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Example 26 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class BaseModelMock method makeImage.

private Image makeImage(int index) {
    // Create <Image/>
    Image image = new Image();
    image.setID("Image:" + index);
    // Create <Pixels/>
    Pixels pixels = new Pixels();
    pixels.setID("Pixels:" + index);
    pixels.setSizeX(new PositiveInteger(SIZE_X));
    pixels.setSizeY(new PositiveInteger(SIZE_Y));
    pixels.setSizeZ(new PositiveInteger(SIZE_Z));
    pixels.setSizeC(new PositiveInteger(SIZE_C));
    pixels.setSizeT(new PositiveInteger(SIZE_T));
    pixels.setDimensionOrder(DIMENSION_ORDER);
    pixels.setType(PIXEL_TYPE);
    // Create <BinData/>
    for (int i = 0; i < SIZE_Z * SIZE_C * SIZE_T; i++) {
        BinData binData = new BinData();
        binData.setBigEndian(false);
        binData.setCompression(Compression.NONE);
        binData.setLength(new NonNegativeLong((long) (SIZE_X * SIZE_Y * BYTES_PER_PIXEL)));
        pixels.addBinData(binData);
    }
    // Create <Channel/> under <Pixels/>
    for (int i = 0; i < SIZE_C; i++) {
        Channel channel = new Channel();
        channel.setID("Channel:" + i);
        pixels.addChannel(channel);
    }
    // Put <Pixels/> under <Image/>
    image.setPixels(pixels);
    return image;
}
Also used : PositiveInteger(ome.xml.model.primitives.PositiveInteger) NonNegativeLong(ome.xml.model.primitives.NonNegativeLong) BinData(ome.xml.model.BinData) Channel(ome.xml.model.Channel) Image(ome.xml.model.Image) Pixels(ome.xml.model.Pixels)

Example 27 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project digilib by robcast.

the class BioFormatsDocuImage method writeImage.

@Override
public void writeImage(String mt, OutputStream ostream) throws ImageOpException, FileOpException {
    logger.debug("writeImage");
    File outFile;
    String filext = ".jpg";
    if (mt.equals("image/png")) {
        filext = ".png";
    }
    try {
        outFile = File.createTempFile("biof_temp", filext);
    } catch (IOException e) {
        throw new FileOpException(e.toString());
    }
    // save image to file
    ImageWriter iw = new ImageWriter();
    /*
         * try { //iw.setMetadataRetrieve(new DummyMetadata());
         * //iw.setSeries(0); //iw.setId(outFile.getAbsolutePath());
         * //logger.debug("writer="+iw); } catch (FormatException e) { throw new
         * FileOpException(e.toString()); } catch (IOException e) { // TODO
         * Auto-generated catch block e.printStackTrace(); } /* if
         * (mt.endsWith("png")) { iw = }
         */
    BufferedImageWriter writer = BufferedImageWriter.makeBufferedImageWriter(iw);
    try {
        logger.debug("setting metadata " + meta);
        iw.setMetadataRetrieve(meta);
        logger.debug("writing to file  " + outFile);
        writer.setId(outFile.getAbsolutePath());
        logger.debug("fixing metadata " + meta);
        iw.setInterleaved(reader.isInterleaved());
        iw.setWriteSequentially(true);
        meta.setPixelsSizeX(new PositiveInteger(img.getWidth()), 0);
        meta.setPixelsSizeY(new PositiveInteger(img.getHeight()), 0);
        meta.setPixelsSizeC(new PositiveInteger(img.getColorModel().getNumComponents()), 0);
        logger.debug("saving image " + img);
        writer.saveImage(0, img);
        logger.debug("closing file");
        writer.close();
    } catch (FormatException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    } catch (IOException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    // now send file
    FileInputStream inFile = null;
    try {
        inFile = new FileInputStream(outFile);
        byte[] dataBuffer = new byte[4096];
        int len;
        while ((len = inFile.read(dataBuffer)) != -1) {
            // copy out file
            ostream.write(dataBuffer, 0, len);
        }
    } catch (IOException e) {
        throw new FileOpException(e.toString());
    } finally {
        try {
            if (inFile != null) {
                inFile.close();
            }
        } catch (IOException e) {
        // nothing to do
        }
    }
}
Also used : PositiveInteger(ome.xml.model.primitives.PositiveInteger) FileOpException(digilib.io.FileOpException) BufferedImageWriter(loci.formats.gui.BufferedImageWriter) ImageWriter(loci.formats.ImageWriter) BufferedImageWriter(loci.formats.gui.BufferedImageWriter) IOException(java.io.IOException) File(java.io.File) FormatException(loci.formats.FormatException) FileInputStream(java.io.FileInputStream)

Example 28 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class Exporter method run.

// -- Exporter API methods --
/**
 * Executes the plugin.
