigned short int[NX*NY*mult*numberOfSlices];
+ else
+ image = new unsigned short int[NX*NY*mult];
+
+
+
+ // === Ecc ===
+
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+
+ if (!multiframe) {
+
+ for (int i=0; i<numberOfSlices; i++)
+ {
+ Ecc.str(rootfilename);
+ Ecc << Ecc.str() << "_s" << i << "_Ecc.txt";
+
+ std::ifstream fromEcc( Ecc.str().c_str() );
+ if ( !fromEcc )
+ {
+ std::cout << "Can't open file [" << Ecc.str() << "]" << std::endl;
+ exit(0);
+ }
+ std::cout << "Open file [" << Ecc.str() << "] : OK" << std::endl;
+
+ if (X2)
+ LoadImageX2(fromEcc, image);
+ else
+ LoadImage(fromEcc, image);
+ fromEcc.close();
+
+ dcmImageName = Ecc.str() + ".dcm";
+
+ MakeDicomImage(image, NX, NY, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i, multiframe );
+ } // end : for (int i=0; i<numberOfSlices
+ delete []image;
+}
+
+
+ if (multiframe) {
+
+ for (int i=0; i<numberOfSlices; i++)
+ {
+ Ecc.str(rootfilename);
+ Ecc << Ecc.str() << "_s" << i << "_Ecc.txt";
+
+ std::ifstream fromEcc( Ecc.str().c_str() );
+ if ( !fromEcc )
+ {
+ std::cout << "Can't open file [" << Ecc.str() << "]" << std::endl;
+ exit(0);
+ }
+
+ std::cout << "Open file [" << Ecc.str() << "] : OK" << std::endl;
+ if (X2)
+ LoadImageX2(fromEcc ,&image[NX*NY*i] );
+ else
+ LoadImage(fromEcc, &image[NX*NY*i] );
+
+ fromEcc.close();
+ } // end : for (int i=0; i<numberOfSlices
+
+ dcmImageName = deb + "_Ecc.dcm";
+ MakeDicomImage(image, NX, NY, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, 0, multiframe );
+
+ } // end : if (multiframe)
+
+
+
+// === perf ===
+
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+
+ if (!multiframe) {
+ for (int i=0; i<numberOfSlices; i++)
+ {
+ perf.str(rootfilename);
+ perf << perf.str() << "_s" << i << "_perf.txt";
+
+ std::ifstream fromperf( perf.str().c_str() );
+ if ( !fromperf )
+ {
+ std::cout << "Can't open file [" << perf.str() << "]" << std::endl;
+ exit(0);
+ }
+ std::cout << "Open file [" << perf.str() << "] : OK" << std::endl;
+
+ if (X2)
+ LoadImageX2(fromperf ,image );
+ else
+ LoadImage(fromperf, image );
+
+ fromperf.close();
+
+ dcmImageName = Ecc.str() + ".dcm";
+ MakeDicomImage(image, NX, NY, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i, multiframe );
+
+ } // end : for (int i=0; i<numberOfSlices
+ }
+
+
+ if (multiframe) {
+ for (int i=0; i<numberOfSlices; i++)
+ {
+ perf.str(rootfilename);
+ perf << perf.str() << "_s" << i << "_perf.txt";
+
+ std::ifstream fromperf( perf.str().c_str() );
+ if ( !fromperf )
+ {
+ std::cout << "Can't open file [" << perf.str() << "]" << std::endl;
+ exit(0);
+ }
+ std::cout << "Open file [" << perf.str() << "] : OK" << std::endl;
+
+ if (X2)
+ LoadImageX2(fromperf, &image[NX*NY*i]);
+ else
+ LoadImage(fromperf, &image[NX*NY*i] );
+
+ fromperf.close();
+ } // end : for (int i=0; i<numberOfSlices
+
+ dcmImageName = deb + "_perf.dcm";
+ MakeDicomImage(image, NX, NY, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, numberOfSlices, multiframe );
+ }
+
+
+
+// === WashoutTc ===
+
+
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+
+ if (multiframe) {
+ for (int i=0; i<numberOfSlices; i++)
+ {
+ WashoutTc.str(rootfilename);
+ WashoutTc << WashoutTc.str() << "_s" << i << "_WashoutTc.txt";
+
+ std::ifstream fromWashoutTc( WashoutTc.str().c_str() );
+ if ( !fromWashoutTc )
+ {
+ std::cout << "Can't open file [" << WashoutTc.str() << "]" << std::endl;
+ exit(0);
+ }
+ std::cout << "Open file [" << WashoutTc.str() << "] : OK" << std::endl;
+
+ if (X2)
+ LoadImageX2(fromWashoutTc, &image[NX*NY*i]);
+ else
+ LoadImage(fromWashoutTc, &image[NX*NY*i] );
+ fromWashoutTc.close();
+
+ } // end : for (int i=0; i<numberOfSlices
+
+ dcmImageName = deb + "_WashoutTc.dcm";
+ MakeDicomImage(image, NX, NY, dcmImageName, patientName, numberOfSlices, strStudyUID, strSerieUID, serieDescr, numberOfSlices, multiframe );
+ }
+
+
+ if (!multiframe) {
+
+ for (int i1=0; i1<numberOfSlices; i1++)
+ {
+ WashoutTc.str(rootfilename);
+ WashoutTc << WashoutTc.str() << "_s" << i1 << "_WashoutTc.txt";
+
+ std::ifstream fromWashoutTc( WashoutTc.str().c_str() );
+ if ( !fromWashoutTc )
+ {
+ std::cout << "Can't open file [" << WashoutTc.str() << "]" << std::endl;
+ exit(0);
+ }
+
+ std::cout << "Open file [" << WashoutTc.str() << "] : OK" << std::endl;
+ if (X2)
+ LoadImageX2(fromWashoutTc,image );
+ else
+ LoadImage(fromWashoutTc,image );
+ fromWashoutTc.close();
+
+ dcmImageName = Ecc.str() + ".dcm";
+ MakeDicomImage(image, NX, NY, dcmImageName, patientName, 1, strStudyUID, strSerieUID, serieDescr, i1, multiframe );
+ } // end : for (int i=0; i<numberOfSlices
+
+ }
+
+ delete []image;
+ return 1;
+}
+
+// =====================================================================================================================
+
+void LoadImage(std::ifstream &from, unsigned short int *image)
+{
+// in any file ".txt" :
+
+/*
+XY Dimensions 47 50
+ 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ ...
