Examples with OMEXMLMetadataRoot ome.xml.meta.OMEXMLMetadataRoot used on opensource projects

Example 6 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method addMetadataOnly.

/**
 * @see OMEXMLService#addMetadataOnly(OMEXMLMetadata, int, boolean)
 */
public void addMetadataOnly(OMEXMLMetadata omexmlMeta, int image, boolean resolve) {
    if (resolve) {
        omexmlMeta.resolveReferences();
    }
    MetadataOnly meta = new MetadataOnly();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    Pixels pix = root.getImage(image).getPixels();
    pix.setMetadataOnly(meta);
}

Example 7 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method addModuloAlong.

@Override
public void addModuloAlong(OMEXMLMetadata meta, CoreMetadata core, int imageIdx) {
    meta.resolveReferences();
    if (core.moduloZ.length() == 1 && core.moduloC.length() == 1 && core.moduloT.length() == 1) {
        // nothing to populate
        return;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
    Image image;
    try {
        image = root.getImage(imageIdx);
    } catch (IndexOutOfBoundsException ieeb) {
        // and exiting without doing anything.
        return;
    }
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null)
        annotations = new StructuredAnnotations();
    int annotationIndex = annotations.sizeOfXMLAnnotationList();
    final Set<String> knownModulos = new HashSet<String>();
    if (annotationIndex > 0) {
        // Check which modulo annotations are already present.
        for (int idx = 0; idx < annotationIndex; idx++) {
            if (ModuloAnnotation.MODULO_NS.equals(meta.getXMLAnnotationNamespace(idx))) {
                // ignore this annotation if it is not linked to the current Image
                boolean ignore = true;
                String xmlID = meta.getXMLAnnotationID(idx);
                for (int link = 0; link < image.sizeOfLinkedAnnotationList(); link++) {
                    if (xmlID.equals(image.getLinkedAnnotation(link).getID())) {
                        ignore = false;
                        break;
                    }
                }
                if (ignore) {
                    continue;
                }
                String value = meta.getXMLAnnotationValue(idx);
                try {
                    Document doc = XMLTools.parseDOM(value);
                    NodeList modulos = doc.getElementsByTagName("Modulo");
                    for (int m = 0; m < modulos.getLength(); m++) {
                        Node modulo = modulos.item(m);
                        NodeList children = modulo.getChildNodes();
                        for (int c = 0; c < children.getLength(); c++) {
                            Node child = children.item(c);
                            String name = child.getNodeName();
                            knownModulos.add(name);
                        }
                    }
                } catch (Exception e) {
                    LOGGER.warn("Could not parse XML from annotation: {}", value, e);
                }
            }
        }
        // Calculate the next annotation ID that should be used.
        String lastAnnotationID = meta.getXMLAnnotationID(annotationIndex - 1);
        String lastIndex = lastAnnotationID.substring(lastAnnotationID.lastIndexOf(":") + 1);
        try {
            int index = Integer.parseInt(lastIndex);
            while (index >= annotationIndex) {
                annotationIndex++;
            }
        } catch (NumberFormatException e) {
        }
    }
    int imageAnnotation = 0;
    if (core.moduloZ.length() > 1 && !knownModulos.contains("ModuloAlongZ")) {
        createModulo(meta, core.moduloZ, annotations, image, imageIdx, annotationIndex, imageAnnotation);
        annotationIndex++;
        imageAnnotation++;
    }
    if (core.moduloC.length() > 1 && !knownModulos.contains("ModuloAlongC")) {
        createModulo(meta, core.moduloC, annotations, image, imageIdx, annotationIndex, imageAnnotation);
        annotationIndex++;
        imageAnnotation++;
    }
    if (core.moduloT.length() > 1 && !knownModulos.contains("ModuloAlongT")) {
        createModulo(meta, core.moduloT, annotations, image, imageIdx, annotationIndex, imageAnnotation);
        annotationIndex++;
        imageAnnotation++;
    }
    root.setStructuredAnnotations(annotations);
    meta.setRoot(root);
}

Example 8 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method removeBinData.

