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added NeXus support. Still a lot of testing will be needed, documentation updated, etc.

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nemu
2011-04-08 09:24:32 +00:00
parent 00d591fbff
commit 49619fcffb
18 changed files with 865 additions and 236 deletions
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343
src/classes/PRunDataHandler.cpp
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@ -29,6 +29,10 @@
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <cstdio>
#include <ctime>
#include <iostream>
@ -50,6 +54,10 @@ using namespace std;
#include "MuSR_td_PSI_bin.h"
#include "mud.h"
#ifdef PNEXUS_ENABLED
#include "PNeXus.h"
#endif
#include "PRunDataHandler.h"
#define ROOT_ALL 0
@ -610,7 +618,7 @@ Bool_t PRunDataHandler::FileExistsCheck(PMsrRunBlock &runInfo, const UInt_t idx)
else if (!runInfo.GetFileFormat(idx)->CompareTo("root-ppc")) // post pile up corrected histos
ext = TString("root");
else if (!runInfo.GetFileFormat(idx)->CompareTo("nexus"))
ext = TString("nexus");
ext = TString("NXS");
else if (!runInfo.GetFileFormat(idx)->CompareTo("psi-bin"))
ext = TString("bin");
else if (!runInfo.GetFileFormat(idx)->CompareTo("psi-mdu"))
@ -640,7 +648,7 @@ Bool_t PRunDataHandler::FileExistsCheck(PMsrRunBlock &runInfo, const UInt_t idx)
assert(0);
}
pstr->ToUpper();
cerr << endl << ">> **ERROR** File Format '" << pstr->Data() << "' unsupported.";
cerr << endl << ">> PRunDataHandler::FileExistsCheck: **ERROR** File Format '" << pstr->Data() << "' unsupported.";
cerr << endl << ">> support file formats are:";
cerr << endl << ">> ROOT-NPP -> root not post pileup corrected for lem";
cerr << endl << ">> ROOT-PPC -> root post pileup corrected for lem";
@ -794,7 +802,7 @@ Bool_t PRunDataHandler::FileExistsCheck(const Bool_t fileName, const Int_t idx)
}
// check for input/output templates
if ((fAny2ManyInfo->inTemplate.Length() == 0) || (fAny2ManyInfo->outTemplate.Length() == 0)) {
cerr << endl << ">> PRunDataHandler::FileExistsCheck(): **ERROR** when using run lists, input/ouput templates are needed as well." << endl;
cerr << endl << ">> PRunDataHandler::FileExistsCheck(): **ERROR** when using run lists, input/output templates are needed as well." << endl;
return false;
}
// make the input file name according to the input template
@ -1214,8 +1222,106 @@ Bool_t PRunDataHandler::ReadRootFile(UInt_t tag)
*/
Bool_t PRunDataHandler::ReadNexusFile()
{
cout << endl << "PRunDataHandler::ReadNexusFile(): Sorry, not yet implemented, ask Alex Amato and Stephen Cottrell ...";
return false;
#ifdef PNEXUS_ENABLED
cout << endl << ">> PRunDataHandler::ReadNexusFile(): Will read nexus file " << fRunPathName.Data() << " ...";
PDoubleVector histoData;
PRawRunData runData;
TString str;
Double_t dval;
PNeXus *nxs_file = new PNeXus(fRunPathName.Data());
if (!nxs_file->IsValid()) {
cerr << endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file.";
cerr << endl << ">> Error Message: " << nxs_file->GetErrorMsg().data() << endl;
return false;
}
// get header information
// get/set run title
str = TString(nxs_file->GetRunTitle());
runData.SetRunTitle(str);
// get/set run number
runData.SetRunNumber(nxs_file->GetRunNumber());
// get/set temperature
runData.SetTemperature(0, nxs_file->GetSampleTemperature(), 0.0);
// get/set field
dval = nxs_file->GetMagneticField();
str = TString(nxs_file->GetMagneticFieldUnits());
// since field has to be given in Gauss, check the units
Double_t factor=1.0;
if (!str.CompareTo("gauss", TString::kIgnoreCase))
factor=1.0;
else if (!str.CompareTo("tesla", TString::kIgnoreCase))
factor=1.0e4;
else
factor=1.0;
runData.SetField(factor*dval);
// get/set implantation energy
runData.SetEnergy(PMUSR_UNDEFINED);
// get/set moderator HV
runData.SetTransport(PMUSR_UNDEFINED);
// get/set RA HV's (LEM specific)
for (UInt_t i=0; i<4; i++)
runData.SetRingAnode(i, PMUSR_UNDEFINED);
// get/set setup
runData.SetSetup(nxs_file->GetRunNotes());
// get/set sample
runData.SetSample(nxs_file->GetSampleName());
// get/set orientation
runData.SetOrientation("??");
// get/set time resolution (ns)
runData.SetTimeResolution(nxs_file->GetTimeResolution());
// get/set start/stop time
runData.SetStartTime(nxs_file->GetStartTime());
runData.SetStartDate(nxs_file->GetStartDate());
runData.SetStopTime(nxs_file->GetStopTime());
runData.SetStopDate(nxs_file->GetStopDate());
// get t0, firstGoodBin, lastGoodBin, data
UInt_t t0=nxs_file->GetT0();
PIntPair goodDataBin;
goodDataBin.first = nxs_file->GetFirstGoodBin();
goodDataBin.second = nxs_file->GetLastGoodBin();
PDoubleVector data;
for (Int_t i=0; i<nxs_file->GetNoHistos(); i++) {
runData.AppendT0(t0);
runData.AppendGoodDataBin(goodDataBin);
data.clear();
for (UInt_t j=0; j<nxs_file->GetHisto(i)->size(); j++) {
data.push_back((Double_t)nxs_file->GetHisto(i)->at(j));
}
runData.AppendDataBin(data);
}
data.clear();
// keep run name from the msr-file
runData.SetRunName(fRunName);
// keep the information
fData.push_back(runData);
// clean up
if (nxs_file) {
delete nxs_file;
nxs_file = 0;
}
#else
cout << endl << ">> PRunDataHandler::ReadNexusFile(): Sorry, not enabled at configuration level, i.e. --enable-NeXus when executing configure" << endl << endl;
#endif
return true;
}
//--------------------------------------------------------------------------
@ -1620,6 +1726,7 @@ Bool_t PRunDataHandler::ReadPsiBinFile()
}
runData.SetStopDate(sDateTime[0]);
runData.SetStopTime(sDateTime[1]);
sDateTime.clear();
// fill raw data
PDoubleVector histoData;
@ -2988,21 +3095,10 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
// generate output file name if needed
if (!fAny2ManyInfo->useStandardOutput || (fAny2ManyInfo->compressionTag > 0)) {
if (fln.Length() == 0) {
Int_t start = fRunPathName.Last('/');
Int_t end = fRunPathName.Last('.');
if (end == -1) {
cerr << endl << ">> PRunDataHandler::WriteRootFile(): **ERROR** couldn't generate the output file name ..." << endl;
Bool_t ok = false;
fln = GetFileName(".root", ok);
if (!ok)
return false;
}
// cut out the filename (get rid of the extension, and the path)
Char_t str1[1024], str2[1024];
strncpy(str1, fRunPathName.Data(), sizeof(str1));
for (Int_t i=0; i<end-start-1; i++) {
str2[i] = str1[i+start+1];
}
str2[end-start-1] = 0;
fln = fAny2ManyInfo->outPath + str2 + ".root";
} else {
