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

Example 11 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve 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 12 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve 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 13 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve 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 14 with MetadataRetrieve

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

the class FormatWriter method getPlaneCount.

/**
 * Retrieve the total number of planes in given series.
 */
protected int getPlaneCount(int series) {
    MetadataRetrieve r = getMetadataRetrieve();
    int z = r.getPixelsSizeZ(series).getValue().intValue();
    int t = r.getPixelsSizeT(series).getValue().intValue();
    int c = r.getPixelsSizeC(series).getValue().intValue();
    c /= r.getChannelSamplesPerPixel(series, 0).getValue().intValue();
    return z * c * t;
}

Example 15 with MetadataRetrieve

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

the class FormatWriter method seekToPlaneOffset.

/**
 * Seek to the given (x, y) coordinate of the image that starts at
 * the given offset.
 */
protected void seekToPlaneOffset(long baseOffset, int x, int y) throws IOException {
    out.seek(baseOffset);
    MetadataRetrieve r = getMetadataRetrieve();
    int samples = getSamplesPerPixel();
    int pixelType = FormatTools.pixelTypeFromString(r.getPixelsType(series).toString());
    int bpp = FormatTools.getBytesPerPixel(pixelType);
    if (interleaved)
        bpp *= samples;
    int sizeX = r.getPixelsSizeX(series).getValue().intValue();
    out.skipBytes(bpp * (y * sizeX + x));
}