/**
 * @see OMEXMLService#removeBinData(OMEXMLMetadata)
 */
@Override
public void removeBinData(OMEXMLMetadata omexmlMeta) {
    omexmlMeta.resolveReferences();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    List<Image> images = root.copyImageList();
    for (Image img : images) {
        Pixels pix = img.getPixels();
        List<BinData> binData = pix.copyBinDataList();
        for (BinData bin : binData) {
            pix.removeBinData(bin);
        }
        pix.setMetadataOnly(null);
    }
    omexmlMeta.setRoot(root);
}

Example 9 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class FileWriteSPW method cleanup.

/**
 * Close the file writer.
 */
public void cleanup() {
    // No of planes expected for each image = 1 if not FLIM
    int validPlanes = 1;
    if (delays != null) {
        validPlanes = sizet;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
    Plate plate = root.getPlate(0);
    StructuredAnnotations anns = root.getStructuredAnnotations();
    ArrayList<Image> invalidImages = new ArrayList<>();
    // if not record those images as being invalid
    for (int i = 0; i < expectedImages.length; i++) {
        if (expectedImages[i] < validPlanes) {
            Image im = root.getImage(i);
            invalidImages.add(im);
            // remove modulo Annotation if FLIM
            if (delays != null) {
                XMLAnnotation ann = (XMLAnnotation) im.getLinkedAnnotation(0);
                anns.removeXMLAnnotation(ann);
            }
        }
    }
    // Now remove all limked wellSnmples and then invalid images
    for (int i = 0; i < invalidImages.size(); i++) {
        Image im = invalidImages.get(i);
        List<WellSample> list = im.copyLinkedWellSampleList();
        if (!list.isEmpty()) {
            WellSample wellSample = im.getLinkedWellSample(0);
            Well well = wellSample.getWell();
            well.removeWellSample(wellSample);
        }
        root.removeImage(im);
    }
    if (writer != null) {
        try {
            writer.close();
        } catch (IOException e) {
            System.err.println("Failed to close file writer.");
        }
    }
}

Example 10 with OMEXMLMetadataRoot

use of ome.xml.meta.OMEXMLMetadataRoot in project bioformats by openmicroscopy.

the class ImageConverter method testConvert.