 */
public void run() {
    String outfile = null;
    Boolean splitZ = null;
    Boolean splitC = null;
    Boolean splitT = null;
    Boolean padded = null;
    Boolean saveRoi = null;
    String compression = null;
    Boolean windowless = Boolean.FALSE;
    if (plugin.arg != null) {
        outfile = Macro.getValue(plugin.arg, "outfile", null);
        String z = Macro.getValue(plugin.arg, "splitZ", null);
        String c = Macro.getValue(plugin.arg, "splitC", null);
        String t = Macro.getValue(plugin.arg, "splitT", null);
        String zeroPad = Macro.getValue(plugin.arg, "padded", null);
        String sr = Macro.getValue(plugin.arg, "saveRoi", null);
        compression = Macro.getValue(plugin.arg, "compression", null);
        String id = Macro.getValue(plugin.arg, "imageid", null);
        splitZ = z == null ? null : Boolean.valueOf(z);
        splitC = c == null ? null : Boolean.valueOf(c);
        splitT = t == null ? null : Boolean.valueOf(t);
        padded = zeroPad == null ? null : Boolean.valueOf(zeroPad);
        saveRoi = sr == null ? null : Boolean.valueOf(sr);
        if (id != null) {
            try {
                int imageID = Integer.parseInt(id);
                ImagePlus plus = WindowManager.getImage(imageID);
                if (plus != null)
                    imp = plus;
            } catch (Exception e) {
            // nothing to do, we use the current imagePlus
            }
        }
        String w = Macro.getValue(plugin.arg, "windowless", null);
        if (w != null) {
            windowless = Boolean.valueOf(w);
        }
        plugin.arg = null;
    }
    if (outfile == null) {
        String options = Macro.getOptions();
        if (options != null) {
            String save = Macro.getValue(options, "save", null);
            if (save != null)
                outfile = save;
        }
    }
    // create a temporary file if window less
    if (windowless && (outfile == null || outfile.length() == 0)) {
        File tmp = null;
        try {
            String name = removeExtension(imp.getTitle());
            String n = name + ".ome.tif";
            tmp = File.createTempFile(name, ".ome.tif");
            File p = tmp.getParentFile();
            File[] list = p.listFiles();
            // make sure we delete a previous tmp file with same name if any
            if (list != null) {
                File toDelete = null;
                for (int i = 0; i < list.length; i++) {
                    if (list[i].getName().equals(n)) {
                        toDelete = list[i];
                        break;
                    }
                }
                if (toDelete != null) {
                    toDelete.delete();
                }
            }
            outfile = new File(p, n).getAbsolutePath();
            if (Recorder.record)
                Recorder.recordPath("outputfile", outfile);
            IJ.log("exporter outputfile " + outfile);
        } catch (Exception e) {
        // fall back to window mode.
        } finally {
            if (tmp != null)
                tmp.delete();
        }
    }
    File f = null;
    if (outfile == null || outfile.length() == 0) {
        // open a dialog prompting for the filename to save
        // NB: Copied and adapted from ij.io.SaveDIalog.jSaveDispatchThread,
        // so that the save dialog has a file filter for choosing output format.
        String dir = null, name = null;
        JFileChooser fc = GUITools.buildFileChooser(new ImageWriter(), false);
        fc.setDialogTitle("Bio-Formats Exporter");
        String defaultDir = OpenDialog.getDefaultDirectory();
        if (defaultDir != null)
            fc.setCurrentDirectory(new File(defaultDir));
        // set OME-TIFF as the default output format
        FileFilter[] ff = fc.getChoosableFileFilters();
        FileFilter defaultFilter = null;
        for (int i = 0; i < ff.length; i++) {
            if (ff[i] instanceof ExtensionFileFilter) {
                ExtensionFileFilter eff = (ExtensionFileFilter) ff[i];
                if (i == 0 || eff.getExtension().equals("ome.tif")) {
                    defaultFilter = eff;
                    break;
                }
            }
        }
        if (defaultFilter != null)
            fc.setFileFilter(defaultFilter);
        int returnVal = fc.showSaveDialog(IJ.getInstance());
        if (returnVal != JFileChooser.APPROVE_OPTION) {
            Macro.abort();
            return;
        }
        f = fc.getSelectedFile();
        dir = fc.getCurrentDirectory().getPath() + File.separator;
        name = fc.getName(f);
        if (f.exists()) {
            int ret = JOptionPane.showConfirmDialog(fc, "The file " + f.getName() + " already exists. \n" + "Would you like to replace it?", "Replace?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
            if (ret != JOptionPane.OK_OPTION)
                f = null;
        } else {
            // ensure filename matches selected filter
            FileFilter filter = fc.getFileFilter();
            if (filter instanceof ExtensionFileFilter) {
                ExtensionFileFilter eff = (ExtensionFileFilter) filter;
                String[] ext = eff.getExtensions();
                String lName = name.toLowerCase();
                boolean hasExtension = false;
                for (int i = 0; i < ext.length; i++) {
                    if (lName.endsWith("." + ext[i])) {
                        hasExtension = true;
