Examples with Length ome.units.quantity.Length used on opensource projects

Example 61 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class LociFunctions method getPixelsPhysicalSizeY.

public void getPixelsPhysicalSizeY(Double[] sizeY) {
    int imageIndex = r.getSeries();
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Length y = retrieve.getPixelsPhysicalSizeY(imageIndex);
    if (y != null) {
        sizeY[0] = y.value(UNITS.MICROMETER).doubleValue();
    }
    if (sizeY[0] == null)
        sizeY[0] = new Double(Double.NaN);
}

Example 62 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class LociFunctions method getPlanePositionZ.

public void getPlanePositionZ(Double[] positionZ, Double no) {
    int imageIndex = r.getSeries();
    int planeIndex = getPlaneIndex(r, no.intValue());
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Length val = null;
    if (planeIndex >= 0) {
        val = retrieve.getPlanePositionZ(imageIndex, planeIndex);
    }
    if (val == null) {
        val = new Length(Double.NaN, UNITS.REFERENCEFRAME);
    }
    positionZ[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue();
}

Example 63 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class LociFunctions method getPlanePositionX.

public void getPlanePositionX(Double[] positionX, Double no) {
    int imageIndex = r.getSeries();
    int planeIndex = getPlaneIndex(r, no.intValue());
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Length val = null;
    if (planeIndex >= 0) {
        val = retrieve.getPlanePositionX(imageIndex, planeIndex);
    }
    positionX[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue();
}

Example 64 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class FormatReaderTest method testEmissionWavelengths.

@Test(groups = { "all", "fast", "automated" })
public void testEmissionWavelengths() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "EmissionWavelengths";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int c = 0; c < config.getChannelCount(); c++) {
            Length realWavelength = retrieve.getChannelEmissionWavelength(i, c);
            Length expectedWavelength = config.getEmissionWavelength(c);
            if (realWavelength == null && expectedWavelength == null) {
                continue;
            }
            if (!isAlmostEqual(expectedWavelength, realWavelength)) {
                result(testName, false, "Series " + i + " channel " + c + " (expected " + expectedWavelength + ", actual " + realWavelength + ")");
            }
        }
    }
    result(testName, true);
}

Example 65 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class FormatReaderTest method testPhysicalSizeX.

@Test(groups = { "all", "fast", "automated" })
public void testPhysicalSizeX() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "PhysicalSizeX";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        Length expectedSize = config.getPhysicalSizeX();
        Length realSize = retrieve.getPixelsPhysicalSizeX(i);
        if (!isAlmostEqual(realSize, expectedSize)) {
            result(testName, false, "Series " + i + " (expected " + expectedSize + ", actual " + realSize + ")");
        }
    }
    result(testName, true);
}