Examples with Calibration uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtos.Calibration used on opensource projects

Example 16 with Calibration

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

the class CalibrationReaderTest method canGetIntensityConverter.

@Test
void canGetIntensityConverter() {
    final Calibration.Builder builder = Calibration.newBuilder();
    final IntensityCalibration.Builder intensityBuilder = builder.getIntensityCalibrationBuilder();
    intensityBuilder.setIntensityUnit(IntensityUnit.PHOTON);
    intensityBuilder.setCountPerPhoton(gain);
    final Calibration c = builder.build();
    final CalibrationReader reader = new CalibrationReader(c);
    final TypeConverter<IntensityUnit> intensityConverter = reader.getIntensityConverter(IntensityUnit.COUNT);
    Assertions.assertEquals(intensityConverter.from(), IntensityUnit.PHOTON);
    Assertions.assertEquals(intensityConverter.to(), IntensityUnit.COUNT);
    final TypeConverter<IntensityUnit> intensityConverter2 = CalibrationHelper.getIntensityConverter(c, IntensityUnit.COUNT);
    Assertions.assertEquals(intensityConverter2.from(), IntensityUnit.PHOTON);
    Assertions.assertEquals(intensityConverter2.to(), IntensityUnit.COUNT);
    Assertions.assertEquals(intensityConverter.getFunction(), intensityConverter2.getFunction());
}

Example 17 with Calibration

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

the class PeakResultsReaderTest method checkEqual.

private static void checkEqual(ResultsFileFormat fileFormat, boolean showDeviations, boolean showEndFrame, boolean showId, boolean showPrecision, boolean showCategory, boolean sort, MemoryPeakResults expectedResults, MemoryPeakResults actualResults) {
    Assertions.assertNotNull(actualResults, "Input results are null");
    Assertions.assertEquals(expectedResults.size(), actualResults.size(), "Size differ");
    final PeakResult[] expected = expectedResults.toArray();
    final PeakResult[] actual = actualResults.toArray();
    if (sort) {
        // Results should be sorted by time
        Arrays.sort(expected, (o1, o2) -> o1.getFrame() - o2.getFrame());
    }
    // TSF requires the bias be subtracted
    // double bias = expectedResults.getCalibration().getBias();
    final DoubleDoubleBiPredicate deltaD = TestHelper.doublesIsCloseTo(1e-5, 0);
    final FloatFloatBiPredicate deltaF = TestHelper.floatsIsCloseTo(1e-5, 0);
    for (int i = 0; i < actualResults.size(); i++) {
        final PeakResult p1 = expected[i];
        final PeakResult p2 = actual[i];
        final ObjectArrayFormatSupplier msg = new ObjectArrayFormatSupplier("%s @ [" + i + "]", 1);
        Assertions.assertEquals(p1.getFrame(), p2.getFrame(), msg.set(0, "Peak"));
        if (fileFormat == ResultsFileFormat.MALK) {
            TestAssertions.assertTest(p1.getXPosition(), p2.getXPosition(), deltaF, msg.set(0, "X"));
            TestAssertions.assertTest(p1.getYPosition(), p2.getYPosition(), deltaF, msg.set(0, "Y"));
            TestAssertions.assertTest(p1.getIntensity(), p2.getIntensity(), deltaF, msg.set(0, "Intensity"));
            continue;
        }
        Assertions.assertEquals(p1.getOrigX(), p2.getOrigX(), msg.set(0, "Orig X"));
        Assertions.assertEquals(p1.getOrigY(), p2.getOrigY(), msg.set(0, "Orig Y"));
        Assertions.assertNotNull(p2.getParameters(), msg.set(0, "Params is null"));
        if (showEndFrame) {
            Assertions.assertEquals(p1.getEndFrame(), p2.getEndFrame(), msg.set(0, "End frame"));
        }
        if (showId) {
            Assertions.assertEquals(p1.getId(), p2.getId(), msg.set(0, "ID"));
        }
        if (showDeviations) {
            Assertions.assertNotNull(p2.getParameterDeviations(), msg.set(0, "Deviations"));
        }
        if (showCategory) {
            Assertions.assertEquals(p1.getCategory(), p2.getCategory(), msg.set(0, "Category"));
        }
        // Binary should be exact for float numbers
        if (fileFormat == ResultsFileFormat.BINARY) {
            Assertions.assertEquals(p1.getOrigValue(), p2.getOrigValue(), msg.set(0, "Orig value"));
            Assertions.assertEquals(p1.getError(), p2.getError(), msg.set(0, "Error"));
            Assertions.assertEquals(p1.getNoise(), p2.getNoise(), msg.set(0, "Noise"));
            Assertions.assertEquals(p1.getMeanIntensity(), p2.getMeanIntensity(), msg.set(0, "Mean intensity"));
            Assertions.assertArrayEquals(p1.getParameters(), p2.getParameters(), msg.set(0, "Params"));
            if (showDeviations) {
                Assertions.assertArrayEquals(p1.getParameterDeviations(), p2.getParameterDeviations(), msg.set(0, "Params StdDev"));
            }
            if (showPrecision) {
                Assertions.assertEquals(p1.getPrecision(), p2.getPrecision(), msg.set(0, "Precision"));
            }
            continue;
        }
        // Otherwise have an error
        TestAssertions.assertTest(p1.getOrigValue(), p2.getOrigValue(), deltaF, msg.set(0, "Orig value"));
        TestAssertions.assertTest(p1.getError(), p2.getError(), deltaD, msg.set(0, "Error"));
        TestAssertions.assertTest(p1.getNoise(), p2.getNoise(), deltaF, msg.set(0, "Noise"));
        TestAssertions.assertTest(p1.getMeanIntensity(), p2.getMeanIntensity(), deltaF, msg.set(0, "Mean intensity"));
        TestAssertions.assertArrayTest(p1.getParameters(), p2.getParameters(), deltaF, msg.set(0, "Params"));
        if (showDeviations) {
            TestAssertions.assertArrayTest(p1.getParameterDeviations(), p2.getParameterDeviations(), deltaF, msg.set(0, "Params StdDev"));
        }
        if (showPrecision) {
            // Handle NaN precisions
            final double pa = p1.getPrecision();
            final double pb = p2.getPrecision();
            if (!Double.isNaN(pa) || !Double.isNaN(pb)) {
                TestAssertions.assertTest(p1.getPrecision(), p2.getPrecision(), deltaD, msg.set(0, "Precision"));
            }
        }
    }
    // Check the header information
    Assertions.assertEquals(expectedResults.getName(), actualResults.getName(), "Name");
    Assertions.assertEquals(expectedResults.getConfiguration(), actualResults.getConfiguration(), "Configuration");
    final Rectangle r1 = expectedResults.getBounds();
    final Rectangle r2 = actualResults.getBounds();
    if (r1 != null) {
        Assertions.assertNotNull(r2, "Bounds");
        Assertions.assertEquals(r1.x, r2.x, "Bounds x");
        Assertions.assertEquals(r1.y, r2.y, "Bounds y");
        Assertions.assertEquals(r1.width, r2.width, "Bounds width");
        Assertions.assertEquals(r1.height, r2.height, "Bounds height");
    } else {
        Assertions.assertNull(r2, "Bounds");
    }
    final Calibration c1 = expectedResults.getCalibration();
    final Calibration c2 = actualResults.getCalibration();
    if (c1 != null) {
        Assertions.assertNotNull(c2, "Calibration");
        // Be lenient and allow no TimeUnit to match TimeUnit.FRAME
        boolean ok = c1.equals(c2);
        if (!ok && new CalibrationReader(c1).getTimeUnitValue() == TimeUnit.TIME_UNIT_NA_VALUE) {
            switch(fileFormat) {
                case BINARY:
                case MALK:
                case TEXT:
                case TSF:
                    final CalibrationWriter writer = new CalibrationWriter(c1);
                    writer.setTimeUnit(TimeUnit.FRAME);
                    ok = writer.getCalibration().equals(c2);
                    break;
                default:
                    // Do not assume frames for other file formats
                    break;
            }
        }
        Assertions.assertTrue(ok, "Calibration");
    } else {
        Assertions.assertNull(c2, "Calibration");
    }
    final PSF p1 = expectedResults.getPsf();
    final PSF p2 = actualResults.getPsf();
    if (p1 != null) {
        Assertions.assertNotNull(p2, "PSF");
        Assertions.assertTrue(p1.equals(p2), "PSF");
    } else {
        Assertions.assertNull(p2, "PSF");
    }
}