Examples with CompositeImage ij.CompositeImage used on opensource projects

Example 11 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class AutoscaleTest method setup.

/**
 * Reads the image and performs some initial tests.
 */
private ImagePlus setup(int pixelType, boolean autoscale, boolean crop, double calib, int sizeC) {
    final String pix = FormatTools.getPixelTypeString(pixelType);
    final String id = "autoscale&pixelType=" + pix + "&sizeX=" + WIDTH + "&sizeY=" + HEIGHT + "&sizeC=" + sizeC + ".fake";
    ImagePlus[] imps = null;
    try {
        final ImporterOptions options = new ImporterOptions();
        options.setId(id);
        options.setAutoscale(autoscale);
        options.setCrop(crop);
        if (crop)
            options.setCropRegion(0, CROP_REGION);
        imps = BF.openImagePlus(options);
    } catch (FormatException exc) {
        fail(exc.getMessage());
        LOGGER.debug("", exc);
    } catch (IOException exc) {
        fail(exc.getMessage());
        LOGGER.debug("", exc);
    }
    assertTrue(imps != null && imps.length == 1);
    final ImagePlus imp = imps[0];
    assertEquals(sizeC > 1, imp instanceof CompositeImage);
    // check calibration function
    final Calibration cal = imp.getCalibration();
    final int calFunction = cal.getFunction();
    if (calib == 0) {
        assertFalse(calFunction == Calibration.STRAIGHT_LINE);
    } else {
        assertTrue(calFunction == Calibration.STRAIGHT_LINE);
        double[] coeffs = cal.getCoefficients();
        assertTrue(coeffs.length >= 1);
        assertEquals(calib, coeffs[0], 0.0);
    }
    dump(pix, sizeC, autoscale, crop, imp);
    return imp;
}

Example 12 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method compositeSubcaseTester.

/**
 * tests BF's options.setColormode(composite) - alternate, later definition
 */
private void compositeSubcaseTester(int sizeC, boolean indexed) {
    int pixType = FormatTools.UINT8, sizeX = 60, sizeY = 30, sizeZ = 2, sizeT = 3, numSeries = 1, rgb = -1, lutLen = -1;
    boolean falseColor = false;
    String path = constructFakeFilename("colorComposite", pixType, sizeX, sizeY, sizeZ, sizeC, sizeT, numSeries, indexed, rgb, falseColor, lutLen);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE);
        options.setId(path);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    xyzctTest(imp, sizeX, sizeY, sizeZ, sizeC, sizeT);
    assertTrue(imp.isComposite());
    CompositeImage ci = (CompositeImage) imp;
    assertTrue(ci.hasCustomLuts());
    assertEquals(CompositeImage.COMPOSITE, ci.getMode());
    colorTests(ci, sizeC, DEFAULT_COLOR_ORDER);
    stackInZctOrderTest(imp, sizeZ, sizeC, sizeT, indexed, falseColor);
    pixelsTest(imp, pixType, indexed, falseColor);
}

Example 13 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method colorCompositeTester.

/**
 * tests BF's options.setColorMode(composite)
 */
private void colorCompositeTester(boolean virtual, int pixType, boolean indexed, int channels, int chanPerPlane, boolean falseColor, int numSeries) {
    int sizeX = 55, sizeY = 71, sizeZ = 3, sizeT = 4;
    // reportedly works in BF as long as numSeries*sizeC*3 <= 25
    String path = constructFakeFilename("colorComposite", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorCompositeTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE);
        options.setId(path);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    int lutLen = 3;
    int expectedSizeC = effectiveC(channels, chanPerPlane, lutLen, indexed, falseColor);
    xyzctTest(imp, sizeX, sizeY, sizeZ, expectedSizeC, sizeT);
    if ((expectedSizeC >= 2) && (expectedSizeC <= 7)) {
        assertTrue(imp.isComposite());
        CompositeImage ci = (CompositeImage) imp;
        assertTrue(ci.hasCustomLuts());
        assertEquals(CompositeImage.COMPOSITE, ci.getMode());
        colorTests(ci, expectedSizeC, DEFAULT_COLOR_ORDER);
    } else // expectedSizeC < 2 or > 7 - we should have gotten back a regular ImagePlus
    {
        assertFalse(imp.isComposite());
        imagePlusLutTest(imp, indexed, falseColor, DEFAULT_COLOR_ORDER[0]);
    }
    stackInCztOrderTest(imp, sizeZ, expectedSizeC, sizeT, indexed, falseColor);
// TODO : i've done no pixel testing
}

Example 14 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method getColorTable.

