#define PATH_MAX 2048
#endif
-
-
bool Bruker2Dicom::Execute()
{
// ----- Check input directory name -----
bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
-
+
//if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
if ( ! boost::filesystem::is_directory(InputDirName) )
{
throw ( BrukerHopelessException ("Output directory creation failure "));
}
- std::string strDirNamein(InputDirName);
- GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
- std::string strDirNameout(OutputDirName);
-
-/*
- if (listonly)
- {
- std::cout << "------------List of found files ------------" << std::endl;
- dirList.Print();
- std::cout << std::endl;
- return 1;
- }
-*/
-
//
// e.g : at level 0, in : B67d1.Bp1
//
// 1 2 3 4 5 6 AdjStatePerStudy subject
//
+ std::string strDirNamein(InputDirName);
+
+/* */
+ GDCM_NAME_SPACE::DirList dirList(strDirNamein, false, true); // DON'T get recursively the list of files
+
GDCM_NAME_SPACE::DirListType fileNames;
fileNames = dirList.GetFilenames();
- bool canOpen;
- std::string outputFileName;
+ std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
- // BrukerDataSet br_subject;
- std::string subject;
- subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
- GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
- "subject";
- if (verbose)
- std::cout << " Subject : [" << subject << "]" << std::endl;
-
- bool subjectFound;
- canOpen =br_subject.LoadFile(subject);
- if (!canOpen)
+ std::string subject = path +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "subject";
+
+ std::string acqp = path +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "acqp";
+
+ if ( boost::filesystem::is_regular(subject) )
+ subjectFound = true;
+ else
+ subjectFound = false; // user passed only a 'serie', not a 'study
+
+ if ( boost::filesystem::is_regular(acqp) )
+ acqpFound= true;
+ else
+ acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
+
+ int type;
+ if (subjectFound ) type = 1; // user passed a 'study
+ else if (acqpFound) type = 2; // user passed a 'serie'
+ else type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
+ /* */
+
+ // 1 : if subjectFound : user passed a Single Study Directory
+ // 2 : if NOT subjectFound and acqpFound : user passed a Serie Directory
+ // 3 : if NOT subjectFound and NOT acqpFound : user passed a 'non Study Directory' (Hope it's a set of Single Study Directories)
+
+ //int type = CheckUserDirectory(InputDirName);
+
+ switch (type)
{
- //std::cout << "Hopeless! no 'subject' found" << std::endl;
- //throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
-
- std::cout << "Not too much hope! no 'subject' found (Desperate try will be performed -default values- )" << std::endl;
- subjectFound = false;
- }
- else
- {
- br_subject.FillMap();
- subjectFound = true;
+ case 1: {
+ bool canOpen = br_subject.LoadFile(subject);
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open"));
+ }
+ else
+ {
+ br_subject.FillMap();
+
+ // get info for 'Study Description'
+ BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
+ subject_name = b_name.GetStringValue()[0];
+ strPatientName = subject_name;
+ cleanString(subject_name);
+ DealWithSingleStudyDirectory (fileNames);
+ }
+ break;
+ }
+
+ case 2: {
+ subject_name = "defaultPatName";
+ strPatientName = subject_name;
+ DealWithSingleStudyDirectory (fileNames);
+ break;
+ }
+
+ case 3: {
+ std::cout << " User passed a 'non study' directory; Hope it's a *non recursive* 'set of studies' directory! (recursive not yet dealt with)" << std::endl;
+ DealWithMultiStudyDirectory (fileNames);
+ break;
+ }
}
- //br_subject.PrintSelf();
+}
- // get info for 'Study Description'
+// ----------------------------------------------------------------------------------------------------------
- if (subjectFound)
- {
- BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
- subject_name = b_name.GetStringValue()[0];
- strPatientName = subject_name;
- cleanString(subject_name);
- }
- else
- subject_name ="defaultPatName";
-
+void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames)
+{
+ GDCM_NAME_SPACE::DirListType::iterator it;
+
+ for (it = dirNames.begin();
+ it != dirNames.end();
+ ++it)
+ {
+ if ( boost::filesystem::is_directory(*it) )
+ {
+ subjectFound = false;
+ if (verbose)
+ std::cout << "in 'DealWithMultiStudyDirectory' [" << *it << "] is a directory" << std::endl;
+
+ GDCM_NAME_SPACE::DirList dirList(*it, false, true); // DON'T get recursively the list of files
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
+ std::string subject = path +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "subject";
+ if (! boost::filesystem::is_regular(subject) )
+ {
+ std::cout << "no [" << subject << "] file found" << std::endl;
+ continue;
+ }
+
+ bool canOpen = br_subject.LoadFile(subject);
+ if (!canOpen)
+ {
+ std::cout << "Hopeless! 'subject' found / cannot be open" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! 'subject' found in root input directory / cannot be open"));
+ }
+ else
+ {
+ br_subject.FillMap();
+ subjectFound = true; // Hope so! (full checking needed!)
