Examples with DistanceUnit uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit used on opensource projects

Example 6 with DistanceUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit in project GDSC-SMLM by aherbert.

the class Fire method initialise.

/**
 * Initialise this instance with localisation results for the FIRE computation.
 *
 * @param results the results
 * @param results2 the second set of results (can be null)
 */
public void initialise(MemoryPeakResults results, MemoryPeakResults results2) {
    this.results = verify(results);
    this.results2 = verify(results2);
    if (this.results == null) {
        return;
    }
    nmPerUnit = 1;
    DistanceUnit unit = null;
    units = "unknown";
    final CalibrationReader cal = results.getCalibrationReader();
    if (cal != null) {
        try {
            nmPerUnit = cal.getDistanceConverter(DistanceUnit.NM).convert(1);
            units = UnitHelper.getShortName(DistanceUnit.NM);
            unit = DistanceUnit.NM;
        } catch (final ConversionException ex) {
            IJ.log(pluginTitle + " Warning: Ignoring invalid distance calibration for primary results");
        }
    } else {
        IJ.log(pluginTitle + " Warning: No calibration exists for primary results");
    }
    // Calibration must match between datasets
    if (this.results2 != null) {
        CalibrationReader cal2 = results.getCalibrationReader();
        if (unit == null) {
            if (cal2 != null) {
                IJ.log(pluginTitle + " Warning: Ignoring calibration for secondary results since no calibration" + " exists for primary results");
            }
        } else {
            // The calibration must match
            try {
                // Try to create a converter and check it is the same conversion
                if (cal2 != null && cal2.getDistanceConverter(DistanceUnit.NM).convert(1) != nmPerUnit) {
                    // Set to null to mark invalid
                    cal2 = null;
                }
            } catch (final ConversionException ex) {
                // Set to null to mark invalid
                cal2 = null;
            } finally {
                if (cal2 == null) {
                    this.results = null;
                    IJ.error(pluginTitle, "Error: Calibration between the two input datasets does not match");
                }
            }
        }
    }
    // Use the float data bounds. This prevents problems if the data is far from the origin.
    dataBounds = results.getDataBounds(null);
    if (this.results2 != null) {
        final Rectangle2D dataBounds2 = results.getDataBounds(null);
        dataBounds = dataBounds.createUnion(dataBounds2);
    }
}

Example 7 with DistanceUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit in project GDSC-SMLM by aherbert.

the class AbstractPeakResults method isCalibratedForPrecision.

/**
 * Checks if the results have a valid calibration to compute the localisation precision. This
 * requires the pixel size and camera gain, or alternatively the units to be in nm and photons,
 * and camera CCD type.
 *
 * @return true, if is calibrated for precision
 */
public boolean isCalibratedForPrecision() {
    if (calibration != null) {
        if (!calibrationReader.isCcdCamera()) {
            return false;
        }
        final DistanceUnit du = calibrationReader.getDistanceUnit();
        final IntensityUnit iu = calibrationReader.getIntensityUnit();
        if (du == DistanceUnit.NM && iu == IntensityUnit.PHOTON) {
            return true;
        }
        return isCalibrated();
    }
    return false;
}

Example 8 with DistanceUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit in project GDSC-SMLM by aherbert.

the class AbstractPeakResults method isCalibrated.

/**
 * Checks if the results have a basic calibration. This requires the pixel size and camera gain
 * with the distance and intensity units.
 *
 * @return true, if is calibrated
 */
public boolean isCalibrated() {
    if (calibration != null) {
        final DistanceUnit du = calibrationReader.getDistanceUnit();
        final IntensityUnit iu = calibrationReader.getIntensityUnit();
        // @formatter:off
        return (du != null && calibrationReader.getNmPerPixel() > 0) && (iu != null && calibrationReader.getCountPerPhoton() > 0);
    // @formatter:on
    }
    return false;
}

Example 9 with DistanceUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit in project GDSC-SMLM by aherbert.

the class TrackPopulationAnalysis method showInputDialog.

private boolean showInputDialog(List<MemoryPeakResults> combinedResults) {
    // Show a list box containing all the clustered results.
    // This should remember the last set of chosen items.
    final MultiDialog md = ResultsManager.createMultiDialog(TITLE, MemoryPeakResults::hasId);
    md.setSelected(settings.input);
    md.setHelpUrl(HelpUrls.getUrl("track-population-analysis"));
    md.showDialog();
    if (md.wasCancelled()) {
        return false;
    }
    final List<String> selected = md.getSelectedResults();
    if (selected.isEmpty()) {
        IJ.error(TITLE, "No results were selected");
        return false;
    }
    settings.input = selected;
    for (final String name : selected) {
        final MemoryPeakResults r = MemoryPeakResults.getResults(name);
        if (r != null) {
            combinedResults.add(r);
        }
    }
    // Check calibration exists for the first set of results
    if (combinedResults.isEmpty() || !checkCalibration(combinedResults.get(0))) {
        return false;
    }
    // Check the calibration is the same for the rest
    final CalibrationReader cal = combinedResults.get(0).getCalibrationReader();
    final double nmPerPixel = cal.getNmPerPixel();
    final double exposureTime = cal.getExposureTime();
    final DistanceUnit distanceUnit = cal.getDistanceUnit();
    for (int i = 1; i < combinedResults.size(); i++) {
        final MemoryPeakResults results = combinedResults.get(i);
        if (!results.hasCalibration() || results.getCalibrationReader().getExposureTime() != exposureTime || results.getNmPerPixel() != nmPerPixel || results.getDistanceUnit() != distanceUnit) {
            IJ.error(TITLE, "The exposure time, pixel pitch and distance unit must match across all the results");
            return false;
        }
    }
    return true;
}

Example 10 with DistanceUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit in project GDSC-SMLM by aherbert.

the class TranslateResults method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    final TranslateResultsSettings.Builder settings = SettingsManager.readTranslateResultsSettings(0).toBuilder();
    // Show a dialog allowing the results set to be filtered
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Select a dataset to translate");
    ResultsManager.addInput(gd, settings.getInputOption(), InputSource.MEMORY);
    gd.addNumericField("x", settings.getDx(), 3);
    gd.addNumericField("y", settings.getDy(), 3);
    gd.addNumericField("z", settings.getDz(), 3);
    gd.addChoice("Distance_unit", SettingsManager.getDistanceUnitNames(), settings.getDistanceUnitValue());
    gd.addHelp(HelpUrls.getUrl("translate-results"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.setInputOption(ResultsManager.getInputSource(gd));
    settings.setDx(gd.getNextNumber());
    settings.setDy(gd.getNextNumber());
    settings.setDz(gd.getNextNumber());
    settings.setDistanceUnitValue(gd.getNextChoiceIndex());
    SettingsManager.writeSettings(settings);
    final MemoryPeakResults results = ResultsManager.loadInputResults(settings.getInputOption(), false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    TypeConverter<DistanceUnit> converter;
    try {
        converter = results.getDistanceConverter(settings.getDistanceUnit());
    } catch (final DataException ex) {
        IJ.error(TITLE, "Unit conversion error: " + ex.getMessage());
        return;
    }
    final float x = (float) converter.convertBack(settings.getDx());
    final float y = (float) converter.convertBack(settings.getDy());
    final float z = (float) converter.convertBack(settings.getDz());
    // Reset the 2D bounds
    if (x != 0 || y != 0) {
        results.setBounds(null);
    }
    results.forEach((PeakResultProcedure) peakResult -> {
        final float[] params = peakResult.getParameters();
        params[PeakResult.X] += x;
        params[PeakResult.Y] += y;
        params[PeakResult.Z] += z;
    });
}