                        break;
                    }
                }
                if (!hasExtension && ext.length > 0) {
                    // append chosen extension
                    name = name + "." + ext[0];
                }
                f = fc.getSelectedFile();
                String filePath = f.getAbsolutePath();
                if (!filePath.endsWith("." + ext[0])) {
                    f = new File(filePath + '.' + ext[0]);
                }
                if (f.exists()) {
                    int ret1 = JOptionPane.showConfirmDialog(fc, "The file " + f.getName() + " already exists. \n" + "Would you like to replace it?", "Replace?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
                    if (ret1 != JOptionPane.OK_OPTION)
                        f = null;
                }
            }
        }
        if (f == null)
            Macro.abort();
        else {
            // do some ImageJ bookkeeping
            OpenDialog.setDefaultDirectory(dir);
            if (Recorder.record)
                Recorder.recordPath("save", dir + name);
        }
        if (dir == null || name == null)
            return;
        outfile = new File(dir, name).getAbsolutePath();
        if (outfile == null)
            return;
    }
    if (windowless) {
        if (splitZ == null)
            splitZ = Boolean.FALSE;
        if (splitC == null)
            splitC = Boolean.FALSE;
        if (splitT == null)
            splitT = Boolean.FALSE;
        if (padded == null)
            padded = Boolean.FALSE;
    }
    if (splitZ == null || splitC == null || splitT == null) {
        // ask if we want to export multiple files
        GenericDialog multiFile = new GenericDialog("Bio-Formats Exporter - Multiple Files");
        multiFile.addCheckbox("Write_each_Z_section to a separate file", false);
        multiFile.addCheckbox("Write_each_timepoint to a separate file", false);
        multiFile.addCheckbox("Write_each_channel to a separate file", false);
        multiFile.addCheckbox("Use zero padding for filename indexes", false);
        multiFile.showDialog();
        splitZ = multiFile.getNextBoolean();
        splitT = multiFile.getNextBoolean();
        splitC = multiFile.getNextBoolean();
        padded = multiFile.getNextBoolean();
        if (multiFile.wasCanceled())
            return;
    }
    try (IFormatWriter w = new ImageWriter().getWriter(outfile)) {
        int ptype = 0;
        int channels = 1;
        switch(imp.getType()) {
            case ImagePlus.GRAY8:
            case ImagePlus.COLOR_256:
                ptype = FormatTools.UINT8;
                break;
            case ImagePlus.COLOR_RGB:
                channels = 3;
                ptype = FormatTools.UINT8;
                break;
            case ImagePlus.GRAY16:
                ptype = FormatTools.UINT16;
                break;
            case ImagePlus.GRAY32:
                ptype = FormatTools.FLOAT;
                break;
        }
        String title = imp.getTitle();
        w.setWriteSequentially(true);
        FileInfo fi = imp.getOriginalFileInfo();
        String xml = fi == null ? null : fi.description == null ? null : fi.description.indexOf("xml") == -1 ? null : fi.description;
        OMEXMLService service = null;
        IMetadata store = null;
        try {
            ServiceFactory factory = new ServiceFactory();
            service = factory.getInstance(OMEXMLService.class);
            store = service.createOMEXMLMetadata(xml);
        } catch (DependencyException de) {
        } catch (ServiceException se) {
        }
        if (store == null)
            IJ.error("OME-XML Java library not found.");
        OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) store.getRoot();
        if (root.sizeOfROIList() > 0) {
            while (root.sizeOfROIList() > 0) {
                ROI roi = root.getROI(0);
                root.removeROI(roi);
            }
            store.setRoot(root);
        }
        if (xml == null) {
            store.createRoot();
        } else if (store.getImageCount() > 1) {
            // the original dataset had multiple series
            // we need to modify the IMetadata to represent the correct series
            ArrayList<Integer> matchingSeries = new ArrayList<Integer>();
            for (int series = 0; series < store.getImageCount(); series++) {
                String type = store.getPixelsType(series).toString();
                int pixelType = FormatTools.pixelTypeFromString(type);
                if (pixelType == ptype) {
                    String imageName = store.getImageName(series);
                    if (title.indexOf(imageName) >= 0) {
                        matchingSeries.add(series);
                    }
                }
            }
            int series = 0;
            if (matchingSeries.size() > 1) {
                for (int i = 0; i < matchingSeries.size(); i++) {
                    int index = matchingSeries.get(i);
                    String name = store.getImageName(index);
                    boolean valid = true;
                    for (int j = 0; j < matchingSeries.size(); j++) {
                        if (i != j) {
                            String compName = store.getImageName(matchingSeries.get(j));
                            if (compName.indexOf(name) >= 0) {
                                valid = false;
                                break;
                            }
