Examples with MetadataRetrieve loci.formats.meta.MetadataRetrieve used on opensource projects

Example 41 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class LociFunctions method getPlaneTimingDeltaT.

public void getPlaneTimingDeltaT(Double[] deltaT, Double no) {
    int imageIndex = r.getSeries();
    int planeIndex = getPlaneIndex(r, no.intValue());
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Double val = Double.NaN;
    if (planeIndex >= 0) {
        Time valTime = retrieve.getPlaneDeltaT(imageIndex, planeIndex);
        if (valTime != null) {
            val = valTime.value(UNITS.SECOND).doubleValue();
        }
    }
    deltaT[0] = val;
}

Example 42 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class LociFunctions method getPixelsPhysicalSizeZ.

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

Example 43 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class LociFunctions method getPlanePositionY.

public void getPlanePositionY(Double[] positionY, 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.getPlanePositionY(imageIndex, planeIndex);
    }
    if (val == null) {
        val = new Length(Double.NaN, UNITS.REFERENCEFRAME);
    }
    positionY[0] = val == null ? Double.NaN : val.value(UNITS.REFERENCEFRAME).doubleValue();
}

Example 44 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class LociFunctions method getPlaneIndex.

// -- Utility methods --
/**
 * Finds the Plane index corresponding to the given image plane number.
 */
private static int getPlaneIndex(IFormatReader r, int no) {
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    int imageIndex = r.getSeries();
    int planeCount = retrieve.getPlaneCount(imageIndex);
    int[] zct = r.getZCTCoords(no);
    for (int i = 0; i < planeCount; i++) {
        Integer theC = retrieve.getPlaneTheC(imageIndex, i).getValue();
        Integer theT = retrieve.getPlaneTheT(imageIndex, i).getValue();
        Integer theZ = retrieve.getPlaneTheZ(imageIndex, i).getValue();
        if (zct[0] == theZ.intValue() && zct[1] == theC.intValue() && zct[2] == theT.intValue()) {
            return i;
        }
    }
    return -1;
}

Example 45 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class LociFunctions method getPlaneTimingExposureTime.

public void getPlaneTimingExposureTime(Double[] exposureTime, Double no) {
    int imageIndex = r.getSeries();
    int planeIndex = getPlaneIndex(r, no.intValue());
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Double val = null;
    if (planeIndex >= 0) {
        Time valTime = retrieve.getPlaneExposureTime(imageIndex, planeIndex);
        if (valTime != null) {
            val = valTime.value(UNITS.SECOND).doubleValue();
        }
    }
    exposureTime[0] = val == null ? new Double(Double.NaN) : val;
}