Program: gdcm
Module: $RCSfile: Dense2007ToDicom.cxx,v $
Language: C++
- Date: $Date: 2008/03/17 13:16:10 $
- Version: $Revision: 1.6 $
+ Date: $Date: 2008/03/28 15:36:57 $
+ Version: $Revision: 1.7 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmFileHelper.h"
#include "gdcmDebug.h"
#include "gdcmDirList.h"
-
+#include "gdcmUtil.h"
#include "gdcmArgMgr.h"
/**
* Hope they don't change soon!
*/
+void LoadPeakStrain(std::ifstream &from, std::string imageName, const char * patientname, std::string studyUID);
+void LoadStrain(std::ifstream &from, std::string imageName, const char * patientname, bool createMultiFrame, std::string studyUID);
+void MakeDicomImage(float *tabVal, float *X, float *Y, float *Z, int NP, std::string dcmImageName,
+ const char * patientname, int nbFrames, std::string studyUID, std::string serieUID);
-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 verbose;
+bool verbose;
int main(int argc, char *argv[])
{
" Converts the '.txt' files into 16 bits Dicom Files, ",
" usage: ",
" Dense2007ToDicom strain=...strain.txt peak_strain=...peak_strain.txt ",
+ " [patientname = Patient's name] ",
+ " [m]ultiframe ",
" [verbose] [debug] ",
" ",
" verbose : user wants to run the program in 'verbose mode' ",
const char *strain = am->ArgMgrWantString("strain",usage);
const char *peak_strain = am->ArgMgrWantString("peak_strain",usage);
+
+ const char *patientName = am->ArgMgrGetString("patientname");
+ bool createMultiFrame = (am->ArgMgrDefined("m") != 0);
+
if (am->ArgMgrDefined("debug"))
GDCM_NAME_SPACE::Debug::DebugOn();
- verbose = am->ArgMgrDefined("verbose");
+ verbose = ( 0 != am->ArgMgrDefined("verbose") );
// if unused Param we give up
if ( am->ArgMgrPrintUnusedLabels() )
// ----- Begin Processing -----
-
std::ifstream fromPeakStrain( peak_strain );
if ( !fromPeakStrain )
{
- std::cout << "Can't open file" << peak_strain << std::endl;
+ 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;
+ std::cout << "Can't open file [" << strain << "]" << std::endl;
exit(0);
- }
+ }
+
+ std::string strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
- std::cout << "Success in open file" << peak_strain << std::endl;
- LoadPeakStrain(fromPeakStrain, peak_strain);
+ std::cout << "Success in open file [" << peak_strain << "]" << std::endl;
+ LoadPeakStrain(fromPeakStrain, peak_strain, patientName,strStudyUID);
fromPeakStrain.close();
- std::cout << "Success in open file" << strain << std::endl;
- LoadStrain(fromStrain, strain);
+ std::cout << "Success in open file [" << strain << "]" << std::endl;
+ LoadStrain(fromStrain, strain, patientName, createMultiFrame, strStudyUID);
fromStrain.close();
return 1;
}
// =====================================================================================================================
-void LoadPeakStrain(std::ifstream &from, std::string textFileName)
+void LoadPeakStrain(std::ifstream &from, std::string textFileName, const char * patientname,std::string studyUID)
{
// in sax_base_slice0_peak_strain.txt :
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;
-
+
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;
-
+
float phase_encX, phase_encY, phase_encZ;
from >> phase_encX;
from >> phase_encY;
from >> str1;
from >> str1;
from >> str1;
-
+
float slice_selX, slice_selY, slice_selZ;
from >> slice_selX;
from >> slice_selY;
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,
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;
}
}
-
- from >> Y[i];
+
+ from >> Y[i];
for (;;) {
if (!from.get(c))
break;
from.putback(c);
break;
}
- }
+ }
from >> Z[i];
-
+
} // end for i<NP
std::cout << "--------------- Ecc_strain ------------------" << std::endl;
float *ecc_strain = new float[NP];
for (i=0; i<NP; i++) {
- from >> ecc_strain[i];
- if (verbose)
- std::cout << ecc_strain[i] << std::endl;
+ from >> ecc_strain[i];
+ if (verbose)
+ std::cout << ecc_strain[i] << std::endl;
}
+ delete []ecc_strain;
std::cout << "--------------- Err_strain ------------------" << std::endl;
float *err_strain = new float[NP];
for (i=0; i<NP; i++) {
- from >> err_strain[i];
- if (verbose)
- std::cout << err_strain[i] << std::endl;
+ from >> err_strain[i];
+ if (verbose)
+ std::cout << err_strain[i] << std::endl;
}
-
+ delete []err_strain;
+
std::cout << "--------------- E11_strain ------------------" << std::endl;
float *e11_strain = new float[NP];
for (i=0; i<NP; i++) {
- from >> e11_strain[i];
- if (verbose)
- std::cout << e11_strain[i] << std::endl;
+ from >> e11_strain[i];
+ if (verbose)
+ std::cout << e11_strain[i] << std::endl;
}
-
+ delete []e11_strain;
+
std::cout << "--------------- E22_strain ------------------" << std::endl;
float *e22_strain = new float[NP];
for (i=0; i<NP; i++) {
- from >> e22_strain[i];
- if (verbose)
- std::cout << e22_strain[i] << std::endl;
+ from >> e22_strain[i];
+ if (verbose)
+ std::cout << e22_strain[i] << std::endl;
}
-
- std::string dcmImageName;
+ delete []e22_strain;
+ std::string dcmImageName;
+ std::string serieUID;
+
//followed by their peak Ecc strain, an array of NP elements,
+ serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
dcmImageName = textFileName + "_peak_Ecc_strain.dcm";
- MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName);
+ MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
//followed by their peak Err strain, an array of NP elements,
+ serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
dcmImageName = textFileName + "_peak_Err_strain.dcm";
- MakeDicomImage(err_strain, X, Y, Z, NP, dcmImageName);
-
+ MakeDicomImage(err_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
+
//followed by their peak E11 strain, an array of NP elements,
+ serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
dcmImageName = textFileName + "_peak_E11_strain.dcm";
- MakeDicomImage(e11_strain, X, Y, Z, NP, dcmImageName);
-
+ MakeDicomImage(e11_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
+
//followed by their Peak E22 strain, an array of NP elements,
+ serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
dcmImageName = textFileName + "_peak_E22_strain.dcm";
- MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName);
+ MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
}
// =====================================================================================================================
-void LoadStrain(std::ifstream &from, std::string textFileName)
+void LoadStrain(std::ifstream &from, std::string textFileName, const char * patientname, bool createMultiFrame, std::string studyUID)
{
// in sax_base_slice0_strain.txt :
return;
std::string str1;
- int NP; // Number of Pints
+ int NP; // Number of Points
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 >> 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;
-
+
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;
-
+
float phase_encX, phase_encY, phase_encZ;
from >> phase_encX;
from >> phase_encY;
from >> Z[i];
}
+char frame[10];
+std::string dcmImageName;
+std::string serieUID;
+
+std::cout << "=======================================================================================" << createMultiFrame << std::endl;
+if(!createMultiFrame) { // One image per file here (single frame)
+
+serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+float *ecc_strain = new float[NP];
+for (int nbr_of_frames=0; nbr_of_frames < NCF; nbr_of_frames++)
+{
+sprintf(frame, "_%d", nbr_of_frames);
+
std::cout << "--------------- Ecc_strain ------------------" << std::endl;
- float *ecc_strain = new float[NP];
for (i=0; i<NP; i++) {
from >> ecc_strain[i];
if (verbose)
std::cout << ecc_strain[i] << std::endl;
}
-
+//followed by their Ecc strain, an array of NP elements,
+ dcmImageName = textFileName + frame + "_Ecc_strain.dcm";
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
+}// end for nbr_of_frames
