#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
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);
if (!canOpen)
{
std::cout << "Hopeless! no 'subject' found" << std::endl;
- exit(0); /// \TODO throw an exception !
+ throw ( BrukerHopelessException ("Hopeless! no 'subject' found in root input directory "));
+ //exit(0); /// \TODO throw an exception !
}
else
{
}
//br_subject.PrintSelf();
- // get info for 'Study Description'
-
+ // get info for 'Study Description'
BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
std::string subject_name = b_name.GetStringValue()[0];
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)
cleanString(acqp_method);
BrukerFieldData b_list_size = br_acqp.GetFieldData("ACQ_O1_list_size");
- b_list_size.PrintSelf(); //JP
+ //b_list_size.PrintSelf(); //JP
nbSlices = b_list_size.GetIntValue()[0];
if (verbose)
printf ("outputDirName [%s]\n", outputDirName);
-
- DealWithNiveau1(*it, outputDirName);
+ try {
+ DealWithNiveau1(*it, outputDirName);
+ }
+ 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
}
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;
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)
##$PVM_SPackArrNSlices=( 2 )
7 1
*/
- DealWithNiveau2(*it,outputDirName );
+ try {
+ DealWithNiveau2(*it,outputDirName );
+ }
+ catch (BrukerHopelessException &e)
+ {
+ std::cout << "And Exception was thrown in DealWithNiveau2 (" << e.what() << ") " << std::endl;
+ continue;
+ }
}
}
}
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::GDCM_FILESEPARATOR,
GDCM_NAME_SPACE::Util::GetName(*it).c_str(),
str_isa_func_name.c_str());
- }
- DealWithNiveau3(*it, outputDirName);
+ }
+ try {
+ DealWithNiveau3(*it, outputDirName);
+ }
+ 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;
+ }
}
}
}
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
sprintf(char_d3proc,"%s%c%s", level3Directory.c_str(), GDCM_NAME_SPACE::GDCM_FILESEPARATOR,"d3proc" );
if (verbose)
- std::cout << "try d3proc: --- => [" << 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;
// GDCM_NAME_SPACE::GDCM_FILESEPARATOR +
// "d3proc";
if (verbose)
- std::cout << "try reco --- => [" << char_reco << "]" << std::endl;
+ std::cout << "reco --- => [" << char_reco << "]" << std::endl;
std::string str_reco(char_reco);
canOpen = br_reco.LoadFile(str_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 !
}
}
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 !
}
//std::cout << "------------------------------------------------------------------------------------------------" << std::cout;
// br_reco.PrintSelf();
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, ...}
res = CreateDirectory( currentOutputMhdDirName );
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
if (!fp)
{
std::cout << "Cannot open [" << original2dseqName << "] for reading" << std::endl;
- exit (0);
+ throw ( BrukerHopelessException ("Hopeless! Cannot open '2dseq'"));
+ //exit (0);
}
unsigned char *buffer_2dseq = new unsigned char[NX*NY*pixelSize*nbSlices*nbInstants];
// 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
{
if (!fp)
{
std::cout << "Cannot open [" << output2dseqSliceFileName << "] for writting" << std::endl;
+ throw ( BrukerHopelessException ("Hopeless! Cannot open 2dseq file for writting"));
}
else
{
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
{
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++)
// 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 *code[] ={ "ADC", "adc", "TTP", "ttp", "PEAK", "peak", "" }; // add more carto file name identifiers if necessary; end with ""
int icode;
GDCM_NAME_SPACE::DirListType::iterator it;
char file_name_ident[500];
while (code[icode][0] != 0)
{
- sprintf(file_name_ident, "2dseq_%s",code[icode]); // e.g "2dseq_ADC"
+ sprintf(file_name_ident, "2dseq.%s",code[icode]); // e.g "2dseq_ADC"
std::string::size_type loc = (*it).rfind(file_name_ident);
if ( loc != std::string::npos )
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);
{
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
{
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 !!!
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();
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();
// 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]
/// \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] << " " <<
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;
-
+ << " File is unwrittable" << std::endl;
+ file->Delete();
+ fileH->Delete();
+ throw ( BrukerHopelessException ("Level 1 Unable to write Dicom file "));
+ }
if (verbose)
file->Print();
git://git.creatis.insa-lyon.fr / creaBruker.git / blobdiff