Examples with PeakResultProcedure uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure used on opensource projects

Example 21 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class Filter method filter2.

/**
 * Filter the results.
 *
 * <p>The number of consecutive rejections are counted per frame. When the configured number of
 * failures is reached all remaining results for the frame are rejected. This assumes the results
 * are ordered by the frame.
 *
 * <p>Note that this method is to be used to score a set of results that may have been extracted
 * from a larger set since the number of consecutive failures before each peak are expected to be
 * stored in the origY property. Set this to zero and the results should be identical to
 * {@link #filter(MemoryPeakResults, int)}
 *
 * @param results the results
 * @param failures the number of failures to allow per frame before all peaks are rejected
 * @return the filtered results
 */
public MemoryPeakResults filter2(MemoryPeakResults results, final int failures) {
    final MemoryPeakResults newResults = new MemoryPeakResults();
    final FrameCounter counter = new FrameCounter();
    newResults.copySettings(results);
    setup(results);
    results.forEach((PeakResultProcedure) peak -> {
        counter.advanceAndReset(peak.getFrame());
        counter.increment(peak.getOrigY());
        final boolean isPositive;
        if (counter.getCount() > failures) {
            isPositive = false;
        } else {
            isPositive = accept(peak);
        }
        if (isPositive) {
            counter.reset();
            newResults.add(peak);
        } else {
            counter.increment();
        }
    });
    end();
    return newResults;
}

Example 22 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class Filter method scoreSubset.

/**
 * Filter the results and return the performance score. Allows benchmarking the filter by marking
 * the results as true or false.
 *
 * <p>Any input PeakResult with an original value that is not zero will be treated as a true
 * result, all other results are false. The filter is run and the results are marked as true
 * positive, false negative and false positive.
 *
 * <p>The number of consecutive rejections are counted per frame. When the configured number of
 * failures is reached all remaining results for the frame are rejected. This assumes the results
 * are ordered by the frame.
 *
 * <p>Note that this method is to be used to score a subset that was generated using
 * {@link #filterSubset(MemoryPeakResults, int, double[])} since the number of consecutive
 * failures before each peak are expected to be stored in the origX property.
 *
 * @param resultsList a list of results to analyse
 * @param failures the number of failures to allow per frame before all peaks are rejected
 * @param tn The initial true negatives (used when the results have been pre-filtered)
 * @param fn The initial false negatives (used when the results have been pre-filtered)
 * @return the score
 */
public ClassificationResult scoreSubset(List<MemoryPeakResults> resultsList, final int failures, int tn, int fn) {
    final int[] s = new int[4];
    s[TN] = tn;
    s[FN] = fn;
    for (final MemoryPeakResults peakResults : resultsList) {
        setup(peakResults);
        final FrameCounter counter = new FrameCounter();
        peakResults.forEach((PeakResultProcedure) peak -> {
            counter.advanceAndReset(peak.getFrame());
            final boolean isTrue = peak.getOrigValue() != 0;
            counter.increment(peak.getOrigX());
            final boolean isPositive;
            if (counter.getCount() > failures) {
                isPositive = false;
            } else {
                isPositive = accept(peak);
            }
            if (isPositive) {
                counter.reset();
            } else {
                counter.increment();
            }
            if (isTrue) {
                if (isPositive) {
                    s[TP]++;
                } else {
                    s[FN]++;
                }
            } else if (isPositive) {
                s[FP]++;
            } else {
                s[TN]++;
            }
        });
        end();
    }
    return new ClassificationResult(s[TP], s[FP], s[TN], s[FN]);
}

Example 23 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class HysteresisFilter method setup.

@Override
public void setup(MemoryPeakResults peakResults) {
    ok = new HashSet<>();
    // Create a set of candidates and valid peaks
    final MemoryPeakResults traceResults = new MemoryPeakResults();
    // Initialise peaks to check
    final LinkedList<PeakResult> candidates = new LinkedList<>();
    peakResults.forEach((PeakResultProcedure) result -> {
        switch(getStatus(result)) {
            case OK:
                ok.add(result);
                traceResults.add(result);
                break;
            case CANDIDATE:
                candidates.add(result);
                traceResults.add(result);
                break;
            default:
                break;
        }
    });
    if (candidates.isEmpty()) {
        // No candidates for tracing so just return
        return;
    }
    double distanceThreshold;
    switch(searchDistanceMode) {
        case 1:
            distanceThreshold = searchDistance / peakResults.getNmPerPixel();
            break;
        case 0:
        default:
            distanceThreshold = getSearchDistanceUsingCandidates(peakResults, candidates);
    }
    if (distanceThreshold <= 0) {
        return;
    }
    // This must be in frames
    int myTimeThreshold;
    if (timeThresholdMode == 1) {
        // time threshold is in Seconds.
        // Default to 1 frame if not calibrated.
        myTimeThreshold = 1;
        if (peakResults.hasCalibration()) {
            // Convert time threshold in seconds to frames
            final CalibrationReader cr = peakResults.getCalibrationReader();
            final double et = cr.getExposureTime();
            if (et > 0) {
                myTimeThreshold = (int) Math.round((this.timeThreshold / et));
            }
        }
    } else {
        // frames
        myTimeThreshold = (int) this.timeThreshold;
    }
    if (myTimeThreshold <= 0) {
        return;
    }
    // Trace through candidates
    final TraceManager tm = new TraceManager(traceResults);
    tm.setTraceMode(TraceMode.LATEST_FORERUNNER);
    tm.traceMolecules(distanceThreshold, myTimeThreshold);
    final Trace[] traces = tm.getTraces();
    for (final Trace trace : traces) {
        if (trace.size() > 1) {
            // Check if the trace touches a valid point
            boolean isOk = false;
            for (int i = 0; i < trace.size(); i++) {
                if (ok.contains(trace.get(i))) {
                    isOk = true;
                    break;
                }
            }
            // Add the entire trace to the OK points
            if (isOk) {
                for (int i = 0; i < trace.size(); i++) {
                    ok.add(trace.get(i));
                }
            }
        }
    }
}

