Examples with Calibrator loci.plugins.in.Calibrator used on opensource projects

Example 1 with Calibrator

use of loci.plugins.in.Calibrator in project bioformats by openmicroscopy.

the class LociFunctions method openThumbImage.

public void openThumbImage(String title, Double no) throws FormatException, IOException {
    ImporterOptions options = new ImporterOptions();
    options.setWindowless(true);
    options.setId(r.getCurrentFile());
    options.setCrop(true);
    options.setSpecifyRanges(true);
    options.setSeriesOn(r.getSeries(), true);
    int[] zct = r.getZCTCoords(no.intValue());
    options.setCBegin(r.getSeries(), zct[1]);
    options.setZBegin(r.getSeries(), zct[0]);
    options.setTBegin(r.getSeries(), zct[2]);
    options.setCEnd(r.getSeries(), zct[1]);
    options.setZEnd(r.getSeries(), zct[0]);
    options.setTEnd(r.getSeries(), zct[2]);
    ImportProcess process = new ImportProcess(options);
    process.execute();
    ImagePlusReader reader = new ImagePlusReader(process);
    final ImagePlus imp = reader.openThumbImagePlus()[0];
    Calibrator calibrator = new Calibrator(process);
    calibrator.applyCalibration(imp);
    process.getReader().close();
    imp.show();
}

Example 2 with Calibrator

use of loci.plugins.in.Calibrator in project bioformats by openmicroscopy.

the class LociFunctions method openSubImage.

public void openSubImage(String title, Double no, Double x, Double y, Double w, Double h) throws FormatException, IOException {
    ImporterOptions options = new ImporterOptions();
    options.setWindowless(true);
    options.setId(r.getCurrentFile());
    options.setCrop(true);
    options.setSpecifyRanges(true);
    options.setSeriesOn(r.getSeries(), true);
    int[] zct = r.getZCTCoords(no.intValue());
    options.setCBegin(r.getSeries(), zct[1]);
    options.setZBegin(r.getSeries(), zct[0]);
    options.setTBegin(r.getSeries(), zct[2]);
    options.setCEnd(r.getSeries(), zct[1]);
    options.setZEnd(r.getSeries(), zct[0]);
    options.setTEnd(r.getSeries(), zct[2]);
    Region region = new Region(x.intValue(), y.intValue(), w.intValue(), h.intValue());
    options.setCropRegion(r.getSeries(), region);
    ImportProcess process = new ImportProcess(options);
    process.execute();
    ImagePlusReader reader = new ImagePlusReader(process);
    final ImagePlus imp = reader.openImagePlus()[0];
    Calibrator calibrator = new Calibrator(process);
    calibrator.applyCalibration(imp);
    process.getReader().close();
    imp.show();
}