                        }
                    }
                    if (valid) {
                        series = index;
                        break;
                    }
                }
            } else if (matchingSeries.size() == 1)
                series = matchingSeries.get(0);
            ome.xml.model.Image exportImage = root.getImage(series);
            List<ome.xml.model.Image> allImages = root.copyImageList();
            for (ome.xml.model.Image img : allImages) {
                if (!img.equals(exportImage)) {
                    root.removeImage(img);
                }
            }
            store.setRoot(root);
        }
        store.setPixelsSizeX(new PositiveInteger(imp.getWidth()), 0);
        store.setPixelsSizeY(new PositiveInteger(imp.getHeight()), 0);
        store.setPixelsSizeZ(new PositiveInteger(imp.getNSlices()), 0);
        store.setPixelsSizeC(new PositiveInteger(channels * imp.getNChannels()), 0);
        store.setPixelsSizeT(new PositiveInteger(imp.getNFrames()), 0);
        if (store.getImageID(0) == null) {
            store.setImageID(MetadataTools.createLSID("Image", 0), 0);
        }
        if (store.getPixelsID(0) == null) {
            store.setPixelsID(MetadataTools.createLSID("Pixels", 0), 0);
        }
        // reset the pixel type, unless the only change is signedness
        // this prevents problems if the user changed the bit depth of the image
        boolean applyCalibrationFunction = false;
        try {
            int originalType = -1;
            if (store.getPixelsType(0) != null) {
                originalType = FormatTools.pixelTypeFromString(store.getPixelsType(0).toString());
            }
            if (ptype != originalType && (store.getPixelsType(0) == null || !FormatTools.isSigned(originalType) || FormatTools.getBytesPerPixel(originalType) != FormatTools.getBytesPerPixel(ptype))) {
                store.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(ptype)), 0);
            } else if (FormatTools.isSigned(originalType)) {
                applyCalibrationFunction = true;
            }
        } catch (EnumerationException e) {
        }
        if (store.getPixelsBinDataCount(0) == 0 || store.getPixelsBinDataBigEndian(0, 0) == null) {
            store.setPixelsBinDataBigEndian(Boolean.FALSE, 0, 0);
        }
        if (store.getPixelsDimensionOrder(0) == null) {
            try {
                store.setPixelsDimensionOrder(DimensionOrder.fromString(ORDER), 0);
            } catch (EnumerationException e) {
            }
        }
        LUT[] luts = new LUT[imp.getNChannels()];
        for (int c = 0; c < imp.getNChannels(); c++) {
            if (c >= store.getChannelCount(0) || store.getChannelID(0, c) == null) {
                String lsid = MetadataTools.createLSID("Channel", 0, c);
                store.setChannelID(lsid, 0, c);
            }
            store.setChannelSamplesPerPixel(new PositiveInteger(channels), 0, 0);
            if (imp instanceof CompositeImage) {
                luts[c] = ((CompositeImage) imp).getChannelLut(c + 1);
            }
        }
        Calibration cal = imp.getCalibration();
        store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(cal.pixelWidth), 0);
        store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(cal.pixelHeight), 0);
        store.setPixelsPhysicalSizeZ(FormatTools.getPhysicalSizeZ(cal.pixelDepth), 0);
        store.setPixelsTimeIncrement(new Time(new Double(cal.frameInterval), UNITS.SECOND), 0);
        if (imp.getImageStackSize() != imp.getNChannels() * imp.getNSlices() * imp.getNFrames()) {
            if (!windowless) {
                IJ.showMessageWithCancel("Bio-Formats Exporter Warning", "The number of planes in the stack (" + imp.getImageStackSize() + ") does not match the number of expected planes (" + (imp.getNChannels() * imp.getNSlices() * imp.getNFrames()) + ")." + "\nIf you select 'OK', only " + imp.getImageStackSize() + " planes will be exported. If you wish to export all of the " + "planes,\nselect 'Cancel' and convert the Image5D window " + "to a stack.");
            }
            store.setPixelsSizeZ(new PositiveInteger(imp.getImageStackSize()), 0);
            store.setPixelsSizeC(new PositiveInteger(1), 0);
            store.setPixelsSizeT(new PositiveInteger(1), 0);
        }
        Object info = imp.getProperty("Info");
        if (info != null) {
            String imageInfo = info.toString();
            if (imageInfo != null) {
                String[] lines = imageInfo.split("\n");
                for (String line : lines) {
                    int eq = line.lastIndexOf("=");
                    if (eq > 0) {
                        String key = line.substring(0, eq).trim();
                        String value = line.substring(eq + 1).trim();
                        if (key.endsWith("BitsPerPixel")) {
                            w.setValidBitsPerPixel(Integer.parseInt(value));
                            break;
                        }
                    }
                }
            }
        }
        // NB: Animation rate code copied from ij.plugin.Animator#doOptions().
        final int rate;
        if (cal.fps != 0.0) {
            rate = (int) cal.fps;
        } else if (cal.frameInterval != 0.0 && cal.getTimeUnit().equals("sec")) {
            rate = (int) (1.0 / cal.frameInterval);
        } else {
            // NB: Code from ij.plugin.Animator#animationRate initializer.
            // The value is 7 by default in ImageJ, so must be 7 here as well.
            rate = (int) Prefs.getDouble(Prefs.FPS, 7.0);
        }
        if (rate > 0)
            w.setFramesPerSecond(rate);
        String[] outputFiles = new String[] { outfile };
        int sizeZ = store.getPixelsSizeZ(0).getValue();
        int sizeC = store.getPixelsSizeC(0).getValue();
        int sizeT = store.getPixelsSizeT(0).getValue();
        if (splitZ || splitC || splitT) {
            int nFiles = 1;
            if (splitZ) {
                nFiles *= sizeZ;
            }
            if (splitC) {
                nFiles *= sizeC;
            }
            if (splitT) {
                nFiles *= sizeT;
            }
            outputFiles = new String[nFiles];
            int dot = outfile.indexOf(".", outfile.lastIndexOf(File.separator));
            String base = outfile.substring(0, dot);
            String ext = outfile.substring(dot);
            int nextFile = 0;
            for (int z = 0; z < (splitZ ? sizeZ : 1); z++) {
                for (int c = 0; c < (splitC ? sizeC : 1); c++) {
                    for (int t = 0; t < (splitT ? sizeT : 1); t++) {
                        int index = FormatTools.getIndex(ORDER, sizeZ, sizeC, sizeT, sizeZ * sizeC * sizeT, z, c, t);
                        String pattern = base + (splitZ ? "_Z%z" : "") + (splitC ? "_C%c" : "") + (splitT ? "_T%t" : "") + ext;
                        outputFiles[nextFile++] = FormatTools.getFilename(0, index, store, pattern, padded);
                    }
                }
            }
        }
        if (!w.getFormat().startsWith("OME")) {
            if (splitZ) {
                store.setPixelsSizeZ(new PositiveInteger(1), 0);
            }
            if (splitC) {
                store.setPixelsSizeC(new PositiveInteger(1), 0);
            }
            if (splitT) {
                store.setPixelsSizeT(new PositiveInteger(1), 0);
            }
        }
        // prompt for options
        String[] codecs = w.getCompressionTypes();
        ImageProcessor proc = imp.getImageStack().getProcessor(1);
        Image firstImage = proc.createImage();
        firstImage = AWTImageTools.makeBuffered(firstImage, proc.getColorModel());
        int thisType = AWTImageTools.getPixelType((BufferedImage) firstImage);
        if (proc instanceof ColorProcessor) {
            thisType = FormatTools.UINT8;
        } else if (proc instanceof ShortProcessor) {
            thisType = FormatTools.UINT16;
        }
        boolean notSupportedType = !w.isSupportedType(thisType);
        if (notSupportedType) {
            IJ.error("Pixel type (" + FormatTools.getPixelTypeString(thisType) + ") not supported by this format.");
            return;
        }
        if (codecs != null && codecs.length > 1) {
            boolean selected = false;
            if (compression != null) {
                for (int i = 0; i < codecs.length; i++) {
                    if (codecs[i].equals(compression)) {
                        selected = true;
                        break;
                    }
                }
            }
            if (!selected && !windowless) {
                GenericDialog gd = new GenericDialog("Bio-Formats Exporter Options");
                gd.addChoice("Compression type: ", codecs, codecs[0]);
                if (saveRoi != null) {
                    gd.addCheckbox("Export ROIs", saveRoi.booleanValue());
                } else {
                    gd.addCheckbox("Export ROIs", true);
                }
                gd.showDialog();
                saveRoi = gd.getNextBoolean();
                if (gd.wasCanceled())
                    return;
                compression = gd.getNextChoice();
            }
        }
        boolean in = false;
        if (outputFiles.length > 1) {
            for (int i = 0; i < outputFiles.length; i++) {
                if (new File(outputFiles[i]).exists()) {
                    in = true;
                    break;
                }
            }
        }
        if (in && !windowless) {
            int ret1 = JOptionPane.showConfirmDialog(null, "Some files already exist. \n" + "Would you like to replace them?", "Replace?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
            if (ret1 != JOptionPane.OK_OPTION) {
                return;
            }
            // Delete the files overwrite does not correctly work
            for (int i = 0; i < outputFiles.length; i++) {
                new File(outputFiles[i]).delete();
            }
        }
        // delete the file.
        if (f != null)
            f.delete();
        if (compression != null) {
            w.setCompression(compression);
        }
        // Save ROI's
        if (saveRoi != null && saveRoi.booleanValue()) {
            ROIHandler.saveROIs(store);
        }
        w.setMetadataRetrieve(store);
        // convert and save slices
        int size = imp.getImageStackSize();
        ImageStack is = imp.getImageStack();
        boolean doStack = w.canDoStacks() && size > 1;
        int start = doStack ? 0 : imp.getCurrentSlice() - 1;
        int end = doStack ? size : start + 1;
        boolean littleEndian = false;
        if (w.getMetadataRetrieve().getPixelsBigEndian(0) != null) {
            littleEndian = !w.getMetadataRetrieve().getPixelsBigEndian(0).booleanValue();
        } else if (w.getMetadataRetrieve().getPixelsBinDataCount(0) == 0) {
            littleEndian = !w.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
        }
        byte[] plane = null;
        w.setInterleaved(false);
        int[] no = new int[outputFiles.length];
        for (int i = start; i < end; i++) {
            if (doStack) {
                BF.status(false, "Saving plane " + (i + 1) + "/" + size);
                BF.progress(false, i, size);
            } else
                BF.status(false, "Saving image");
            proc = is.getProcessor(i + 1);
            if (proc instanceof RecordedImageProcessor) {
                proc = ((RecordedImageProcessor) proc).getChild();
            }
            int x = proc.getWidth();
            int y = proc.getHeight();
            if (proc instanceof ByteProcessor) {
                if (applyCalibrationFunction) {
                    // don't alter 'pixels' directly as that will
                    // affect the open ImagePlus
                    byte[] pixels = (byte[]) proc.getPixels();
                    plane = new byte[pixels.length];
                    float[] calibration = proc.getCalibrationTable();
                    for (int pixel = 0; pixel < pixels.length; pixel++) {
                        plane[pixel] = (byte) calibration[pixels[pixel] & 0xff];
                    }
                } else {
                    plane = (byte[]) proc.getPixels();
                }
            } else if (proc instanceof ShortProcessor) {
                short[] pixels = (short[]) proc.getPixels();
                if (applyCalibrationFunction) {
                    // don't alter 'pixels' directly as that will
                    // affect the open ImagePlus
                    plane = new byte[pixels.length * 2];
                    float[] calibration = proc.getCalibrationTable();
                    for (int pixel = 0; pixel < pixels.length; pixel++) {
                        short v = (short) calibration[pixels[pixel] & 0xffff];
                        DataTools.unpackBytes(v, plane, pixel * 2, 2, littleEndian);
                    }
                } else {
                    plane = DataTools.shortsToBytes(pixels, littleEndian);
                }
            } else if (proc instanceof FloatProcessor) {
                plane = DataTools.floatsToBytes((float[]) proc.getPixels(), littleEndian);
            } else if (proc instanceof ColorProcessor) {
                byte[][] pix = new byte[3][x * y];
                ((ColorProcessor) proc).getRGB(pix[0], pix[1], pix[2]);
                plane = new byte[3 * x * y];
                System.arraycopy(pix[0], 0, plane, 0, x * y);
                System.arraycopy(pix[1], 0, plane, x * y, x * y);
                System.arraycopy(pix[2], 0, plane, 2 * x * y, x * y);
                if (i == start) {
                    sizeC /= 3;
                }
            }
            int fileIndex = 0;
            if (doStack) {
                int[] coords = FormatTools.getZCTCoords(ORDER, sizeZ, sizeC, sizeT, size, i);
                int realZ = sizeZ;
                int realC = sizeC;
                int realT = sizeT;
                if (!splitZ) {
                    coords[0] = 0;
                    realZ = 1;
                }
                if (!splitC) {
                    coords[1] = 0;
                    realC = 1;
                }
                if (!splitT) {
                    coords[2] = 0;
                    realT = 1;
                }
                fileIndex = FormatTools.getIndex(ORDER, realZ, realC, realT, realZ * realC * realT, coords[0], coords[1], coords[2]);
            }
            if (notSupportedType) {
                IJ.error("Pixel type not supported by this format.");
            } else {
                w.changeOutputFile(outputFiles[fileIndex]);
                int currentChannel = FormatTools.getZCTCoords(ORDER, sizeZ, sizeC, sizeT, imp.getStackSize(), i)[1];
                if (luts[currentChannel] != null) {
                    // expand to 16-bit LUT if necessary
                    int bpp = FormatTools.getBytesPerPixel(thisType);
                    if (bpp == 1) {
                        w.setColorModel(luts[currentChannel]);
                    } else if (bpp == 2) {
                        int lutSize = luts[currentChannel].getMapSize();
                        byte[][] lut = new byte[3][lutSize];
                        luts[currentChannel].getReds(lut[0]);
                        luts[currentChannel].getGreens(lut[1]);
                        luts[currentChannel].getBlues(lut[2]);
                        short[][] newLut = new short[3][65536];
                        int bins = newLut[0].length / lut[0].length;
                        for (int c = 0; c < newLut.length; c++) {
                            for (int q = 0; q < newLut[c].length; q++) {
                                int index = q / bins;
                                newLut[c][q] = (short) ((lut[c][index] * lut[0].length) + (q % bins));
                            }
                        }
                        w.setColorModel(new Index16ColorModel(16, newLut[0].length, newLut, littleEndian));
                    }
                } else if (!proc.isDefaultLut()) {
                    w.setColorModel(proc.getColorModel());
                }
                w.saveBytes(no[fileIndex]++, plane);
            }
        }
        w.close();
    } catch (FormatException e) {
        WindowTools.reportException(e);
    } catch (IOException e) {
        WindowTools.reportException(e);
    }
}
Also used : ServiceFactory(loci.common.services.ServiceFactory) ArrayList(java.util.ArrayList) Image(java.awt.Image) BufferedImage(java.awt.image.BufferedImage) CompositeImage(ij.CompositeImage) OMEXMLService(loci.formats.services.OMEXMLService) Index16ColorModel(loci.formats.gui.Index16ColorModel) ImageProcessor(ij.process.ImageProcessor) RecordedImageProcessor(loci.plugins.util.RecordedImageProcessor) IMetadata(loci.formats.meta.IMetadata) FileInfo(ij.io.FileInfo) List(java.util.List) ArrayList(java.util.ArrayList) ImageStack(ij.ImageStack) FloatProcessor(ij.process.FloatProcessor) DependencyException(loci.common.services.DependencyException) ROI(ome.xml.model.ROI) FormatException(loci.formats.FormatException) IFormatWriter(loci.formats.IFormatWriter) JFileChooser(javax.swing.JFileChooser) ServiceException(loci.common.services.ServiceException) OMEXMLMetadataRoot(ome.xml.meta.OMEXMLMetadataRoot) File(java.io.File) ExtensionFileFilter(loci.formats.gui.ExtensionFileFilter) EnumerationException(ome.xml.model.enums.EnumerationException) ByteProcessor(ij.process.ByteProcessor) ImageWriter(loci.formats.ImageWriter) Time(ome.units.quantity.Time) ColorProcessor(ij.process.ColorProcessor) CompositeImage(ij.CompositeImage) GenericDialog(ij.gui.GenericDialog) RecordedImageProcessor(loci.plugins.util.RecordedImageProcessor) ExtensionFileFilter(loci.formats.gui.ExtensionFileFilter) FileFilter(javax.swing.filechooser.FileFilter) PositiveInteger(ome.xml.model.primitives.PositiveInteger) LUT(ij.process.LUT) Calibration(ij.measure.Calibration) IOException(java.io.IOException) ImagePlus(ij.ImagePlus) ServiceException(loci.common.services.ServiceException) DependencyException(loci.common.services.DependencyException) EnumerationException(ome.xml.model.enums.EnumerationException) FormatException(loci.formats.FormatException) IOException(java.io.IOException) ShortProcessor(ij.process.ShortProcessor) PositiveInteger(ome.xml.model.primitives.PositiveInteger)

Example 29 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class MetadataTools method populatePixels.

/**
 * Populates the Pixels element of the given metadata store, using core
 * metadata from the given reader.  If the {@code doPlane} flag is set,
 * then the Plane elements will be populated as well. If the
 * {@code doImageName} flag is set, then the image name will be populated as
 * well.
 *
 * @param store       The metadata store whose Pixels should be populated
 * @param r           The format reader whose core metadata should be used
 * @param doPlane     Specifies whether Plane elements should be populated
 * @param doImageName Specifies whether the Image name should be populated
 */
public static void populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName) {
    if (store == null || r == null)
        return;
    int oldSeries = r.getSeries();
    for (int i = 0; i < r.getSeriesCount(); i++) {
        r.setSeries(i);
        String imageName = null;
        if (doImageName) {
            Location f = new Location(r.getCurrentFile());
            imageName = f.getName();
            if (r.getSeriesCount() > 1) {
                imageName += " #" + (i + 1);
            }
        }
        String pixelType = FormatTools.getPixelTypeString(r.getPixelType());
        populateMetadata(store, r.getCurrentFile(), i, imageName, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount());
        store.setPixelsInterleaved(r.isInterleaved(), i);
        store.setPixelsSignificantBits(new PositiveInteger(r.getBitsPerPixel()), i);
        try {
            OMEXMLService service = new ServiceFactory().getInstance(OMEXMLService.class);
            if (service.isOMEXMLRoot(store.getRoot())) {
                MetadataStore baseStore = r.getMetadataStore();
                if (service.isOMEXMLMetadata(baseStore)) {
                    OMEXMLMetadata omeMeta;
                    try {
                        omeMeta = service.getOMEMetadata(service.asRetrieve(baseStore));
                        if (omeMeta.getTiffDataCount(i) == 0 && omeMeta.getPixelsBinDataCount(i) == 0) {
                            service.addMetadataOnly(omeMeta, i, i == 0);
                        }
                    } catch (ServiceException e) {
                        LOGGER.warn("Failed to add MetadataOnly", e);
                    }
                }
            }
        } catch (DependencyException exc) {
            LOGGER.warn("Failed to add MetadataOnly", exc);
        }
        if (doPlane) {
            for (int q = 0; q < r.getImageCount(); q++) {
                int[] coords = r.getZCTCoords(q);
                store.setPlaneTheZ(new NonNegativeInteger(coords[0]), i, q);
                store.setPlaneTheC(new NonNegativeInteger(coords[1]), i, q);
                store.setPlaneTheT(new NonNegativeInteger(coords[2]), i, q);
            }
        }
    }
    r.setSeries(oldSeries);
}
Also used : MetadataStore(loci.formats.meta.MetadataStore) PositiveInteger(ome.xml.model.primitives.PositiveInteger) ServiceException(loci.common.services.ServiceException) ServiceFactory(loci.common.services.ServiceFactory) OMEXMLMetadata(loci.formats.ome.OMEXMLMetadata) NonNegativeInteger(ome.xml.model.primitives.NonNegativeInteger) DependencyException(loci.common.services.DependencyException) OMEXMLService(loci.formats.services.OMEXMLService) Location(loci.common.Location)

Example 30 with PositiveInteger

use of ome.xml.model.primitives.PositiveInteger in project bioformats by openmicroscopy.

the class FormatWriter method checkParams.

// -- Helper methods --
/**
 * Ensure that the arguments that are being passed to saveBytes(...) are
 * valid.
 * @throws FormatException if any of the arguments is invalid.
 */
protected void checkParams(int no, byte[] buf, int x, int y, int w, int h) throws FormatException {
    MetadataRetrieve r = getMetadataRetrieve();
    MetadataTools.verifyMinimumPopulated(r, series);
    if (buf == null)
        throw new FormatException("Buffer cannot be null.");
    int z = r.getPixelsSizeZ(series).getValue().intValue();
    int t = r.getPixelsSizeT(series).getValue().intValue();
    int c = r.getChannelCount(series);
    int planes = z * c * t;
    if (no < 0)
        throw new FormatException(String.format("Plane index:%d must be >= 0", no));
    if (no >= planes) {
        throw new FormatException(String.format("Plane index:%d must be < %d", no, planes));
    }
    int sizeX = r.getPixelsSizeX(series).getValue().intValue();
    int sizeY = r.getPixelsSizeY(series).getValue().intValue();
    if (x < 0)
        throw new FormatException(String.format("X:%d must be >= 0", x));
    if (y < 0)
        throw new FormatException(String.format("Y:%d must be >= 0", y));
    if (x >= sizeX) {
        throw new FormatException(String.format("X:%d must be < %d", x, sizeX));
    }
    if (y >= sizeY) {
        throw new FormatException(String.format("Y:%d must be < %d", y, sizeY));
    }
    if (w <= 0)
        throw new FormatException(String.format("Width:%d must be > 0", w));
    if (h <= 0)
        throw new FormatException(String.format("Height:%d must be > 0", h));
    if (x + w > sizeX)
        throw new FormatException(String.format("(w:%d + x:%d) must be <= %d", w, x, sizeX));
    if (y + h > sizeY)
        throw new FormatException(String.format("(h:%d + y:%d) must be <= %d", h, y, sizeY));
    int pixelType = FormatTools.pixelTypeFromString(r.getPixelsType(series).toString());
    int bpp = FormatTools.getBytesPerPixel(pixelType);
    PositiveInteger samples = r.getChannelSamplesPerPixel(series, 0);
    if (samples == null)
        samples = new PositiveInteger(1);
    int minSize = bpp * w * h * samples.getValue();
    if (buf.length < minSize) {
        throw new FormatException("Buffer is too small; expected " + minSize + " bytes, got " + buf.length + " bytes.");
    }
    if (!DataTools.containsValue(getPixelTypes(compression), pixelType)) {
        throw new FormatException("Unsupported image type '" + FormatTools.getPixelTypeString(pixelType) + "'.");
    }
}
Also used : PositiveInteger(ome.xml.model.primitives.PositiveInteger) MetadataRetrieve(loci.formats.meta.MetadataRetrieve)

Aggregations

PositiveInteger (ome.xml.model.primitives.PositiveInteger)42 NonNegativeInteger (ome.xml.model.primitives.NonNegativeInteger)17 FormatException (loci.formats.FormatException)16 ServiceFactory (loci.common.services.ServiceFactory)14 OMEXMLService (loci.formats.services.OMEXMLService)14 Location (loci.common.Location)13 CoreMetadata (loci.formats.CoreMetadata)13 MetadataStore (loci.formats.meta.MetadataStore)13 ServiceException (loci.common.services.ServiceException)11 Time (ome.units.quantity.Time)11 ArrayList (java.util.ArrayList)10 Length (ome.units.quantity.Length)10 IOException (java.io.IOException)9 DependencyException (loci.common.services.DependencyException)9 Image (ome.xml.model.Image)7 Timestamp (ome.xml.model.primitives.Timestamp)7 OMEXMLMetadata (loci.formats.ome.OMEXMLMetadata)6 EnumerationException (ome.xml.model.enums.EnumerationException)6 RandomAccessInputStream (loci.common.RandomAccessInputStream)5 TiffWriter (loci.formats.out.TiffWriter)5