main (int argc, char *argv[])
{
int i, j, k, val;
int curr_line;
int last_dwp, this_dwp;
int last_start;
SEASAT_header_ext *hdr;
FILE *fpin_dat, *fpin_hdr;
FILE *fpout_dat, *fpout_hdr;
FILE *fptmp;
unsigned char buf[SAMPLES_PER_LINE];
double tbuf[O_SAMP_PER_LINE], fbuf[SAMPLES_PER_LINE], fbuf2[SAMPLES_PER_LINE];
double total[O_SAMP_PER_LINE];
int dwp_positions[256];
double ave;
int ndwps;
double ovpulse[10][O_SAMP_PER_LINE];
complexFloat *b;
fftwf_plan b_longb, b_longf;
double op[O_SAMP_PER_LINE];
char indat[256], inhdr[256];
char outdat[256], outhdr[256], outdis[256];
char tmp[256];
int ocnt, this_line;
double ocal[20];
char intmp[256];
if (argc != 3) {
printf("Usage: %s <in> <out>\n",argv[0]);
printf("\tin - input data and header file base name\n");
printf("\tout - output data and header file base name\n\n");
exit(1);
}
strcpy(indat,argv[1]); strcat(indat,".dat");
strcpy(inhdr,argv[1]); strcat(inhdr,".hdr");
strcpy(outdat,argv[2]); strcat(outdat,".dat");
strcpy(outhdr,argv[2]); strcat(outhdr,".hdr");
hdr = (SEASAT_header_ext *) malloc(sizeof(SEASAT_header_ext));
printf("\t%s: opening input files...\n",argv[0]);
fpin_dat = fopen(indat,"rb");
if (fpin_dat == NULL) {printf("ERROR: Unable to open input data file %s\n",indat); exit(1);}
fpin_hdr = fopen(inhdr,"r");
if (fpin_hdr == NULL) {printf("ERROR: Unable to open input header file %s\n",inhdr); exit(1);}
b = (complexFloat *) fftwf_malloc(sizeof(fftwf_complex)*O_SAMP_PER_FFT);
b_longb = fftwf_plan_dft_1d(O_SAMP_PER_FFT, (fftwf_complex *) b, (fftwf_complex *)b, FFTW_BACKWARD, FFTW_MEASURE);
b_longf = fftwf_plan_dft_1d(O_SAMP_PER_FFT, (fftwf_complex *) b, (fftwf_complex *)b, FFTW_FORWARD, FFTW_MEASURE);
for (i=0; i<O_SAMP_PER_LINE; i++) { tbuf[i] = 0.0; total[i] = 0;}
/* Start reading the input file header - get the first DWP */
val=get_values(fpin_hdr,hdr);
if (val!=20) {printf("ERROR: unable to read from header file\n"); exit(1);}
last_dwp = hdr->delay;
printf("\tfound initial dwp of %i\n",last_dwp);
this_dwp = last_dwp;
curr_line = 0;
ndwps = 0;
dwp_positions[ndwps++] = 0;
printf("Set dwp position %i to %i\n",ndwps-1,dwp_positions[ndwps-1]);
last_start = 1;
printf("\treading file; creating oversampled average\n");
double sum = 0.0;
/* Loop through the entire file creating averaged calibration pulses */
while (val == 20) {
this_line = 0;
/* read, oversample, and sum lines until DWP shift is found in the hdr file */
while (this_dwp == last_dwp) {
fread(buf,SAMPLES_PER_LINE,1,fpin_dat);
if (this_line < 10000) {
for (i=0; i<SAMPLES_PER_LINE; i++) fbuf[i] = (double) buf[i];
fft_oversamp(fbuf,SAMPLES_PER_LINE,EXPANSION_FACTOR,op);
for (i=0; i<O_SAMP_PER_LINE; i++) /* if (op[i]>=4.0 && op[i]<28.0) */ { tbuf[i] += op[i]; total[i]++; }
this_line++;
if ((int)this_line%100==0) printf("\toversampling line %i\n",curr_line);
}
curr_line++;
val=get_values(fpin_hdr,hdr);
if (val!=20) break;
this_dwp = hdr->delay;
