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Merge pull request #406 from mpaolone/development
Various ALERT updates
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160 changes: 160 additions & 0 deletions
160
common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/HipoExtractor.java
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| package org.jlab.detector.pulse; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import org.jlab.io.base.DataBank; | ||
| import org.jlab.io.base.DataEvent; | ||
| import org.jlab.jnp.hipo4.data.Bank; | ||
| import org.jlab.jnp.hipo4.data.Event; | ||
| import org.jlab.jnp.hipo4.data.SchemaFactory; | ||
| import org.jlab.utils.groups.IndexedTable; | ||
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| /** | ||
| * For now, a place to store standard boilerplate for waveform/pulse HIPO | ||
| * manipulations. No bounds checking regarding number of samples. | ||
| * | ||
| * Here an IndexedTable object from CCDB is used to pass initialization parameters | ||
| * to the extractor. If that object is null, the @{link org.jlab.detector.pulse.IExtractor.extract} | ||
| * method should know what to do, e.g., hardcoded, channel-independent parameters. | ||
| * | ||
| * FIXME: Passing the #samples around is obviously bad, and there's probably a | ||
| * few non-horrible ways that can be addressed without changing bank format. | ||
| * | ||
| * @author baltzell | ||
| */ | ||
| public abstract class HipoExtractor implements IExtractor { | ||
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| /** | ||
| * @param n number of samples in readout | ||
| * @param it CCDB table containing extraction initialization parameters | ||
| * @param event the event to modify | ||
| * @param schema bank schema factory | ||
| * @param wfBankName name of the input waveform bank | ||
| * @param adcBankName name of the output ADC bank | ||
| */ | ||
| public void update(int n, IndexedTable it, Event event, SchemaFactory schema, String wfBankName, String adcBankName) { | ||
| Bank wf = new Bank(schema.getSchema(wfBankName)); | ||
| event.read(wf); | ||
| if (wf.getRows() > 0) { | ||
| Bank adc = new Bank(schema.getSchema(adcBankName)); | ||
| update(n, it, wf, adc); | ||
| event.remove(schema.getSchema(adcBankName)); | ||
| if (adc.getRows() > 0) event.write(adc); | ||
| } | ||
| } | ||
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| /** | ||
| * This could be overriden, e.g., for non-standard ADC banks. | ||
| * @param n number of samples in readout | ||
| * @param it CCDB table containing extraction initialization parameters | ||
| * @param event the event to modify | ||
| * @param wfBankName name of the input waveform bank | ||
| * @param adcBankName name of the output ADC bank | ||
| */ | ||
| public void update(int n, IndexedTable it, DataEvent event, String wfBankName, String adcBankName) { | ||
| DataBank wf = event.getBank(wfBankName); | ||
| if (wf.rows() > 0) { | ||
| event.removeBank(adcBankName); | ||
| List<Pulse> pulses = getPulses(n, it, wf); | ||
| if (pulses != null && !pulses.isEmpty()) { | ||
| DataBank adc = event.createBank(adcBankName, pulses.size()); | ||
| for (int i=0; i<pulses.size(); ++i) { | ||
| copyIndices(wf, adc, i, i); | ||
| adc.setInt("ADC", i, (int)pulses.get(i).integral); | ||
| adc.setFloat("time", i, pulses.get(i).time); | ||
| } | ||
| event.appendBank(adc); | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * This could be overriden, e.g., for non-standard ADC banks. | ||
| * @param n number of samples in readout | ||
| * @param it CCDB table containing extraction initialization parameters | ||
| * @param wfBank input waveform bank | ||
| * @param adcBank output ADC bank | ||
| */ | ||
| protected void update(int n, IndexedTable it, Bank wfBank, Bank adcBank) { | ||
| if (wfBank.getRows() > 0) { | ||
| List<Pulse> pulses = getPulses(n, it, wfBank); | ||
| adcBank.reset(); | ||
| adcBank.setRows(pulses!=null ? pulses.size() : 0); | ||
| if (pulses!=null && !pulses.isEmpty()) { | ||
| for (int i=0; i<pulses.size(); ++i) { | ||
| copyIndices(wfBank, adcBank, pulses.get(i).id, i); | ||
| adcBank.putInt("ADC", i, (int)pulses.get(i).integral); | ||
| adcBank.putFloat("time", i, pulses.get(i).time); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| private static void copyIndices(Bank src, Bank dest, int isrc, int idest) { | ||
| dest.putByte("sector", idest, src.getByte("sector",isrc)); | ||
| dest.putByte("layer", idest, src.getByte("layer",isrc)); | ||
| dest.putShort("component", idest, src.getShort("component",isrc)); | ||
| dest.putByte("order", idest, src.getByte("order",isrc)); | ||
| dest.putShort("id", idest, (short)isrc); | ||
| } | ||
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| private static void copyIndices(DataBank src, DataBank dest, int isrc, int idest) { | ||
| dest.setByte("sector", idest, src.getByte("sector",isrc)); | ||
| dest.setByte("layer", idest, src.getByte("layer",isrc)); | ||
| dest.setShort("component", idest, src.getShort("component",isrc)); | ||
| dest.setByte("order", idest, src.getByte("order",isrc)); | ||
| dest.setShort("id", idest, (short)isrc); | ||
| } | ||
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| private static int[] getIndices(Bank bank, int row) { | ||
| return new int[] { | ||
| bank.getShort("sector", row), | ||
| bank.getShort("layer", row), | ||
| bank.getShort("component", row), | ||
| bank.getShort("order", row)}; | ||
| } | ||
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| private static int[] getIndices(DataBank bank, int row) { | ||
| return new int[] { | ||
| bank.getShort("sector", row), | ||
| bank.getShort("layer", row), | ||
| bank.getShort("component", row), | ||
| bank.getShort("order", row)}; | ||
| } | ||
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| private List<Pulse> getPulses(int n, IndexedTable it, DataBank wfBank) { | ||
| List<Pulse> pulses = null; | ||
| short[] samples = new short[n]; | ||
| for (int i=0; i<wfBank.rows(); ++i) { | ||
| for (int j=0; j<n; ++j) | ||
| samples[j] = wfBank.getShort(String.format("s%d",j+1), i); | ||
| List<Pulse> p = it==null ? extract(null, i, samples) : | ||
| extract(it.getNamedEntry(getIndices(wfBank,i)), i, samples); | ||
| if (p!=null && !p.isEmpty()) { | ||
| if (pulses == null) pulses = new ArrayList<>(); | ||
| pulses.addAll(p); | ||
| } | ||
| } | ||
| return pulses; | ||
| } | ||
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| private List<Pulse> getPulses(int n, IndexedTable it, Bank wfBank) { | ||
| List<Pulse> pulses = null; | ||
| short[] samples = new short[n]; | ||
| for (int i=0; i<wfBank.getRows(); ++i) { | ||
| for (int j=0; j<n; ++j) | ||
| samples[j] = wfBank.getShort(String.format("s%d",j+1), i); | ||
| // FIXME: Can speed this up (but looks like not for DataBank?): | ||
| //samples[j] = wfBank.getShort(String.format(5+j,j+1), i); | ||
| List p = it==null ? extract(null, i, samples) : | ||
| extract(it.getNamedEntry(getIndices(wfBank,i)), i, samples); | ||
| if (p!=null && !p.isEmpty()) { | ||
| if (pulses == null) pulses = new ArrayList<>(); | ||
| pulses.addAll(p); | ||
| } | ||
| } | ||
| return pulses; | ||
| } | ||
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| } |
10 changes: 10 additions & 0 deletions
10
common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/IExtractor.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,10 @@ | ||
| package org.jlab.detector.pulse; | ||
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| import java.util.List; | ||
| import org.jlab.utils.groups.NamedEntry; | ||
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| public interface IExtractor <T> { | ||
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| public List<T> extract(NamedEntry pars, int id, short... samples); | ||
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| } |
65 changes: 65 additions & 0 deletions