// -- Utility methods --
/**
 * A utility method for converting a file from the command line.
 */
public boolean testConvert(IFormatWriter writer, String[] args) throws FormatException, IOException {
    nextOutputIndex.clear();
    options.setValidate(validate);
    writer.setMetadataOptions(options);
    firstTile = true;
    boolean success = parseArgs(args);
    if (!success) {
        return false;
    }
    if (printVersion) {
        CommandLineTools.printVersion();
        return true;
    }
    CommandLineTools.runUpgradeCheck(args);
    if (in == null || out == null) {
        printUsage();
        return false;
    }
    if (new Location(out).exists()) {
        if (overwrite == null) {
            LOGGER.warn("Output file {} exists.", out);
            LOGGER.warn("Do you want to overwrite it? ([y]/n)");
            BufferedReader r = new BufferedReader(new InputStreamReader(System.in, Constants.ENCODING));
            String choice = r.readLine().trim().toLowerCase();
            overwrite = !choice.startsWith("n");
        }
        if (!overwrite) {
            LOGGER.warn("Exiting; next time, please specify an output file that " + "does not exist.");
            return false;
        } else {
            new Location(out).delete();
        }
    }
    if (map != null)
        Location.mapId(in, map);
    long start = System.currentTimeMillis();
    LOGGER.info(in);
    reader = new ImageReader();
    if (stitch) {
        reader = new FileStitcher(reader);
        Location f = new Location(in);
        String pat = null;
        if (!f.exists()) {
            pat = in;
        } else {
            pat = FilePattern.findPattern(f);
        }
        if (pat != null)
            in = pat;
    }
    if (separate)
        reader = new ChannelSeparator(reader);
    if (merge)
        reader = new ChannelMerger(reader);
    if (fill)
        reader = new ChannelFiller(reader);
    minMax = null;
    if (autoscale) {
        reader = new MinMaxCalculator(reader);
        minMax = (MinMaxCalculator) reader;
    }
    reader.setMetadataOptions(options);
    reader.setGroupFiles(group);
    reader.setMetadataFiltered(true);
    reader.setOriginalMetadataPopulated(true);
    OMEXMLService service = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        reader.setMetadataStore(service.createOMEXMLMetadata());
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    reader.setId(in);
    MetadataStore store = reader.getMetadataStore();
    MetadataTools.populatePixels(store, reader, false, false);
    boolean dimensionsSet = true;
    if (width == 0 || height == 0) {
        // otherwise default to series 0
        if (series >= 0) {
            reader.setSeries(series);
        }
        width = reader.getSizeX();
        height = reader.getSizeY();
        dimensionsSet = false;
    }
    if (channel >= reader.getEffectiveSizeC()) {
        throw new FormatException("Invalid channel '" + channel + "' (" + reader.getEffectiveSizeC() + " channels in source file)");
    }
    if (timepoint >= reader.getSizeT()) {
        throw new FormatException("Invalid timepoint '" + timepoint + "' (" + reader.getSizeT() + " timepoints in source file)");
    }
    if (zSection >= reader.getSizeZ()) {
        throw new FormatException("Invalid Z section '" + zSection + "' (" + reader.getSizeZ() + " Z sections in source file)");
    }
    if (store instanceof MetadataRetrieve) {
        try {
            String xml = service.getOMEXML(service.asRetrieve(store));
            OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) store.getRoot();
            IMetadata meta = service.createOMEXMLMetadata(xml);
            if (series >= 0) {
                Image exportImage = new Image(root.getImage(series));
                Pixels exportPixels = new Pixels(root.getImage(series).getPixels());
                exportImage.setPixels(exportPixels);
                OMEXMLMetadataRoot newRoot = (OMEXMLMetadataRoot) meta.getRoot();
                while (newRoot.sizeOfImageList() > 0) {
                    newRoot.removeImage(newRoot.getImage(0));
                }
                newRoot.addImage(exportImage);
                meta.setRoot(newRoot);
                meta.setPixelsSizeX(new PositiveInteger(width), 0);
                meta.setPixelsSizeY(new PositiveInteger(height), 0);
                if (autoscale) {
                    store.setPixelsType(PixelType.UINT8, 0);
                }
                if (channel >= 0) {
                    meta.setPixelsSizeC(new PositiveInteger(1), 0);
                }
                if (zSection >= 0) {
                    meta.setPixelsSizeZ(new PositiveInteger(1), 0);
                }
                if (timepoint >= 0) {
                    meta.setPixelsSizeT(new PositiveInteger(1), 0);
                }
                writer.setMetadataRetrieve((MetadataRetrieve) meta);
            } else {
                for (int i = 0; i < reader.getSeriesCount(); i++) {
                    meta.setPixelsSizeX(new PositiveInteger(width), 0);
                    meta.setPixelsSizeY(new PositiveInteger(height), 0);
                    if (autoscale) {
                        store.setPixelsType(PixelType.UINT8, i);
                    }
