Examples with ImageProcessorReader loci.plugins.util.ImageProcessorReader used on opensource projects

Example 16 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class ImagePlusReader method readProcessors.

/**
 * HACK: This method mainly exists to prompt the user for a missing
 * LuraWave license code, in the case of LWF-compressed Flex.
 *
 * @see ImportProcess#setId()
 */
private ImageProcessor[] readProcessors(ImportProcess process, int no, Region r, boolean thumbnail) throws FormatException, IOException {
    final ImageProcessorReader reader = process.getReader();
    final ImporterOptions options = process.getOptions();
    boolean first = true;
    for (int i = 0; i < LuraWave.MAX_TRIES; i++) {
        String code = LuraWave.initLicenseCode();
        try {
            if (thumbnail) {
                return reader.openThumbProcessors(no);
            }
            return reader.openProcessors(no, r.x, r.y, r.width, r.height);
        } catch (FormatException exc) {
            if (options.isQuiet() || options.isWindowless())
                throw exc;
            if (!LuraWave.isLicenseCodeException(exc))
                throw exc;
            // prompt user for LuraWave license code
            code = LuraWave.promptLicenseCode(code, first);
            if (code == null)
                throw exc;
            if (first)
                first = false;
        }
    }
    throw new FormatException(LuraWave.TOO_MANY_TRIES);
}

Example 17 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class ImagePlusReader method readImages.

private List<ImagePlus> readImages(boolean thumbnail) throws FormatException, IOException {
    final ImporterOptions options = process.getOptions();
    final ImageProcessorReader reader = process.getReader();
    List<ImagePlus> imps = new ArrayList<ImagePlus>();
    // beginning timing
    startTiming();
    // read in each image series
    for (int s = 0; s < reader.getSeriesCount(); s++) {
        if (!options.isSeriesOn(s))
            continue;
        final ImagePlus imp = readImage(s, thumbnail);
        imps.add(imp);
    }
    // concatenate compatible images
    imps = concatenate(imps);
    // colorize images, as appropriate
    imps = applyColors(imps);
    // split dimensions, as appropriate
    imps = splitDims(imps);
    // when all image windows are closed, the Bio-Formats reader is closed
    if (options.isVirtual()) {
        process.getVirtualReader().setRefCount(imps.size());
    }
    // end timing
    finishTiming();
    return imps;
}

Example 18 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class RangeDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    ImageProcessorReader r = process.getReader();
    int seriesCount = process.getSeriesCount();
    // construct dialog
    GenericDialog gd = new GenericDialog("Bio-Formats Range Options");
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        r.setSeries(s);
        gd.addMessage(process.getSeriesLabel(s).replaceAll("_", " "));
        String suffix = seriesCount > 1 ? "_" + (s + 1) : "";
        // if (r.isOrderCertain()) {
        if (r.getEffectiveSizeC() > 1) {
            gd.addNumericField("C_Begin" + suffix, process.getCBegin(s) + 1, 0);
            gd.addNumericField("C_End" + suffix, process.getCEnd(s) + 1, 0);
            gd.addNumericField("C_Step" + suffix, process.getCStep(s), 0);
        }
        if (r.getSizeZ() > 1) {
            gd.addNumericField("Z_Begin" + suffix, process.getZBegin(s) + 1, 0);
            gd.addNumericField("Z_End" + suffix, process.getZEnd(s) + 1, 0);
            gd.addNumericField("Z_Step" + suffix, process.getZStep(s), 0);
        }
        if (r.getSizeT() > 1) {
            gd.addNumericField("T_Begin" + suffix, process.getTBegin(s) + 1, 0);
            gd.addNumericField("T_End" + suffix, process.getTEnd(s) + 1, 0);
            gd.addNumericField("T_Step" + suffix, process.getTStep(s), 0);
        }
    // }
    // else {
    // gd.addNumericField("Begin" + suffix, process.getCBegin(s) + 1, 0);
    // gd.addNumericField("End" + suffix, process.getCEnd(s) + 1, 0);
    // gd.addNumericField("Step" + suffix, process.getCStep(s), 0);
    // }
    }
    WindowTools.addScrollBars(gd);
    return gd;
}

Example 19 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class RangeDialog method needPrompt.

