+/*
+ # ---------------------------------------------------------------------
+ #
+ # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
+ # pour la Santé)
+ # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
+ # Previous Authors : Laurent Guigues, Jean-Pierre Roux
+ # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
+ #
+ # This software is governed by the CeCILL-B license under French law and
+ # abiding by the rules of distribution of free software. You can use,
+ # modify and/ or redistribute the software under the terms of the CeCILL-B
+ # license as circulated by CEA, CNRS and INRIA at the following URL
+ # http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ # or in the file LICENSE.txt.
+ #
+ # As a counterpart to the access to the source code and rights to copy,
+ # modify and redistribute granted by the license, users are provided only
+ # with a limited warranty and the software's author, the holder of the
+ # economic rights, and the successive licensors have only limited
+ # liability.
+ #
+ # The fact that you are presently reading this means that you have had
+ # knowledge of the CeCILL-B license and that you accept its terms.
+ # ------------------------------------------------------------------------
+*/
#include "bruker2dicom.h"
#include <boost/filesystem/path.hpp>
#include <boost/filesystem/operations.hpp>
bool Bruker2Dicom::Execute()
{
+ int dimension = 1;
// ----- Check input directory name -----
bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
switch (type)
{
- case 1: {
+ case 1: {
bool canOpen = br_subject.LoadFile(subject);
if (!canOpen)
{
subject_name = b_name.GetStringValue()[0];
strPatientName = subject_name;
cleanString(subject_name);
- DealWithSingleStudyDirectory (fileNames);
+ DealWithSingleStudyDirectory (fileNames, dimension);
}
break;
}
case 2: {
subject_name = "defaultPatName";
strPatientName = subject_name;
- DealWithSingleStudyDirectory (fileNames);
+ DealWithSingleStudyDirectory (fileNames, dimension);
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);
+ DealWithMultiStudyDirectory (fileNames, dimension);
break;
}
}
// ----------------------------------------------------------------------------------------------------------
-void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames)
+void Bruker2Dicom::DealWithMultiStudyDirectory (GDCM_NAME_SPACE::DirListType &dirNames, int dimension)
{
GDCM_NAME_SPACE::DirListType::iterator it;
subject_name = b_name.GetStringValue()[0];
strPatientName = subject_name;
cleanString(subject_name);
- DealWithSingleStudyDirectory(fileNames);
+ DealWithSingleStudyDirectory(fileNames,dimension);
}
}
else
// ----------------------------------------------------------------------------------------------------------
-void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames)
+void Bruker2Dicom::DealWithSingleStudyDirectory (GDCM_NAME_SPACE::DirListType &fileNames, int dimension)
{
bool res;
// creation directory : 'nom du patient'
std::string tempStringPatDir(OutputDirName);
- tempStringPatDir = tempStringPatDir + GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name;
+
+ tempStringPatDir = tempStringPatDir + "/"+ subject_name;
+ //GDCM_NAME_SPACE::GDCM_FILESEPARATOR + subject_name; //FCY TO MODIFY
res=CreateDirectory(tempStringPatDir);
if (!res) {
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'
if (verbose)
printf ("outputDirName [%s]\n", outputDirName);
try {
- DealWithNiveau1(*it, strOutputDirName);
+ DealWithNiveau1(*it, strOutputDirName, dimension);
}
catch (BrukerHopelessException &e)
{
// =====================================================================
-void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName) {
+void Bruker2Dicom::DealWithNiveau1(std::string &level1Directory, std::string ¤tOutputDirName, int dimension) {
//
// e.g. : at level 1, in B67d1.Bp1/6
//
7 1
*/
try {
- DealWithNiveau2(*it, strOutputDirName);
+ DealWithNiveau2(*it, strOutputDirName, dimension);
}
catch (BrukerHopelessException &e)
{
// =====================================================================
-void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName) {
+void Bruker2Dicom::DealWithNiveau2(std::string &level2Directory, std::string ¤tOutputDirName, int dimension) {
// e.g. : at level 2 in B67d1.Bp1/6/pdata
//
++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
{
}
std::string strOutputDirName(outputDirName);
try {
- DealWithNiveau3(*it, strOutputDirName);
+ DealWithNiveau3(*it, strOutputDirName, dimension);
}
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 ¤tOutputDirName){
+void Bruker2Dicom::DealWithNiveau3(std::string &level3Directory, std::string ¤tOutputDirName, int dimension){
//
// e.g. at level 3, in
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;
} else {
if (verbose)
std::cout << "[" << str_reco << "] successfully Mapped" << std::endl;
- }
+ }
//std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
// br_reco.PrintSelf();
// 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];
+
+ double fovX;
+ double fovY;
+ fovX= fov.GetDoubleValue()[0];
+ if(fov.GetDoubleValue().size() > 1)
+ 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];
+ double sizeX;
+ double sizeY;
+ sizeX = size.GetDoubleValue()[0];
+
+ if(fov.GetDoubleValue().size() > 1)
+ sizeY = size.GetDoubleValue()[1];
if (verbose)
std::cout << "SIZE (ds reco) " << sizeX << " " << sizeY << std::endl;
- double spatResolX = fovX / sizeX;
- double spatResolY = fovY / sizeY;
+ double spatResolX;
+ double spatResolY;
+ spatResolX = fovX / sizeX;
+ if(fov.GetDoubleValue().size() > 1)
+ 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)
-
+ double sliceDistance;
+ if(dimension > 1)
+ {
BrukerFieldData bsliceDistance = br_method.GetFieldData("PVM_SPackArrSliceDistance");
- double sliceDistance = bsliceDistance.GetDoubleValue()[0];
-
+ sliceDistance = bsliceDistance.GetDoubleValue()[0];
+ }
if (verbose)
std::cout << "SPackArrSliceDistance (ds method) " << sliceDistance << std::endl;
if (verbose)
std::cout << "nbSlices " << nbSlices << std::endl;
int k;
+ if(dimension ==1)
+ nbSlices = 1;
int nbInstants = nbFrames/nbSlices;
if (verbose)
std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
// This one will be important!
// ---------------------------
try {
- imageSet = CreateImageSet ( );
+ imageSet = CreateImageSet ( dimension);
}
catch (BrukerInitException& e)
{
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();
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'
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);
}
// ===========================================================================================
-std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( )
+std::vector<BrukerImage> Bruker2Dicom::CreateImageSet ( int dimension)
{
std::vector<BrukerImage> imageSet;
- br_acqp.SetLoopStructure();
+ br_acqp.SetLoopStructure(dimension);
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()") );
+ throw ( BrukerInitException ("ObjectVaryingProperties.init() failure in Bruker2Dicom::CreateImageSet()") );
}
br_acqp.SetImageLoopStructure();
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
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");
// 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));
// file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
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!
git://git.creatis.insa-lyon.fr / creaBruker.git / blobdiff