void os2d(complexFloat *v, complexFloat *vo, int dim, int os)
{
int i;
int forward_fft = 1;
int inverse_fft = -1;
int osize;
/* printf("os2d(): dim = %d\tos = %d\n", dim, os); */
/* calculate total size of oversampled array */
osize = dim*dim*os*os;
/* printf("os2d(): total size of oversampled array (osize) = %d\n", osize); */
/* 2-D fft vector 'v' */
fft2d (v, dim, forward_fft);
/* make sure 'vo' = 0.0 */
for (i = 0; i < osize; i++)
*(vo+i) = Czero();
/* zero pad 'v' into 'vout' */
zeroPad(v, vo, dim, os);
/* inverse FFT 'vo' */
fft2d (vo, dim*os, inverse_fft);
return;
}
QString
MetaBundle::prettyTime( uint seconds, bool showHours ) //static
{
QString s = QChar( ':' );
s.append( zeroPad( seconds % 60 ) ); //seconds
seconds /= 60;
if( showHours && seconds >= 60)
{
s.prepend( zeroPad( seconds % 60 ) ); //minutes
s.prepend( ':' );
seconds /= 60;
}
//don't zeroPad the last one, as it can be greater than 2 digits
s.prepend( QString::number( seconds ) ); //hours or minutes depending on above if block
return s;
}
inline
void findPeak(double *idata, place * odata, int siz, int pitch) {
place p = {0u, 0.0};
zeroPad(idata, siz, pitch);
unsigned int n = siz * pitch;
#pragma omp declare reduction (maxer: place : omp_out = pmax(omp_out, omp_in))
#pragma omp parallel for reduction(maxer: p)
for (unsigned int i = 0; i<n; i++) {
p = pmax(p, {n, fabs(idata[n])});
}
*odata = p;
}
int main(int argc, char* argv[])
{
// Single byte to be read from the data files
char c;
// Counters to keep track of cuts
unsigned long waveformCtr = 0;
unsigned long linearGateCtr = 0;
unsigned long muonVetoCtr = 0;
unsigned long overflowCtr = 0;
unsigned long bgAnalysisCtr = 0;
unsigned long sAnalysisCtr = 0;
// Variables for the background output files
int bg_counter = 0;
int bg_file_number = 0;
std::ofstream bg_out_file;
// Variables for the signal output files
int s_counter = 0;
int s_file_number = 0;
std::ofstream s_out_file;
// Run Info output
std::ofstream infoOut;
// Saved waveforms
std::ofstream waveformOut;
// LabView headers
int no_samples = 0;
int no_channels = 0;
// Timestamp of current trigger
std::string timestamp;
// Waveform buffers
int csi [35000] = {} ;
int csi_raw[35000] = {} ;
int mv [35000] = {} ;
// Buffer to store bit shifted samples
int _tmpC = 0;
// Medians of CsI and muon veto
int med_csi = 0;
int med_mv = 0;
// Buffers used for median calculation as well as overflow detection
unsigned int med_csi_sum = 0;
unsigned int med_mv_sum = 0;
unsigned int med_csi_arr [256] = {} ;
unsigned int med_mv_arr [256] = {};
bool med_csi_found = false;
bool med_mv_found = false;
bool overflow = false;
// Buffers for SPE integration
int spe_charge_dist[300] = {};
int spe_integration_ctr = 0;
int spe_integration_charge = 0;
// Buffers for peaks in pretrace
int bg_pe_pt[52] = {};
int s_pe_pt[52] = {};
// Buffer for baseline
int baseline_hist[32] = {};
// Rising and falling threshold crossings used for linear gate detection
int _previous_c = 0;
int gate_down = 0;
int gate_up = 0;
// Waveform contains a gate or muon veto fired more than three times
bool linear_gate = false;
bool muon_veto_flag = false;
// Photoelectron counter for all interesting regions
// pt = pretrace, roi = region of interest, iw = integration window
unsigned int s_pt_ct = 0;
unsigned int bg_pt_ct = 0;
unsigned int s_roi_ct = 0;
unsigned int bg_roi_ct = 0;
unsigned int s_iw_ct = 0;
unsigned int bg_iw_ct = 0;
unsigned int PE_max_PT = 10;
// Buffers to store current peak width in CsI and muon veto waveform
int above_pe_threshold = 0;
int current_peak_width = 0;
int current_pe_width = 0;
int m_peak_width = 0;
// Peak thresholds
int peak_height_threshold = 3;
int peak_width_threshold = 4;
// Peak locations in CsI, Muon locations in muon veto
std::vector<int> peaks;
std::vector<int> peak_heights;
int peak_height_dist[100] = {};
int peak_amplitude = 0;
std::vector<int> pe_beginnings;
std::vector<int> pe_endings;
std::vector<int> muon_peaks;
std::vector<int> muon_onset_arr;
// Keep track of all peak/pe locations in the full minute
int peak_distribution[350][350] = {};
int charge_distribution[350][350] = {};
for (int i1 = 0; i1 < 350; i1++)
{
for (int i2 = 0; i2 < 350; i2++)
{
peak_distribution[i1][i2] = 0;
charge_distribution[i1][i2] = 0;
}
}
// Get peak width distribution
int peak_width_distribution[51] = {};
// Charge of PE in PT
int current_spe_q = 0;
// Integration window buffers
int s_q_arr [1500] = {};
int bg_q_arr [1500] = {};
int running_charge = 0;
// LogLikelihood prefactors & estimators
double lnL_pf_real[1500] = {};
double lnL_pf_flat[1500] = {};
double lnL_real = 0;
double lnL_flat = 0;
// Big pulse detection
bool bP_detected = false;
int _t_bP_idx = 0;
std::vector<int> bP_onset_arr;
std::vector<int> bP_charge_arr;
// Calculate prefactors for loglikelihood analysis
// timing and fraction from NIMA paper
double r = 0.41;
double tf = 527.0;
double ts = 5600.0;
// total integration window is 3 us long -> tMax = 1500
double _tFast = 1.0 / ((1.0 + r) * tf * (1 - exp(-1500.0 / tf)));
double _tSlow = r / ((1.0 + r) * ts * (1 - exp(-1500.0 / ts)));
// Calculate prefactor for each time step
for (int i = 0; i < 1500; i++)
{
lnL_pf_real[i] = log(_tFast * exp(-(double)i / tf) + _tSlow * exp(-(double)i / ts));
lnL_pf_flat[i] = log(1.0 / 1500.0);
}
// Threshold buffer and measured rise times
double thresholds [3] = {};
double bg_rt [3] = {};
double s_rt [3] = {};
// Buffers used during window analysis
int idx_0 = 0;
int idx_w_offset = 0;
int i_peak = 0;
int i_pe = 0;
int q_int = 0;
double _t1 = 0.0;
double _t2 = 0.0;
std::string main_dir;
int current_time;
int single_time;
std::string out_dir;
std::string current_zip_file;
std::string time_name_in_zip;
// Save waveforms as ascii - Counter,cuts etc
int save_wf_ctr = 0;
int no_total_peaks[2] = { 100, 200 };
int minimum_no_peaks_iw = 6;
int rt1090_bottom_left[2] = { 750, 1150 };
int rt050_bottom_left[2] = { 235, 345 };
int rt1090_upper_right[2] = { 1080, 1280 };
int rt050_upper_right[2] = { 520, 760 };
bool save_waveforms = false;
bool passed_cuts_bg = false;
bool passed_cuts_s = false;
bool passed_cut = false;
// Set main run directory, e.g. Run-15-10-02-27-32-23/151002
// Set current time to be analzyed as index of sorted number of total files in folder, e.g. 0-1439 for a full day
// Set output directory, eg Output/ Run-15-10-02-27-32-23/151002
int data_set = 0;
if (argc == 6)
{
data_set = atoi(argv[1]);
main_dir = std::string(argv[2]);
current_time = atoi(argv[3]);
out_dir = std::string(argv[4]);
single_time = atoi(argv[5]);
}
else
{
std::cout << "Arguments not matching! Aborting now!" << std::endl;
return 1;
}
unsigned int BG_PT[2] = {};
unsigned int BG_ROI[2] = {};
unsigned int S_PT[2] = {};
unsigned int S_ROI[2] = {};
switch (data_set)
{
case 1: BG_PT[0] = 0;
BG_PT[1] = 19975;
BG_ROI[0] = 19975;
BG_ROI[1] = 27475;
S_PT[0] = 7500;
S_PT[1] = 27475;
S_ROI[0] = 27475;
S_ROI[1] = 34975;
PE_max_PT = 10;
break;
case 2: BG_PT[0] = 0;
BG_PT[1] = 20000;
BG_ROI[0] = 20000;
BG_ROI[1] = 27400;
S_PT[0] = 7400;
S_PT[1] = 27400;
S_ROI[0] = 27400;
S_ROI[1] = 35000;
PE_max_PT = 20;
break;
case 3: BG_PT[0] = 0;
BG_PT[1] = 17500;
BG_ROI[0] = 17500;
BG_ROI[1] = 25000;
S_PT[0] = 7500;
S_PT[1] = 25000;
S_ROI[0] = 25000;
S_ROI[1] = 32500;
PE_max_PT = 30;
break;
default: std::cout << "Arguments not matching! Aborting now!" << std::endl;
return 1;
}
// Full analysis -> Converts $(Process) from condor submit to the current time file
if (single_time == 0)
{
// Buffers used to process data files and to step through directories
std::vector<std::string> time_files;
DIR *dpdf;
struct dirent *epdf;
// Find all time files and sort them
time_files.clear();
dpdf = opendir(main_dir.c_str());
if (dpdf != NULL)
{
std::string _tmp;
while (epdf = readdir(dpdf))
{
_tmp = epdf->d_name;
if (_tmp != "." && _tmp != ".." && _tmp.substr(7) == "zip")
{
time_files.push_back(_tmp.substr(0, 6));
}
}
}
// Sort time files by time in ascending order to convert current_time index to proper file
std::sort(time_files.begin(), time_files.end(), timeSort);
// Prepare paths to zipped and unzipped files
current_zip_file = main_dir + "/" + time_files[current_time] + ".zip";
time_name_in_zip = time_files[current_time];
}
// Single file analysis -> Directly convert input to current time file
else
{
current_zip_file = main_dir + "/" + zeroPad(current_time,6) +".zip";
time_name_in_zip = zeroPad(current_time,6);
}
//Open the ZIP archive
int err = 0;
int zidx = 0;
int fileSize = 0;
zip *z = zip_open(current_zip_file.c_str(), 0, &err);
//Search for the file of given name
const char *name = time_name_in_zip.c_str();
struct zip_stat st;
zip_stat_init(&st);
zip_stat(z, name, 0, &st);
//Alloc memory for its uncompressed contents
char *contents = new char[st.size];
// Unzip the compressed file into memory
zip_file *f = zip_fopen(z, time_name_in_zip.c_str(), 0);
fileSize = st.size;
zip_fread(f, contents, fileSize);
zip_fclose(f);
//And close the archive
zip_close(z);
// Create signal, background and info output files
bg_out_file.open((out_dir + "/" + fileName(atoi(time_name_in_zip.c_str()), "B-")).c_str(), std::ofstream::out | std::ofstream::trunc);
s_out_file.open((out_dir + "/" + fileName(atoi(time_name_in_zip.c_str()), "S-")).c_str(), std::ofstream::out | std::ofstream::trunc);
infoOut.open((out_dir + "/" + fileName(atoi(time_name_in_zip.c_str()), "I-")).c_str(), std::ofstream::out | std::ofstream::trunc);
if (save_waveforms)
{
waveformOut.open((out_dir + "/" + fileName(atoi(time_name_in_zip.c_str()), "W-")).c_str(), std::ofstream::out | std::ofstream::trunc);
}
// Begin data processing if file has been properly opened
if(err == 0)
{
waveformCtr = 0;
zidx = 0;
// Begin reading byte-stream
while (zidx < fileSize)
{
// Read LabView header and get the total number of samples written for each channel in the next chunk of data
for (int i=0;i<4;i++)
{
c = contents[zidx++];
no_samples = no_samples << 8 | (unsigned char) c;
}
// Read LabView header and get the total number of channels written in next chunk of data (always 2 in our case)
for (int i=0;i<4;i++)
{
c = contents[zidx++];
no_channels = no_channels << 8 | (unsigned char) c;
}
// Takes care of LabViews closing bit...
if (no_samples > 350070)
{
break;
}
// ----------------------------------------------------------------
// Process XYZ consecutive waveforms without encountering another
// LabView header inbetween
// ----------------------------------------------------------------
for (int wf=0; wf < (int) (no_samples/35007); wf++)
{
// A new waveform begins
waveformCtr += 1;
// -------------------------------------------------------------
// Reset all major waveform specific variables
// -------------------------------------------------------------
timestamp.clear();
overflow = false;
linear_gate = false;
muon_veto_flag = false;
_previous_c = 128;
gate_down = 0;
gate_up = 0;
memset(med_csi_arr,0,sizeof med_csi_arr);
memset(med_mv_arr,0,sizeof med_mv_arr );
med_csi_found = false;
med_mv_found = false;
med_csi_sum = 0;
med_mv_sum = 0;
above_pe_threshold = 0;
current_peak_width = 0;
current_pe_width = 0;
current_spe_q = 0;
m_peak_width = 0;
peaks.clear();
peak_heights.clear();
pe_beginnings.clear();
pe_endings.clear();
muon_peaks.clear();
spe_integration_ctr = 0;
spe_integration_charge = 0;
passed_cuts_s = false;
passed_cuts_bg = false;
passed_cut = false;
peak_amplitude = 0;
bP_detected = false;
_t_bP_idx = 0;
// -------------------------------------------------------------
// Read current timestamp
// -------------------------------------------------------------
for(int i=0; i<7; i++)
{
c = contents[zidx++];
c = contents[zidx++];
timestamp += zeroPad((int) c, 2);
}
// ---------------------------------------------------------------
// Read the full CsI and muon veto waveforms from the zip-stream
// + Apply bit transformation
// + Determine if a linear gate is present
// ---------------------------------------------------------------
for(int i=0; i<35000; i++)
{
//--------------
// CsI
//--------------
c = contents[zidx++];
// bit transformation to get rid of empty bins
_tmpC = (int) c - (int) floor(((double) c + 5.0)/11.0);
if (i<20000){ med_csi_arr[_tmpC + 128] += 1; }
csi[i] = _tmpC;
csi_raw[i] = _tmpC;
if (i == 0) { _previous_c = _tmpC; }
// Gate check
if (_tmpC <= 18 && _previous_c > 18) { gate_down++; }
if (_previous_c <= 18 && _tmpC > 18) { gate_up++; }
_previous_c = _tmpC;
// Overflow check
if (!overflow && (c >= 127 || c == -128))
{
overflow = true;
overflowCtr += 1;
}
//--------------
// Muon Veto
//--------------
c = contents[zidx++];
_tmpC = (int) c + (int) ((signbit((int) c) ? -1 : 1 ) * floor((4.0 - abs((double) c))/11.0));
med_mv_arr[_tmpC + 128] += 1;
mv[i] = _tmpC;
}
// ---------------------------------------
// Calculate the median of both channels
// ---------------------------------------
for(int i=0; i<256; i++)
{
if (!med_csi_found)
{
med_csi_sum += med_csi_arr[i];
if (med_csi_sum >= 10000)
{
med_csi = i-128;
med_csi_found=true;
}
}
if (!med_mv_found)
{
med_mv_sum += med_mv_arr[i];
if (med_mv_sum >= 10000)
{
med_mv = i-128;
med_mv_found=true;
}
}
}
// ----------------------------------------------
// Adjust linear gate counter if wf is gated
// ----------------------------------------------
if (gate_down != gate_up || med_csi < 50)
{
linear_gate = true;
linearGateCtr += 1;
}
// -----------------------------------------------
// Find peaks and photoelectrons in waveforms
// -----------------------------------------------
current_peak_width = 0;
peak_amplitude = 0;
bP_detected = false;
for (int i = 0; i < 35000; i++)
{
// -------------------------------------------
// Analyze CsI[Na] waveform
// -------------------------------------------
csi[i] = med_csi - csi[i];
// Simple peak finder using threshold crossing with history
if (csi[i] >= peak_height_threshold)
{
current_peak_width++;
peak_amplitude = csi[i] > peak_amplitude ? csi[i] : peak_amplitude;
}
else
{
if (current_peak_width >= peak_width_threshold)
{
peaks.push_back(i - current_peak_width);
pe_beginnings.push_back((i - current_peak_width - 2) >= 0 ? (i - current_peak_width - 2) : 0);
pe_endings.push_back((i + 1) <= 34999 ? (i + 1) : 34999);
peak_width_distribution[(current_peak_width < 50) ? current_peak_width : 50] += 1;
peak_heights.push_back(peak_amplitude);
// Check for large energy depositions
if (!bP_detected && current_peak_width >= 35 && !linear_gate && !overflow)
{
bP_detected = true;
bP_onset_arr.push_back(i - current_peak_width);
}
}
current_peak_width = 0;
peak_amplitude = 0;
}
// -------------------------------------------
// Analyze muon veto waveform
// -------------------------------------------
mv[i] = med_mv - mv[i];
// Peak finder
if (mv[i] >= 10) { m_peak_width++; }
else
{
if (m_peak_width >= 3)
{
muon_peaks.push_back(i-m_peak_width);
}
m_peak_width = 0;
}
}
// If there was a big pulse in the trace integrate it
// But only if there was no linear gate or overflow
if (bP_detected && !linear_gate && !overflow)
{
int _t_charge = 0;
for (int i = bP_onset_arr.back(); i < (1500 + bP_onset_arr.back()); i++)
{
_t_charge += (csi[i] >= peak_height_threshold) ? csi[i] : 0;
}
bP_charge_arr.push_back(_t_charge);
}
// Raise muon veto flag if more than three muons have been found
// If less than 3 have been found fill the vector with -1 for postprocessing
int muons_found = muon_peaks.size();
if (muons_found > 0)
{
if (linear_gate)
{
muon_onset_arr.push_back(muon_peaks[0]);
}
else
{
for (std::vector<int>::size_type idx = 0; idx < muons_found; idx++)
{
muon_onset_arr.push_back(muon_peaks[idx]);
}
}
}
if (muons_found > 3)
{
muon_veto_flag = true;
muonVetoCtr += 1;
}
else { muon_peaks.resize(3, -1); }
// Add PE peaks to peak height distribution
if (peak_heights.size() > 0 && !overflow && !linear_gate)
{
for (int idx = 0; idx < peak_heights.size(); idx++)
{
peak_height_dist[(peak_heights[idx] < 100) ? peak_heights[idx] : 99]++;
}
}
// ========================================================================
// Check that there is at least one PE in the trace, there is no overflow,
// no linear gate and no muon veto flag, otherwise continue to next
// waveform without bothering to analyze this one
// ========================================================================
bool analyze = false;
if (data_set == 1 && !overflow && !linear_gate && !muon_veto_flag) { analyze = true; }
if (data_set == 2 && !overflow && !linear_gate) { analyze = true; }
if (data_set == 3 && !overflow && !linear_gate) { analyze = true; }
if (analyze && pe_beginnings.size() > 0)
{
// -------------------------------------------------------------
// Integrate all SPE found in the PT and histogram their charge
// -------------------------------------------------------------
for (std::vector<int>::size_type idx = 0; idx < pe_beginnings.size(); idx++)
{
if (pe_beginnings[idx] < BG_PT[1])
{
current_spe_q = 0;
for (int i = pe_beginnings[idx]; i <= pe_endings[idx]; i++)
{
current_spe_q += csi[i];
}
if (current_spe_q >= -50 && current_spe_q < 250) { spe_charge_dist[(current_spe_q+50)] += 1; }
}
else { break; }
}
// -------------------------------------------------------------
// Determine number of PE in different regions
// -------------------------------------------------------------
bg_pt_ct = 0;
bg_roi_ct = 0;
bg_iw_ct = 0;
s_pt_ct = 0;
s_roi_ct = 0;
s_iw_ct = 0;
if (peaks.size() > 0)
{
for (std::vector<int>::size_type idx = 0; idx < peaks.size(); idx++)
{
if (peaks[idx] >= BG_PT[0] && peaks[idx] < BG_PT[1]) { bg_pt_ct += 1; }
if (peaks[idx] >= S_PT[0] && peaks[idx] < S_PT[1]) { s_pt_ct += 1; }
if (peaks[idx] >= BG_ROI[0] && peaks[idx] < BG_ROI[1]) { bg_roi_ct += 1; }
if (peaks[idx] >= S_ROI[0] && peaks[idx] < S_ROI[1]) { s_roi_ct += 1; }
}
// Distribution of charge (only add >= 3)
if (true)
{
int sz = peaks.size() / 2;
if (sz < 350)
{
int cpi = 0;
for (int idx = 0; idx < 35000; idx++)
{
// Add sample if it is within one of the PE regions identified previously
if (idx >= pe_beginnings[cpi] && idx <= pe_endings[cpi])
{
charge_distribution[sz][idx / 100] += csi[idx];
if (idx >= pe_endings[cpi])
{
if (++cpi >= pe_beginnings.size()){ break; }
}
}
}
}
}
}
// Histogram baseline and peaks in pretrace
if (!overflow && !linear_gate && !muon_veto_flag)
{
int _t_med_csi_bin = med_csi - 85;
if (_t_med_csi_bin >= 0 && _t_med_csi_bin <=30) { baseline_hist[_t_med_csi_bin]++; }
else { baseline_hist[31]++; }
if (bg_pt_ct <= 50) { bg_pe_pt[bg_pt_ct]++; }
else { bg_pe_pt[51]++; }
if (s_pt_ct <= 50) { s_pe_pt[s_pt_ct]++; }
else { s_pe_pt[51]++; }
}
// -------------------------------------------------------------
// Only analzye BG region if there are a maximum of PE_max_PT
// & at least one PE in ROI
// -------------------------------------------------------------
if (bg_pt_ct <= PE_max_PT && bg_roi_ct > 0)
{
bgAnalysisCtr += 1;
// Reset window parameters
idx_0 = 0;
i_peak = 0;
i_pe = 0;
q_int = 0;
lnL_real = 0.0;
lnL_flat = 0.0;
_t1 = 0.0;
_t2 = 0.0;
// -------------------------------------------------------------
// Determine onset of integration window by finding the first
// PE in the region of interest
// -------------------------------------------------------------
for (int i = 0; i < peaks.size(); i++)
{
if (peaks[i] >= BG_ROI[0])
{
idx_0 = peaks[i];
i_peak = i;
break;
}
}
idx_0 -= 3;
// -------------------------------------------------------------
// Only analyze if the full integration window is within the ROI
// -------------------------------------------------------------
if (idx_0 < (BG_ROI[1] - 1500))
{
// --------------------------------------------------------------
// Determine number of peaks in integration window (magic bullet)
// --------------------------------------------------------------
for (int i = i_peak; i < peaks.size(); i++)
{
bg_iw_ct += (peaks[i] - idx_0 < 1500) ? 1 : 0;
}
// -------------------------------------------------------------
// Integrate over all PE found in the integration window
// -------------------------------------------------------------
i_pe = i_peak;
for (int i = 0; i < 1500; i++)
{
// Get proper 'real' index that includes the onset offset
idx_w_offset = i + idx_0;
// Add sample if it is within one of the PE regions identified previously as well as update loglikelihood estimators
if (i_pe < pe_beginnings.size() && idx_w_offset >= pe_beginnings[i_pe] && idx_w_offset <= pe_endings[i_pe])
{
q_int += csi[idx_w_offset];
lnL_real += lnL_pf_real[i] * csi[idx_w_offset];
lnL_flat += lnL_pf_flat[i] * csi[idx_w_offset];
if (idx_w_offset == pe_endings[i_pe]) { i_pe++; }
}
// Keep track of charge integration to determine rise times later
bg_q_arr[i] = q_int;
}
// -------------------------------------------------------------
// Determine rise times
// -------------------------------------------------------------
// Calculate charge thresholds
thresholds[0] = 0.1*bg_q_arr[1499];
thresholds[1] = 0.5*bg_q_arr[1499];
thresholds[2] = 0.9*bg_q_arr[1499];
// Determine threshold crossing times
for (int i = 0; i < 1499; i++)
{
_t1 = (double)bg_q_arr[i];
_t2 = (double)bg_q_arr[i + 1];
for (int j = 0; j < 3; j++)
{
if (_t1 < thresholds[j] && _t2 >= thresholds[j]){ bg_rt[j] = i + (thresholds[j] - _t1) / (_t2 - _t1); }
}
}
// -------------------------------------------------------------
// If waveforms are being saved check whether cuts are passed
// -------------------------------------------------------------
if (save_waveforms)
{
int rt1090 = (bg_rt[2] - bg_rt[0]);
int rt050 = bg_rt[1];
bool bottom_left_cut = (rt1090 >= rt1090_bottom_left[0]) && (rt1090 <= rt1090_bottom_left[1]) && (rt050 >= rt050_bottom_left[0]) && (rt050 <= rt050_bottom_left[1]);
bool upper_right_cut = (rt1090 >= rt1090_upper_right[0]) && (rt1090 <= rt1090_upper_right[1]) && (rt050 >= rt050_upper_right[0]) && (rt050 <= rt050_upper_right[1]);
bool min_peak_cut = (bg_iw_ct >= minimum_no_peaks_iw);
bool total_peak_cut = (peaks.size() >= no_total_peaks[0]) && (peaks.size() <= no_total_peaks[1]);
passed_cuts_bg = (bottom_left_cut || upper_right_cut) && min_peak_cut && total_peak_cut;
}
// -------------------------------------------------------------
// Write analysis results to file
// -------------------------------------------------------------
bg_out_file << timestamp << " " << med_csi << " " << med_mv << " ";
bg_out_file << bg_pt_ct << " " << bg_roi_ct << " ";
bg_out_file << bg_iw_ct << " " << idx_0 << " " << bg_q_arr[1499] << " " << lnL_real << " " << lnL_flat << " ";
bg_out_file << bg_rt[0] << " " << bg_rt[1] << " " << bg_rt[2] << " ";
bg_out_file << muon_peaks[0] << " " << muon_peaks[1] << " " << muon_peaks[2] << " " << peaks.size() << std::endl;
// Keeps track of how many BG waveforms have actually been analyzed
bg_counter++;
}
}
// -------------------------------------------------------------
// Only analzye S region if there are a maximum of PE_max_PT
// & at least one PE in ROI
// -------------------------------------------------------------
if (s_pt_ct <= PE_max_PT && s_roi_ct > 0)
{
sAnalysisCtr += 1;
// Reset window parameters
idx_0 = 0;
i_peak = 0;
i_pe = 0;
q_int = 0;
lnL_real = 0.0;
lnL_flat = 0.0;
_t1 = 0.0;
_t2 = 0.0;
// -------------------------------------------------------------
// Determine onset of integration window by finding the first
// PE in the region of interest
// -------------------------------------------------------------
for (int i = 0; i < peaks.size(); i++)
{
if (peaks[i] >= S_ROI[0])
{
idx_0 = peaks[i];
i_peak = i;
break;
}
}
idx_0 -= 3;
// -------------------------------------------------------------
// Only analyze if the full integration window is within the ROI
// -------------------------------------------------------------
if (idx_0 < (S_ROI[1] - 1500))
{
// --------------------------------------------------------------
// Determine number of peaks in integration window (magic bullet)
// --------------------------------------------------------------
for (int i = i_peak; i < peaks.size(); i++)
{
s_iw_ct += (peaks[i] - idx_0 < 1500) ? 1 : 0;
}
i_pe = i_peak;
// -------------------------------------------------------------
// Integrate over all PE found in the integration window
// -------------------------------------------------------------
for (int i = 0; i < 1500; i++)
{
// Get proper 'real' index that includes the onset offset
idx_w_offset = i + idx_0;
// Add sample if it is within one of the PE regions identified previously & update loglikelihood estimators
if (i_pe < pe_beginnings.size() && idx_w_offset >= pe_beginnings[i_pe] && idx_w_offset <= pe_endings[i_pe])
{
q_int += csi[idx_w_offset];
lnL_real += lnL_pf_real[i] * csi[idx_w_offset];
lnL_flat += lnL_pf_flat[i] * csi[idx_w_offset];
if (idx_w_offset == pe_endings[i_pe]) { i_pe++; }
}
// Keep track of charge integration to determine rise times later
s_q_arr[i] = q_int;
}
// -------------------------------------------------------------
// Determine rise times
// -------------------------------------------------------------
// Calculate charge thresholds
thresholds[0] = 0.1*s_q_arr[1499];
thresholds[1] = 0.5*s_q_arr[1499];
thresholds[2] = 0.9*s_q_arr[1499];
// Determine threshold crossing times
for (int i = 0; i < 1499; i++)
{
_t1 = (double)s_q_arr[i];
_t2 = (double)s_q_arr[i + 1];
for (int j = 0; j < 3; j++)
{
if (_t1 < thresholds[j] && _t2 >= thresholds[j]){ s_rt[j] = i + (thresholds[j] - _t1) / (_t2 - _t1); }
}
}
// -------------------------------------------------------------
// If waveforms are being saved check whether cuts are passed
// -------------------------------------------------------------
if (save_waveforms)
{
int rt1090 = (s_rt[2] - s_rt[0]);
int rt050 = s_rt[1];
bool bottom_left_cut = (rt1090 >= rt1090_bottom_left[0]) && (rt1090 <= rt1090_bottom_left[1]) && (rt050 >= rt050_bottom_left[0]) && (rt050 <= rt050_bottom_left[1]);
bool upper_right_cut = (rt1090 >= rt1090_upper_right[0]) && (rt1090 <= rt1090_upper_right[1]) && (rt050 >= rt050_upper_right[0]) && (rt050 <= rt050_upper_right[1]);
bool min_peak_cut = (s_iw_ct >= minimum_no_peaks_iw);
bool total_peak_cut = (peaks.size() >= no_total_peaks[0]) && (peaks.size() <= no_total_peaks[1]);
passed_cuts_s = (bottom_left_cut || upper_right_cut) && min_peak_cut && total_peak_cut;
}
// -------------------------------------------------------------
// Write analysis results to file
// -------------------------------------------------------------
s_out_file << timestamp << " " << med_csi << " " << med_mv << " ";
s_out_file << s_pt_ct << " " << s_roi_ct << " ";
s_out_file << s_iw_ct << " " << idx_0 << " " << s_q_arr[1499] << " " << lnL_real << " " << lnL_flat << " ";
s_out_file << s_rt[0] << " " << s_rt[1] << " " << s_rt[2] << " ";
s_out_file << muon_peaks[0] << " " << muon_peaks[1] << " " << muon_peaks[2] << " " << peaks.size() << std::endl;
// Keeps track of how many BG waveforms have actually been analyzed
s_counter++;
}
}
}
// -------------------------------------------------------------
// Save waveform if cuts have been passed for either ROI
// -------------------------------------------------------------
if (save_waveforms && passed_cut)
{
for (int idx = 0; idx < 35000; idx++)
{
waveformOut << csi_raw[idx] << " ";
}
waveformOut << gate_up << " " << gate_down << " " << med_csi << " ";
for (int idx = 0; idx < pe_beginnings.size(); idx++)
{
waveformOut << pe_beginnings[idx] << " " << pe_endings[idx] << " ";
}
waveformOut << std::endl;
}
}
}
}
// Before exiting, make sure that both output files are properly closed to prevent data loss.
if (bg_out_file.is_open()) { bg_out_file.close(); }
if (s_out_file.is_open()) { s_out_file.close(); }
// Write run info
if (infoOut.is_open())
{
infoOut << "Total number of Waveforms processed" << std::endl;
infoOut << waveformCtr << std::endl;
infoOut << "Number of triggers with linear gates in CsI channel" << std::endl;
infoOut << linearGateCtr << std::endl;
infoOut << "Number of triggers with overflows in either channel" << std::endl;
infoOut << overflowCtr << std::endl;
infoOut << "Number of triggers with more than 3 muons in muon veto channel" << std::endl;
infoOut << muonVetoCtr << std::endl;
infoOut << "Number of triggers that have actually been analyzed in the background window (less than x PE/peaks in PT + at least one PE/peak in ROI)" << std::endl;
infoOut << bgAnalysisCtr << std::endl;
infoOut << "Number of triggers that have actually been analyzed in the signal window (less than x PE/peaks in PT + at least one PE/peak in ROI)" << std::endl;
infoOut << sAnalysisCtr << std::endl;
infoOut << "Maximum number of PE/peaks in the pretrace" << std::endl;
infoOut << PE_max_PT << std::endl;
infoOut << "Background pretrace start" << std::endl;
infoOut << BG_PT[0] << std::endl;
infoOut << "Background pretrace stop" << std::endl;
infoOut << BG_PT[1] << std::endl;
infoOut << "Background ROI start" << std::endl;
infoOut << BG_ROI[0] << std::endl;
infoOut << "Background ROI stop" << std::endl;
infoOut << BG_ROI[1] << std::endl;
infoOut << "Signal pretrace start" << std::endl;
infoOut << S_PT[0] << std::endl;
infoOut << "Signal pretrace stop" << std::endl;
infoOut << S_PT[1] << std::endl;
infoOut << "Signal ROI start" << std::endl;
infoOut << S_ROI[0] << std::endl;
infoOut << "Signal ROI stop" << std::endl;
infoOut << S_ROI[1] << std::endl;
infoOut << "Unzipped file size" << std::endl;
infoOut << fileSize << std::endl;
infoOut << "SPE charge histogram" << std::endl;
for (int idx = 0; idx < 300; idx++)
{
infoOut << spe_charge_dist[idx] << " ";
}
infoOut << std::endl;
infoOut << "Background - Peaks in pretrace histogram" << std::endl;
for (int idx = 0; idx < 52; idx++)
{
infoOut << bg_pe_pt[idx] << " ";
}
infoOut << std::endl;
infoOut << "Signal - Peaks in pretrace histogram" << std::endl;
for (int idx = 0; idx < 52; idx++)
{
infoOut << s_pe_pt[idx] << " ";
}
infoOut << std::endl;
infoOut << "CsI baseline histogram" << std::endl;
for (int idx = 0; idx < 32; idx++)
{
infoOut << baseline_hist[idx] << " ";
}
infoOut << std::endl;
infoOut << "Peak width distribution" << std::endl;
for (int idx = 0; idx < 51; idx++)
{
infoOut << peak_width_distribution[idx] << " ";
}
infoOut << std::endl;
infoOut << "PE amplitudes" << std::endl;
for (int idx = 0; idx < 100; idx++)
{
infoOut << peak_height_dist[idx] << " ";
}
infoOut << std::endl;
infoOut << "Big pulse onsets" << std::endl;
for (int idx = 0; idx < bP_onset_arr.size(); idx++)
{
infoOut << bP_onset_arr[idx] << " ";
}
infoOut << std::endl;
infoOut << "Big pulse charges" << std::endl;
for (int idx = 0; idx < bP_charge_arr.size(); idx++)
{
infoOut << bP_charge_arr[idx] << " ";
}
infoOut << std::endl;
infoOut << "All muon onsets - If linear gate present only the first is recorded" << std::endl;
for (int idx = 0; idx < muon_onset_arr.size(); idx++)
{
infoOut << muon_onset_arr[idx] << " ";
}
infoOut << std::endl;
infoOut << "Charge distribution in full waveform" << std::endl;
for (int idx_1 = 0; idx_1 < 350; idx_1++)
{
bool printLine = false;
for (int idx_2 = 0; idx_2 < 350; idx_2++)
{
if (charge_distribution[idx_1][idx_2] > 0)
{
printLine = true;
break;
}
}
if (printLine)
{
infoOut << idx_1 << " ";
for (int idx_2 = 0; idx_2 < 350; idx_2++)
{
if (charge_distribution[idx_1][idx_2] > 0) { infoOut << idx_2 << " " << charge_distribution[idx_1][idx_2] << " "; }
}
infoOut << std::endl;
}
}
infoOut.close();
}
return 0;
}
static void itsaWriteMerged(struct chromInfo *chromList, DNA *allDna,
bits32 *offsetArray, bits32 *listArray, bits32 *index13, char *output)
/* Write out a file that contains a single splix that is the merger of
* all of the individual splixes in list. As a side effect will replace
* offsetArray with suffix array and listArray with traverse array */
{
FILE *f = mustOpen(output, "w+");
/** Allocate header and fill out easy constant fields. */
struct itsaFileHeader *header;
AllocVar(header);
header->majorVersion = ITSA_MAJOR_VERSION;
header->minorVersion = ITSA_MINOR_VERSION;
/* Figure out sizes of names and sequence for each chromosome. */
struct chromInfo *chrom;
bits32 chromNamesSize = 0;
bits64 dnaDiskSize = 1; /* For initial zero. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
chromNamesSize += strlen(chrom->name) + 1;
dnaDiskSize += chrom->size + 1; /* Include separating zeroes. */
}
/* Fill in most of rest of header fields */
header->chromCount = slCount(chromList);
header->chromNamesSize = roundUpTo4(chromNamesSize);
header->dnaDiskSize = roundUpTo4(dnaDiskSize);
bits32 chromSizesSize = header->chromCount*sizeof(bits32);
/* Write header. */
mustWrite(f, header, sizeof(*header));
/* Write chromosome names. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
mustWrite(f, chrom->name, strlen(chrom->name)+1);
zeroPad(f, header->chromNamesSize - chromNamesSize);
/* Write chromosome sizes. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
mustWrite(f, &chrom->size, sizeof(chrom->size));
int chromSizesSizePad = chromSizesSize - header->chromCount * sizeof(bits32);
zeroPad(f, chromSizesSizePad);
/* Write out chromosome DNA and zeros before, between, and after. */
mustWrite(f, allDna, dnaDiskSize);
zeroPad(f, header->dnaDiskSize - dnaDiskSize);
verboseTime(1, "Wrote %lld bases of DNA including zero padding", header->dnaDiskSize);
/* Calculate and write suffix array. Convert index13 to index of array as opposed to index
* of sequence. */
bits64 arraySize = 0;
off_t suffixArrayFileOffset = ftello(f);
int slotCount = itsaSlotCount;
int slotIx;
for (slotIx=0; slotIx < slotCount; ++slotIx)
{
int slotSize = finishAndWriteOneSlot(offsetArray, listArray, index13[slotIx], allDna, f);
/* Convert index13 to hold the position in the suffix array where the first thing matching
* the corresponding 13-base prefix is found. */
if (slotSize != 0)
index13[slotIx] = arraySize+1; /* The +1 is so we can keep 0 for not found. */
else
index13[slotIx] = 0;
arraySize += slotSize;
if ((slotIx % 200000 == 0) && slotIx != 0)
{
verboseDot();
if (slotIx % 10000000 == 0)
verbose(1, "fine sort bucket %d of %d\n", slotIx, slotCount);
}
}
verbose(1, "fine sort bucket %d of %d\n", slotCount, slotCount);
verboseTime(1, "Wrote %lld suffix array positions", arraySize);
/* Now we're done with the offsetArray and listArray buffers, so use them for the
* next phase. */
bits32 *suffixArray = offsetArray;
offsetArray = NULL; /* Help make some errors more obvious */
bits32 *traverseArray = listArray;
listArray = NULL; /* Help make some errors more obvious */
/* Read the suffix array back from the file. */
fseeko(f, suffixArrayFileOffset, SEEK_SET);
mustRead(f, suffixArray, arraySize*sizeof(bits32));
verboseTime(1, "Read suffix array back in");
/* Calculate traverse array and cursor arrays */
memset(traverseArray, 0, arraySize*sizeof(bits32));
UBYTE *cursorArray = needHugeMem(arraySize);
itsaFillInTraverseArray(allDna, suffixArray, arraySize, traverseArray, cursorArray);
verboseTime(1, "Filled in traverseArray");
/* Write out traverse array. */
mustWrite(f, traverseArray, arraySize*sizeof(bits32));
verboseTime(1, "Wrote out traverseArray");
/* Write out 13-mer index. */
mustWrite(f, index13, itsaSlotCount*sizeof(bits32));
verboseTime(1, "Wrote out index13");
/* Write out bits of cursor array corresponding to index. */
for (slotIx=0; slotIx<itsaSlotCount; ++slotIx)
{
bits32 indexPos = index13[slotIx];
if (indexPos == 0)
fputc(0, f);
else
fputc(cursorArray[indexPos-1], f);
}
verboseTime(1, "Wrote out cursors13");
/* Update a few fields in header, and go back and write it out again with
* the correct magic number to indicate it's complete. */
header->magic = ITSA_MAGIC;
header->arraySize = arraySize;
header->size = sizeof(*header) // header
+ header->chromNamesSize + // chromosome names
+ header->chromCount * sizeof(bits32) // chromosome sizes
+ header->dnaDiskSize // dna sequence
+ sizeof(bits32) * arraySize // suffix array
+ sizeof(bits32) * arraySize // traverse array
+ sizeof(bits32) * itsaSlotCount // index13
+ sizeof(UBYTE) * itsaSlotCount; // cursors13
rewind(f);
mustWrite(f, header, sizeof(*header));
carefulClose(&f);
verbose(1, "Completed %s is %lld bytes\n", output, header->size);
}
std::string encode(const std::string & word) const{
assert(!word.empty());
return zeroPad(upperFront(word)+
encodeDigits(word.substr(1)));
}
std::string encode(const std::string& word) const {
return zeroPad(upperFront(head(word)) + tail(encodedDigits(word)));
}
