--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: Dense2007ToDicom.cxx,v $
+ Language: C++
+ Date: $Date: 2007/07/10 11:00:50 $
+ 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 <fstream>
+#include <iostream>
+//#include <values.h>
+
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+
+#include "gdcmArgMgr.h"
+
+/**
+ * \brief
+ * Converts the "Dense" ".txt" (2007 version) files into 16 bits Dicom Files,
+ * Hope they don't change soon!
+ */
+
+
+void LoadPeakStrain(std::ifstream &from, std::string imageName);
+void LoadStrain(std::ifstream &from, std::string imageName);
+void MakeDicomImage(float *tabVal, float *X, float *Y, float *Z, int NP, std::string dcmImageName);
+
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ " \n Dense2007ToDicom :\n ",
+ " Converts the '.txt' files into 16 bits Dicom Files, ",
+ " usage: ",
+ " Dense2007ToDicom strain=...strain.txt peak_strain=...peak_strain.txt ",
+ " [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;
+ }
+
+ const char *strain = am->ArgMgrWantString("strain",usage);
+ const char *peak_strain = am->ArgMgrWantString("peak_strain",usage);
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ int verbose = am->ArgMgrDefined("verbose");
+
+
+ // 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::ifstream fromPeakStrain( peak_strain );
+ if ( !fromPeakStrain )
+ {
+ std::cout << "Can't open file" << peak_strain << std::endl;
+ exit(0);
+ }
+
+ std::ifstream fromStrain( strain );
+ if ( !fromStrain )
+ {
+ std::cout << "Can't open file" << strain << std::endl;
+ exit(0);
+ }
+
+ std::cout << "Success in open file" << peak_strain << std::endl;
+ LoadPeakStrain(fromPeakStrain, peak_strain);
+ fromPeakStrain.close();
+
+ std::cout << "Success in open file" << strain << std::endl;
+ LoadStrain(fromStrain, strain);
+ fromStrain.close();
+
+}
+
+// =====================================================================================================================
+
+void LoadPeakStrain(std::ifstream &from, std::string textFileName)
+{
+// in sax_base_slice0_peak_strain.txt :
+
+/*
+Number of material points (NP) = 181
+Origin of (readout, phase enc, slice sel) coordinates in 3D = 87.3243 3.19392
+88.2381
+Readout direction in 3D = -0.162314 -0.0771294 -0.983720
+Phase Enc. direction in 3D = -0.540606 -0.827052 0.154046
+Slice select direction in 3D = 0.825469 -0.556809 -0.0925458
+The following are the (readout, phase enc, slice sel) coordinates (mm) of the grid points for which strains are calculated,
+followed by their peak Ecc strain, an array of NP elements,
+followed by their peak Err strain, an array of NP elements,
+followed by their peak E11 strain, an array of NP elements,
+followed by their Peak E22 strain, an array of NP elements,
+ 42.0000 10.0000 0.000000
+ ...
+ -0.154905 -0.0840482 -0.157350 -0.221403 -0.168118 -0.131331
+ -0.153781 -0.148481 -0.166602 -0.232858 -0.222650 -0.213712
+ ...
+*/
+
+ if (!from)
+ return;
+
+ std::string str1;
+ int NP;
+
+ //Number of material points (NP) = 181
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> NP;
+
+ std::cout << "NP : " << NP << std::endl;
+
+ //Origin of (readout, phase enc, slice sel) coordinates in 3D = 87.3243 3.19392 88.2381
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float readout, phase_enc, slice_sel;
+ from >> readout;
+ from >> phase_enc;
+ from >> slice_sel;
+ std::cout << " readout " << readout << " phase_enc " << phase_enc << " slice_sel " << slice_sel << std::endl;
+
+ // Readout direction in 3D = -0.162314 -0.0771294 -0.983720
+
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float readoutX, readoutY, readoutZ;
+ from >> readoutX;
+ from >> readoutY;
+ from >> readoutZ;
+ std::cout << " readoutX " << readoutX << " readoutY " << readoutY << " readoutZ " << readoutZ << std::endl;
+
+// Phase Enc. direction in 3D = -0.540606 -0.827052 0.154046
+
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float phase_encX, phase_encY, phase_encZ;
+ from >> phase_encX;
+ from >> phase_encY;
+ from >> phase_encZ;
+ std::cout << " phase_encX " << phase_encX << " phase_encY " << phase_encY << " phase_encZ " << phase_encZ << std::endl;
+
+// Slice select direction in 3D = 0.825469 -0.556809 -0.0925458
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float slice_selX, slice_selY, slice_selZ;
+ from >> slice_selX;
+ from >> slice_selY;
+ from >> slice_selZ;
+ std::cout << " slice_selX " << slice_selX << " slice_selY " << slice_selY << " slice_selZ " << slice_selZ << std::endl;
+
+
+
+// Skip 5 lines :
+/*
+The following are the (readout, phase enc, slice sel) coordinates (mm) of the grid points for which strains are calculated,
+followed by their peak Ecc strain, an array of NP elements,
+followed by their peak Err strain, an array of NP elements,
+followed by their peak E11 strain, an array of NP elements,
+followed by their Peak E22 strain, an array of NP elements,
+*/
+
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------stop skipping ---------------- " << std::endl;
+
+ float *X = new float[NP];
+ float *Y = new float[NP];
+ float *Z = new float[NP];
+
+ char c;
+ int i;
+ for (i=0; i<NP; i++) {
+ from >> X[i];
+ for (;;) {
+ if (!from.get(c))
+ break;
+ if (!isspace(c)) {
+ from.putback(c);
+ break;
+ }
+ }
+ from >> Y[i];
+ for (;;) {
+ if (!from.get(c))
+ break;
+ if (!isspace(c)) {
+ from.putback(c);
+ break;
+ }
+ }
+ from >> Z[i];
+ }
+
+ std::cout << "--------------- Ecc_strain ------------------" << std::endl;
+ float *ecc_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> ecc_strain[i];
+ std::cout << ecc_strain[i] << std::endl;
+ }
+
+ std::cout << "--------------- Err_strain ------------------" << std::endl;
+ float *err_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> err_strain[i];
+ std::cout << err_strain[i] << std::endl;
+ }
+
+ std::cout << "--------------- E11_strain ------------------" << std::endl;
+ float *e11_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> e11_strain[i];
+ std::cout << e11_strain[i] << std::endl;
+ }
+
+ std::cout << "--------------- E22_strain ------------------" << std::endl;
+ float *e22_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> e22_strain[i];
+ std::cout << e22_strain[i] << std::endl;
+ }
+
+ std::string dcmImageName;
+
+//followed by their peak Ecc strain, an array of NP elements,
+ dcmImageName = textFileName + "_peak_Ecc_strain.dcm";
+ MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName);
+
+//followed by their peak Err strain, an array of NP elements,
+ dcmImageName = textFileName + "_peak_Err_strain.dcm";
+ MakeDicomImage(err_strain, X, Y, Z, NP, dcmImageName);
+
+//followed by their peak E11 strain, an array of NP elements,
+ dcmImageName = textFileName + "_peak_E11_strain.dcm";
+ MakeDicomImage(e11_strain, X, Y, Z, NP, dcmImageName);
+
+//followed by their Peak E22 strain, an array of NP elements,
+ dcmImageName = textFileName + "_peak_E22_strain.dcm";
+ MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName);
+}
+
+// =====================================================================================================================
+
+void LoadStrain(std::ifstream &from, std::string textFileName)
+{
+
+// in sax_base_slice0_strain.txt :
+/*
+Number of cine frames = 18
+Temporal resolution = 32.0000 ms
+First frame starts at 48.0000 ms
+Number of material points (NP) = 181
+Origin of (readout, phase enc, slice sel) coordinates in 3D = 87.324341 3.193918 88.238113
+Readout direction in 3D = -0.162314 -0.0771294 -0.983720
+Phase Enc. direction in 3D = -0.540606 -0.827052 0.154046
+Slice select direction in 3D = 0.825469 -0.556809 -0.0925458
+The following are the (readout, phase enc, slice sel) coordinates (mm) of the grid points for which strains are calculated,
+followed by their Ecc strain, an array of dimensions(NP, number of cine frames),
+followed by their Err strain, an array of dimensions(NP, number of cine frames),
+followed by their E11 strain, an array of dimensions(NP, number of cine frames),
+followed by their E22 strain, an array of dimensions(NP, number of cine frames),
+Note that RV Err, E11 and E22 strains are not calculated due to the small thickness.