                    if (channel >= 0) {
                        meta.setPixelsSizeC(new PositiveInteger(1), 0);
                    }
                    if (zSection >= 0) {
                        meta.setPixelsSizeZ(new PositiveInteger(1), 0);
                    }
                    if (timepoint >= 0) {
                        meta.setPixelsSizeT(new PositiveInteger(1), 0);
                    }
                }
                writer.setMetadataRetrieve((MetadataRetrieve) meta);
            }
        } catch (ServiceException e) {
            throw new FormatException(e);
        }
    }
    writer.setWriteSequentially(true);
    if (writer instanceof TiffWriter) {
        ((TiffWriter) writer).setBigTiff(bigtiff);
    } else if (writer instanceof ImageWriter) {
        IFormatWriter w = ((ImageWriter) writer).getWriter(out);
        if (w instanceof TiffWriter) {
            ((TiffWriter) w).setBigTiff(bigtiff);
        }
    }
    String format = writer.getFormat();
    LOGGER.info("[{}] -> {} [{}]", new Object[] { reader.getFormat(), out, format });
    long mid = System.currentTimeMillis();
    int total = 0;
    int num = writer.canDoStacks() ? reader.getSeriesCount() : 1;
    long read = 0, write = 0;
    int first = series == -1 ? 0 : series;
    int last = series == -1 ? num : series + 1;
    long timeLastLogged = System.currentTimeMillis();
    for (int q = first; q < last; q++) {
        reader.setSeries(q);
        firstTile = true;
        if (!dimensionsSet) {
            width = reader.getSizeX();
            height = reader.getSizeY();
        }
        int writerSeries = series == -1 ? q : 0;
        writer.setSeries(writerSeries);
        writer.setInterleaved(reader.isInterleaved() && !autoscale);
        writer.setValidBitsPerPixel(reader.getBitsPerPixel());
        int numImages = writer.canDoStacks() ? reader.getImageCount() : 1;
        int startPlane = (int) Math.max(0, firstPlane);
        int endPlane = (int) Math.min(numImages, lastPlane);
        numImages = endPlane - startPlane;
        if (channel >= 0) {
            numImages /= reader.getEffectiveSizeC();
        }
        if (zSection >= 0) {
            numImages /= reader.getSizeZ();
        }
        if (timepoint >= 0) {
            numImages /= reader.getSizeT();
        }
        total += numImages;
        int count = 0;
        for (int i = startPlane; i < endPlane; i++) {
            int[] coords = reader.getZCTCoords(i);
            if ((zSection >= 0 && coords[0] != zSection) || (channel >= 0 && coords[1] != channel) || (timepoint >= 0 && coords[2] != timepoint)) {
                continue;
            }
            String outputName = FormatTools.getFilename(q, i, reader, out, zeroPadding);
            if (outputName.equals(FormatTools.getTileFilename(0, 0, 0, outputName))) {
                writer.setId(outputName);
                if (compression != null)
                    writer.setCompression(compression);
            } else {
                int tileNum = outputName.indexOf(FormatTools.TILE_NUM);
                int tileX = outputName.indexOf(FormatTools.TILE_X);
                int tileY = outputName.indexOf(FormatTools.TILE_Y);
                if (tileNum < 0 && (tileX < 0 || tileY < 0)) {
                    throw new FormatException("Invalid file name pattern; " + FormatTools.TILE_NUM + " or both of " + FormatTools.TILE_X + " and " + FormatTools.TILE_Y + " must be specified.");
                }
            }
            int outputIndex = 0;
            if (nextOutputIndex.containsKey(outputName)) {
                outputIndex = nextOutputIndex.get(outputName);
            }
            long s = System.currentTimeMillis();
            long m = convertPlane(writer, i, outputIndex, outputName);
            long e = System.currentTimeMillis();
            read += m - s;
            write += e - m;
            nextOutputIndex.put(outputName, outputIndex + 1);
            if (i == endPlane - 1) {
                nextOutputIndex.remove(outputName);
            }
            // log number of planes processed every second or so
            if (count == numImages - 1 || (e - timeLastLogged) / 1000 > 0) {
                int current = (count - startPlane) + 1;
                int percent = 100 * current / numImages;
                StringBuilder sb = new StringBuilder();
                sb.append("\t");
                int numSeries = last - first;
                if (numSeries > 1) {
                    sb.append("Series ");
                    sb.append(q);
                    sb.append(": converted ");
                } else
                    sb.append("Converted ");
                LOGGER.info(sb.toString() + "{}/{} planes ({}%)", new Object[] { current, numImages, percent });
                timeLastLogged = e;
            }
            count++;
        }
    }
    writer.close();
    long end = System.currentTimeMillis();
    LOGGER.info("[done]");
    // output timing results
    float sec = (end - start) / 1000f;
    long initial = mid - start;
    float readAvg = (float) read / total;
    float writeAvg = (float) write / total;
    LOGGER.info("{}s elapsed ({}+{}ms per plane, {}ms overhead)", new Object[] { sec, readAvg, writeAvg, initial });
    return true;
}