if (curr_line%1000==1) printf("\tskipping line %i\n",curr_line);
}
/* check if we found a new DWP or hit end of file */
if (this_dwp != last_dwp) {
printf("\tread to line %i. New DWP is %i\n",curr_line,this_dwp);
dwp_positions[ndwps++] = curr_line;
printf("Set dwp position %i to %i\n",ndwps-1,dwp_positions[ndwps-1]);
} else if (val!=20) {
printf("\tread to end of file\n");
dwp_positions[ndwps] = curr_line;
printf("Set dwp position %i to %i\n",ndwps,dwp_positions[ndwps]);
}
/* average the summed up pulse */
sum = 0.0;
for (i=0; i<O_SAMP_PER_LINE; i++) {
if (total[i] != 0) tbuf[i] = tbuf[i]/total[i];
else tbuf[i] = 0.0;
sum += tbuf[i];
}
sum = sum / (double) O_SAMP_PER_LINE;
/* write the averaged normalized pulse to output file */
sprintf(tmp,"%s%.7i.ov.pulse",argv[1],last_start);
fptmp = fopen(tmp,"w");
if (fptmp == NULL) {printf("ERROR: Unable to open output data file %s\n",tmp); exit(1);}
for (i=0; i<O_SAMP_PER_LINE; i++) {
fprintf(fptmp,"%lf\n",(tbuf[i]-sum));
ovpulse[ndwps-1][i] = tbuf[i]-sum; /* save averaged pulses as we go */
}
fclose(fptmp);
/* calculate the spectra - just for fun (?) */
spectra(fpin_dat,dwp_positions[(ndwps-1)],10002,ave,&ocnt,ocal);
sprintf(intmp,"%s%.7i.spectra.out",argv[1],dwp_positions[(ndwps-1)]);
rename("spectra.out",intmp);
sprintf(intmp,"%s%.7i.spectra.fixed",argv[1],dwp_positions[(ndwps-1)]);
rename("spectra.fixed",intmp);
/* Since the spectra ALWAYS shows a peak at 0.25, we remove that here */
for (k=0; k<O_SAMP_PER_LINE; k++) { b[k].real = tbuf[k]; b[k].imag = 0.0; }
for (k=O_SAMP_PER_LINE; k<O_SAMP_PER_FFT; k++) { b[k].real = 0.0; b[k].imag = 0.0; }
fftwf_execute(b_longf);
fptmp = fopen("b.freq","w");
for (k=0; k<O_SAMP_PER_LINE; k++) {
tbuf[k] = sqrt(b[k].real*b[k].real+b[k].imag*b[k].imag)/(double)O_SAMP_PER_LINE;
fprintf(fptmp,"%i %lf\n",k,tbuf[k]);
}
fclose(fptmp);
// printf("Removing freq at location %i (value %lf)\n",O_SAMP_PER_FFT/4,
// sqrt(b[O_SAMP_PER_FFT/4].real*b[O_SAMP_PER_FFT/4].real+
// b[O_SAMP_PER_FFT/4].imag*b[O_SAMP_PER_FFT/4].imag)/(double)O_SAMP_PER_FFT);
// b[O_SAMP_PER_FFT/4].real = 0.0;
// b[O_SAMP_PER_FFT/4].imag = 0.0;
// printf("Removing freq at location %i (value %lf)\n",3*O_SAMP_PER_FFT/4,
// sqrt(b[3*O_SAMP_PER_FFT/4].real*b[3*O_SAMP_PER_FFT/4].real+
// b[3*O_SAMP_PER_FFT/4].imag*b[3*O_SAMP_PER_FFT/4].imag)/(double)O_SAMP_PER_FFT);
// b[3*O_SAMP_PER_FFT/4].real = 0.0;
// b[3*O_SAMP_PER_FFT/4].imag = 0.0;
printf("Removing freq at location 4095 - 4097\n");
// b[4093].real = 0.0;
// b[4093].imag = 0.0;
// b[4094].real = 0.0;
// b[4094].imag = 0.0;
b[4095].real = 0.0;
b[4095].imag = 0.0;
b[4096].real = 0.0;
b[4096].imag = 0.0;
b[4097].real = 0.0;
b[4097].imag = 0.0;
// b[4098].real = 0.0;
// b[4098].imag = 0.0;
// b[4099].real = 0.0;
// b[4099].imag = 0.0;
printf("Removing freq at location 1365\n");
b[1365].real = 0.0;
b[1365].imag = 0.0;
fptmp = fopen("b.freq2","w");
for (k=0; k<O_SAMP_PER_LINE; k++) {
tbuf[k] = sqrt(b[k].real*b[k].real+b[k].imag*b[k].imag)/(double)O_SAMP_PER_LINE;
fprintf(fptmp,"%i %lf\n",k,tbuf[k]);
}
fclose(fptmp);
fftwf_execute(b_longb);
/* average the summed up pulse */
sum = 0.0;
for (k=0; k<O_SAMP_PER_LINE; k++)
{
tbuf[k] = sqrt(b[k].real*b[k].real+b[k].imag*b[k].imag)/(double)O_SAMP_PER_LINE;
sum += tbuf[k];
}
sum = sum / (double) O_SAMP_PER_LINE;
fptmp = fopen("b.time2","w");
for (k=0; k<O_SAMP_PER_LINE; k++) {
tbuf[k] -= sum;
fprintf(fptmp,"%i %lf\n",k,tbuf[k]);
ovpulse[ndwps-1][k] = tbuf[k]; /* save averaged pulses as we go */
}
fclose(fptmp);
last_dwp = this_dwp;
last_start = curr_line;
}
printf("\n");
fclose(fpin_dat);
fclose(fpin_hdr);
fpin_dat = fopen(indat,"rb");
if (fpin_dat == NULL) {printf("ERROR: Unable to open input data file %s\n",indat); exit(1);}
printf("Opening output file\n");
fpout_dat = fopen(outdat,"wb");
if (fpout_dat == NULL) {printf("ERROR: Unable to open output data file %s\n",outdat); exit(1);}
printf("Number of DWPs is %i\n",ndwps);
/* Now that we have the pulses, apply them to the data file */
sum = 0.0; curr_line =0;
for (k=0; k<ndwps; k++) {
printf("%i : trying range of %i to %i\n",k,dwp_positions[k],dwp_positions[k+1]);
for (j=dwp_positions[k]; j<dwp_positions[k+1]; j++) {
fread(buf,SAMPLES_PER_LINE,1,fpin_dat);
sum =0.0;
for (i=0; i<SAMPLES_PER_LINE; i++) { fbuf[i] = (double) buf[i]; sum += fbuf[i]; }
sum = sum / SAMPLES_PER_LINE;
for (i=0; i<SAMPLES_PER_LINE; i++) fbuf[i] -= sum;
match_pulse(fbuf,ovpulse[k],fbuf2);
for (i=0; i<SAMPLES_PER_LINE; i++) { buf[i] = (int) (fbuf2[i]+sum); }
fwrite(buf,SAMPLES_PER_LINE,1,fpout_dat);
curr_line+=1.0;
}
}
sprintf(tmp,"cp %s %s\n",inhdr,outhdr);
system(tmp);
printf("Done correcting file, wrote %i lines of output\n\n",curr_line);
fclose(fpout_dat);
exit(0);
}
/**
* Read the instrument group
* @param mtd_entry :: The node for the current workspace
* @param local_workspace :: The workspace to attach the instrument
*/
void LoadNexusProcessed::readInstrumentGroup(NXEntry & mtd_entry, API::MatrixWorkspace_sptr local_workspace)
{
//Instrument information
NXInstrument inst = mtd_entry.openNXInstrument("instrument");
if ( ! inst.containsGroup("detector") )
{
g_log.information() << "Detector block not found. The workspace will not contain any detector information.\n";
return;
}
//Populate the spectra-detector map
NXDetector detgroup = inst.openNXDetector("detector");
//Read necessary arrays from the file
// Detector list contains a list of all of the detector numbers. If it not present then we can't update the spectra
// map
int ndets(-1);
boost::shared_array<int> det_list(NULL);
try
{
NXInt detlist_group = detgroup.openNXInt("detector_list");
ndets = detlist_group.dim0();
detlist_group.load();
det_list.swap(detlist_group.sharedBuffer());
}
catch(std::runtime_error &)
{
g_log.information() << "detector_list block not found. The workspace will not contain any detector information."
<< std::endl;
return;
}
//Detector count contains the number of detectors associated with each spectra
NXInt det_count = detgroup.openNXInt("detector_count");
det_count.load();
//Detector index - contains the index of the detector in the workspace
NXInt det_index = detgroup.openNXInt("detector_index");
det_index.load();
int nspectra = det_index.dim0();
//Spectra block - Contains spectrum numbers for each workspace index
// This might not exist so wrap and check. If it doesn't exist create a default mapping
bool have_spectra(true);
boost::shared_array<int> spectra(NULL);
try
{
NXInt spectra_block = detgroup.openNXInt("spectra");
spectra_block.load();
spectra.swap(spectra_block.sharedBuffer());
}
catch(std::runtime_error &)
{
have_spectra = false;
}
//Now build the spectra list
int *spectra_list = new int[ndets];
API::Axis *axis1 = local_workspace->getAxis(1);
int index=0;
for(int i = 1; i <= nspectra; ++i)
{
int spectrum(-1);
if( have_spectra ) spectrum = spectra[i-1];
else spectrum = i+1 ;
if ((i >= m_spec_min && i < m_spec_max )||(m_list && find(m_spec_list.begin(), m_spec_list.end(),
i) != m_spec_list.end()))
{
if( m_axis1vals.empty() )
{
axis1->spectraNo(index) = spectrum;
}
else
{
axis1->setValue(index, m_axis1vals[i-1]);
}
++index;
}
int offset = det_index[i-1];
int detcount = det_count[i-1];
for(int j = 0; j < detcount; j++)
{
spectra_list[offset + j] = spectrum;
}
}
local_workspace->replaceSpectraMap(new SpectraDetectorMap(spectra_list, det_list.get(), ndets));
delete[] spectra_list;
}
/**
* Reads the data from the file. It is assumed that the provided file stream has its position
* set such that the first call to getline will be give the first line of data
* @param file :: A reference to a file stream
* @returns A pointer to a new workspace
*/
API::Workspace_sptr LoadAscii::readData(std::ifstream & file) const
{
// Get the first line and find the number of spectra from the number of columns
std::string line;
getline(file,line);
boost::trim(line);
std::list<std::string> columns;
const int numCols = splitIntoColumns(columns, line);
if( numCols < 2 )
{
g_log.error() << "Invalid data format found in file \"" << getPropertyValue("Filename") << "\"\n";
throw std::runtime_error("Invalid data format. Fewer than 2 columns found.");
}
size_t numSpectra(0);
bool haveErrors(false);
bool haveXErrors(false);
// Assume single data set with no errors
if( numCols == 2 )
{
numSpectra = numCols/2;
}
// Data with errors
else if( (numCols-1) % 2 == 0 )
{
numSpectra = (numCols - 1)/2;
haveErrors = true;
}
// Data with errors on both X and Y (4-column file)
else if( numCols == 4 )
{
numSpectra = 1;
haveErrors = true;
haveXErrors = true;
}
else
{
g_log.error() << "Invalid data format found in file \"" << getPropertyValue("Filename") << "\"\n";
g_log.error() << "LoadAscii requires the number of columns to be an even multiple of either 2 or 3.";
throw std::runtime_error("Invalid data format.");
}
// A quick check at the number of lines won't be accurate enough as potentially there
// could be blank lines and comment lines
int numBins(0), lineNo(0);
std::vector<DataObjects::Histogram1D> spectra(numSpectra);
std::vector<double> values(numCols, 0.);
do
{
++lineNo;
boost::trim(line);
if( this->skipLine(line) ) continue;
columns.clear();
int lineCols = this->splitIntoColumns(columns, line);
if( lineCols != numCols )
{
std::ostringstream ostr;
ostr << "Number of columns changed at line " << lineNo;
throw std::runtime_error(ostr.str());
}
try
{
fillInputValues(values, columns); //ignores nans and replaces them with 0
}
catch(boost::bad_lexical_cast&)
{
g_log.error() << "Invalid value on line " << lineNo << " of \""
<< getPropertyValue("Filename") << "\"\n";
throw std::runtime_error("Invalid value encountered.");
}
for (size_t i = 0; i < numSpectra; ++i)
{
spectra[i].dataX().push_back(values[0]);
spectra[i].dataY().push_back(values[i*2+1]);
if( haveErrors )
{
spectra[i].dataE().push_back(values[i*2+2]);
}
else
{
spectra[i].dataE().push_back(0.0);
}
if( haveXErrors )
{
// Note: we only have X errors with 4-column files.
// We are only here when i=0.
spectra[i].dataDx().push_back(values[3]);
}
else
{
spectra[i].dataDx().push_back(0.0);
}
}
++numBins;
}
while(getline(file,line));
MatrixWorkspace_sptr localWorkspace = boost::dynamic_pointer_cast<MatrixWorkspace>
(WorkspaceFactory::Instance().create("Workspace2D",numSpectra,numBins,numBins));
try
{
localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create(getProperty("Unit"));
}
catch (Exception::NotFoundError&)
{
// Asked for dimensionless workspace (obviously not in unit factory)
}
for (size_t i = 0; i < numSpectra; ++i)
{
localWorkspace->dataX(i) = spectra[i].dataX();
localWorkspace->dataY(i) = spectra[i].dataY();
localWorkspace->dataE(i) = spectra[i].dataE();
// Just have spectrum number start at 1 and count up
localWorkspace->getAxis(1)->spectraNo(i) = static_cast<specid_t>(i+1);
}
return localWorkspace;
}