+
+ BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
+ subject_name = b_name.GetStringValue()[0];
+ strPatientName = subject_name;
+ cleanString(subject_name);
+ DealWithSingleStudyDirectory(fileNames);
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "[" << *it << "] is NOT a directory; skipped!" << std::endl;
+ }
+ }
+}
+
+// ----------------------------------------------------------------------------------------------------------
+
+void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames)
+{
+ bool res;
// creation directory : 'nom du patient'
std::string tempStringPatDir(OutputDirName);
tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
-
+
res=CreateDirectory(tempStringPatDir);
if (!res) {
std::cout << "[" << tempStringPatDir << "] Directory creation failure " << std::endl;
throw ( BrukerHopelessException ("Patient directory creation failure "));
- }
+ }
- std::string subject_entry;
- std::string subject_position;
- std::string subject_date;
- std::string subject_study_name;
-
if (subjectFound)
{
BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
subject_study_name = "defStudyName"; // Why not?
}
// subject_name is already in 'Patient Name'
- strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
-
+ if (0) // We don't realy need so much information for 'Study'
+ strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
+ else
+ strStudyDescr = /*subject_name + "." + */ subject_study_name /*+ "." + subject_entry + "." + subject_position + "." + subject_date*/;
+
// creation directory : 'nom de la Study'
-
+
std::string tempStringStudyDir(OutputDirName);
tempStringStudyDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + strStudyDescr;
-
+
res=CreateDirectory(tempStringStudyDir);
if (!res) {
std::cout << "[" << tempStringStudyDir << "] Directory creation failure " << std::endl;
throw ( BrukerHopelessException ("Study directory creation failure "));
}
-
+
char outputDirName[(unsigned int) PATH_MAX+2];
strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
// (this is level ZERO)
// each Directory (name : 1, 2, 3, ...) will be a Dicom Serie
// -----------------------------------------------------
-
+
+ /// \TODO better use directory iterator, from boost! // JPR
GDCM_NAME_SPACE::DirListType::iterator it;
for (it = fileNames.begin();
if (verbose)
std::cout << "[" << *it << "] is a directory" << std::endl;
+ //if((*it) == "AdjResult") // avoid trouble with new version 'AdjResult' directory
+ if(GDCM_NAME_SPACE::Util::GetName(*it) == "AdjResult")
+ continue;
+
//BrukerDataSet br_acqp;
std::string strAcqp;
strAcqp = (*it) +
BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
b_method.PrintSelf();
acqp_method = b_method.GetStringValue()[0];
-
+
cleanString(acqp_method);
//std::cout << "out of br_acqp.FillMap 3" << std::endl;
BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
//std::cout << "out of br_acqp.FillMap 4" << std::endl;
//b_list_size.PrintSelf(); //JP
-
+
nbSlices = b_list_size.GetIntValue()[0];
//std::cout << "out of br_acqp.FillMap 5" << std::endl;
strSerieDescr = GDCM_NAME_SPACE::Util::GetName(*it)
+ "." + acqp_scan_name
+ "." + acqp_method.c_str();
- sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(), //OutputDirName.c_str(),
+ sprintf(outputDirName, "%s%c%s", tempStringStudyDir.c_str(), //OutputDirName.c_str(),
GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
strSerieDescr.c_str() );
-
+
std::cout << " ================================================================================\n"
<< " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
<< " ================================================================================"
<< std::endl;
-
-
+ std::string strOutputDirName(outputDirName);
if (verbose)
- printf ("outputDirName [%s]\n", outputDirName);
+ printf ("outputDirName [%s]\n", outputDirName);
try {
- DealWithNiveau1(*it, outputDirName);
+ DealWithNiveau1(*it, strOutputDirName);
}