// -- ImporterDialog methods --
@Override
protected boolean needPrompt() {
    if (process.isWindowless() || !options.isSpecifyRanges())
        return false;
    ImageProcessorReader r = process.getReader();
    int seriesCount = process.getSeriesCount();
    int currentSeries = r.getSeries();
    for (int s = 0; s < seriesCount; s++) {
        r.setSeries(s);
        if (options.isSeriesOn(s) && r.getImageCount() > 1) {
            r.setSeries(currentSeries);
            return true;
        }
    }
    r.setSeries(currentSeries);
    return false;
}

Example 20 with ImageProcessorReader

use of loci.plugins.util.ImageProcessorReader in project bioformats by openmicroscopy.

the class RangeDialog method harvestResults.

@Override
protected boolean harvestResults(GenericDialog gd) {
    ImageProcessorReader r = process.getReader();
    int seriesCount = process.getSeriesCount();
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        r.setSeries(s);
        int sizeC = r.getEffectiveSizeC();
        int sizeZ = r.getSizeZ();
        int sizeT = r.getSizeT();
        boolean certain = r.isOrderCertain();
        int cBegin = process.getCBegin(s);
        int cEnd = process.getCEnd(s);
        int cStep = process.getCStep(s);
        int zBegin = process.getZBegin(s);
        int zEnd = process.getZEnd(s);
        int zStep = process.getZStep(s);
        int tBegin = process.getTBegin(s);
        int tEnd = process.getTEnd(s);
        int tStep = process.getTStep(s);
        // if (certain) {
        if (r.getEffectiveSizeC() > 1) {
            cBegin = (int) gd.getNextNumber() - 1;
            cEnd = (int) gd.getNextNumber() - 1;
            cStep = (int) gd.getNextNumber();
        }
        if (r.getSizeZ() > 1) {
            zBegin = (int) gd.getNextNumber() - 1;
            zEnd = (int) gd.getNextNumber() - 1;
            zStep = (int) gd.getNextNumber();
        }
        if (r.getSizeT() > 1) {
            tBegin = (int) gd.getNextNumber() - 1;
            tEnd = (int) gd.getNextNumber() - 1;
            tStep = (int) gd.getNextNumber();
        }
        // }
        // else {
        // cBegin = (int) gd.getNextNumber() - 1;
        // cEnd = (int) gd.getNextNumber() - 1;
        // cStep = (int) gd.getNextNumber();
        // }
        int maxC = certain ? sizeC : r.getImageCount();
        if (cBegin < 0)
            cBegin = 0;
        if (cBegin >= maxC)
            cBegin = maxC - 1;
        if (cEnd < cBegin)
            cEnd = cBegin;
        if (cEnd >= maxC)
            cEnd = maxC - 1;
        if (cStep < 1)
            cStep = 1;
        if (zBegin < 0)
            zBegin = 0;
        if (zBegin >= sizeZ)
            zBegin = sizeZ - 1;
        if (zEnd < zBegin)
            zEnd = zBegin;
        if (zEnd >= sizeZ)
            zEnd = sizeZ - 1;
        if (zStep < 1)
            zStep = 1;
        if (tBegin < 0)
            tBegin = 0;
        if (tBegin >= sizeT)
            tBegin = sizeT - 1;
        if (tEnd < tBegin)
            tEnd = tBegin;
        if (tEnd >= sizeT)
            tEnd = sizeT - 1;
        if (tStep < 1)
            tStep = 1;
        options.setCBegin(s, cBegin);
        options.setCEnd(s, cEnd);
        options.setCStep(s, cStep);
        options.setZBegin(s, zBegin);
        options.setZEnd(s, zEnd);
        options.setZStep(s, zStep);
        options.setTBegin(s, tBegin);
        options.setTEnd(s, tEnd);
        options.setTStep(s, tStep);
    }
    return true;
}