+ 42.0000 10.0000 0.000000
+ 44.0000 10.0000 0.000000
+ ...
+ -0.0622793 -0.0840482 -0.157350 -0.196722 -0.105844 -0.131331
+ -0.153781 -0.00940573 -0.0542236 -0.100403 -0.0369671 -0.0696840
+*/
+
+ if (!from)
+ return;
+
+ std::string str1;
+ int NP; // Number of Pints
+ int NCF; // Number of cine frames
+ float TR; // Temporal resolution
+ float FFS; // First frame starts
+
+ // Number of cine frames = 18
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> NCF;
+
+ // Temporal resolution = 32.0000 ms
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> TR;
+ from >> str1;
+
+ // First frame starts at 48.0000 ms
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> FFS;
+ from >> str1;
+
+ //Number of material points (NP) = 181
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> NP;
+
+ std::cout << "NP : " << NP << std::endl;
+
+ //Origin of (readout, phase enc, slice sel) coordinates in 3D = 87.324341 3.193918 88.238113
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float readout, phase_enc, slice_sel;
+ from >> readout;
+ from >> phase_enc;
+ from >> slice_sel;
+ std::cout << " readout " << readout << " phase_enc " << phase_enc << " slice_sel " << slice_sel << std::endl;
+
+ // Readout direction in 3D = -0.162314 -0.0771294 -0.983720
+
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float readoutX, readoutY, readoutZ;
+ from >> readoutX;
+ from >> readoutY;
+ from >> readoutZ;
+ std::cout << " readoutX " << readoutX << " readoutY " << readoutY << " readoutZ " << readoutZ << std::endl;
+
+// Phase Enc. direction in 3D = -0.540606 -0.827052 0.154046
+
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float phase_encX, phase_encY, phase_encZ;
+ from >> phase_encX;
+ from >> phase_encY;
+ from >> phase_encZ;
+ std::cout << " phase_encX " << phase_encX << " phase_encY " << phase_encY << " phase_encZ " << phase_encZ << std::endl;
+
+// Slice select direction in 3D = 0.825469 -0.556809 -0.0925458
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1;
+
+ float slice_selX, slice_selY, slice_selZ;
+ from >> slice_selX;
+ from >> slice_selY;
+ from >> slice_selZ;
+ std::cout << " slice_selX " << slice_selX << " slice_selY " << slice_selY << " slice_selZ " << slice_selZ << std::endl;
+
+
+
+// Skip 6 lines :
+/*
+The following are the (readout, phase enc, slice sel) coordinates (mm) of the grid points for which strains are calculated,
+followed by their Ecc strain, an array of dimensions(NP, number of cine frames),
+followed by their Err strain, an array of dimensions(NP, number of cine frames),
+followed by their E11 strain, an array of dimensions(NP, number of cine frames),
+followed by their E22 strain, an array of dimensions(NP, number of cine frames),
+Note that RV Err, E11 and E22 strains are not calculated due to the small thickness.
+*/
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------start skipping 1 line---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------stop skipping ---------------- " << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+std::cout << "------------stop skipping ---------------- " << std::endl;
+
+ float *X = new float[NP];
+ float *Y = new float[NP];
+ float *Z = new float[NP];
+
+ char c;
+ int i;
+ for (i=0; i<NP; i++) {
+
+ from >> X[i];
+ for (;;) {
+ if (!from.get(c))
+ break;
+ if (!isspace(c)) {
+ from.putback(c);
+ break;
+ }
+ }
+ from >> Y[i];
+ for (;;) {
+ if (!from.get(c))
+ break;
+ if (!isspace(c)) {
+ from.putback(c);
+ break;
+ }
+ }
+ from >> Z[i];
+ }
+
+ std::cout << "--------------- Ecc_strain ------------------" << std::endl;
+ float *ecc_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> ecc_strain[i];
+ std::cout << ecc_strain[i] << std::endl;
+ }
+
+ std::cout << "--------------- Err_strain ------------------" << std::endl;
+ float *err_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> err_strain[i];
+ std::cout << err_strain[i] << std::endl;
+ }
+
+ std::cout << "--------------- E11_strain ------------------" << std::endl;
+ float *e11_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> e11_strain[i];
+ std::cout << e11_strain[i] << std::endl;
+ }
+
+ std::cout << "--------------- E22_strain ------------------" << std::endl;
+ float *e22_strain = new float[NP];
+ for (i=0; i<NP; i++) {
+ from >> e22_strain[i];
+ std::cout << e22_strain[i] << std::endl;
+ }
+
+ std::string dcmImageName;
+
+//followed by their Ecc strain, an array of NP elements,
+ dcmImageName = textFileName + "_Ecc_strain.dcm";
+ MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName);
+
+//followed by their Err strain, an array of NP elements,
+ dcmImageName = textFileName + "_Err_strain.dcm";
+ MakeDicomImage(err_strain, X, Y, Z, NP, dcmImageName);
+
+//followed by their E11 strain, an array of NP elements,
+ dcmImageName = textFileName + "_E11_strain.dcm";
+ MakeDicomImage(e11_strain, X, Y, Z, NP, dcmImageName);
+
+//followed by their E22 strain, an array of NP elements,
+ dcmImageName = textFileName + "_E22_strain.dcm";
+ MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName);
+
+}
+
+
+// =====================================================================================================================
+
+
+void MakeDicomImage(float *tabVal, float *X, float *Y, float *Z, int NP, std::string dcmImageName)
+{
+ float minX = 999., minY = 999., minZ = 999.;
+ float maxX = 0., maxY = 0., maxZ = 0.;
+ int i;
+ for (i=0; i<NP; i++) {
+ // std::cout << X[i] << " " << Y[i] << " " << Z[i] << std::endl;
+ if(maxX < X[i])
+ maxX = X[i];
+ if(maxY < Y[i])
+ maxY = Y[i];
+ if(maxZ < Z[i])
+ maxZ = Z[i];
+
+ if(minX > X[i])
+ minX = X[i];
+ if(minY > Y[i])
+ minY = Y[i];
+ if(minZ > Z[i])
+ minZ = Z[i];
+
+ }
+ std::cout << "Min X,Y,Z " << minX << " " << minY << " " << minZ << std::endl;
+ std::cout << "Max X,Y,Z " << maxX << " " << maxY << " " << maxZ << std::endl;
+ std::cout << "Size X,Y,Z " << maxX-minX << " " << maxY-minY << " " << maxZ-minZ << std::endl;
+
+
+ uint16_t *img = new uint16_t[int(maxX*maxY)];
+
+ for(int i3=0;i3<int(maxX*maxY);i3++)
+ img[i3] = 0;
+
+ for(int i2=0; i2<NP; i2++) {
+ img[ int(maxX -(X[i2]-1))+ int((maxY -Y[i2])* maxX) ] = int(tabVal[i2]*100);
+ }
+
+ // 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 << (int)maxX;
+ file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << (int)maxY;
+ 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
+
+/*
+ // 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)
+ fileH->SetImageData((uint8_t *)img,int(maxX*maxY)*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();
+}
projects / gdcm.git / commitdiff