+delete []ecc_strain;
+
+serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+float *err_strain = new float[NP];
+for (int nbr_of_frames=0; nbr_of_frames < NCF; nbr_of_frames++)
+{
+sprintf(frame, "_%d", nbr_of_frames);
std::cout << "--------------- Err_strain ------------------" << std::endl;
- float *err_strain = new float[NP];
for (i=0; i<NP; i++) {
from >> err_strain[i];
if (verbose)
std::cout << err_strain[i] << std::endl;
}
-
+//followed by their Err strain, an array of NP elements,
+ dcmImageName = textFileName + frame + "_Err_strain.dcm";
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(err_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
+}// end for nbr_of_frames
+delete []err_strain;
+
+serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+float *e11_strain = new float[NP];
+for (int nbr_of_frames=0; nbr_of_frames < NCF; nbr_of_frames++)
+{
+sprintf(frame, "_%d", nbr_of_frames);
std::cout << "--------------- E11_strain ------------------" << std::endl;
- float *e11_strain = new float[NP];
for (i=0; i<NP; i++) {
from >> e11_strain[i];
if (verbose)
std::cout << e11_strain[i] << std::endl;
}
-
+//followed by their E11 strain, an array of NP elements,
+ dcmImageName = textFileName + frame + "_E11_strain.dcm";
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(e11_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
+}// end for nbr_of_frames
+delete []e11_strain;
+
+serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+float *e22_strain = new float[NP];
+for (int nbr_of_frames=0; nbr_of_frames < NCF; nbr_of_frames++)
+{
+sprintf(frame, "_%d", nbr_of_frames);
std::cout << "--------------- E22_strain ------------------" << std::endl;
- float *e22_strain = new float[NP];
for (i=0; i<NP; i++) {
from >> e22_strain[i];
if (verbose)
std::cout << e22_strain[i] << std::endl;
- }
+ }
+//followed by their E22 strain, an array of NP elements,
+ dcmImageName = textFileName + frame + "_E22_strain.dcm";
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName, patientname, 1, studyUID, serieUID);
+} // end for nbr_of_frames
+delete [] e22_strain;
+
+} // end of single frame
+
+
+else // generate Multiframe files
+{
- std::string dcmImageName;
+serieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+float *ecc_strain = new float[NP*NCF];
+ std::cout << "--------------- Ecc_strain ------------------" << std::endl;
+ for (i=0; i<NP*NCF; i++) {
+ from >> ecc_strain[i];
+ if (verbose)
+ std::cout << ecc_strain[i] << std::endl;
+ }
//followed by their Ecc strain, an array of NP elements,
dcmImageName = textFileName + "_Ecc_strain.dcm";
- MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName);
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(ecc_strain, X, Y, Z, NP, dcmImageName, patientname, NCF, studyUID, serieUID);
+delete []ecc_strain;
-//followed by their Err strain, an array of NP elements,
+
+
+float *err_strain = new float[NP*NCF];
+ std::cout << "--------------- Err_strain ------------------" << std::endl;
+ for (i=0; i<NP*NCF; i++) {
+ from >> err_strain[i];
+ if (verbose)
+ std::cout << err_strain[i] << std::endl;
+ }
+//followed by their Ecc 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,
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(err_strain, X, Y, Z, NP, dcmImageName, patientname, NCF, studyUID, serieUID);
+delete []err_strain;
+
+
+
+float *e11_strain = new float[NP*NCF];
+ std::cout << "--------------- E11_strain ------------------" << std::endl;
+ for (i=0; i<NP*NCF; i++) {
+ from >> e11_strain[i];
+ if (verbose)
+ std::cout << e11_strain[i] << std::endl;
+ }
+//followed by their Ecc 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,
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(e11_strain, X, Y, Z, NP, dcmImageName, patientname, NCF, studyUID, serieUID);
+delete []e11_strain;
+
+
+
+float *e22_strain = new float[NP*NCF];
+ std::cout << "--------------- E22_strain ------------------" << std::endl;
