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

Example 1 with ImporterOptions

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

the class LociFunctions method openImagePlus.

public void openImagePlus(String path) {
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setId(path);
        options.setSeriesOn(series, true);
        imps = BF.openImagePlus(options);
        for (ImagePlus imp : imps) imp.show();
    } catch (IOException exc) {
        IJ.handleException(exc);
    } catch (FormatException exc) {
        IJ.handleException(exc);
    }
}

Example 2 with ImporterOptions

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

the class LociFunctions method openThumbImagePlus.

public void openThumbImagePlus(String path) {
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setId(path);
        options.setSeriesOn(series, true);
        imps = BF.openThumbImagePlus(options);
        for (ImagePlus imp : imps) imp.show();
    } catch (IOException exc) {
        IJ.handleException(exc);
    } catch (FormatException exc) {
        IJ.handleException(exc);
    }
}

Example 3 with ImporterOptions

use of loci.plugins.in.ImporterOptions 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 4 with ImporterOptions

use of loci.plugins.in.ImporterOptions 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();
}

Example 5 with ImporterOptions

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

the class BF method openThumbImagePlus.

public static ImagePlus[] openThumbImagePlus(String path) throws FormatException, IOException {
    ImporterOptions options = new ImporterOptions();
    options.setId(path);
    return openThumbImagePlus(options);
}