// note - the following code relies on setZctPosition() being called previously. Otherwise regular ImagePlus case
// won't work. In general this method not designed for general use but actually just for use by getPixelValue().
/**
 * gets the color table from any kind of ImagePlus (composite or not) - not for general use
 */
private LUT getColorTable(ImagePlus imp, int channel) {
    if (imp instanceof CompositeImage)
        return ((CompositeImage) imp).getChannelLut(channel + 1);
    // else a regular ImagePlus
    IndexColorModel icm = (IndexColorModel) imp.getProcessor().getColorModel();
    // TODO - maybe I can cast from IndexColorModel to LUT here - depends what IJ did.
    // otherwise make a LUT
    byte[] reds = new byte[256], greens = new byte[256], blues = new byte[256];
    icm.getReds(reds);
    icm.getGreens(greens);
    icm.getBlues(blues);
    return new LUT(reds, greens, blues);
}

Example 15 with CompositeImage

use of ij.CompositeImage in project bioformats by openmicroscopy.

the class ImporterTest method colorDefaultTester.

/**
 * tests BF's options.setColorMode(composite)
 */
private void colorDefaultTester(boolean virtual, int pixType, boolean indexed, int channels, int chanPerPlane, boolean falseColor, int numSeries, boolean wantLutDefined) {
    int sizeX = 55, sizeY = 71, sizeZ = 3, sizeT = 4;
    // reportedly works in BF as long as numSeries*sizeC*3 <= 25
    String path = constructFakeFilename("colorDefault", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorDefaultTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        options.setColorMode(ImporterOptions.COLOR_MODE_DEFAULT);
        if (indexed && wantLutDefined) {
            for (int s = 0; s < numSeries; s++) // set the first channel lut to pink to force COLOR mode as return
            options.setCustomColor(s, 0, Color.PINK);
        }
        options.setId(path);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    int lutLen = 3;
    int expectedSizeC = effectiveC(channels, chanPerPlane, lutLen, indexed, falseColor);
    xyzctTest(imp, sizeX, sizeY, sizeZ, expectedSizeC, sizeT);
    if ((expectedSizeC >= 2) && (expectedSizeC <= 7)) {
        assertTrue(imp.isComposite());
        CompositeImage ci = (CompositeImage) imp;
        assertEquals(chanPerPlane > 1, ci.hasCustomLuts());
        Color[] colorOrder;
        int expectedType;
        if (// TODO : apparently need another test here for channelFiller.isFilled() case so 1/1/indexed works
        chanPerPlane > 1) {
            expectedType = CompositeImage.COMPOSITE;
            colorOrder = DEFAULT_COLOR_ORDER;
        } else if (indexed && wantLutDefined) {
            // TODO - left working here. this case doesn't work yet.
            // have to figure how BF calcs hasChannelLut so I can exercise it here
            expectedType = CompositeImage.COLOR;
            colorOrder = new Color[] { Color.PINK, Color.WHITE, Color.WHITE, Color.WHITE, Color.WHITE, Color.WHITE, Color.WHITE, Color.WHITE };
        } else {
            expectedType = CompositeImage.GRAYSCALE;
            colorOrder = DEFAULT_COLOR_ORDER;
        }
        assertEquals(expectedType, ci.getMode());
        colorTests(ci, expectedSizeC, colorOrder);
    } else // expectedSizeC < 2 or > 7 - we should have gotten back a regular ImagePlus
    {
        assertFalse(imp.isComposite());
        imagePlusLutTest(imp, indexed, falseColor, DEFAULT_COLOR_ORDER[0]);
    }
    stackInCztOrderTest(imp, sizeZ, expectedSizeC, sizeT, indexed, falseColor);
// TODO : i've done no pixel testing
}