+ for (i=0; i<NP*NCF; i++) {
+ from >> e22_strain[i];
+ if (verbose)
+ std::cout << e22_strain[i] << std::endl;
+ }
+//followed by their Ecc strain, an array of NP elements,
dcmImageName = textFileName + "_E22_strain.dcm";
- MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName);
-
+ std::cout << "Try to make image :[" << dcmImageName << "]" << std::endl;
+ MakeDicomImage(e22_strain, X, Y, Z, NP, dcmImageName, patientname, NCF, studyUID, serieUID);
+delete []e22_strain;
+
+} // end of Multiframe
}
// =====================================================================================================================
-void MakeDicomImage(float *tabVal, float *X, float *Y, float *Z, int NP, std::string dcmImageName)
+void MakeDicomImage(float *tabVal, float *X, float *Y, float *Z, int NP, std::string dcmImageName, const char * patientName, int nbFrames, std::string studyUID, std::string serieUID)
{
+
+std::cout << "=============================================================================="
+ << "enter MakeDicomImage [" << dcmImageName << "] [" << patientName << "]" << std::endl;
float minX = 99999., minY = 99999., minZ = 99999.;
float maxX = 0., maxY = 0., maxZ = 0.;
int i;
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+0.5)*int(maxY+0.5)];
- uint16_t *img = new uint16_t[int(maxX*4.)*int(maxY*4.)];
-
- // Set whole image to 0
- for(int i3=0;i3<int(maxX*4.)*int(maxY*4.);i3++)
-// for(int i3=0;i3<int(maxX+0.5)*int(maxY+0.5);i3++)
- img[i3] = 0;
+ int lgrFrame = int(maxX*4.)*int(maxY*4.);
+ uint16_t *img = new uint16_t[lgrFrame*nbFrames ];
- for(int i2=0; i2<NP; i2++) {
-
+ // Set whole image to 0
+ for(int i3=0; i3<lgrFrame*nbFrames; i3++)
+ img[i3] = 0;
+
+for(int i4=0; i4<nbFrames; i4++)
+ for(int i2=0; i2<NP; i2++) {
int ordX = int(X[i2]*4.-30);
int ordY = int(maxY*4.) - int(Y[i2]*4.)+30;
-// img[ /*int(maxX) -*/ int(X[i2]+0.5-1) + (int(maxY+0.5) - int(Y[i2]+0.5)) * int(maxX+0.5) ] = int(tabVal[i2]*100);
-
-// img[ /*int(maxX) -*/ int(X[i2]*4.-30) + (int(maxY*4.) - int(Y[i2]*4.)+30) * int(maxX*4.) ] = int(tabVal[i2]*100);
- img[ /*int(maxX) -*/ ordX + ordY * int(maxX*4.) ] = int(tabVal[i2]*100);
+ img[ lgrFrame*i4 + ordX + ordY * int(maxX*4.) ] = int(tabVal[i2 + NP*i4]*100);
// Try to round up, just to see.
- for(int iii=ordY-3; iii<ordY+4; iii++) for(int jjj=ordX-3; jjj<ordX+4; jjj++)
- img[ jjj + iii * int(maxX*4.) ] = int(tabVal[i2]*100);
- std::cout << int(X[i2]*4.) << " " << int(Y[i2]*4.) << " = " << int(tabVal[i2]*100) << std::endl;
- }
-
+ for(int iii=ordY-3; iii<ordY+4; iii++)
+ for(int jjj=ordX-3; jjj<ordX+4; jjj++)
+ img[ lgrFrame*i4 + jjj + iii * int(maxX*4.) ] = int(tabVal[i2 + NP*i4]*100);
+ }
+
+ std::cout << "===========sortie recup points" << std::endl;
// 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*4.);
str.str("");
str << (int)(maxY*4.);
file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
-
+
// Set the pixel type
// 16; //8, 16, 32
file->InsertEntryString("16",0x0028,0x0100,"US"); // Bits Allocated
// 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");
+
+ int pos = 0; // get the usefull part of the name
+/*
+ for(i=0, pos=0; pos<dcmImageName.size()-4; pos++, i++) {
+ if( dcmImageName[i]=='.' &&dcmImageName[i+1]=='t' && dcmImageName[i+2]=='x' && dcmImageName[i+3]=='t'
+ && dcmImageName[i+3]=='_') {
+ pos+=5;
+ break;
+ }
+ }
+*/
+ file->InsertEntryString(&(dcmImageName.c_str()[pos]),0x0008,0x103e, "LO"); // Series Description
/*
// Set Rescale Intercept
str.str("");
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)); // troubles when maxX, mayY are *actually* float!
- fileH->SetImageData((uint8_t *)img,int(maxX*4.)*int(maxY*4.)*sizeof(uint16_t));
+
+ fileH->SetImageData((uint8_t *)img,int(maxX*4.)*int(maxY*4.)*nbFrames*sizeof(uint16_t));
fileH->SetWriteModeToRaw();
fileH->SetWriteTypeToDcmExplVR();
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff