Program: gdcm
Module: $RCSfile: DenseMultiFramesToDicom.cxx,v $
Language: C++
- Date: $Date: 2006/07/20 17:15:28 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2007/10/29 17:13:59 $
+ Version: $Revision: 1.10 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <iostream>
//#include <values.h>
+#if defined(__BORLANDC__)
+#include <ctype.h>
+#endif
+
#include "gdcmFile.h"
#include "gdcmFileHelper.h"
#include "gdcmDebug.h"
* WARNING : directory must contain ONLY .txt files
*/
-
void Load(std::ifstream &from, std::string imageName, std::string patName,
- std::string strStudyUID, int serieNumber);
+ std::string strStudyUID, std::string strSerieUID, int serieNumber, int verbose);
//std::ifstream& eatwhite(std::ifstream& is);
int main(int argc, char *argv[])
{
START_USAGE(usage)
- " \n DenseMultiframeToDicom :\n ",
+ " \n DenseMultiFramesToDicom : \n",
" - explores recursively the given (single Patient, single Study) directory",
" - examines the '.txt' files ",
" - Converts the files into 16 bits Dicom files, ",
" WARNING : directory must contain ONLY .txt files ",
" usage: ",
- " DenseMultiframeToDicom dirin=rootDirectoryName ",
+ " DenseMultiFramesToDicom dirin=rootDirectoryName ",
" [studyUID = ] [patName = ] ",
" [listonly] [verbose] [debug] ",
" ",
- "studyUID : *aware* user wants to add the serie ",
+ " studyUID : *aware* user wants to add the serie ",
" to an already existing study ",
" verbose : user wants to run the program in 'verbose mode' ",
" debug : *developer* wants to run the program in 'debug mode' ",
// ----- Initialize Arguments Manager ------
- gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+ GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
if (argc == 1 || am->ArgMgrDefined("usage"))
{
dirNamein = am->ArgMgrGetString("dirin",".");
if (am->ArgMgrDefined("debug"))
- gdcm::Debug::DebugOn();
+ GDCM_NAME_SPACE::Debug::DebugOn();
int verbose = am->ArgMgrDefined("verbose");
int listonly = am->ArgMgrDefined("listonly");
- std::string patName = am->ArgMgrGetString("patname", "g^PatientName");
+ std::string patName = am->ArgMgrGetString("patname", dirNamein);
+
+ bool userDefinedStudy = ( 0 != am->ArgMgrDefined("studyUID") );
- bool userDefinedStudy = am->ArgMgrDefined("studyUID");
- const char *studyUID = am->ArgMgrGetString("studyUID");
+ const char *studyUID;
+ if (userDefinedStudy)
+ studyUID = am->ArgMgrGetString("studyUID");
+
+ // not described *on purpose* in the Usage !
+ bool userDefinedSerie = ( 0 != am->ArgMgrDefined("serieUID") );
+
+ const char *serieUID;
+ if(userDefinedSerie)
+ serieUID = am->ArgMgrGetString("serieUID");
-// not described *on purpose* in the Usage !
- bool userDefinedSerie = am->ArgMgrDefined("serieUID");
- const char *serieUID = am->ArgMgrGetString("serieUID");
-
-
// if unused Param we give up
if ( am->ArgMgrPrintUnusedLabels() )
{
// ----- Begin Processing -----
- if ( ! gdcm::DirList::IsDirectory(dirNamein) )
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirNamein) )
{
std::cout << "KO : [" << dirNamein << "] is not a Directory."
<< std::endl;
}
else
{
- std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
+ if (verbose)
+ std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
}
std::string strDirNamein(dirNamein);
- gdcm::DirList dirList(strDirNamein, true); // (recursively) the list of files
+ GDCM_NAME_SPACE::DirList dirList(strDirNamein, true); // (recursively) the list of files
if (listonly)
{
std::string filenameout;
std::string strStudyUID;
- strStudyUID = gdcm::Util::CreateUniqueUID();
+ std::string strSerieUID;
+
+ if (userDefinedStudy)
+ strSerieUID = studyUID;
+ else
+ strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+
+ if (userDefinedStudy)
+ strSerieUID = serieUID;
+ else
+ strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+
+
int serieNumber =0;
- gdcm::DirListType fileNames;
+ GDCM_NAME_SPACE::DirListType fileNames;
fileNames = dirList.GetFilenames();
- for (gdcm::DirListType::iterator it = fileNames.begin();
+ for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
it != fileNames.end();
++it)
- {
-
-
+ {
+ if ( GDCM_NAME_SPACE::Util::GetName((*it)).c_str()[0] == '.' )
+ {
+ // skip hidden files
+ continue;
+ }
+ int sz = (*it).size();
+ if ( (*it).c_str()[sz-1] != 't')
+ {
+ // skip non .txt files
+ continue;
+ }
std::ifstream from( (*it).c_str() );
if ( !from )
{
}
else
{
- std::cout << "Success in open file" << *it << std::endl;
- Load(from, *it, patName, strStudyUID, serieNumber);
- serieNumber++;
+ if (verbose)
+ std::cout << "Success in open file" << *it << std::endl;
+ Load(from, *it, patName, strStudyUID, strSerieUID, serieNumber, verbose);
+ serieNumber+=2;
//return 0;
}
}
+ return 1;
}
void Load(std::ifstream &from, std::string imageName, std::string patName,
- std::string strStudyUID, int serieNumber)
+ std::string strStudyUID, std::string strSerieUID, int serieNumber, int verbose)
{
+ if (verbose)
+ std::cout << " ========= Deal with file [" << imageName << "]" << std::endl;
if (!from)
return;
-
+ if (verbose)
+ std::cout << " ========= Create Parametric images" << std::endl;
/* was OK for single frames
eg :
---------------------------
from >> str1;
from >> str1; // 52x59x14
- std::cout << "[" << str1 << "]" << std::endl;
+ if(verbose)
+ std::cout << "[" << str1 << "]" << std::endl;
sscanf( str1.c_str(),"%dx%dx%d", &nx,&ny,&nf);
std::cout << nx << " " << ny << " " << nf << std::endl;
- // Skip 4 lines.
- for (int k=0; k<4; k++)
- {
+ std::getline(from, str1);
+
+ from >> str1; // Temporal
+ from >> str1; // Resolution
+ from >> str1; // =
+
+ from >> str1;
+
+ float temporalResolution;
+ sscanf( str1.c_str(),"%f",&temporalResolution);
+ if(verbose)
+ std::cout << "temporal Resolution = " << temporalResolution << std::endl;
+ std::getline(from, str1);
+
+ from >> str1; // First
+ from >> str1; // frame
+ from >> str1; // starts
+ from >> str1; // at
+
+ from >> str1;
+ float timeStart;
+ sscanf( str1.c_str(),"%f",&timeStart);
+ std::cout << "time Start = " << timeStart << std::endl;
+ std::getline(from, str1);
+
+ // Skip 3 lines.
+ for (int k=0; k<2; k++) //
+ {
std::getline(from, str1);
std::cout << str1 << std::endl;
}
- //float *f = new float(nx*ny);
+ //float *f = new float(nx*ny);
+ // -->float *f = new float[nx*ny]; // Would be better !
float *f = (float *) malloc(nx*ny*nf*sizeof(float));
// float mini = FLT_MAX, maxi = FLT_MIN;
float val;
-
-
- std::string strSerieUID;
- strSerieUID = gdcm::Util::CreateUniqueUID();
-
- for (int l=0; l<nf; l++) // Loop on the frames
- {
+
+ int imageNumber = 0;
+ float currentTime;
+ currentTime = timeStart;
+ int l1;
+ for (l1=0; l1<nf; l1++) // Loop on the frames
+ {
+ //std::cout << "Frame nb " << l1 << std::endl;
for( int j=0; j<ny; j++)
- {
- int l =0;
+ {
for (int i=0; i<nx; i++)
{
+ str1="";
//eatwhite(from);
char c;
- for (;;)
+ for (;;) //eatwhite(from);
{
if (!from.get(c))
+ {
+ std::cout << " !from.get(c) ";
break;
- if (!isspace(c))
+ }
+ if (!isspace(c) )
{
+ //std::cout << " !isspace(c) ";
from.putback(c);
break;
}
- }
- from >> str1;
+ } //end eatwhite(from);
+
+ // trouble : when space is missing "-0.0990263-8.8778"
+ // is not interpreted as TWO values :-(
+ // from >> str1;
+
+ int first = 1;
+ char previous = 'z';
+ for(;;)
+ {
+ from.get(c);
+ if ( c == ' ')
+ break;
+ if ( first != 1 && c == '-' && previous != 'e')
+ {
+ from.putback(c);
+ //std::cout << " One more gauffre in frame:" << std::dec << l
+ // << ", line : " << j << " element " << i << std::endl;
+ break;
+ }
+
+ first=0;
+ previous = c;
+ str1=str1+c;
+ }
+
val = (float)atof(str1.c_str());
- // std::cout << " " << val;
+ //std::cout << " " << val;
*(f+ /*l*nx*ny + */j*nx+i) = val;
if(from.eof())
{
- std::cout << "Missing values at [" << j <<"," << i << "]"
+ std::cout << "Missing values at [" << std::dec << j <<"," << i << "]"
<< std::endl;
break;
}
- l++;
}
- std::cout << std::endl;
+ //std::cout << std::endl;
//std::cout << std::endl << " line nb : " << j
// << " line length : " << l << std::endl;
-
}
-
// std::cout << "mini : "<< mini << " maxi : " << maxi << std::endl;
/*
ptr++;
}
*/
- uint16_t *img = new uint16_t[ny*nx];
- uint16_t *ptr = img;
+ int16_t *img = new int16_t[ny*nx];
+ int16_t *ptr = img;
float *tmp = f /* + l*ny*nx */ ; // start on image nb l.
for( int k=0; k<ny*nx; k++)
{
- if(*tmp < 0) // artefacted pixel
+ if(*tmp > 1.0) // artefacted pixel
*ptr = 0;
else /// \todo FIXME : what about max threshold ?
*ptr = (int16_t)(*tmp *100);
- //std::cout << std::dec << "[" << *tmp <<" : " << *ptr << "] ";
+ // std::cout << std::dec << "[" << *tmp <<" : " << *ptr << "] ";
tmp ++;
ptr++;
}
- // gdcm::Debug::DebugOn();
+ // GDCM_NAME_SPACE::Debug::DebugOn();
std::ostringstream str;
- gdcm::File *file;
- file = gdcm::File::New();
+ GDCM_NAME_SPACE::File *file;
+ file = GDCM_NAME_SPACE::File::New();
// Set the image size
str.str("");
file->InsertEntryString("15",0x0028,0x0102,"US"); // High Bit
// Set the pixel representation // 0/1 1 : signed
- file->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
+ 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
// 0020 0032 DS 3 Image Position (Patient)
char charImagePosition[256];
- sprintf(charImagePosition,"0.0\\0.0\\%f",float(l%nf));
+ sprintf(charImagePosition,"0.0\\0.0\\%f",float(l1%nf));
// 0020 0x1041 DS 1 Slice Location
- sprintf(charImagePosition,"%f",float(l%nf));
+ sprintf(charImagePosition,"%f",float(l1%nf));
file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
//0008 103e LO 1 Series Description
//0020 0011 "IS" Series Number
sprintf(charImagePosition,"%04d",serieNumber);
file->InsertEntryString(charImagePosition,0x0020,0x0011, "IS");
-
+
+//0020 0011 "IS" Instance Number
+ sprintf(charImagePosition,"%04d",imageNumber);
+ file->InsertEntryString(charImagePosition,0x0020,0x0013, "IS");
+
+//0018 1060 "DS" Time Trigger
+ sprintf(charImagePosition,"%f",currentTime);
+ file->InsertEntryString(charImagePosition,0x0018,0x1060, "DS");
+
// file->Print();
- gdcm::FileHelper *fh;
- fh = gdcm::FileHelper::New(file);
+ GDCM_NAME_SPACE::FileHelper *fh;
+ fh = GDCM_NAME_SPACE::FileHelper::New(file);
// cast is just to avoid warnings (*no* conversion)
fh->SetImageData((uint8_t *)img,nx*ny*sizeof(uint16_t));
fh->SetWriteModeToRaw();
fh->SetWriteTypeToDcmExplVR();
-
char numero[10];
- sprintf(numero, "%02d", l);
+ sprintf(numero, "%02d", l1);
std::string fileName = imageName + "." + numero + ".dcm";
- std::cout << "fileName " << fileName << std::endl;
+ if(verbose)
+ std::cout << "fileName " << fileName << std::endl;
if( !fh->Write(fileName))
std::cout << "Failed for [" << fileName << "]\n"
<< " File is unwrittable" << std::endl;
- delete img;
+ delete img;
+ currentTime += temporalResolution;
+ imageNumber ++;
+
} // end loop on frames
+
+ // Anatomical Images.
+ std::cout << " ========= Create Anatomical images" << std::endl;
+
+ strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ imageNumber = 0;
+ currentTime = timeStart;
+
+ for (int fr=0; fr<nf; fr++) // Loop on the frames
+ {
+ //std::cout << "Frame nb " << l << std::endl;
+ for( int j=0; j<ny; j++)
+ {
+ int l =0;
+ for (int i=0; i<nx; i++)
+ {
+ //eatwhite(from);
+ char c;
+ for (;;)
+ {
+ if (!from.get(c))
+ break;
+ if (!isspace(c))
+ {
+ from.putback(c);
+ break;
+ }
+ }
+ from >> str1;
+ val = (float)atof(str1.c_str());
+ // std::cout << " " << val;
+ *(f+ /*l*nx*ny + */j*nx+i) = val;
+
+ if(from.eof())
+ {
+ std::cout << "Missing values at [" << std::dec << j <<"," << i << "]"
+ << std::endl;
+ break;
+ }
+ l++;
+ }
+ }
+
+ uint16_t *img = new uint16_t[ny*nx];
+ uint16_t *ptr = img;
+ float *tmp = f /* + l*ny*nx */ ; // start on image nb l.
+ for( int k=0; k<ny*nx; k++)
+ {
+ *ptr = (int16_t)(*tmp);
+ tmp ++;
+ ptr++;
+ }
+ std::ostringstream str;
+ GDCM_NAME_SPACE::File *file;
+ file = GDCM_NAME_SPACE::File::New();
+
+ // Set the image size
+ str.str("");
+ str << nx;
+ file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << ny;
+ 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 1 : signed
+ file->InsertEntryString("0",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");
+*/
+
+// 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
+
+// 0020 0032 DS 3 Image Position (Patient)
+ char charImagePosition[256];
+ sprintf(charImagePosition,"0.0\\0.0\\%f",float(l1%nf));
+
+// 0020 0x1041 DS 1 Slice Location
+ sprintf(charImagePosition,"%f",float(l1%nf));
+ file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
+
+//0008 103e LO 1 Series Description
+ file->InsertEntryString(imageName,0x0008,0x103e, "LO");
+
+ file->InsertEntryString(strStudyUID,0x0020,0x000d,"UI");
+ file->InsertEntryString(strSerieUID,0x0020,0x000e,"UI");
+ file->InsertEntryString(patName,0x0010,0x0010, "PN"); // Patient's Name
+
+//0020 0011 "IS" Series Number
+ sprintf(charImagePosition,"%04d",serieNumber+1);
+ file->InsertEntryString(charImagePosition,0x0020,0x0011, "IS");
+
+//0020 0011 "IS" Instance Number
+ sprintf(charImagePosition,"%04d",imageNumber);
+ file->InsertEntryString(charImagePosition,0x0020,0x0013, "IS");
+
+//0018 1060 "DS" Time Trigger
+ sprintf(charImagePosition,"%f",currentTime);
+ file->InsertEntryString(charImagePosition,0x0018,0x1060, "DS");
+ // file->Print();
+
+ GDCM_NAME_SPACE::FileHelper *fh;
+ fh = GDCM_NAME_SPACE::FileHelper::New(file);
+ // cast is just to avoid warnings (*no* conversion)
+ fh->SetImageData((uint8_t *)img,nx*ny*sizeof(uint16_t));
+ fh->SetWriteModeToRaw();
+ fh->SetWriteTypeToDcmExplVR();
+
+ fh->SetWriteTypeToDcmExplVR();
+
+ char numero[10];
+ sprintf(numero, "%02d", l1);
+ std::string fileName = imageName + ".Anatomical." + numero + ".dcm";
+ std::cout << "fileName " << fileName << std::endl;
+
+ if( !fh->Write(fileName))
+ std::cout << "Failed for [" << fileName << "]\n"
+ << " File is unwrittable" << std::endl;
+
+ delete img;
+ currentTime += temporalResolution;
+ imageNumber ++;
+
+ } // end loop on frames
+
from.close();
-}
+} // end void Load(
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff