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Raw data file write/read now uses absolute channel values in multidetector systems. Flat field and bad channel corrections and angular conversion debugged

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git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorSoftware@135 951219d9-93cf-4727-9268-0efd64621fa3
This commit is contained in:
bergamaschi
2012-03-02 11:01:53 +00:00
parent 5e086b9ee6
commit 461fd8824f
9 changed files with 709 additions and 207 deletions
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315
slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp
View File

@ -105,6 +105,7 @@ multiSlsDetector::multiSlsDetector(int id) : slsDetectorUtils(), shmId(-1)
thisMultiDetector->dataBytes=0;
thisMultiDetector->numberOfChannels=0;
thisMultiDetector->maxNumberOfChannels=0;
@ -225,15 +226,15 @@ multiSlsDetector::multiSlsDetector(int id) : slsDetectorUtils(), shmId(-1)
&thisMultiDetector->fileIndex);
#ifdef VERBOSE
cout << "filling bad channel mask" << endl;
#endif
/** fill the BadChannelMask \sa fillBadChannelMask */
fillBadChannelMask();
// #ifdef VERBOSE
// cout << "filling bad channel mask" << endl;
// #endif
// /** fill the BadChannelMask \sa fillBadChannelMask */
// fillBadChannelMask();
#ifdef VERBOSE
cout << "done" << endl;
#endif
// #ifdef VERBOSE
// cout << "done" << endl;
// #endif
}
@ -297,7 +298,8 @@ int multiSlsDetector::addSlsDetector(int id, int pos) {
thisMultiDetector->dataBytes+=detectors[pos]->getDataBytes();
thisMultiDetector->numberOfChannels+=detectors[pos]->getNChans()*detectors[pos]->getNChips()*detectors[pos]->getNMods();
thisMultiDetector->numberOfChannels+=detectors[pos]->getTotalNumberOfChannels();
thisMultiDetector->maxNumberOfChannels-=detectors[j]->getMaxNumberOfChannels();
#ifdef VERBOSE
cout << "Detector added " << thisMultiDetector->numberOfDetectors<< endl;
@ -528,7 +530,8 @@ int multiSlsDetector::removeSlsDetector(int pos) {
if (detectors[j]) {
thisMultiDetector->dataBytes-=detectors[j]->getDataBytes();
thisMultiDetector->numberOfChannels-=detectors[j]->getNChans()*detectors[pos]->getNChips()*detectors[pos]->getNMods();
thisMultiDetector->numberOfChannels-=detectors[j]->getTotalNumberOfChannels();
thisMultiDetector->maxNumberOfChannels-=detectors[j]->getMaxNumberOfChannels();
delete detectors[j];
thisMultiDetector->numberOfDetectors--;
@ -738,7 +741,7 @@ int multiSlsDetector::getThresholdEnergy(int pos) {
ret=detectors[i]->getThresholdEnergy();
if (ret1==-100)
ret1=ret;
else if (ret!=ret1)
else if (ret<(ret1-200) || ret>(ret1+200))
ret1=FAIL;
}
@ -767,11 +770,17 @@ int multiSlsDetector::setThresholdEnergy(int e_eV, int pos, detectorSettings ise
for (i=posmin; i<posmax; i++) {
if (detectors[i]) {
ret=detectors[i]->setThresholdEnergy(e_eV,-1,isettings);
#ifdef VERBOSE
cout << "detetcor " << i << " threshold " << ret << endl;
#endif
if (ret1==-100)
ret1=ret;
else if (ret!=ret1)
else if (ret<(ret1-200) || ret>(ret1+200))
ret1=FAIL;
#ifdef VERBOSE
cout << "return value " << ret1 << endl;
#endif
}
}
@ -1350,14 +1359,14 @@ float* multiSlsDetector::decodeData(int *datain) {
float *dataout=new float[thisMultiDetector->numberOfChannels];
int ich=0;
float *detp;
int *datap=datain;
int *datap=datain;
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
if (detectors[i]) {
detp=detectors[i]->decodeData(datap);
datap+=detectors[i]->getDataBytes();
for (int j=0; j<detectors[i]->getNChans()*detectors[i]->getNChips()*detectors[i]->getNMods(); j++) {
datap+=detectors[i]->getDataBytes()/sizeof(int);
for (int j=0; j<detectors[i]->getTotalNumberOfChannels(); j++) {
dataout[ich]=detp[j];
ich++;
}
@ -1429,7 +1438,7 @@ int multiSlsDetector::setFlatFieldCorrection(string fname){
for (int ichan=0; ichan<nch; ichan++) {
if (detectors[idet]) {
if (ichdet>=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods()) {
if (ichdet>=detectors[idet]->getTotalNumberOfChannels()) {
ichdet=0;
detectors[idet]->setBadChannelCorrection(nbad,badlist,1);
idet++;
@ -1468,13 +1477,18 @@ int multiSlsDetector::setFlatFieldCorrection(string fname){
idet=0;
ichdet=0;
int detoff=0;
for (int ichan=0; ichan<nch; ichan++) {
if (detectors[idet]) {
if (ichdet>=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods()) {
detectors[idet]->setFlatFieldCorrection(ffcoefficients+ichdet, fferrors+ichdet);
ichdet=ichan;
if (ichdet>=detectors[idet]->getTotalNumberOfChannels()) {
#ifdef VERBOSE
cout << "Set flat field detector " << idet << "(offset "<< detoff << ")" << endl;
#endif
detectors[idet]->setFlatFieldCorrection(ffcoefficients+detoff, fferrors+detoff);
ichdet=0;//ichan;
detoff=ichan;
idet++;
}
}
@ -1487,9 +1501,13 @@ int multiSlsDetector::setFlatFieldCorrection(string fname){
ffcoefficients[ichan]=0.;
fferrors[ichan]=1.;
}
ichdet++;
}
if (detectors[idet]) {
detectors[idet]->setFlatFieldCorrection(ffcoefficients+ichdet, fferrors+ichdet);
#ifdef VERBOSE
cout << "**Set flat field detector " << idet << "(offset "<< detoff << ")" << endl;
#endif
detectors[idet]->setFlatFieldCorrection(ffcoefficients+detoff, fferrors+detoff);
}
} else {
std::cout<< "Flat field data from file " << fname << " are not valid (" << nmed << "///" << xmed[nmed/2] << std::endl;
@ -1500,7 +1518,7 @@ int multiSlsDetector::setFlatFieldCorrection(string fname){
}
return -1;
}
} else {
} else {
std::cout<< "Flat field from file " << fname << " is not valid " << nch << std::endl;
thisMultiDetector->correctionMask&=~(1<<FLAT_FIELD_CORRECTION);
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
@ -1531,7 +1549,7 @@ int multiSlsDetector::setFlatFieldCorrection(float *corr, float *ecorr) {
else
ep=NULL;
detectors[idet]->setFlatFieldCorrection(p, ep);
ichdet+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
ichdet+=detectors[idet]->getTotalNumberOfChannels();
}
}
return 0;
@ -1559,7 +1577,7 @@ int multiSlsDetector::getFlatFieldCorrection(float *corr, float *ecorr) {
else
ep=NULL;
detectors[idet]->getFlatFieldCorrection(p, ep);
ichdet+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
ichdet+=detectors[idet]->getTotalNumberOfChannels();
}
}
return 0;
@ -1590,10 +1608,16 @@ int multiSlsDetector::getFlatFieldCorrection(float *corr, float *ecorr) {
int multiSlsDetector::flatFieldCorrect(float* datain, float *errin, float* dataout, float *errout){
int ichdet=0;
float *pdata, *perr=errin;
for (int idet=0; idet<thisMultiDetector->numberOfDetectors; idet++) {
if (detectors[idet]) {
detectors[idet]->flatFieldCorrect(datain+ichdet, errin+ichdet, dataout+ichdet, errout+ichdet);
ichdet+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
#ifdef VERBOSE
cout << " detector " << idet << " offset " << ichdet << endl;
#endif
if (errin)
perr+=ichdet;
detectors[idet]->flatFieldCorrect(datain+ichdet, perr, dataout+ichdet, errout+ichdet);
ichdet+=detectors[idet]->getTotalNumberOfChannels();//detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
}
}
return 0;
@ -1677,10 +1701,13 @@ int multiSlsDetector::getRateCorrection(){
int multiSlsDetector::rateCorrect(float* datain, float *errin, float* dataout, float *errout){
int ichdet=0;
float *perr=errin;
for (int idet=0; idet<thisMultiDetector->numberOfDetectors; idet++) {
if (detectors[idet]) {
detectors[idet]->rateCorrect(datain+ichdet, errin+ichdet, dataout+ichdet, errout+ichdet);
ichdet+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
if (errin)
perr+=ichdet;
detectors[idet]->rateCorrect(datain+ichdet, perr, dataout+ichdet, errout+ichdet);
ichdet+=detectors[idet]->getTotalNumberOfChannels();
}
}
return 0;
@ -1696,9 +1723,16 @@ int multiSlsDetector::setBadChannelCorrection(string fname){
fname=string(thisMultiDetector->badChanFile);
int ret=setBadChannelCorrection(fname, nbad, badlist);
if (ret==0)
#ifdef VERBOSE
cout << "file contained " << ret << " badcahns" << endl;
#endif
if (ret==0) {
thisMultiDetector->correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
nbad=0;
} else {
thisMultiDetector->correctionMask|=(1<<DISCARD_BAD_CHANNELS);
strcpy(thisMultiDetector->badChanFile,fname.c_str());
}
return setBadChannelCorrection(nbad,badlist,0);
@ -1717,9 +1751,12 @@ int multiSlsDetector::setBadChannelCorrection(int nbad, int *badlist, int ff) {
for (int ich=0; ich<nbad; ich++) {
if (detectors[idet]) {
while ((badlist[ich]-choff)>=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods()) {
if ((badlist[ich]-choff)>=detectors[idet]->getTotalNumberOfChannels()) {
#ifdef VERBOSE
cout << "setting " << nbaddet << " badchans to detector " << idet << endl;
#endif
detectors[idet]->setBadChannelCorrection(nbaddet,badlist,0);
choff+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
choff+=detectors[idet]->getTotalNumberOfChannels();
nbaddet=0;
idet++;
if (detectors[idet]==NULL)
@ -1727,10 +1764,26 @@ int multiSlsDetector::setBadChannelCorrection(int nbad, int *badlist, int ff) {
}
badlistdet[nbaddet]=(badlist[ich]-choff);
nbaddet++;
cout << nbaddet << " " << badlist[ich] << " " << badlistdet[nbaddet-1] << endl;
}
}
if (nbaddet>0) {
if (detectors[idet]) {
#ifdef VERBOSE
cout << "setting " << nbaddet << " badchans to detector " << idet << endl;
#endif
detectors[idet]->setBadChannelCorrection(nbaddet,badlist,0);
choff+=detectors[idet]->getTotalNumberOfChannels();
nbaddet=0;
idet++;
}
}
nbaddet=0;
for (int i=idet; i<thisMultiDetector->numberOfDetectors; i++) {
#ifdef VERBOSE
cout << "setting " << 0 << " badchans to detector " << i << endl;
#endif
if (detectors[i]) {
detectors[i]->setBadChannelCorrection(nbaddet,badlist,0);
}
@ -1740,12 +1793,17 @@ int multiSlsDetector::setBadChannelCorrection(int nbad, int *badlist, int ff) {
nbaddet=0;
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
if (detectors[idet]) {
#ifdef VERBOSE
cout << "setting " << 0 << " badchans to detector " << idet << endl;
#endif
detectors[idet]->setBadChannelCorrection(nbaddet,badlist,0);
}
}
thisMultiDetector->correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
}
#ifdef VERBOSE
cout << (thisMultiDetector->correctionMask&(1<<DISCARD_BAD_CHANNELS)) << endl;
#endif
return thisMultiDetector->correctionMask&(1<<DISCARD_BAD_CHANNELS);
}
@ -1784,6 +1842,9 @@ int multiSlsDetector::readAngularConversion(string fname) {
for (int idet=0; idet<thisMultiDetector->numberOfDetectors; idet++) {
if (detectors[idet]) {
#ifdef VERBOSE
cout << " detector " << idet << endl;
#endif
detectors[idet]->readAngularConversion(infile);
}
}
@ -1918,6 +1979,24 @@ int multiSlsDetector::setChannel(long long reg, int ichan, int ichip, int imod)
/**
sets the value of s angular conversion parameter
\param c can be ANGULAR_DIRECTION, GLOBAL_OFFSET, FINE_OFFSET, BIN_SIZE
\param v the value to be set
\returns the actual value
*/
float multiSlsDetector::setAngularConversionParameter(angleConversionParameter c, float v) {
float ret=slsDetectorUtils::setAngularConversionParameter(c,v);
for (int idet=0; idet<thisMultiDetector->numberOfDetectors; idet++) {
if (detectors[idet]) {
detectors[idet]->setAngularConversionParameter(c,v);
}
}
return ret;
}
@ -1931,10 +2010,10 @@ float* multiSlsDetector::convertAngles(float pos) {
if (detectors[idet]) {
p=detectors[idet]->convertAngles(pos);
for (int ich=0; ich<detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods(); ich++) {
for (int ich=0; ich<detectors[idet]->getTotalNumberOfChannels(); ich++) {
ang[choff+ich]=p[ich];
}
choff+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
choff+=detectors[idet]->getTotalNumberOfChannels();
delete [] p;
}
}
@ -1953,12 +2032,12 @@ int multiSlsDetector::getBadChannelCorrection(int *bad) {
bd = new int[nd];
nd=detectors[idet]->getBadChannelCorrection(bd);
for (int id=0; id<nd; id++) {
if (bd[id]<detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods()) {
if (bd[id]<detectors[idet]->getTotalNumberOfChannels()) {
if (bad) bad[ntot]=choff+bd[id];
ntot++;
}
}
choff+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
choff+=detectors[idet]->getTotalNumberOfChannels();
delete [] bd;
}
}
@ -2408,7 +2487,7 @@ int multiSlsDetector::setDynamicRange(int p) {
if (detectors[idet]) {
ret1=detectors[idet]->setDynamicRange(p);
thisMultiDetector->dataBytes+=detectors[idet]->getDataBytes();
thisMultiDetector->numberOfChannels+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
thisMultiDetector->numberOfChannels+=detectors[idet]->getTotalNumberOfChannels();
if (ret==-100)
ret=ret1;
else if (ret!=ret1)
@ -2459,7 +2538,7 @@ int multiSlsDetector::setNumberOfModules(int p, dimension d) {
}
ret+=detectors[idet]->setNumberOfModules(nm);
thisMultiDetector->dataBytes+=detectors[idet]->getDataBytes();
thisMultiDetector->numberOfChannels+=detectors[idet]->getNChans()*detectors[idet]->getNChips()*detectors[idet]->getNMods();
thisMultiDetector->numberOfChannels+=detectors[idet]->getTotalNumberOfChannels();
}
}
return ret;
@ -2471,7 +2550,7 @@ int multiSlsDetector::decodeNMod(int i, int &id, int &im) {
cout << " Module " << i << " belongs to detector ";
#endif
if (i<0 || i>=setNumberOfModules()) {
if (i<0 || i>=getMaxNumberOfModules()) {
id=-1;
im=-1;
#ifdef VERBOSE
@ -3090,3 +3169,161 @@ int multiSlsDetector::loadImageToDetector(imageType t, string s) {
int multiSlsDetector::testFunction(int times) {
}
int multiSlsDetector::writeDataFile(string fname, float *data, float *err, float *ang, char dataformat, int nch) {
#ifdef VERBOSE
cout << "using overloaded multiSlsDetector function to write formatted data file " << endl;
#endif
ofstream outfile;
int idata, choff=0, off=0;
float *pe=err, *pa=ang;
int nch_left=nch, n;
if (nch_left<=0)
nch_left=getTotalNumberOfChannels();
if (data==NULL)
return FAIL;
// args|=0x10; // one line per channel!
outfile.open (fname.c_str(),ios_base::out);
if (outfile.is_open())
{
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
if (detectors[i]) {
n=detectors[i]->getTotalNumberOfChannels();
if (nch_left<n)
n=nch_left;
detectors[i]->writeDataFile(outfile,n, data+off, pe, pa, dataformat, choff);
nch_left-=n;
choff+=detectors[i]->getMaxNumberOfChannels();
off+=n;
if (pe)
pe=pe+off;
if (pa)
pa=pa+off;
}
}
outfile.close();
return OK;
} else {
std::cout<< "Could not open file " << fname << "for writing"<< std::endl;
return FAIL;
}
}
int multiSlsDetector::writeDataFile(string fname, int *data) {
ofstream outfile;
int choff=0, off=0;
#ifdef VERBOSE
cout << "using overloaded multiSlsDetector function to write raw data file " << endl;
#endif
if (data==NULL)
return FAIL;
outfile.open (fname.c_str(),ios_base::out);
if (outfile.is_open())
{
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
if (detectors[i]) {
detectors[i]->writeDataFile(outfile, detectors[i]->getTotalNumberOfChannels(), data+off, choff);
choff+=detectors[i]->getMaxNumberOfChannels();
off+=detectors[i]->getTotalNumberOfChannels();
}
}
outfile.close();
return OK;
} else {
std::cout<< "Could not open file " << fname << "for writing"<< std::endl;
return FAIL;
}
}
int multiSlsDetector::readDataFile(string fname, float *data, float *err, float *ang, char dataformat){
#ifdef VERBOSE
cout << "using overloaded multiSlsDetector function to read formatted data file " << endl;
#endif
ifstream infile;
int ichan, iline=0;
int interrupt=0;
string str;
int choff=0, off=0;
float *pe=err, *pa=ang;
#ifdef VERBOSE
std::cout<< "Opening file "<< fname << std::endl;
#endif
infile.open(fname.c_str(), ios_base::in);
if (infile.is_open()) {
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
if (detectors[i]) {
iline+=detectors[i]->readDataFile(detectors[i]->getTotalNumberOfChannels(), infile, data+off, pe, pa, dataformat, choff);
choff+=detectors[i]->getMaxNumberOfChannels();
off+=detectors[i]->getTotalNumberOfChannels();
if (pe)
pe=pe+off;
if (pa)
pa=pa+off;
}
}
infile.close();
} else {
std::cout<< "Could not read file " << fname << std::endl;
return -1;
}
return iline;
}
int multiSlsDetector::readDataFile(string fname, int *data) {
#ifdef VERBOSE
cout << "using overloaded multiSlsDetector function to read raw data file " << endl;
#endif
ifstream infile;
int ichan, iline=0;
int interrupt=0;
string str;
int choff=0, off=0;
#ifdef VERBOSE
std::cout<< "Opening file "<< fname << std::endl;
#endif
infile.open(fname.c_str(), ios_base::in);
if (infile.is_open()) {
for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
if (detectors[i]) {
iline+=detectors[i]->readDataFile(infile, data+off,detectors[i]->getTotalNumberOfChannels(), choff);
choff+=detectors[i]->getMaxNumberOfChannels();
off+=detectors[i]->getTotalNumberOfChannels();
}
}
infile.close();
} else {
std::cout<< "Could not read file " << fname << std::endl;
return -1;
}
return iline;
}

67
slsDetectorSoftware/multiSlsDetector/multiSlsDetector.h
View File

@ -86,6 +86,9 @@ class multiSlsDetector : public slsDetectorUtils {
/** total number of channels for all detectors */
int numberOfChannels;
/** total number of channels for all detectors */
int maxNumberOfChannels;
/** timer values */
@ -273,6 +276,8 @@ class multiSlsDetector : public slsDetectorUtils {
int getTotalNumberOfChannels(){return thisMultiDetector->numberOfChannels;};
int getMaxNumberOfChannels(){return thisMultiDetector->maxNumberOfChannels;};
float getScanStep(int index, int istep){return thisMultiDetector->scanSteps[index][istep];};
/** returns the detector offset (in number of channels)
\param pos position of the detector
@ -894,7 +899,69 @@ class multiSlsDetector : public slsDetectorUtils {
*/
int testFunction(int times=0);
/**
sets the value of s angular conversion parameter
\param c can be ANGULAR_DIRECTION, GLOBAL_OFFSET, FINE_OFFSET, BIN_SIZE
\param v the value to be set
\returns the actual value
*/
float setAngularConversionParameter(angleConversionParameter c, float v);
/**
writes a data file
\param name of the file to be written
\param data array of data values
\param err array of arrors on the data. If NULL no errors will be written
\param ang array of angular values. If NULL data will be in the form chan-val(-err) otherwise ang-val(-err)
\param dataformat format of the data: can be 'i' integer or 'f' float (default)
\param nch number of channels to be written to file. if -1 defaults to the number of installed channels of the detector
\returns OK or FAIL if it could not write the file or data=NULL
\sa mythenDetector::writeDataFile
*/
int writeDataFile(string fname, float *data, float *err=NULL, float *ang=NULL, char dataformat='f', int nch=-1);
/**
writes a data file
\param name of the file to be written
\param data array of data values
\returns OK or FAIL if it could not write the file or data=NULL
\sa mythenDetector::writeDataFile
*/
int writeDataFile(string fname, int *data);
/**
reads a data file
\param name of the file to be read
\param data array of data values to be filled
\param err array of arrors on the data. If NULL no errors are expected on the file
\param ang array of angular values. If NULL data are expected in the form chan-val(-err) otherwise ang-val(-err)
\param dataformat format of the data: can be 'i' integer or 'f' float (default)
\param nch number of channels to be written to file. if <=0 defaults to the number of installed channels of the detector
\returns OK or FAIL if it could not read the file or data=NULL
\sa mythenDetector::readDataFile
*/
int readDataFile(string fname, float *data, float *err=NULL, float *ang=NULL, char dataformat='f');
/**
reads a data file
\param name of the file to be read
\param data array of data values
\returns OK or FAIL if it could not read the file or data=NULL
\sa mythenDetector::readDataFile
*/
int readDataFile(string fname, int *data);
protected: