Examples with BufferedImageReader loci.formats.gui.BufferedImageReader used on opensource projects

Example 1 with BufferedImageReader

use of loci.formats.gui.BufferedImageReader in project bioformats by openmicroscopy.

the class SeriesDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    final int seriesCount = process.getSeriesCount();
    // NB: Load thumbnails only when series count is modest.
    if (seriesCount < MAX_SERIES_THUMBS) {
        // construct thumbnail reader
        thumbReader = new BufferedImageReader(process.getReader());
        // set up the thumbnail panels
        p = new Panel[seriesCount];
        for (int i = 0; i < seriesCount; i++) {
            thumbReader.setSeries(i);
            // a little extra padding
            int sx = thumbReader.getThumbSizeX() + 10;
            int sy = thumbReader.getThumbSizeY();
            p[i] = new Panel();
            p[i].add(Box.createRigidArea(new Dimension(sx, sy)));
            if (options.isForceThumbnails()) {
                // load thumbnail immediately
                ThumbLoader.loadThumb(thumbReader, i, p[i], options.isQuiet());
            }
        }
    }
    GenericDialog gd = new GenericDialog("Bio-Formats Series Options");
    // NB: Provide individual checkboxes only when series count is manageable.
    if (seriesCount < MAX_SERIES_TOGGLES) {
        // NB: We need to add the checkboxes in groups, to prevent an
        // exception from being thrown if there are more than 512 series.
        // See also:
        // http://dev.loci.wisc.edu/trac/java/ticket/408 and
        // http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980
        final int nGroups = (seriesCount + MAX_COMPONENTS - 1) / MAX_COMPONENTS;
        int nextSeries = 0;
        for (int i = 0; i < nGroups; i++) {
            final int nRows = Math.min(MAX_COMPONENTS, seriesCount - nextSeries);
            final String[] labels = new String[nRows];
            final boolean[] defaultValues = new boolean[nRows];
            for (int row = 0; row < nRows; row++) {
                labels[row] = process.getSeriesLabel(nextSeries);
                defaultValues[row] = options.isSeriesOn(nextSeries);
                nextSeries++;
            }
            gd.addCheckboxGroup(nRows, 1, labels, defaultValues);
        }
        // extract checkboxes, for "Select All" and "Deselect All" functions
        boxes = WindowTools.getCheckboxes(gd).toArray(new Checkbox[0]);
        // rebuild dialog so that the thumbnails and checkboxes line up correctly
        rebuildDialog(gd, nGroups);
    } else {
        // too many series; display a simple text field for specifying series
        gd.addMessage("Please specify the image series you wish to import.\n" + "Use commas to list multiple series. You can also use\n" + "a dash to represent a range of series. For example,\n" + "to import series 1, 3, 4, 5, 7, 8, 9, 12, 15 & 16,\n" + "you could write: 1, 3-5, 7-9, 12, 15-16\n \n" + "There are " + seriesCount + " total series.");
        gd.addStringField("Series_list: ", "1");
    }
    return gd;
}

Example 2 with BufferedImageReader

use of loci.formats.gui.BufferedImageReader in project bioformats by openmicroscopy.

the class FormatReaderTest method setupReader.

// -- Helper methods --
/**
 * Sets up the current IFormatReader.
 */
private void setupReader() {
    // Remove external SlideBook6Reader class for testing purposes
    ImageReader ir = new ImageReader();
    reader = new BufferedImageReader(new FileStitcher(new Memoizer(ir, Memoizer.DEFAULT_MINIMUM_ELAPSED, new File(""))));
    reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.NO_OVERLAYS));
    reader.setNormalized(true);
    reader.setOriginalMetadataPopulated(false);
    reader.setMetadataFiltered(true);
    MetadataStore store = null;
    try {
        store = omexmlService.createOMEXMLMetadata();
    } catch (ServiceException e) {
        LOGGER.warn("Could not parse OME-XML", e);
    }
    reader.setMetadataStore(store);
}

Example 3 with BufferedImageReader

use of loci.formats.gui.BufferedImageReader in project bioformats by openmicroscopy.

the class ImageInfo method configureReaderPreInit.

public void configureReaderPreInit() throws FormatException, IOException {
    if (omexml) {
        reader.setOriginalMetadataPopulated(originalMetadata);
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            reader.setMetadataStore(service.createOMEXMLMetadata(null, omexmlVersion));
        } catch (DependencyException de) {
            throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
        } catch (ServiceException se) {
            throw new FormatException(se);
        }
    }
    // check file format
    if (reader instanceof ImageReader) {
        // determine format
        ImageReader ir = (ImageReader) reader;
        if (new Location(id).exists()) {
            LOGGER.info("Checking file format [{}]", ir.getFormat(id));
        }
    } else {
        // verify format
        LOGGER.info("Checking {} format [{}]", reader.getFormat(), reader.isThisType(id) ? "yes" : "no");
    }
    LOGGER.info("Initializing reader");
    if (stitch) {
        reader = new FileStitcher(reader, true);
        Location f = new Location(id);
        String pat = null;
        if (!f.exists()) {
            ((FileStitcher) reader).setUsingPatternIds(true);
            pat = id;
        } else {
            pat = FilePattern.findPattern(f);
        }
        if (pat != null)
            id = pat;
    }
    if (expand)
        reader = new ChannelFiller(reader);
    if (separate)
        reader = new ChannelSeparator(reader);
    if (merge)
        reader = new ChannelMerger(reader);
    if (cache) {
        if (cachedir != null) {
            reader = new Memoizer(reader, 0, new File(cachedir));
        } else {
            reader = new Memoizer(reader, 0);
        }
    }
    minMaxCalc = null;
    if (minmax || autoscale)
        reader = minMaxCalc = new MinMaxCalculator(reader);
    dimSwapper = null;
    if (swapOrder != null || shuffleOrder != null) {
        reader = dimSwapper = new DimensionSwapper(reader);
    }
    reader = biReader = new BufferedImageReader(reader);
    reader.close();
    reader.setNormalized(normalize);
    reader.setMetadataFiltered(filter);
    reader.setGroupFiles(group);
    options.setMetadataLevel(doMeta ? MetadataLevel.ALL : MetadataLevel.MINIMUM);
    options.setValidate(validate);
    reader.setMetadataOptions(options);
    reader.setFlattenedResolutions(flat);
}

Example 4 with BufferedImageReader

use of loci.formats.gui.BufferedImageReader in project bioformats by openmicroscopy.

the class FormatReaderTest method testUnflattenedSubimagePixelsHashes.

/*
  @Test(groups = {"all", "pixels"})
  public void testReorderedPixelsHashes() {
    if (config == null) throw new SkipException("No config tree");
    String testName = "testReorderedPixelsHashes";
    if (!initFile()) result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
      for (int i=0; i<reader.getSeriesCount() && success; i++) {
        reader.setSeries(i);
        config.setSeries(i);

        for (int j=0; j<3; j++) {
          int index = (int) (Math.random() * reader.getImageCount());
          reader.openBytes(index);
        }

        String md5 = TestTools.md5(reader.openBytes(0));
        String expected1 = config.getMD5();
        String expected2 = config.getAlternateMD5();

        if (!md5.equals(expected1) && !md5.equals(expected2)) {
          success = false;
          msg = expected1 == null && expected2 == null ? "no configuration" :
            "series " + i;
        }
      }
    }
    catch (Throwable t) {
      LOGGER.info("", t);
      success = false;
    }
    result(testName, success, msg);
  }
  */
@Test(groups = { "all", "pixels", "automated" })
public void testUnflattenedSubimagePixelsHashes() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testUnflattenedSubimagePixelsHashes";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        IFormatReader resolutionReader = new BufferedImageReader(new FileStitcher());
        resolutionReader.setFlattenedResolutions(false);
        resolutionReader.setNormalized(true);
        resolutionReader.setOriginalMetadataPopulated(false);
        resolutionReader.setMetadataFiltered(true);
        resolutionReader.setId(id);
        // check the MD5 of the first plane in each resolution
        for (int i = 0; i < resolutionReader.getSeriesCount() && success; i++) {
            resolutionReader.setSeries(i);
            for (int r = 0; r < resolutionReader.getResolutionCount() && success; r++) {
                resolutionReader.setResolution(r);
                config.setSeries(resolutionReader.getCoreIndex());
                int w = (int) Math.min(Configuration.TILE_SIZE, resolutionReader.getSizeX());
                int h = (int) Math.min(Configuration.TILE_SIZE, resolutionReader.getSizeY());
                String expected1 = config.getTileMD5();
                String expected2 = config.getTileAlternateMD5();
                String md5 = null;
                try {
                    md5 = TestTools.md5(resolutionReader.openBytes(0, 0, 0, w, h));
                } catch (Throwable e) {
                    if (TestTools.isOutOfMemory(e)) {
                        result(testName, true, "Image too large");
                        return;
                    }
                    LOGGER.warn("", e);
                }
                if (md5 == null && expected1 == null && expected2 == null) {
                    success = true;
                } else if (!md5.equals(expected1) && !md5.equals(expected2) && (expected1 != null || expected2 != null)) {
                    success = false;
                    msg = "series " + i + ", resolution " + r;
                }
            }
        }
        resolutionReader.close();
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 5 with BufferedImageReader

use of loci.formats.gui.BufferedImageReader in project bioformats by openmicroscopy.

the class FormatReaderTest method testUnflattenedPixelsHashes.

@Test(groups = { "all", "pixels", "automated" })
public void testUnflattenedPixelsHashes() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testUnflattenedPixelsHashes";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        IFormatReader resolutionReader = new BufferedImageReader(new FileStitcher());
        resolutionReader.setFlattenedResolutions(false);
        resolutionReader.setNormalized(true);
        resolutionReader.setOriginalMetadataPopulated(false);
        resolutionReader.setMetadataFiltered(true);
        resolutionReader.setId(id);
        // check the MD5 of the first plane in each resolution
        for (int i = 0; i < resolutionReader.getSeriesCount() && success; i++) {
            resolutionReader.setSeries(i);
            for (int r = 0; r < resolutionReader.getResolutionCount() && success; r++) {
                resolutionReader.setResolution(r);
                config.setSeries(resolutionReader.getCoreIndex());
                long planeSize = -1;
                try {
                    planeSize = DataTools.safeMultiply32(resolutionReader.getSizeX(), resolutionReader.getSizeY(), resolutionReader.getRGBChannelCount(), FormatTools.getBytesPerPixel(resolutionReader.getPixelType()));
                } catch (IllegalArgumentException e) {
                    continue;
                }
                if (planeSize < 0 || !TestTools.canFitInMemory(planeSize)) {
                    continue;
                }
                String md5 = TestTools.md5(resolutionReader.openBytes(0));
                String expected1 = config.getMD5();
                String expected2 = config.getAlternateMD5();
                if (expected1 == null && expected2 == null) {
                    continue;
                }
                if (!md5.equals(expected1) && !md5.equals(expected2)) {
                    success = false;
                    msg = "series " + i + ", resolution " + r;
                }
            }
        }
        resolutionReader.close();
    } catch (Throwable t) {
        if (TestTools.isOutOfMemory(t)) {
            result(testName, true, "Image too large");
            return;
        }
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}