#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 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;
bool canOpen;
std::string outputFileName;
+
// BrukerDataSet br_subject;
std::string subject;
subject = GDCM_NAME_SPACE::Util::GetPath(*(fileNames.begin()))+
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'
-
- /*
- BrukerFieldData b_protocol_location=br_acqp.GetFieldData("ACQ_protocol_location");
- acqp_protocol_location = b_protocol_location.GetStringValue()[0];
- cleanString(acqp_protocol_location);
-*/
+ // get info for 'Study Description'
+
BrukerFieldData b_name=br_subject.GetFieldData("SUBJECT_name_string");
std::string subject_name = b_name.GetStringValue()[0];
- strPatientName = subject_name;
+ 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);
-
+ 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);
-
+ 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;
+ 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);
+ 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;
-
+
+ // subject_name is already in 'Patient Name'
+ strStudyDescr = /*subject_name + "." + */ subject_study_name + "." + subject_entry + "." + subject_position + "." + subject_date;
+
char outputDirName[(unsigned int) PATH_MAX+2];
strStudyUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
-
+ serieNumber = 0;
// -----------------------------------------------------
// Iterate to ALL the objets(files/directories) found in the input directory
// (this is level ZERO)
nbSlices = b_list_size.GetIntValue()[0];
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(),
GDCM_NAME_SPACE::GDCM_FILESEPARATOR,
strSerieDescr.c_str() );
-
+
std::cout << " ================================================================================\n"
- << " === [" << GDCM_NAME_SPACE::Util::GetName(*it) << "] -> [" << strSerieDescr << "]\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"
- << " ================================================================================"
- << std::endl;
-*/
+
if (verbose)
printf ("outputDirName [%s]\n", outputDirName);
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;
it != fileNames.end();
++it)
{
- if ( ! boost::filesystem::is_directory(*it) )
+ if ( boost::filesystem::is_regular(*it) )
+ //if ( ! boost::filesystem::is_directory(*it) )
{
if (verbose)
- std::cout << "--- [" << *it << "] is a file" << std::endl;
+ std::cout << "--- [" << *it << "] is a file." << std::endl;
}
}
if (!canOpen)
{
std::cout << "Hopeless! neither 'method' nor 'imnd' found" << std::endl;
- exit(0); /// \TODO throw an exception !
+ throw ( BrukerHopelessException ("Hopeless! neither 'method' nor 'imnd' found "));
+ //exit(0); /// \TODO throw an exception !
}
}
if (verbose)
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
{
if ( ! boost::filesystem::is_directory(*it) )
{
- std::cout << "--- --- [" << *it << "] is a file" << std::endl;
+ std::cout << "--- --- [" << *it << "] is a file.." << std::endl;
}
}
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 << "--- => [" << 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 << "--- => [" << 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, ...}
std::cout << "FOV (ds method) " << fovX << " " << fovY << 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];
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)
+ {
+ std::cout << "Exception " << e.what() << std::endl;
+ return;
+ }
+ 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
{
fwrite( buffer_2dseq, NX*NY*pixelSize, nbSlices, fp);
}
fclose(fp);
+ serieNumber ++;
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
} // end if mhd
if (dicom)
day,
strStudyUID,
strSerieUID,
- strStudyDescr,
+ strStudyDescr,
strSerieDescr,
- strStudyTimeDate,
+ strStudyTimeDate,
0,// index frame number
GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE
);
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
{
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++)
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);
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++;
}
void Bruker2Dicom::dealWithCarto(GDCM_NAME_SPACE::DirListType &fileNames, int NX, int NY, int nbSlices,
double fovX, double fovY, double sliceDistance,
char *copyFile, std::string ¤tOutputDirName,
- char *outputMhdFileName, char *output2dseqCartoName)
+ char *outputMhdFileName, char *output2dseqCartoName)
{
// -----------------------------------------------------
// deal with MatLab-generated Carto file.
it != fileNames.end();
++it)
{
- if ( ! boost::filesystem::is_directory(*it) )
+ if ( boost::filesystem::is_regular(*it) )
+ //if ( ! boost::filesystem::is_directory(*it) )
{
if (verbose)
- std::cout << "--- [" << *it << "] is a file" << std::endl;
+ std::cout << "--- [" << *it << "] is a file..." << std::endl;
icode = 0;
<< NX*NY*sizeof(double)*nbSlices << std::endl;
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());
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()));
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++;
}
}
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") {
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 ("Bruker2Dicom::CreateImageSet failure ") );
+ }
br_acqp.SetImageLoopStructure();
br_acqp.SetBrukerImageList();
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
)
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] << " " <<
git://git.creatis.insa-lyon.fr / creaBruker.git / blobdiff