+*/
+
+ if (!from)
+ return;
+
+ std::string str1;
+
+ from >> str1;
+ from >> str1;
+
+ int NX, NY;
+ from >> NX;
+ from >> NY;
+ std::cout << "NX, NY : " << NX << ", " << NY << std::endl;
+
+ float pixelValue;
+
+ int i, j;
+ for( i=0;i<NY;i++)
+ for(j=0;j<NX;j++) {
+ from >> pixelValue;
+ image[i*NX+j] = (unsigned short int)(pixelValue * 1000.)
+ }
+}
+
+
+// =====================================================================================================================
+
+void LoadImageX2(std::ifstream &from, unsigned short int *image )
+{
+// in any file ".txt" :
+
+/*
+XY Dimensions 47 50
+ 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ ...
+*/
+
+ if (!from)
+ return;
+
+ std::string str1;
+
+ from >> str1;
+ from >> str1;
+
+ int NX, NY;
+ from >> NX;
+ from >> NY;
+ std::cout << "NX, NY : " << NX << ", " << NY << std::endl;
+
+ float pixelValue;
+
+ int i, j;
+ for( i=0;i<NY;i++) {
+ for(j=0;j<NX;j++) {
+ from >> pixelValue;
+ pixelValue*=1000.;
+ image[i*4*NX + j*2] = image[i*4*NX + j*2+1] = image[(i*4+2)*NX + j*2] = image[(i*4+2)*NX + j*2+1] = (unsigned short int)(pixelValue);
+ }
+ }
+
+}
+// =====================================================================================================================================
+
+
+void MakeDicomImage(unsigned short int *tabVal, int X, int Y, std::string dcmImageName, const char * patientName, int nbFrames, std::string studyUID, std::string serieUID, std::string SerieDescr, int imgNum, bool m)
+{
+
+ // GDCM_NAME_SPACE::Debug::DebugOn();
+
+ std::ostringstream str;
+
+ GDCM_NAME_SPACE::File *file;
+ file = GDCM_NAME_SPACE::File::New();
+
+ // Set the image size
+ str.str("");
+ str << X;
+ file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << Y;
+ file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
+
+ // Set the pixel type
+ // 16; //8, 16, 32
+ file->InsertEntryString("16",0x0028,0x0100,"US"); // Bits Allocated
+
+ str.str("");
+ str << 16; // may be 12 or 16 if componentSize =16
+ file->InsertEntryString("16",0x0028,0x0101,"US"); // Bits Stored
+ file->InsertEntryString("15",0x0028,0x0102,"US"); // High Bit
+
+ // Set the pixel representation // 0/1 , 0=unsigned
+ file->InsertEntryString("1",0x0028,0x0103, "US"); // Pixel Representation
+
+ // Set the samples per pixel // 1:Grey level, 3:RGB
+ file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
+
+
+ if (nbFrames != 1)
+ {
+ str.str("");
+ str << nbFrames;
+ file->InsertEntryString(str.str(),0x0028,0x0008,"IS"); // Number of Frames
+ }
+
+ if (strlen(patientName) != 0)
+ file->InsertEntryString(patientName,0x0010,0x0010, "PN"); // Patient's Name
+
+ file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
+ file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
+
+ file->InsertEntryString(SerieDescr,0x0008,0x103e, "LO"); // Series Description
+
+// 0020 0037 DS 6 Image Orientation (Patient)
+ file->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial (Tant pis!)
+
+// 0020 0032 DS 3 Image Position (Patient)
+ char charImagePosition[256];
+ sprintf(charImagePosition,"0.0\\0.0\\%f",(float)imgNum);
+ file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient)
+
+// 0020 0x1041 DS 1 Slice Location
+ sprintf(charImagePosition,"%f",float(imgNum));
+ file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
+/*
+ // Set Rescale Intercept
+ str.str("");
+ str << div;
+ file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
+
+ // Set Rescale Slope
+ str.str("");
+ str << mini;
+ file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
+*/
+
+ GDCM_NAME_SPACE::FileHelper *fileH;
+ fileH = GDCM_NAME_SPACE::FileHelper::New(file);
+ // cast is just to avoid warnings (*no* conversion is performed)
+ //fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*sizeof(uint16_t)); // troubles when maxX, mayY are *actually* float!
+
+ fileH->SetImageData((uint8_t *)tabVal,X*Y*nbFrames*sizeof(uint16_t));
+ fileH->SetWriteModeToRaw();
+ fileH->SetWriteTypeToDcmExplVR();
+
+ if( !fileH->Write(dcmImageName))
+ std::cout << "Failed for [" << dcmImageName << "]\n"
+ << " File is unwrittable" << std::endl;
+
+ // file->Print();
+
+ // delete img;
+ file->Delete();
+ fileH->Delete();
+}
+
+
+
+// =====================================================================================================================
+
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