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

Example 1 with AngleUnit

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

the class CalibrationReaderTest method canGetAngleConverter.

@Test
void canGetAngleConverter() {
    final Calibration.Builder builder = Calibration.newBuilder();
    final AngleCalibration.Builder psfBuilder = builder.getAngleCalibrationBuilder();
    psfBuilder.setAngleUnit(AngleUnit.RADIAN);
    final Calibration c = builder.build();
    final CalibrationReader reader = new CalibrationReader(c);
    final TypeConverter<AngleUnit> angleConverter = reader.getAngleConverter(AngleUnit.DEGREE);
    Assertions.assertEquals(angleConverter.from(), AngleUnit.RADIAN);
    Assertions.assertEquals(angleConverter.to(), AngleUnit.DEGREE);
    final TypeConverter<AngleUnit> angleConverter2 = CalibrationHelper.getAngleConverter(c, AngleUnit.DEGREE);
    Assertions.assertEquals(angleConverter2.from(), AngleUnit.RADIAN);
    Assertions.assertEquals(angleConverter2.to(), AngleUnit.DEGREE);
    Assertions.assertEquals(angleConverter.getFunction(), angleConverter2.getFunction());
}

Example 2 with AngleUnit

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

the class ConvertResults method showDialog.

private static boolean showDialog(MemoryPeakResults results) {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Convert the current units for the results");
    gd.addHelp(HelpUrls.getUrl("convert-results"));
    final CalibrationReader cr = CalibrationWriter.create(results.getCalibration());
    gd.addChoice("Distance_unit", SettingsManager.getDistanceUnitNames(), cr.getDistanceUnitValue());
    gd.addNumericField("Calibration (nm/px)", cr.getNmPerPixel(), 2);
    gd.addChoice("Intensity_unit", SettingsManager.getIntensityUnitNames(), cr.getIntensityUnitValue());
    gd.addNumericField("Gain (Count/photon)", cr.getCountPerPhoton(), 2);
    gd.addChoice("Angle_unit", SettingsManager.getAngleUnitNames(), cr.getAngleUnitValue());
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    final CalibrationWriter cw = results.getCalibrationWriterSafe();
    final DistanceUnit distanceUnit = SettingsManager.getDistanceUnitValues()[gd.getNextChoiceIndex()];
    cw.setNmPerPixel(Math.abs(gd.getNextNumber()));
    final IntensityUnit intensityUnit = SettingsManager.getIntensityUnitValues()[gd.getNextChoiceIndex()];
    cw.setCountPerPhoton(Math.abs(gd.getNextNumber()));
    final AngleUnit angleUnit = SettingsManager.getAngleUnitValues()[gd.getNextChoiceIndex()];
    // Don't set the calibration with bad values
    if (distanceUnit.getNumber() > 0 && !(cw.getNmPerPixel() > 0)) {
        IJ.error(TITLE, "Require positive nm/pixel for conversion");
        return false;
    }
    if (intensityUnit.getNumber() > 0 && !(cw.getCountPerPhoton() > 0)) {
        IJ.error(TITLE, "Require positive Count/photon for conversion");
        return false;
    }
    final Calibration newCalibration = cw.getCalibration();
    results.setCalibration(newCalibration);
    if (!results.convertToUnits(distanceUnit, intensityUnit, angleUnit)) {
        IJ.error(TITLE, "Conversion failed");
        return false;
    }
    return true;
}

Example 3 with AngleUnit

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

the class AngleUnitTest method check.

private static void check(ExpectedUnit<AngleUnit>... expectedUnits) {
    final int n = expectedUnits.length;
    TypeConverter<AngleUnit> conv;
    for (int i = 0; i < n; i++) {
        final AngleUnit u1 = expectedUnits[i].unit;
        final double v1 = expectedUnits[i].value;
        for (int j = 0; j < n; j++) {
            final AngleUnit u2 = expectedUnits[j].unit;
            conv = UnitConverterUtils.createConverter(u1, u2);
            final double o = conv.convert(v1);
            Assertions.assertEquals(expectedUnits[j].value, o, 1e-5, () -> u1 + " to " + u2);
        }
    }
}

Example 4 with AngleUnit

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

the class CalibrationWriterTest method canWrite.

private static void canWrite(UniformRandomProvider rng) {
    final double qe = rng.nextDouble();
    final double bias = 1 + rng.nextDouble();
    final double exposureTime = 1 + rng.nextDouble();
    final double gain = 1 + rng.nextDouble();
    final double nmPerPixel = 1 + rng.nextDouble();
    final double readNoise = 1 + rng.nextDouble();
    final AngleUnit angleUnit = AngleUnit.values()[rng.nextInt(AngleUnit.values().length - 1)];
    final CameraType cameraType = CameraType.values()[rng.nextInt(CameraType.values().length - 1)];
    final DistanceUnit distanceUnit = DistanceUnit.values()[rng.nextInt(DistanceUnit.values().length - 1)];
    final IntensityUnit intensityUnit = IntensityUnit.values()[rng.nextInt(IntensityUnit.values().length - 1)];
    final CalibrationWriter writer = new CalibrationWriter();
    Assertions.assertEquals(writer.getQuantumEfficiency(), 0);
    Assertions.assertEquals(writer.getBias(), 0);
    Assertions.assertEquals(writer.getExposureTime(), 0);
    Assertions.assertEquals(writer.getCountPerPhoton(), 0);
    Assertions.assertEquals(writer.getNmPerPixel(), 0);
    Assertions.assertEquals(writer.getReadNoise(), 0);
    Assertions.assertFalse(writer.hasQuantumEfficiency());
    Assertions.assertFalse(writer.hasBias());
    Assertions.assertFalse(writer.hasExposureTime());
    Assertions.assertFalse(writer.hasCountPerPhoton());
    Assertions.assertFalse(writer.hasNmPerPixel());
    Assertions.assertFalse(writer.hasReadNoise());
    Assertions.assertEquals(writer.getAngleUnit(), AngleUnit.ANGLE_UNIT_NA);
    Assertions.assertEquals(writer.getCameraType(), CameraType.CAMERA_TYPE_NA);
    Assertions.assertEquals(writer.getDistanceUnit(), DistanceUnit.DISTANCE_UNIT_NA);
    Assertions.assertEquals(writer.getIntensityUnit(), IntensityUnit.INTENSITY_UNIT_NA);
    writer.setQuantumEfficiency(qe);
    writer.setBias(bias);
    writer.setExposureTime(exposureTime);
    writer.setCountPerPhoton(gain);
    writer.setNmPerPixel(nmPerPixel);
    writer.setReadNoise(readNoise);
    writer.setAngleUnit(angleUnit);
    writer.setCameraType(cameraType);
    writer.setDistanceUnit(distanceUnit);
    writer.setIntensityUnit(intensityUnit);
    Assertions.assertEquals(writer.getQuantumEfficiency(), qe);
    Assertions.assertEquals(writer.getBias(), bias);
    Assertions.assertEquals(writer.getExposureTime(), exposureTime);
    Assertions.assertEquals(writer.getCountPerPhoton(), gain);
    Assertions.assertEquals(writer.getNmPerPixel(), nmPerPixel);
    Assertions.assertEquals(writer.getReadNoise(), readNoise);
    Assertions.assertTrue(writer.hasQuantumEfficiency());
    Assertions.assertTrue(writer.hasBias());
    Assertions.assertTrue(writer.hasExposureTime());
    Assertions.assertTrue(writer.hasCountPerPhoton());
    Assertions.assertTrue(writer.hasNmPerPixel());
    Assertions.assertTrue(writer.hasReadNoise());
    Assertions.assertEquals(writer.getAngleUnit(), angleUnit);
    Assertions.assertEquals(writer.getCameraType(), cameraType);
    Assertions.assertEquals(writer.getDistanceUnit(), distanceUnit);
    Assertions.assertEquals(writer.getIntensityUnit(), intensityUnit);
    final CalibrationReader reader = new CalibrationReader(writer.getCalibration());
    Assertions.assertEquals(reader.getQuantumEfficiency(), qe);
    Assertions.assertEquals(reader.getBias(), bias);
    Assertions.assertEquals(reader.getExposureTime(), exposureTime);
    Assertions.assertEquals(reader.getCountPerPhoton(), gain);
    Assertions.assertEquals(reader.getNmPerPixel(), nmPerPixel);
    Assertions.assertEquals(reader.getReadNoise(), readNoise);
    Assertions.assertTrue(reader.hasQuantumEfficiency());
    Assertions.assertTrue(reader.hasBias());
    Assertions.assertTrue(reader.hasExposureTime());
    Assertions.assertTrue(reader.hasCountPerPhoton());
    Assertions.assertTrue(reader.hasNmPerPixel());
    Assertions.assertTrue(reader.hasReadNoise());
    Assertions.assertEquals(reader.getAngleUnit(), angleUnit);
    Assertions.assertEquals(reader.getCameraType(), cameraType);
    Assertions.assertEquals(reader.getDistanceUnit(), distanceUnit);
    Assertions.assertEquals(reader.getIntensityUnit(), intensityUnit);
}