65
common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode3.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,65 @@ | ||
| package org.jlab.detector.pulse; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import org.jlab.utils.groups.NamedEntry; | ||
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| /** | ||
| * Similar to a FADC250 Mode-3 pulse extraction. | ||
| * | ||
| * @author baltzell | ||
| */ | ||
| public class Mode3 extends HipoExtractor { | ||
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| // Fixed extraction parameters: | ||
| final double ped = 2000; | ||
| final double tet = 2000; | ||
| final int nsa = 30; | ||
| final int nsb = 5; | ||
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| /** | ||
| * @param pars CCDB row | ||
| * @param id link to row in source bank | ||
| * @param samples ADC samples | ||
| * @return extracted pulses | ||
| */ | ||
| @Override | ||
| public List<Pulse> extract(NamedEntry pars, int id, short... samples) { | ||
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| List<Pulse> pulses = null; | ||
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| /* | ||
| // Retrive extraction parameters from a CCDB table: | ||
| double ped = pars.getValue("ped").doubleValue(); | ||
| double tet = pars.getValue("tet").doubleValue(); | ||
| int nsa = pars.getValue("nsa").intValue(); | ||
| int nsb = pars.getValue("nsb").intValue(); | ||
| */ | ||
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| // Perform the extraction: | ||
| for (int i=0; i<samples.length-1; ++i) { | ||
| // Check for threshold crossing: | ||
| if (samples[i] > ped+tet && samples[i+1] > samples[i]) { | ||
| int n = 0; | ||
| float integral = 0; | ||
| // Integrate the pulse: | ||
| for (int j=i-nsb; j<=i+nsa; ++j) { | ||
| if (j<0) continue; | ||
| if (j>=samples.length) break; | ||
| integral += samples[j]; | ||
| n++; | ||
| } | ||
| integral -= n * ped; | ||
| Pulse p = new Pulse(integral, i, 0x0, id); | ||
| p.pedestal = (float)(ped); | ||
| // Add the new pulse to the list: | ||
| if (pulses == null) pulses = new ArrayList<>(); | ||
| pulses.add(p); | ||
| // Add a holdoff time before next possible pulse: | ||
| i += nsa; | ||
| } | ||
| } | ||
| return pulses; | ||
| } | ||
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| } |
39 changes: 39 additions & 0 deletions
39
common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode7.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| package org.jlab.detector.pulse; | ||
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| import java.util.List; | ||
| import org.jlab.utils.groups.NamedEntry; | ||
|
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| /** | ||
| * Similar to a Mode-7 FADC250 pulse extraction. | ||
| * | ||
| * @author baltzell | ||
| */ | ||
| public class Mode7 extends Mode3 { | ||
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| /** | ||
| * @param t0 threshold-crossing sample index | ||
| * @param ped pedestal (for calculating pulse half-height) | ||
| * @param samples | ||
| * @return pulse time | ||
| */ | ||
| private static float calculateTime(int t0, float ped, short... samples) { | ||
| for (int j=t0+1; j<samples.length; ++j) { | ||
| if (samples[j] < samples[j-1]) { | ||
| float slope = (samples[j-1]-ped) / (j-t0); | ||
| float offset = samples[j-1] - (j-1)*slope; | ||
| return (samples[j-1]/2 - offset) / slope; | ||
| } | ||
| } | ||
| // Fall back to Mode-3 time: | ||
| return t0; | ||
| } | ||
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| @Override | ||
| public List<Pulse> extract(NamedEntry pars, int id, short... samples) { | ||
| List<Pulse> pulses = super.extract(pars, id, samples); | ||
| for (Pulse p : pulses) | ||
| p.time = calculateTime((int)p.time, p.pedestal, samples); | ||
| return pulses; | ||
| } | ||
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| } |
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