#include "bruker2dicom.h"
#include <boost/filesystem/path.hpp>
#include <boost/filesystem/operations.hpp>
+#include "brukerexception.h"
#ifndef PATH_MAX // If not defined yet : do it
- #define PATH_MAX 2048
+ #define PATH_MAX 2048
#endif
-
-
bool Bruker2Dicom::Execute()
{
- // ----- Check input values -----
+ // ----- Check input directory name -----
bool bigEndian = GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian();
-
+
//if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(InputDirName) )
if ( ! boost::filesystem::is_directory(InputDirName) )
{
std::cout << "OK : [" << InputDirName << "] is a Directory." << std::endl;
}
+ // ----- Check output directory name -----
+
std::string strDirNameOut(OutputDirName);
bool res=CreateDirectory(strDirNameOut);
if (!res) {
std::cout << "[" << OutputDirName << "] Directory creation failure " << std::endl;
- exit (0);
+ //exit (0);
+ 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;
- // 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;
- canOpen =br_subject.LoadFile(subject);
+ std::string path = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()));
- 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;
- exit(0); /// \TODO throw an exception !
- }
- else
- {
- br_subject.FillMap();
+ 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();
+}
+
+// ----------------------------------------------------------------------------------------------------------
+
+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();
- // get info for 'Study Description'
+ 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 "));
+ }
+
+ if (subjectFound)
+ {
+ BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
+ subject_entry = b_entry.GetStringValue()[0];
+ //cleanString(subject_entry);
+ subject_entry = subject_entry.substr(11, subject_entry.size()-11);
- /*
- BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
- acqp_protocol_location = b_protocol_location.GetStringValue()[0];
- cleanString(acqp_protocol_location);
-*/
- BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
- std::string subject_name = b_name.GetStringValue()[0];
- strPatientName = subject_name;
- cleanString(subject_name);
-
- BrukerFieldData b_entry=br_subject.GetFieldData("SUBJECT_entry");
- std::string subject_entry = b_entry.GetStringValue()[0];
- //cleanString(subject_entry);
- subject_entry = subject_entry.substr(11, subject_entry.size()-11);
-
- BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
- std::string subject_position = b_position.GetStringValue()[0];
- //cleanString(subject_position);
- subject_position = subject_position.substr(9, subject_position.size()-9);
-
- BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
- std::string subject_date = b_date.GetStringValue()[0];
- strStudyTimeDate = subject_date;
- cleanString(subject_date);
-
- BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
- std::string subject_study_name = b_study_name.GetStringValue()[0];
- subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
- cleanString(subject_date);
-
- strStudyDescr = subject_name + "." + subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
-
+ BrukerFieldData b_position=br_subject.GetFieldData("SUBJECT_position");
+ subject_position = b_position.GetStringValue()[0];
+ //cleanString(subject_position);
+ subject_position = subject_position.substr(9, subject_position.size()-9);
+
+ BrukerFieldData b_date=br_subject.GetFieldData("SUBJECT_date");
+ subject_date = b_date.GetStringValue()[0];
+ strStudyTimeDate = subject_date;
+ cleanString(subject_date);
+
+ BrukerFieldData b_study_name=br_subject.GetFieldData("SUBJECT_study_name");
+ subject_study_name = b_study_name.GetStringValue()[0];
+ subject_study_name = subject_study_name.substr(1, subject_study_name.size()-2);
+ cleanString(subject_study_name);
+ }
+ else // Desperate trick when file 'subject' is missing
+ {
+ subject_entry = "HeadFirst"; // Why not?
+ subject_position = "Supine"; // Why not?
+ strStudyTimeDate = "06_06_06_6_June_1666"; // Why not?
+ subject_date = "6_June_1666"; // Why not?
+ 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;
+
+ // 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();
-
+ strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ serieNumber = 0;
+ instanceNumber = 0;
+
// -----------------------------------------------------
// Iterate to ALL the objets(files/directories) found in the input directory
// (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();
it != fileNames.end();
++it)
{
- if ( !boost::filesystem::is_regular(*it) ) // check twice !
if ( boost::filesystem::is_directory(*it) )
{
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) +
br_acqp.LoadFile(strAcqp);
br_acqp.FillMap();
+//std::cout << "out of br_acqp.FillMap " << std::endl;
std::string acqp_scan_name;
std::string acqp_method;
std::string acqp_protocol_location;
BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
acqp_protocol_location = b_protocol_location.GetStringValue()[0];
cleanString(acqp_protocol_location);
-
+
+//std::cout << "out of br_acqp.FillMap 1" << std::endl;
BrukerFieldData b_scan_name=br_acqp.GetFieldData("ACQ_scan_name");
+//std::cout << "out of br_acqp.FillMap 11" << std::endl;
acqp_scan_name = b_scan_name.GetStringValue()[0];
+//std::cout << "out of br_acqp.FillMap 12 [" << acqp_scan_name << "]" << std::endl;
cleanString(acqp_scan_name);
-
- BrukerFieldData b_method=br_acqp.GetFieldData("ACQ_method");
- acqp_method = b_method.GetStringValue()[0];
- cleanString(acqp_method);
+//std::cout << "out of br_acqp.FillMap 2" << std::endl;
+ 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");
- b_list_size.PrintSelf(); //JP
-
- nbSlices = b_list_size.GetIntValue()[0];
+//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_protocol_location
+ /* + "." + acqp_protocol_location */ // always the same (in each acquisition)
+ "." + acqp_scan_name
+ "." + acqp_method.c_str();
- sprintf(outputDirName, "%s%c%s", 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::cout << " ================================================================================\n"
- << " ========================= [" << GDCM_NAME_SPACE::Util::GetName(*it).c_str()
- << acqp_protocol_location.c_str()
- << acqp_scan_name.c_str()
- << acqp_method.c_str()
- << "]\n"
+ << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\n"
<< " ================================================================================"
<< std::endl;
-*/
+ std::string strOutputDirName(outputDirName);
if (verbose)
- printf ("outputDirName [%s]\n", outputDirName);
-
- DealWithNiveau1(*it, outputDirName);
+ printf ("outputDirName [%s]\n", outputDirName);
+ try {
+ DealWithNiveau1(*it, strOutputDirName);
+ }
+ catch (BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau1 (" << e.what() << ") " << std::endl;
+ continue;
+ }
}
} // end of : for (GDCM_NAME_SPACE::DirListType::iterator it
}
-
// =====================================================================
-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
//
if (!res) {
std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
- exit (0);
+ throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
+ // exit (0);
}
GDCM_NAME_SPACE::DirList dirList(level1Directory, false, true); // DON'T get recursively the list of files
GDCM_NAME_SPACE::DirListType fileNames;
//if ( ! boost::filesystem::is_directory(*it) )
{
if (verbose)
- std::cout << "--- [" << *it << "] is a file" << std::endl;
+ std::cout << "--- [" << *it << "] is a file." << std::endl;
}
}
it != fileNames.end();
++it)
{
- if ( !boost::filesystem::is_regular(*it) ) // check twice !
if ( boost::filesystem::is_directory(*it) )
{
// will be always "pdata" ...
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;
canOpen = br_method.LoadFile(strMethod);
if (!canOpen)
{
- std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
- exit(0); /// \TODO throw an exception !
+ std::cout << "Hopeless! neither 'method' nor 'imnd' found in ["
+ << level1Directory << "]; we skip it!" << std::endl;
+ continue;
+ //throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
+ //exit(0); /// \TODO throw an exception !
}
}
if (verbose)
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
- */
- DealWithNiveau2(*it,outputDirName );
+ */
+ try {
+ DealWithNiveau2(*it, strOutputDirName);
+ }
+ catch (BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
+ continue;
+ }
}
}
}
// =====================================================================
-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
if (!res) {
std::cout << "[" << currentOutputDirName << "] Directory creation failure " << std::endl;
- exit (0);
+ 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;
it != fileNames.end();
++it)
{
- if ( !boost::filesystem::is_regular(*it) )
- //if ( ! boost::filesystem::is_directory(*it) )
+ if ( ! boost::filesystem::is_directory(*it) )
{
- std::cout << "--- --- [" << *it << "] is a file" << std::endl;
+ std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
}
-
}
-
+
for (it = fileNames.begin();
it != fileNames.end();
++it)
{
- if ( !boost::filesystem::is_regular(*it) ) // check twice !
if ( boost::filesystem::is_directory(*it) )
{
if (verbose)
std::cout << "--- --- [" << *it << "] is a directory" << std::endl;
-
+
// sprintf(outputDirName, "%s%c%s", currentOutputDirName.c_str(),
// GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
// GDCM_NAME_SPACE::Util::GetName(*it).c_str() );
GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
str_isa_func_name.c_str());
- }
- DealWithNiveau3(*it, outputDirName);
+ }
+ std::string strOutputDirName(outputDirName);
+ try {
+ DealWithNiveau3(*it, strOutputDirName);
+ }
+ catch (BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau3 (" << e.what() << "); "
+ << " We skip [" << level2Directory << "]" << std::endl;
+ continue;
+ }
+ catch (BrukerInitException &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;
- exit (0);
+ throw ( BrukerHopelessException ("Hopeless! Level3 output directory creation failure"));
+ //exit (0);
}
GDCM_NAME_SPACE::DirList dirList(level3Directory, false, true); // DON'T get recursively the list of files
fileNames = dirList.GetFilenames();
char original2dseqName [(unsigned int) PATH_MAX+2];
+ char original2dseqName_XXX [(unsigned int) PATH_MAX+2];
char currentOutputMhdDirName [(unsigned int) PATH_MAX+2];
char outputMhdFileName [(unsigned int) PATH_MAX+2];
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 << "--- => [" << char_d3proc << "]" << std::endl;
+ std::cout << "d3proc: --- => [" << char_d3proc << "]" << std::endl;
std::string str_d3proc(char_d3proc);
canOpen = br_d3proc.LoadFile(str_d3proc);
if (!canOpen)
{
std::cout << "Hopeless! no 'd3proc' found" << std::endl;
- exit(0); /// \TODO throw an exception !
+ throw ( BrukerHopelessException ("Hopeless! no 'd3proc' found"));
+ //exit(0); /// \TODO throw an exception !
}
canOpen = br_d3proc.FillMap();
if (!canOpen)
{
std::cout << "Hopeless! FillMap failed on 'd3proc'" << std::endl;
- exit(0); /// \TODO throw an exception !
+ throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'd3proc'"));
+ //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 << "--- => [" << 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)
{
- std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl;
- exit(0); /// \TODO throw an exception !
+ std::cout << "Hopeless! cannot find 'reco' in [" << str_reco << "]" << std::endl;
+ 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();
if (!canOpen)
{
std::cout << "Hopeless! FillMap failed on [" << str_reco << "]" << std::endl;
- exit(0); /// \TODO throw an exception !
- }
+ throw ( BrukerHopelessException ("Hopeless! FillMap failed on 'reco'"));
+ //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;
-
// -------------------end try reco
BrukerFieldData bX = br_d3proc.GetFieldData("IM_SIX");
int NX = bX.GetIntValue()[0];
- std::cout << "IM_SIX " << NX << std::endl;
+ if (verbose)
+ std::cout << "IM_SIX " << NX << std::endl;
BrukerFieldData bY=br_d3proc.GetFieldData("IM_SIY");
int NY = bY.GetIntValue()[0];
- std::cout << "IM_SIY " << NY << std::endl;
+ 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];
- std::cout << "IM_SIZ " << nbFrames << std::endl;
+ 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 clices, etc)
+ /// (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;
- exit (0);
+ throw ( BrukerHopelessException ("Hopeless!FillMap failed on 'reco'"));
+ //exit (0);
}
if (verbose)
std::cout << "Directory creation [" << currentOutputDirName << "]" << std::endl;
} // end if mhd
- std::cout << "nbFrames " << nbFrames << std::endl;
- std::cout << "nbSlices " << nbSlices << std::endl;
+ if (verbose)
+ std::cout << "nbFrames " << nbFrames << std::endl;
+ if (verbose)
+ std::cout << "nbSlices " << nbSlices << std::endl;
int k;
int nbInstants = nbFrames/nbSlices;
- std::cout << "nbInstants (deduced )" << nbInstants << std::endl;
+ if (verbose)
+ std::cout << "nbInstants (deduced)" << nbInstants << std::endl;
int instantNb;
int sliceNb;
FILE *fp; // for MHD files
fp = fopen(original2dseqName, "rb");
if (!fp)
{
- std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
- exit (0);
+ // try 2dseq_Angio2D ?!?
+
+ sprintf( original2dseqName_XXX, "%s%s", original2dseqName, "_Angio2D");
+ fp = fopen(original2dseqName_XXX, "rb");
+ if (!fp)
+ {
+ std::cout << "Cannot open [" << original2dseqName << "] nor [" << original2dseqName_XXX << "] for reading" << std::endl;
+ fclose(fp);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
+ //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);
// This one will be important!
// ---------------------------
- imageSet = CreateImageSet ( );
-
+ try {
+ imageSet = CreateImageSet ( );
+ }
+ catch (BrukerInitException& e)
+ {
+ if (verbose)
+ std::cout << "an Init Exception was thrown in CreateImageSet ( ); " << e.what()
+ << "catched in DealWithNiveau3" << std::endl;
+ //return;
+ throw (e);
+ }
+
+ serieNumber++;
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
if (nbInstants==1) // creer un seul fichier .mhd pour toutes les Slices! (images natives)
{
- std::cout << "Single instant : do not split" << std::endl;
+ if (verbose)
+ std::cout << "Single instant : do not split" << std::endl;
if (mhd)
{
sprintf(outputMhdFileName, "%s%cMhdData_All_the_Slices.mhd", currentOutputMhdDirName,
if (!fp)
{
std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
- exit(0);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
+ //exit(0);
}
else
{
fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
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",fovX/NY, fovY/NY, 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" );
if (!fp)
{
std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
}
else
{
fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
}
fclose(fp);
+ serieNumber ++;
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
} // end if mhd
if (dicom)
{
sprintf(output2dseqSliceFileName, "%s%c2dseq_All_the_Slices.dcm",
currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
-
+
/* ----------- Write Dicom Image ---------------*/
MakeDicomImage(buffer_2dseq,
NX,
NY,
nbFrames,
pixelSize,
- fovX/NY, fovY/NY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
output2dseqSliceFileName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
- strStudyDescr,
+ strStudyDescr,
strSerieDescr,
- strStudyTimeDate,
+ strStudyTimeDate,
0,// index frame number
GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
);
} // end if dicom
} // end if nbInstants = 1
-
+
else // more than ONE instant
{
// Interleaved !
// it's (slice1,slide2, ...)t1 ; (slice1,slide2, ...)t2 ; ...
-
unsigned char *pixelsForCurrentSlice = new unsigned char[NX*NY*pixelSize*nbInstants];
k = 0;
for (sliceNb=0; sliceNb<nbSlices; sliceNb++)
{
- if (mhd)
- {
+ if (mhd)
+ {
sprintf(outputMhdFileName, "%s%cMhdData_%03d.mhd", currentOutputMhdDirName,
GDCM_NAME_SPACE::GDCM_FILESEPARATOR, k );
if (verbose)
if (!fp)
{
std::cout << "Cannot open [" << outputMhdFileName << "] for writting" << std::endl;
- exit(0);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open mhd file for writting"));
+ //exit(0);
}
else
{
fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbInstants);
fprintf(fp, "HeaderSize = %d\n", 0);
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); // slice distance : no meaning for temporal serie
- fprintf(fp, "Position = 0 0 %d\n", sliceNb );
+ //fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, 1.0 ); //
+ fprintf(fp, "ElementSpacing = %lf %lf %lf\n",spatResolX, spatResolY, 1.0 ); //slice distance : no meaning for temporal serie
+ fprintf(fp, "Position = 0 0 %d\n", sliceNb );
fprintf(fp, "Offset = 0 0 0\n" );
fprintf(fp, "CenterOfRotation = 0 0 0\n" );
fprintf(fp, "ElementNumberOfChannels = 1\n" );
if (!fp)
{
std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
- exit (0);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseqSliceFile file for writting"));
+ //exit (0);
}
int frameSize = NX*NY*pixelSize;
for (instantNb=0; instantNb<nbInstants; instantNb++)
1, fp);
}
fclose(fp);
+
// std::cout << "end writting[" << output2dseqSliceFileName << "]" << std::endl;
} // end if mhd
-
- if (dicom)
- {
+
+ if (dicom)
+ {
// desperate try !
- /*
+ /*
sprintf(output2dseqSliceFileName, "%sdummy_buffer",
currentOutputDirName.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR);
fp=fopen(output2dseqSliceFileName, "wb");
1, fp);
}
fclose(fp);
-
+
fp=fopen(output2dseqSliceFileName, "rb");
if (!fp)
{
std::cout << "Cannot open [" << output2dseqSliceFileName << "] for reading" << std::endl;
exit (0);
- }
+ }
fread( pixelsForCurrentSlice,
frameSize*nbInstants,
1, fp);
fclose(fp);
// end of desperate try !
- */
+ */
/* ----------- Write Dicom Image ---------------*/
-
- int frameSize = NX*NY*pixelSize;
+
+ int frameSize = NX*NY*pixelSize;
for (instantNb=0; instantNb<nbInstants; instantNb++)
{
memcpy(pixelsForCurrentSlice + frameSize*instantNb, buffer_2dseq +(nbSlices*instantNb + sliceNb)*frameSize, frameSize);
NY,
nbInstants,
pixelSize,
- fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
output2dseqSliceFileName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
- strStudyDescr,
+ strStudyDescr,
strSerieDescr,
- strStudyTimeDate,
+ strStudyTimeDate,
sliceNb*nbInstants,
GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
);
if (verbose)
std::cout << "--- Output DCM file [" << output2dseqSliceFileName << "]" << std::endl;
- } // en if dicom
+ } // en if dicom
k++;
}
} // end nbInstants == 1
delete [] buffer_2dseq;
/**/
-
-
+
+
// -----------------------------------------------------
// deal with MatLab-generated Carto file.
// -----------------------------------------------------
-
- dealWithCarto(fileNames, NX, NY, nbSlices, fovX, fovY, sliceDistance,
+
+ 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,
- double fovX, double fovY, double sliceDistance,
+ /*double fovX, double fovY, */
+ double spatResolX, double spatResolY, double sliceDistance,
char *copyFile, std::string ¤tOutputDirName,
- char *outputMhdFileName, char *output2dseqCartoName)
+ char *outputMhdFileName, char *output2dseqCartoName)
{
// -----------------------------------------------------
// deal with MatLab-generated Carto file.
// -----------------------------------------------------
-
- char *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak" , ""}; // add more carto file name identifiers if necessary; end with ""
- int icode;
+
+ 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 ( ! boost::filesystem::is_directory(*it) )
{
if (verbose)
- std::cout << "--- [" << *it << "] is a file" << std::endl;
-
- icode = 0;
+ std::cout << "--- [" << *it << "] is a file..." << std::endl;
+ icode = 0;
while (code[icode][0] != 0)
+ {
+ iseparator = 0;
+ while (separator[iseparator][0] != 0)
{
- sprintf(file_name_ident, "2dseq_%s",code[icode]); // e.g "2dseq_ADC"
+ sprintf(file_name_ident, "2dseq%s%s",separator[iseparator],code[icode]); // e.g "2dseq_ADC"
+ //if (verbose)
+ // std::cout << "check name ["<<(*it) << "] for string [" << file_name_ident << "]" << std::endl;
std::string::size_type loc = (*it).rfind(file_name_ident);
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");
if (!fp){
std::cout << "Cannot open [" << *it << "] for reading" << std::endl;
-
+ throw ( BrukerHopelessException ("Level 1 Unable to open 'carto' file "));
}
fread(buffer_carto, NX*NY*sizeof(double), nbSlices, fp);
+ // ?!? sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
std::cout << "Deal with Carto file :[" <<*it << "], computed length : "
<< NX*NY*sizeof(double)*nbSlices << std::endl;
- std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
+ std::string lastFileName = GDCM_NAME_SPACE::Util::GetName((*it).c_str());
if (mhd)
- {
+ {
// Copy the data file in the new directory
sprintf(copyFile, "cp %s %s%c%s", (*it).c_str() ,
currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str());
system(copyFile);
sprintf(outputMhdFileName, "%s%c%s%s",
- currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".mhd" );
+ 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)
fprintf(fp, "BinaryData = True \n" );
fprintf(fp, "BinaryDataByteOrderMSB = False\n" );
fprintf(fp, "DimSize = %d %d %d\n", NX, NY, nbSlices);
- fprintf(fp, "ElementSpacing = %lf %lf %lf\n",fovX/NY, fovY/NY, sliceDistance );
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, "Position = 0 0 0\n" );
fprintf(fp, "Offset = 0 0 0\n" );
fprintf(fp, "CenterOfRotation = 0 0 0\n" );
fclose(fp);
}
if (verbose)
- std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
+ std::cout << "--- end write Carto MHD file [" << outputMhdFileName << "]" << std::endl;
} // end if mhd
// ----------- Write Dicom Image ---------------
if (dicom)
- {
+ {
sprintf(output2dseqCartoName, "%s%c%s%s",
currentOutputDirName.c_str(),GDCM_NAME_SPACE::GDCM_FILESEPARATOR, lastFileName.c_str(), ".dcm" );
if (verbose)
- std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
+ std::cout << "--- end create name output2dseqCartoName file [" << output2dseqCartoName << "]" << std::endl;
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID(); //New SerieUID for each carto.
std::string strNewSerieDescr(strSerieDescr+ "_" +GDCM_NAME_SPACE::Util::GetName((*it).c_str()));
NY,
nbSlices,
8, // pixelSize
- fovX/NY, fovY/NY, sliceDistance,
+ //fovX/NY, fovY/NY, sliceDistance,
+ spatResolX, spatResolY, sliceDistance,
output2dseqCartoName,
- strPatientName,
+ subject_name,
day,
strStudyUID,
strSerieUID,
- strStudyDescr,
+ strStudyDescr,
strNewSerieDescr,
- strStudyTimeDate,
+ strStudyTimeDate,
0,
GDCM_NAME_SPACE::CREATED_IMAGE
);
delete [] buffer_carto;
if (verbose)
- std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
+ std::cout << "--- End writing Carto DICOM file [" << output2dseqCartoName << "]" << std::endl;
break; // don't check for more ident on same file name!
- }
- icode++;
- }
- }
- } // end iterate on files
-}
+ } // end deal with _ADC, -adc, etc
+ iseparator ++;
+ } // end iterate speparators
+ icode++;
+ } // end iterate code
+ } // end boost::filesystem::is_regular(*it)
+ } // 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;
if (verbose)
std::cout << "Check for output directory :[" << OutputDirName << "]."
- <<std::endl;
+ <<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 << "KO : not a dir : [" << OutputDirName << "] (creation failure ?)" << std::endl;
- return 0;
- /// \todo : THROW AN EXCEPTION
+ //return 0;
+ throw ( BrukerHopelessException ("Level 1 output directory creation failure "));
}
else
{
else
{
if (verbose)
- std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
+ std::cout << "Output Directory [" << OutputDirName << "] already exists; Used as is." << std::endl;
}
-
return 1;
-
}
-
// ===========================================================================================
/// \TODO move cleanString to 'crea' ?
GDCM_NAME_SPACE::Util::ReplaceSpecChar(s, repChar);
}
-
-
// ===========================================================================================
-
void Bruker2Dicom::getImhDataType(BrukerFieldData &bDPT, std::string &mhdDataPixelType, int &pixelSize)
{
if(bDPT.GetDataType() == "string")
{
std::string brukerDataPixelType = bDPT.GetStringValue()[0];
- std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
+ if (verbose)
+ std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
//std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
if (brukerDataPixelType == "ip_short") {
else
{
int brukerDataPixelType = bDPT.GetIntValue()[0];
- std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
+ if (verbose)
+ std::cout << "DATTYPE " << brukerDataPixelType << std::endl;
//std::string brukerDataPixelType = br_d3proc.GetFieldData("DATTYPE").GetStringValue()[0];
// 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()") );
+ }
+
br_acqp.SetImageLoopStructure();
br_acqp.SetBrukerImageList();
std::vector<std::vector<int> > brukerImageList = br_acqp.GetBrukerImageList();
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] ;
imageOrientation = imageSet[i].getRotationMatrixRPS2XYZ();
std::cout << "\t Orientation " ;
for(int i1=0; i1<3;i1++)for(int i2=0; i2<3;i2++)
- std::cout << imageOrientation[i1][i2] << " ";
-
+ std::cout << imageOrientation[i1][i2] << " ";CreateImageSet
+
//std::cout << "\t Abs Time " << imageSet[i].getAbsoluteTimePosition();
std::cout << "\t Relat Time " << imageSet[i].getRelativeTimePosition();
return imageSet;
}
-
// ===========================================================================================
void Bruker2Dicom::MakeDicomImage(unsigned char *tabPixels,
std::string &serieUID,
std::string &studyDescr,
std::string &serieDescr,
- std::string &strStudyTimeDate,
+ std::string &strStudyTimeDate,
int imgNum,
- GDCM_NAME_SPACE::ImageContentType contentType
+ GDCM_NAME_SPACE::ImageContentType contentType
)
{
std::ostringstream str;
// 0018 0050 DS 1 Slice Thickness
str.str("");
str << sliceDistance;
- file->InsertEntryString(str.str(),0x0018,0x0050, "DS");
+ 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" , 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
file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0002, 0x0002, "UI"); // [Media Storage SOP Class UID]
file->InsertEntryString("1.2.840.10008.5.1.4.1.1.4" , 0x0008, 0x0016, "UI"); // [SOP Class UID]
// 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");
/// \TODO split into 2 strings!
file->InsertEntryString(strStudyTimeDate.substr(10,11).c_str(),0x0008,0x0020, "DA");
- file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(),0x0008,0x0030, "TM");
+ file->InsertEntryString(strStudyTimeDate.substr(1,8).c_str(), 0x0008,0x0030, "TM");
- file->InsertEntryString(studyDescr,0x0008,0x1030, "LO"); // Study Description
- file->InsertEntryString(serieDescr,0x0008,0x103e, "LO"); // Series Description
+ file->InsertEntryString(studyDescr, 0x0008,0x1030, "LO"); // Study Description
+ file->InsertEntryString(serieDescr, 0x0008,0x103e, "LO"); // Series Description
//0008|0060 [CS] [Modality]
file->InsertEntryString("MR",0x0008,0x0060, "CS");
char charImageOrientation[256];
/*
-std::cout << "try charImageOrientation " <<
+std::cout << "charImageOrientation " <<
imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][0] << " " <<
imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][1] << " " <<
imageSet[imgNum].getRotationMatrixRPS2XYZ()[0][2] << " " <<
file->InsertEntryString(charImageOrientation,0x0020,0x0037, "DS");
-
// 0020 0032 DS 3 Image Position (Patient)
char charImagePosition[256];
imageSet[imgNum].getTranslationVectorRPS2XYZ()[2]);
file->InsertEntryString(charImagePosition,0x0020,0x0032, "DS"); //0020 0032 DS 3 Image Position (Patient)
-
-
// 0020 0x1041 DS 1 Slice Location
// sprintf(charImagePosition,"%f",float(imgNum));
fileH->SetImageData((uint8_t *)tabPixels, X*Y*nbFrames*pixelSize);
fileH->SetWriteModeToRaw();
fileH->SetWriteTypeToDcmExplVR();
- if( !fileH->Write(dcmImageName))
+ if( !fileH->Write(dcmImageName)) {
std::cout << "Failed for [" << dcmImageName << "]\n"
- << " File is unwrittable" << std::endl;
-
- if (verbose)
- file->Print();
+ << " File is unwrittable" << std::endl;
+ file->Delete();
+ fileH->Delete();
+ throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
+ }
+ //if (verbose)
+ // file->Print();
file->Delete();
fileH->Delete();
}
-
-
git://git.creatis.insa-lyon.fr / creaBruker.git / blobdiff