catch (BrukerHopelessException &e)
{
// =====================================================================
-void Bruker2Dicom::DealWithNiveau1(std::string level1Directory, std::string currentOutputDirName) {
+void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName) {
//
// e.g. : at level 1, in B67d1.Bp1/6
//
sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
GDCM_NAME_SPACE::Util::GetName(*it).c_str());
+ std::string strOutputDirName(outputDirName);
//br1.PrintSelf();
std::string strMethod;
br_method.FillMap();
/* a recuperer :
- ##$PVM_Fov (dimension)
+ ##$PVM_Fov (dimension) // ou plutot RECO_fov !
*/
/*
dans method (pour perfusion seulement?) :
##$PVM_NSPacks=2
##$PVM_SPackArrNSlices=( 2 )
7 1
- */
+ */
try {
- DealWithNiveau2(*it, outputDirName);
+ DealWithNiveau2(*it, strOutputDirName);
}
catch (BrukerHopelessException &e)
{
// =====================================================================
-void Bruker2Dicom::DealWithNiveau2(std::string level2Directory, std::string currentOutputDirName) {
-
+void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName) {
+
// e.g. : at level 2 in B67d1.Bp1/6/pdata
//
// acqp fid imnd pdata pulseprogram spnam0 spnam1
throw ( BrukerHopelessException ("Hopeless! Level2 output directory creation failure"));
//exit (0);
}
-
+
GDCM_NAME_SPACE::DirList dirList(level2Directory, false, true); // DON'T get recursively the list of files
GDCM_NAME_SPACE::DirListType fileNames;
{
std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
}
-
}
-
+
for (it = fileNames.begin();
it != fileNames.end();
++it)
{
if ( boost::filesystem::is_directory(*it) )
- {
-
+ {
+
if (verbose)
std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
-
- // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
+
+ // sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
// GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
// GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
// MUST be 'pdata'!
//
// (interest of previous method :
-// If unaware user changed the pdata name, it goes on working
+// If unaware user changed the pdata name, it goes on working
//
std::string str_isa;
str_isa = (*it) +
GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
"isa";
- std::string str_isa_func_name;
+ std::string str_isa_func_name;
canOpen = br_isa.LoadFile(str_isa);
if (!canOpen)
{
sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
- GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
+ GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
}
else
{
GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
str_isa_func_name.c_str());
}
- try {
- DealWithNiveau3(*it, outputDirName);
+ std::string strOutputDirName(outputDirName);
+ try {
+ DealWithNiveau3(*it, strOutputDirName);
}
catch (BrukerHopelessException &e)
{
std::cout << "And Init Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
<< " We skip [" << level2Directory << "]" << std::endl;
continue;
- }
+ }
}
}
}
-
//
// =====================================================================
//
-void Bruker2Dicom::DealWithNiveau3(std::string level3Directory, std::string currentOutputDirName){
+void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName){
//
// e.g. at level 3, in
if (!res)
{
std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
- throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
+ throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
//exit (0);
}
char copyFile[PATH_MAX + PATH_MAX + 5]; // Should be enough!
bool canOpen;
-
+
//-------------- try d3proc;
char char_d3proc[(unsigned int) PATH_MAX+2];
sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
-
+
if (verbose)
std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
- std::string str_d3proc(char_d3proc);
+ std::string str_d3proc(char_d3proc);
canOpen = br_d3proc.LoadFile(str_d3proc);
if (!canOpen)
{
std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
- //exit(0); /// \TODO throw an exception !