fln.Prepend(fAny2ManyInfo->outPath);
}
@ -3183,8 +3279,92 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
* \param fln file name. If empty, the routine will try to construct one
*/
Bool_t PRunDataHandler::WriteNexusFile(TString fln)
{
cout << endl << ">> PRunDataHandler::WriteNexusFile(): will write a nexus data file. Not yet implemented ... " << endl;
{
#ifdef PNEXUS_ENABLED
// generate output file name
if (fln.Length() == 0) {
Bool_t ok = false;
fln = GetFileName(".nxs", ok);
if (!ok)
return false;
} else {
fln.Prepend(fAny2ManyInfo->outPath);
}
// keep the file name if compression is whished
fAny2ManyInfo->outPathFileName.push_back(fln);
if (!fAny2ManyInfo->useStandardOutput)
cout << endl << ">> PRunDataHandler::WriteNexusFile(): writing a NeXus data file (" << fln.Data() << ") ... " << endl;
// create NeXus object
PNeXus *nxs = new PNeXus();
if (nxs == 0) {
cerr << endl << ">> PRunDataHandler::WriteNexusFile(): **ERROR** couldn't invoke the NeXus object." << endl;
return false;
}
// fill necessary data structures
nxs->SetFileName(fln.Data());
nxs->SetIDFVersion(1);
nxs->SetProgramName("any2many");
nxs->SetProgramVersion("$Id$");
nxs->SetRunNumber(fData[0].GetRunNumber());
nxs->SetRunTitle(fData[0].GetRunTitle()->Data());
nxs->SetRunNotes("n/a");
nxs->SetAnalysisTag("n/a");
nxs->SetLab("PSI");
nxs->SetBeamline("n/a");
nxs->SetStartDate(fData[0].GetStartDate()->Data());
nxs->SetStartTime(fData[0].GetStartTime()->Data());
nxs->SetStopDate(fData[0].GetStopDate()->Data());
nxs->SetStopTime(fData[0].GetStopTime()->Data());
nxs->SetSwitchingState(0);
nxs->SetUser("n/a");
nxs->SetExperimentNumber("n/a");
nxs->SetSampleName(fData[0].GetSample()->Data());
nxs->SetSampleTemperature(fData[0].GetTemperature(0));
nxs->SetSampleTemperatureUints("Kelvin");
nxs->SetMagneticField(fData[0].GetField());
nxs->SetMagneticFieldUnits("Gauss");
nxs->SetSampleEnvironment("n/a");
nxs->SetSampleShape("n/a");
nxs->SetMagneticFieldVectorAvailable(0);
nxs->SetExperimentName("n/a");
nxs->SetNoDetectors(fData[0].GetNoOfHistos());
nxs->SetCollimatorType("n/a");
nxs->SetTimeResolution(fData[0].GetTimeResolution());
if (fData[0].GetT0(0) == -1)
nxs->SetT0(0);
else
nxs->SetT0(fData[0].GetT0(0)); // this needs to be changed in the long term, since for continous sources each detector has its one t0!!
if (fData[0].GetGoodDataBin(0).first == -1) {
nxs->SetFirstGoodBin(0);
nxs->SetLastGoodBin(0);
} else {
nxs->SetFirstGoodBin(fData[0].GetGoodDataBin(0).first);
nxs->SetLastGoodBin(fData[0].GetGoodDataBin(0).second);
}
// feed real histogram data
PUIntVector data;
for (UInt_t i=0; i<fData[0].GetNoOfHistos(); i++) {
for (UInt_t j=0; j<fData[0].GetDataBin(i)->size(); j++) {
data.push_back((UInt_t)fData[0].GetDataBin(i)->at(j));
}
nxs->SetHisto(i, data);
data.clear();
}
// write file
nxs->WriteFile(fln);
// clean up
if (nxs != 0) {
delete nxs;
nxs = 0;
}
#else
cout << endl << ">> PRunDataHandler::WriteNexusFile(): Sorry, not enabled at configuration level, i.e. --enable-NeXus when executing configure" << endl << endl;
#endif
return true;
}
@ -3204,21 +3384,10 @@ Bool_t PRunDataHandler::WriteWkmFile(TString fln)
{
// generate output file name
