Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 46 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ImporterTest method colorCustomTester.

/**
 * tests BF's options.setColorMode(custom)
 */
private void colorCustomTester(boolean virtual, int pixType, boolean indexed, int channels, int chanPerPlane, boolean falseColor, int numSeries) {
    int sizeX = 55, sizeY = 71, sizeZ = 3, sizeT = 4;
    String path = constructFakeFilename("colorCustom", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorCustomTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        options.setColorMode(ImporterOptions.COLOR_MODE_CUSTOM);
        int maxChannels = (channels <= 7) ? channels : 7;
        for (int s = 0; s < numSeries; s++) for (int c = 0; c < maxChannels; c++) options.setCustomColor(s, c, CUSTOM_COLOR_ORDER[c]);
        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.COLOR, ci.getMode());
        colorTests(ci, expectedSizeC, CUSTOM_COLOR_ORDER);
    } else // expectedSizeC < 2 or > 7 - we should have gotten back a regular ImagePlus
    {
        assertFalse(imp.isComposite());
        imagePlusLutTest(imp, indexed, falseColor, CUSTOM_COLOR_ORDER[0]);
    }
    stackInCztOrderTest(imp, sizeZ, expectedSizeC, sizeT, indexed, falseColor);
// TODO : i've done no pixel testing
}

Example 47 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ImporterTest method testComboManyOptions.

@Test
public void testComboManyOptions() {
    // note - crop and setTStep both don't work with virtualStacks. No need to test virtual here.
    int pixType = FormatTools.UINT16, sizeX = 106, sizeY = 33, sizeZ = 3, sizeC = 5, sizeT = 7;
    int cropOriginX = 0, cropOriginY = 0, cropSizeX = 55, cropSizeY = 16, start = 1, stepBy = 2;
    // orig is ZCT : this is a deadly swap of all dims
    ChannelOrder swappedOrder = ChannelOrder.CTZ;
    // note - to reuse existing code it is necessary that the crop origin is (0,0)
    String path = constructFakeFilename("superCombo", pixType, sizeX, sizeY, sizeZ, sizeC, sizeT, 1, false, -1, false, -1);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setId(path);
        options.setSwapDimensions(true);
        options.setInputOrder(0, bfChanOrd(swappedOrder));
        options.setCrop(true);
        options.setCropRegion(0, new Region(cropOriginX, cropOriginY, cropSizeX, cropSizeY));
        options.setTStep(0, stepBy);
        options.setTBegin(0, start);
        options.setSplitFocalPlanes(true);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    // we split on Z but that dim was swapped with T
    impsCountTest(imps, sizeT);
    stackCtzSwappedAndCroppedTest(imps, cropSizeX, cropSizeY, sizeZ, sizeC, sizeT, start, stepBy);
}

Example 48 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ImporterTest method memorySpecifyRangeTester.

/**
 * tests BF's options.set?Begin(), options.set?End(), and options.set?Step()
 */
private void memorySpecifyRangeTester(int z, int c, int t, int zFrom, int zTo, int zBy, int cFrom, int cTo, int cBy, int tFrom, int tTo, int tBy) {
    int pixType = FormatTools.UINT8, x = 50, y = 5;
    String path = constructFakeFilename("range", pixType, x, y, z, c, t, -1, false, -1, false, -1);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setId(path);
        // z's
        if (zFrom != 0)
            options.setZBegin(0, zFrom);
        if (zTo != z - 1)
            options.setZEnd(0, zTo);
        if (zBy != 1)
            options.setZStep(0, zBy);
        // c's
        if (cFrom != 0)
            options.setCBegin(0, cFrom);
        if (cTo != c - 1)
            options.setCEnd(0, cTo);
        if (cBy != 1)
            options.setCStep(0, cBy);
        // t's
        if (tFrom != 0)
            options.setTBegin(0, tFrom);
        if (tTo != t - 1)
            options.setTEnd(0, tTo);
        if (tBy != 1)
            options.setTStep(0, tBy);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    // should have the data in one series
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    xyzctTest(imp, x, y, numInSeries(zFrom, zTo, zBy), numInSeries(cFrom, cTo, cBy), numInSeries(tFrom, tTo, tBy));
    // should be in correct order
    seriesInZctOrderTest(imp, false, false, zFrom, zTo, zBy, cFrom, cTo, cBy, tFrom, tTo, tBy);
}

Example 49 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ImporterTest method colorGrayscaleTester.

/**
 * tests BF's options.setColorMode(gray)
 */
private void colorGrayscaleTester(boolean virtual, int pixType, boolean indexed, int channels, int chanPerPlane, boolean falseColor, int numSeries) {
    int sizeX = 55, sizeY = 71, sizeZ = 3, sizeT = 4;
    String path = constructFakeFilename("colorGrayscale", pixType, sizeX, sizeY, sizeZ, channels, sizeT, numSeries, indexed, chanPerPlane, falseColor, -1);
    LOGGER.debug("colorGrayscaleTester: {}", path);
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setVirtual(virtual);
        options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE);
        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;
        assertFalse(ci.hasCustomLuts());
        assertEquals(CompositeImage.GRAYSCALE, 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 50 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class ImporterTest method memoryVirtualStackTester.

/**
 * tests BF's options.setVirtual()
 */
private void memoryVirtualStackTester(boolean desireVirtual) {
    int x = 604, y = 531, z = 7, c = 1, t = 1;
    String path = constructFakeFilename("vstack", FormatTools.UINT16, x, y, z, c, t, -1, false, -1, false, -1);
    // open stack
    ImagePlus[] imps = null;
    try {
        ImporterOptions options = new ImporterOptions();
        options.setAutoscale(false);
        options.setId(path);
        // user specified value here
        options.setVirtual(desireVirtual);
        imps = BF.openImagePlus(options);
    } catch (IOException e) {
        fail(e.getMessage());
    } catch (FormatException e) {
        fail(e.getMessage());
    }
    // test results
    impsCountTest(imps, 1);
    ImagePlus imp = imps[0];
    xyzctTest(imp, x, y, z, c, t);
    assertEquals(desireVirtual, imp.getStack().isVirtual());
}