+ //exit(0); /// \TODO throw an exception !
}
-
+
//-------------- end try d3proc;
-
-
+
+
// -------------------try reco
char char_reco[(unsigned int) PATH_MAX+2];
// GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
// "d3proc";
if (verbose)
- std::cout << "reco --- => [" << char_reco << "]" << std::endl;
- std::string str_reco(char_reco);
+ std::cout << "reco: --- => [" << char_reco << "]" << std::endl;
+
+ std::string str_reco(char_reco);
canOpen = br_reco.LoadFile(str_reco);
if (!canOpen) // we try in directory ../1
std::string lastDirName = GDCM_NAME_SPACE::Util::GetPath(level3Directory);
//lastDirName = GDCM_NAME_SPACE::Util::GetPath(lastDirName);
sprintf(char_reco,"%s%c1%c%s", lastDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"reco" );
- str_reco=char_reco;
+ //str_reco=char_reco;
canOpen = br_reco.LoadFile(str_reco);
if (!canOpen)
{
throw ( BrukerHopelessException ("Hopeless! cannot find 'reco'"));
//exit(0); /// \TODO throw an exception !
}
+ } else {
+ if (verbose)
+ std::cout << "[" << str_reco << "] successfully Loaded " << std::endl;
}
canOpen = br_reco.FillMap();
{
std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
- //exit(0); /// \TODO throw an exception !
+ //exit(0); /// \TODO throw an exception !
+ } else {
+ if (verbose)
+ std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
}
+
//std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
// br_reco.PrintSelf();
// std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
if (verbose)
std::cout << "IM_SIY " << NY << std::endl;
/// \todo : check if there are actually 3 dimensions or only 2
-
+
BrukerFieldData bZ= br_d3proc.GetFieldData("IM_SIZ");
int nbFrames = bZ.GetIntValue()[0];
if (verbose)
std::cout << "IM_SIZ " << nbFrames << std::endl;
// WARNING DATTYPE is, either in {ip_short, ip_int, ip_char, ...}, or in {1, 2, 3, ...}
-
+
BrukerFieldData bDPT = br_d3proc.GetFieldData("DATTYPE");
-
+
std::string mhdDataPixelType;
int pixelSize;
getImhDataType(bDPT, mhdDataPixelType, pixelSize);
-
+
+
+ /*
+
+ // See mail Denis :
+ // En regle generale il vaut mieux que l'on passe par RECO_*
+ // pour extraire les parametres de l'image
+ //
+
BrukerFieldData fov = br_method.GetFieldData("PVM_Fov");
double fovX = fov.GetDoubleValue()[0];
double fovY = fov.GetDoubleValue()[1];
if (verbose)
std::cout << "FOV (ds method) " << fovX << " " << fovY << std::endl;
-
+
BrukerFieldData spatResol = br_method.GetFieldData("PVM_SpatResol");
double spatResolX = spatResol.GetDoubleValue()[0];
double spatResolY = spatResol.GetDoubleValue()[1];
if (verbose)
std::cout << "SpatResol (ds method) " << spatResolX << " " << spatResolY << std::endl;
+
+*/
+
+/* ------ */
+// Better we use 'get' accessors from BrukerImage class, as Denis wrote them
+
+ BrukerFieldData fov = br_reco.GetFieldData("RECO_fov");
+ double fovX = fov.GetDoubleValue()[0];
+ double fovY = fov.GetDoubleValue()[1];
+ if (verbose)
+ std::cout << "FOV (ds reco) " << fovX << " " << fovY << std::endl;
+
+ BrukerFieldData size = br_reco.GetFieldData("RECO_size");
+ double sizeX = size.GetDoubleValue()[0];
+ double sizeY = size.GetDoubleValue()[1];
+
+ if (verbose)
+ std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl;
+
+ double spatResolX = fovX / sizeX;
+ double spatResolY = fovY / sizeY;
+
+ if (verbose)
+ std::cout << "spatResol (ds reco : fov/size) " << spatResolX << " " << spatResolY << std::endl;
+/* ------ */
/// \TODO probabely a more sophisticated accessor will be necessary :
/// (cf : non contiguous slices, overlapping, slice thickness, space between slices, etc)
+
BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
double sliceDistance = bsliceDistance.GetDoubleValue()[0];
+ if (verbose)
+ std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl;
+
+// ----------------------------------------------------------------------------------------
+
if (mhd)
{
sprintf(currentOutputMhdDirName, "%s%c%s", currentOutputDirName.c_str(),
GDCM_NAME_SPACE::GDCM_FILESEPARATOR, "MhdFiles");
- res = CreateDirectory( currentOutputMhdDirName );
+
+ std::string strCurrentOutputMhdDirName(currentOutputMhdDirName);
+ res = CreateDirectory( strCurrentOutputMhdDirName );
if (!res) {
std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
int k;
int nbInstants = nbFrames/nbSlices;
if (verbose)
- std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
+ std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
int instantNb;
int sliceNb;
FILE *fp; // for MHD files
//exit (0);
}
}
-
+
unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
///\ TODO : find a safer way to be sure to read everything!
size_t lgr = fread(buffer_2dseq, 1, NX*NY*pixelSize*nbSlices*nbInstants, fp);
//return;
throw (e);
}
-
+
serieNumber++;
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices );
fprintf(fp, "HeaderSize = %d\n", 0);
//fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n", spatResolX, spatResolY, sliceDistance );
fprintf(fp, "Position = 0 0 %d\n", 0 );
fprintf(fp, "Offset = 0 0 0\n" );
fprintf(fp, "CenterOfRotation = 0 0 0\n" );
{
sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
-
+
/* ----------- Write Dicom Image ---------------*/
MakeDicomImage(buffer_2dseq,
NX,
);
} // end if dicom
} // end if nbInstants = 1
-
+
else // more than ONE instant
{
// Interleaved !
1, fp);
}
fclose(fp);
+
// std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
} // end if mhd
1, fp);
}
fclose(fp);
-
+
fp=fopen(output2dseqSliceFileName, "rb");
if (!fp)
{
*/
/* ----------- Write Dicom Image ---------------*/
-
+
int frameSize = NX*NY*pixelSize;
for (instantNb=0; instantNb<nbInstants; instantNb++)
{
} // end nbInstants == 1
delete [] buffer_2dseq;
/**/
-
-
+
+
// -----------------------------------------------------
// deal with MatLab-generated Carto file.
// -----------------------------------------------------
-
+
dealWithCarto(fileNames, NX, NY, nbSlices, /*fovX, fovY,*/ spatResolX, spatResolY, sliceDistance,
copyFile, currentOutputDirName, outputMhdFileName, output2dseqCartoName);
}
-
// ===========================================================================================
void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
// -----------------------------------------------------
// deal with MatLab-generated Carto file.
// -----------------------------------------------------
-
- char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
- char *separator[] = { "_", ".", "-", "" }; // add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
+
+ const char *code[] = { "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
+ const char *separator[] = { "_", ".", "-", "" }; // add more, if necessary, to ckeck for 2dseq.ADC, 2dseq_ADC, 2dseq-ADC, etc; end with ""
int icode;
int iseparator;
GDCM_NAME_SPACE::DirListType::iterator it;
char file_name_ident[500];
FILE *fp;
-
+
// Iterate to ALL the objets(files/directories) found in the input directory
for (it = fileNames.begin();
it != fileNames.end();
if ( loc != std::string::npos )
{
-
+
///\ TODO : find a safer way to be sure to read everything!
unsigned char *buffer_carto = new unsigned char[NX*NY*sizeof(double)*nbSlices];
fp = fopen ( (*it).c_str(), "rb");
currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
if (verbose)
std::cout << "--- Output Carto MHD file [" << outputMhdFileName << "]" << std::endl;
-
+
FILE *fp;
fp=fopen(outputMhdFileName, "w");
if (!fp)
if (verbose)
std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
break; // don't check for more ident on same file name!
-
+
} // end deal with _ADC, -adc, etc
iseparator ++;
} // end iterate speparators
} // end iterate on all objects (files, dir, etc)
} // end method
+// ==========================================================================================================
+
+int Bruker2Dicom::CheckUserDirectory(std::string &userDirName)
+{
+ GDCM_NAME_SPACE::DirList dirList(userDirName, false, true); // DON'T get recursively the list of files
+
+ GDCM_NAME_SPACE::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+
+ std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
+
+ std::string subject = path +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "subject";
+
+ std::string acqp = path +
+ GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
+ "acqp";
+
+ if ( boost::filesystem::is_regular(subject) )
+ subjectFound = true; // user passed a 'study
+ else
+ subjectFound = false; // user didnt' pass a 'study
+
+ if ( boost::filesystem::is_regular(acqp) )
+ acqpFound= true; // user passes a 'serie', not a 'study'
+ else
+ acqpFound = false; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
+
+ int type;
+ if (subjectFound ) type = 1; // user passed a 'study
+ else if (acqpFound) type = 2; // user passed a 'serie'
+ else type = 3; // user passed a 'non study' directory; Hope it's a 'set of studies' directory!
+
+ return type;
+}
// ==========================================================================================================
-
-bool Bruker2Dicom::CreateDirectory(std::string OutputDirName)
+
+bool Bruker2Dicom::CreateDirectory(std::string &OutputDirName)
{
std::string systemCommand;
<<std::endl;
if ( ! boost::filesystem::is_directory(OutputDirName) ) // dirout not found
{
- std::string strDirNameout(OutputDirName); // to please gcc 4
- systemCommand = "mkdir " + strDirNameout; // create it!
+ systemCommand = "mkdir " + OutputDirName; // create it!
if (verbose)
std::cout << systemCommand << std::endl;
system (systemCommand.c_str());
if (verbose)
std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
}
-
return 1;
-
}
-
// ===========================================================================================
/// \TODO move cleanString to 'crea' ?
l--;
s = s.substr(0, l);
}
-
+
if (s[0] == '<')
s= s.substr(1,l-2);
- std::string repChar("_");
+ std::string repChar("_");
GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
}
-
-
// ===========================================================================================
-
void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
{
if(bDPT.GetDataType() == "string")
// Cross your fingers !!!
// pb : found values : 2, 3, 5
-
+
if (brukerDataPixelType == 2) {
mhdDataPixelType = "MET_USHORT";
pixelSize = 2;
br_acqp.SetLoopStructure();
std::vector<int> tempVect = br_acqp.GetLoopStructure() ;
std::map<std::string, BrukerFieldData> map = br_acqp.GetBrukerHeaderMap();
-
+
bool result = br_acqp.ObjectVaryingProperties.init(map,tempVect);
-
+
if (result == false)
{
throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
BrukerImage image(br_acqp,br_reco);
image.Init(br_acqp,br_reco,1);
-
+
for(int i=0;i<brukerImageList.size();i++)
{
image.Init(br_acqp,br_reco,i);
imageSet.push_back(image);
}
-
+
// Just for checking
/*
-
+
std::vector<std::vector <double> > imageOrientation;
std::vector <double> imagePosition;
for(int i=0;i<brukerImageList.size();i++)
{
// fread(buffer_2dseq, NX*NY*pixelSize*nbSlices*nbInstants, 1, fp);
-
+
imagePosition = imageSet[i].getTranslationVectorRPS2XYZ();
std::cout << "Position " << imagePosition[0] << " "
<< imagePosition[1] << " " << imagePosition[2] ;
std::cout << "\t Orientation " ;
for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
-
+
//std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition();
std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition();
std::string &serieDescr,
std::string &strStudyTimeDate,
int imgNum,
- GDCM_NAME_SPACE::ImageContentType contentType
+ GDCM_NAME_SPACE::ImageContentType contentType
)
{
std::ostringstream str;
GDCM_NAME_SPACE::File *file;
- file = GDCM_NAME_SPACE::File::New();
-
+ file = GDCM_NAME_SPACE::File::New();
+
// Set the image size
str.str("");
str << X;
// Set the pixel type
// //8, 16, 32, 64 (for double ?)
str.str("");
- str << pixelSize*8;
+ str << pixelSize*8;
+
+ // Bits Allocated
file->InsertEntryString(str.str(),0x0028,0x0100,"US"); // Bits Allocated
file->InsertEntryString(str.str(),0x0028,0x0101,"US"); // Bits Stored
// 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
str.str("");
str << spacingX << "\\" << spacingY;
file->InsertEntryString(str.str(),0x0028,0x0030, "DS"); // Pixel Spacing
-
+
// 0018 0050 DS 1 Slice Thickness
str.str("");
str << sliceDistance;
file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
-
+
// 0020 0011 IS 1 Series Number
str.str("");
str << serieNumber;
file->InsertEntryString(str.str(),0x0020,0x0011, "IS");
-
+
// 0020|0013 [IS] [Instance Number]
instanceNumber++;
str.str("");
str << instanceNumber;
file->InsertEntryString(str.str(),0x0020,0x0013, "IS");
-
-
+
// 1.2.840.10008.5.1.4.1.1.4.1 : Enhanced MR Image Storage
- // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
+ // file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
// file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4.1" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
-
// OK : MR is NOT multiframe, but I want just a quick an dirty solution
// 1.2.840.10008.5.1.4.1.1.4 MR Image Storage
// if (strlen(patientName) != 0)
file->InsertEntryString(patientName.c_str(),0x0010,0x0010, "PN"); // Patient's Name
+ file->InsertEntryString(patientName.c_str(),0x0010,0x0020, "LO"); // Patient's ID
file->InsertEntryString(studyUID, 0x0020, 0x000d, "UI");
file->InsertEntryString(serieUID, 0x0020, 0x000e, "UI");
-
+
// 0008 0020 DA 1 Study Date
// 0008 0030 TM 1 Study Time
imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][0],
imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][1],
imageSet[imgNum].getRotationMatrixRPS2XYZ()[1][2] ) ;
-
- file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
+ file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
// 0020 0032 DS 3 Image Position (Patient)
imageSet[imgNum].getTranslationVectorRPS2XYZ()[0],
imageSet[imgNum].getTranslationVectorRPS2XYZ()[1],
imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
-
+
file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient)
-
+ // Private creator
+ /*
+
+0029|0010 [LO] [Private Creator] [CREATIS HEADER ]
+0029|0011 [LO] [Private Creator] [CREATIS for BRUKER to DICOM]
+0029|1031 [LO] [] [4.0.7571167 ]
+0029|1032 [UL] [] [1440000] =0x(15f900)
+
+> $$ Thu Jul 30 17:29:46 2009 CEST (UT+2h) mwiart
+> $$ /opt/PV4.0/data/mwiart/nmr/dha80.Uw1/4/method
+> ##$Method=DtiEpi
+> ##$PVM_DwNDiffDir=3 % 3 directions
+> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b par direction
+> ##$PVM_DwAoImages=1 % 1 image pour b=0
+> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b
+> 1500.000000 3000.000000
+>
+> $$ Wed Dec 2 09:56:01 2009 UTC (UT+0h) mwiart
+> $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/4/method
+> ##$Method=DtiEpi
+> ##$PVM_DwNDiffDir=3 % 3 directions
+> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b par direction
+> ##$PVM_DwAoImages=1 % 1 image pour b=0
+> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b
+> 1500 3000
+>
+> $$ Wed Dec 2 10:14:27 2009 UTC (UT+0h) mwiart
+> $$ /opt/Pv5.0/data/mwiart/nmr/ECI7.Wx1/5/method
+> ##$Method=DtiStandard
+> ##$PVM_DwNDiffDir=1 % 1 direction
+> ##$PVM_DwNDiffExpEach=2 % 2 valeurs de b
+> ##$PVM_DwAoImages=0 % 0 image pour b=0
+> ##$PVM_DwBvalEach=( 2 ) % Valeurs de b
+> 138 1600
+>
+ */
+
+ file->InsertEntryString("CREATIS HEADER", 0x0029,0x0010, "LO");
+ file->InsertEntryString("CREATIS FOR BRUKER-TO-DICOM", 0x0029,0x0011, "LO");
+
+ BrukerFieldData brf_method = br_method.GetFieldData("Method");
+ const std::vector<std::string> method = brf_method.GetStringValue();
+
+ // std::string method = br_method.GetFieldData("Method").GetStringValue();
+ file->InsertEntryString(method[0], 0x0029,0x0100, "LO");
+
+ std::cout << " method[" << method[0] << "]" << std::endl;
+ if (method[0] == "DtiEpi" || method[0] == "DtiStandard")
+ {
+ // const std::vector<int> NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir").GetIntValue();
+ BrukerFieldData brf_NDiffDir = br_method.GetFieldData("PVM_DwNDiffDir");
+ const std::vector<int> NDiffDir = brf_NDiffDir.GetIntValue();
+
+ //const std::vector<int> NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach").GetIntValue();
+ BrukerFieldData brf_NDiffExpEach = br_method.GetFieldData("PVM_DwNDiffExpEach");
+ const std::vector<int> NDiffExpEach =brf_NDiffExpEach.GetIntValue();
+
+// const std::vector<int> AoImages = br_method.GetFieldData("PVM_DwAoImages").GetIntValue();
+ BrukerFieldData brf_AoImages = br_method.GetFieldData("PVM_DwAoImages");
+ const std::vector<int> AoImages = brf_AoImages.GetIntValue();
+
+ BrukerFieldData brf_DwBvalEach = br_method.GetFieldData("PVM_DwBvalEach");
+ const std::vector<double> DwBvalEach = brf_DwBvalEach.GetDoubleValue();
+
+ std::cout << "nb directions : " << NDiffDir[0] << " nb valeurs de b par direction : " << NDiffExpEach[0]
+ << " nb images for b=0 : " << AoImages[0] << std::endl;
+
+ str.str("");
+ str << NDiffDir[0];
+ file->InsertEntryString(str.str(),0x0029,0x0101,"US"); // nb de directions
+ str.str("");
+ str << NDiffExpEach[0];
+ file->InsertEntryString(str.str(),0x0029,0x0102,"US"); // nb valeurs de b par direction
+ str.str("");
+ str << AoImages[0];
+ file->InsertEntryString(str.str(),0x0029,0x0103,"US"); // nb images pour b=0
+
+ str.str("");
+ for (unsigned int i=0; i<NDiffExpEach[0]; i++) {
+ str << DwBvalEach[i];
+ if (i!=AoImages[0])
+ str << "\\";
+ }
+ file->InsertEntryString(str.str(),0x0029,0x0104,"DS"); // Valeurs de b
+ }
// 0020 0x1041 DS 1 Slice Location
// sprintf(charImagePosition,"%f",float(imgNum));
GDCM_NAME_SPACE::FileHelper *fileH;
fileH = GDCM_NAME_SPACE::FileHelper::New(file);
- fileH->SetContentType(contentType);
-
+ fileH->SetContentType(contentType);
+
// 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!
file->Delete();
fileH->Delete();
}
-
-
git://git.creatis.insa-lyon.fr / creaBruker.git / blobdiff