if (fln.Length() == 0) {
Int_t start = fRunPathName.Last('/');
Int_t end = fRunPathName.Last('.');
if (end == -1) {
cerr << endl << ">> PRunDataHandler::WriteWkmFile(): **ERROR** couldn't generate the output file name ..." << endl;
Bool_t ok = false;
fln = GetFileName(".wkm", ok);
if (!ok)
return false;
}
// cut out the filename (get rid of the extension, and the path)
Char_t str1[1024], str2[1024];
strncpy(str1, fRunPathName.Data(), sizeof(str1));
for (Int_t i=0; i<end-start-1; i++) {
str2[i] = str1[i+start+1];
}
str2[end-start-1] = 0;
fln = fAny2ManyInfo->outPath + str2 + ".wkm";
} else {
fln.Prepend(fAny2ManyInfo->outPath);
}
@ -3244,7 +3413,7 @@ Bool_t PRunDataHandler::WriteWkmFile(TString fln)
// save output buffer of the stream
strm_buffer = cout.rdbuf();
// redirect ouput into the file
// redirect output into the file
cout.rdbuf(fout.rdbuf());
}
@ -3266,7 +3435,7 @@ Bool_t PRunDataHandler::WriteWkmFile(TString fln)
} else {
cout << endl << "Field : ??";
}
cout << endl << "Date : ??";
cout << endl << "Date : " << fData[0].GetStartTime()->Data() << " " << fData[0].GetStartDate()->Data() << " / " << fData[0].GetStopTime()->Data() << " " << fData[0].GetStopDate()->Data();
cout << endl << "Setup : " << fData[0].GetSetup()->Data();
cout << endl << "Groups : " << fData[0].GetNoOfHistos();
cout << endl << "Channels : " << static_cast<UInt_t>(fData[0].GetDataBin(0)->size()/fAny2ManyInfo->rebin);
@ -3334,21 +3503,10 @@ Bool_t PRunDataHandler::WritePsiBinFile(TString fln)
// generate output file name if needed
if (!fAny2ManyInfo->useStandardOutput || (fAny2ManyInfo->compressionTag > 0)) {
if (fln.Length() == 0) {
Int_t start = fRunPathName.Last('/');
Int_t end = fRunPathName.Last('.');
if (end == -1) {
cerr << endl << ">> PRunDataHandler::WritePsiBinFile(): **ERROR** couldn't generate the output file name ..." << endl;
Bool_t ok = false;
fln = GetFileName(".bin", ok);
if (!ok)
return false;
}
// cut out the filename (get rid of the extension, and the path)
Char_t str1[1024], str2[1024];
strncpy(str1, fRunPathName.Data(), sizeof(str1));
for (Int_t i=0; i<end-start-1; i++) {
str2[i] = str1[i+start+1];
}
str2[end-start-1] = 0;
fln = fAny2ManyInfo->outPath + str2 + ".bin";
} else {
fln.Prepend(fAny2ManyInfo->outPath);
}
@ -3522,21 +3680,10 @@ Bool_t PRunDataHandler::WriteMudFile(TString fln)
// generate output file name if needed
if (!fAny2ManyInfo->useStandardOutput || (fAny2ManyInfo->compressionTag > 0)) {
if (fln.Length() == 0) {
Int_t start = fRunPathName.Last('/');
Int_t end = fRunPathName.Last('.');
if (end == -1) {
cerr << endl << ">> PRunDataHandler::WriteMudFile(): **ERROR** couldn't generate the output file name ..." << endl;
Bool_t ok = false;
fln = GetFileName(".msr", ok);
if (!ok)
return false;
}
// cut out the filename (get rid of the extension, and the path)
Char_t str1[1024], str2[1024];
strncpy(str1, fRunPathName.Data(), sizeof(str1));
for (Int_t i=0; i<end-start-1; i++) {
str2[i] = str1[i+start+1];
}
str2[end-start-1] = 0;
fln = fAny2ManyInfo->outPath + str2 + ".msr";
} else {
fln.Prepend(fAny2ManyInfo->outPath);
}
@ -3700,21 +3847,10 @@ Bool_t PRunDataHandler::WriteAsciiFile(TString fln)
{