Example 24 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class Filter method score.

/**
 * Filter the results and return the performance score. Allows benchmarking the filter by marking
 * the results as true or false.
 *
 * <p>Any input PeakResult with an original value that is not zero will be treated as a true
 * result, all other results are false. The filter is run and the results are marked as true
 * positive, false negative and false positive.
 *
 * <p>The number of consecutive rejections are counted per frame. When the configured number of
 * failures is reached all remaining results for the frame are rejected. This assumes the results
 * are ordered by the frame.
 *
 * @param resultsList a list of results to analyse
 * @param failures the number of failures to allow per frame before all peaks are rejected
 * @return the score
 */
public ClassificationResult score(List<MemoryPeakResults> resultsList, final int failures) {
    final int[] s = new int[4];
    for (final MemoryPeakResults peakResults : resultsList) {
        setup(peakResults);
        final FrameCounter counter = new FrameCounter();
        peakResults.forEach((PeakResultProcedure) peak -> {
            counter.advanceAndReset(peak.getFrame());
            final boolean isTrue = peak.getOrigValue() != 0;
            final boolean isPositive;
            if (counter.getCount() > failures) {
                isPositive = false;
            } else {
                isPositive = accept(peak);
            }
            if (isPositive) {
                counter.reset();
            } else {
                counter.increment();
            }
            if (isTrue) {
                if (isPositive) {
                    s[TP]++;
                } else {
                    s[FN]++;
                }
            } else if (isPositive) {
                s[FP]++;
            } else {
                s[TN]++;
            }
        });
        end();
    }
    return new ClassificationResult(s[TP], s[FP], s[TN], s[FN]);
}

Example 25 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class PeakResultsReaderTest method writeMatchesRead.

// -=-=-=-=-
private static void writeMatchesRead(RandomSeed seed, boolean sequential, ResultsFileFormat fileFormat, boolean showDeviations, boolean showEndFrame, boolean showId, boolean showPrecision, boolean showCategory, boolean sort) {
    final UniformRandomProvider rg = RngUtils.create(seed.getSeed());
    final MemoryPeakResults out = createResults(rg, 200, showDeviations, showEndFrame, showId, showPrecision, showCategory);
    if (fileFormat == ResultsFileFormat.MALK) {
        final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
        cal.setDistanceUnit(DistanceUnit.NM);
        cal.setIntensityUnit(IntensityUnit.PHOTON);
        out.setCalibration(cal.getCalibration());
        out.setPsf(PsfHelper.create(PSFType.CUSTOM));
    }
    if (fileFormat == ResultsFileFormat.TSF) {
        final CalibrationWriter cal = new CalibrationWriter(out.getCalibration());
        // For now just support using the native float TSF datatype
        cal.setNmPerPixel((float) cal.getNmPerPixel());
        out.setCalibration(cal.getCalibration());
        // TSF converts the width parameters so make sure they are not zero
        out.forEach(new PeakResultProcedure() {

            @Override
            public void execute(PeakResult peakResult) {
                check(peakResult.getParameters());
                if (showDeviations) {
                    check(peakResult.getParameterDeviations());
                }
            }

            private void check(float[] parameters) {
                for (int i = 0; i < parameters.length; i++) {
                    if (parameters[i] == 0) {
                        parameters[i] = 0.1f;
                    }
                }
            }
        });
    }
    // System.out.println(out.getCalibration());
    // System.out.println(out.getPSF().toString());
    // 
    // System.out.println(TextFormat.shortDebugString(out.getCalibration()));
    // 
    // try
    // {
    // Printer printer = JsonFormat.printer()
    // .omittingInsignificantWhitespace()
    // //.includingDefaultValueFields()
    // ;
    // System.out.println(printer.print(out.getCalibration()));
    // System.out.println(printer.print(out.getPSF()));
    // }
    // catch (InvalidProtocolBufferException e)
    // {
    // // This shouldn't happen so throw it
    // }
    final String filename = createFile();
    writeFile(sequential, fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, filename);
    final MemoryPeakResults in = readFile(filename, false);
    checkEqual(fileFormat, showDeviations, showEndFrame, showId, showPrecision, showCategory, sort, out, in);
}