Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 51 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ImporterTest method defaultBehaviorTester.

// ******** specific testers  **********************************
/**
 * tests BioFormats when directly calling BF.openImagePlus(path) (no options set)
 */
private void defaultBehaviorTester(int pixType, int x, int y, int z, int c, int t) {
    String path = constructFakeFilename("default", pixType, x, y, z, c, t, -1, false, -1, false, -1);
    ImagePlus[] imps = null;
    try {
        imps = BF.openImagePlus(path);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    xyzctTest(imp, x, y, z, c, t);
}

Example 52 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class Simple_Read method run.

public void run(String arg) {
    OpenDialog od = new OpenDialog("Open Image File...", arg);
    String dir = od.getDirectory();
    String name = od.getFileName();
    String id = dir + name;
    try {
        ImagePlus[] imps = BF.openImagePlus(id);
        for (ImagePlus imp : imps) imp.show();
    } catch (FormatException exc) {
        IJ.error("Sorry, an error occurred: " + exc.getMessage());
    } catch (IOException exc) {
        IJ.error("Sorry, an error occurred: " + exc.getMessage());
    }
}

Example 53 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ROIHandler method readFromOverlays.

/**
 * Returns rois if any from the overlay.
 * @return See above
 */
public static Roi[] readFromOverlays() {
    ImagePlus image = IJ.getImage();
    Overlay overlay = image.getOverlay();
    if (overlay == null)
        return null;
    return overlay.toArray();
}

Example 54 with ImagePlus

use of ij.ImagePlus 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 55 with ImagePlus

use of ij.ImagePlus 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);
    }
}