// generate output file name
if (fln.Length() == 0) {
Int_t start = fRunPathName.Last('/');
Int_t end = fRunPathName.Last('.');
if (end == -1) {
cerr << endl << ">> PRunDataHandler::WriteAsciiFile(): **ERROR** couldn't generate the output file name ..." << endl;
Bool_t ok = false;
fln = GetFileName(".ascii", ok);
if (!ok)
return false;
}
// cut out the filename (get rid of the extension, and the path)
Char_t str1[1024], str2[1024];
strncpy(str1, fRunPathName.Data(), sizeof(str1));
for (Int_t i=0; i<end-start-1; i++) {
str2[i] = str1[i+start+1];
}
str2[end-start-1] = 0;
fln = fAny2ManyInfo->outPath + str2 + ".ascii";
} else {
fln.Prepend(fAny2ManyInfo->outPath);
}
@ -3740,7 +3876,7 @@ Bool_t PRunDataHandler::WriteAsciiFile(TString fln)
// save output buffer of the stream
strm_buffer = cout.rdbuf();
// redirect ouput into the file
// redirect output into the file
cout.rdbuf(fout.rdbuf());
}
@ -3754,6 +3890,8 @@ Bool_t PRunDataHandler::WriteAsciiFile(TString fln)
if (fData[0].GetSetup()->Length() > 0)
cout << endl << "% setup : " << fData[0].GetSetup()->Data();
cout << endl << "% field : " << fData[0].GetField() << " (G)";
if (fData[0].GetStartTime()->Length() > 0)
cout << endl << "% date : " << fData[0].GetStartTime()->Data() << " " << fData[0].GetStartDate()->Data() << " / " << fData[0].GetStopTime()->Data() << " " << fData[0].GetStopDate()->Data();
if (fData[0].GetNoOfTemperatures() > 0) {
cout << endl << "% temperature : ";
for (UInt_t i=0; i<fData[0].GetNoOfTemperatures()-1; i++) {
@ -4058,6 +4196,51 @@ Int_t PRunDataHandler::GetDataTagIndex(TString &str, const PStringVector* dataTa
return result;
}
//--------------------------------------------------------------------------
// GetFileName (private)
//--------------------------------------------------------------------------
/**
* <p>Construct the file name based on the any2many request.
*
* <b>return:</b>
* - constructed file name
* - empty string
*
* \param extension if the file name to be constructed
* \param ok flag which is 'true' if the file name could be constructed, 'false' otherwise
*/
TString PRunDataHandler::GetFileName(const TString extension, Bool_t &ok)
{
TString fileName = "";
ok = true;
Int_t start = fRunPathName.Last('/');
Int_t end = fRunPathName.Last('.');
if (end == -1) {
cerr << endl << ">> PRunDataHandler::GetFileName(): **ERROR** couldn't generate the output file name ..." << endl;
ok = false;
return fileName;
}
// cut out the filename (get rid of the extension, and the path)
Char_t str1[1024], str2[1024];
strncpy(str1, fRunPathName.Data(), sizeof(str1));
for (Int_t i=0; i<end-start-1; i++) {
str2[i] = str1[i+start+1];
}
str2[end-start-1] = 0;
if (fAny2ManyInfo->inFormat == fAny2ManyInfo->outFormat) { // only rebinning
TString rebinStr;
rebinStr += fAny2ManyInfo->rebin;
fileName = fAny2ManyInfo->outPath + str2 + "_rebin" + rebinStr + extension;
} else { // real conversion
fileName = fAny2ManyInfo->outPath + str2 + extension;
}
return fileName;
}
//--------------------------------------------------------------------------
// FileNameFromTemplate (private)
//--------------------------------------------------------------------------