Examples with ServiceException loci.common.services.ServiceException used on opensource projects

Example 31 with ServiceException

use of loci.common.services.ServiceException in project bioformats by openmicroscopy.

the class Memoizer method setId.

// -- ReaderWrapper API methods --
@Override
public void setId(String id) throws FormatException, IOException {
    StopWatch sw = stopWatch();
    try {
        realFile = new Location(id);
        memoFile = getMemoFile(id);
        if (memoFile == null) {
            // Memoization disabled.
            if (userMetadataStore != null) {
                reader.setMetadataStore(userMetadataStore);
            }
            // EARLY EXIT
            super.setId(id);
            return;
        }
        // Should never throw kryo exceptions
        IFormatReader memo = loadMemo();
        loadedFromMemo = false;
        savedToMemo = false;
        if (memo != null) {
            // loadMemo has already called handleMetadataStore with non-null
            try {
                loadedFromMemo = true;
                reader = memo;
                reader.reopenFile();
            } catch (FileNotFoundException e) {
                LOGGER.info("could not reopen file - deleting invalid memo file: {}", memoFile);
                deleteQuietly(memoFile);
                memo = null;
                reader.close();
                loadedFromMemo = false;
            }
        }
        if (memo == null) {
            OMEXMLService service = getService();
            super.setMetadataStore(service.createOMEXMLMetadata());
            long start = System.currentTimeMillis();
            super.setId(id);
            long elapsed = System.currentTimeMillis() - start;
            // Between setId and saveMemo
            handleMetadataStore(null);
            if (elapsed < minimumElapsed) {
                LOGGER.debug("skipping save memo. elapsed millis: {}", elapsed);
                // EARLY EXIT!
                return;
            }
            // Should never throw.
            savedToMemo = saveMemo();
        }
    } catch (ServiceException e) {
        LOGGER.error("Could not create OMEXMLMetadata", e);
    } finally {
        sw.stop("loci.formats.Memoizer.setId");
    }
}

Example 32 with ServiceException

use of loci.common.services.ServiceException in project bioformats by openmicroscopy.

the class CellVoyagerReader method readInfo.

private void readInfo(final Document msDocument, final Document omeDocument) throws FormatException {
    /*
     * Magnification.
     *
     * We need it early, because the file format reports only un-magnified
     * sizes. So if we are to put proper metadata, we need to make the
     * conversion to size measured at the sample level ourselves. I feel
     * like this is fragile and most likely to change in a future version of
     * the file format.
     */
    final Element msRoot = msDocument.getDocumentElement();
    final double objectiveMagnification = Double.parseDouble(getChildText(msRoot, new String[] { "ObjectiveLens", "Magnification" }));
    // final double zoomLensMagnification = Double.parseDouble(
    // getChildText( msRoot, new String[] { "ZoomLens", "Magnification",
    // "Value" } ) );
    // *
    final double magnification = objectiveMagnification;
    // zoomLensMagnification;
    /*
     * Read the ome.xml file. Since it is malformed, we need to parse all
     * nodes, and add an "ID" attribute to those who do not have it.
     */
    final NodeList nodeList = omeDocument.getElementsByTagName("*");
    for (int i = 0; i < nodeList.getLength(); i++) {
        final Node node = nodeList.item(i);
        if (node.getNodeType() == Node.ELEMENT_NODE) {
            final NamedNodeMap atts = node.getAttributes();
            final Node namedItem = atts.getNamedItem("ID");
            if (namedItem == null) {
                final String name = node.getNodeName();
                final String id = name + ":" + i;
                if (!node.getParentNode().getNodeName().equals("LightSource")) {
                    ((Element) node).setAttribute("ID", id);
                }
            }
        }
    }
    /*
     * For single-slice image, the PhysicalSizeZ can be 0, which will make
     * the metadata read fail. Correct that.
     */
    final Element pszEl = getChild(omeDocument.getDocumentElement(), new String[] { "Image", "Pixels" });
    final double physicalSizeZ = Double.parseDouble(pszEl.getAttribute("PhysicalSizeZ"));
    if (physicalSizeZ <= 0) {
        // default to 1 whatever
        pszEl.setAttribute("PhysicalSizeZ", "" + 1);
    }
    /*
     * Now that the XML document is properly formed, we can build a metadata
     * object from it.
     */
    OMEXMLService service = null;
    String xml = null;
    try {
        xml = XMLTools.getXML(omeDocument);
    } catch (final TransformerConfigurationException e2) {
        LOGGER.debug("", e2);
    } catch (final TransformerException e2) {
        LOGGER.debug("", e2);
    }
    try {
        service = new ServiceFactory().getInstance(OMEXMLService.class);
    } catch (final DependencyException e1) {
        LOGGER.debug("", e1);
    }
    OMEXMLMetadata omeMD = null;
    try {
        omeMD = service.createOMEXMLMetadata(xml);
    } catch (final ServiceException e) {
        LOGGER.debug("", e);
    } catch (final NullPointerException npe) {
        LOGGER.debug("", npe);
        throw npe;
    }
    // Correct pixel size for magnification
    omeMD.setPixelsPhysicalSizeX(FormatTools.createLength(omeMD.getPixelsPhysicalSizeX(0).value().doubleValue() / magnification, omeMD.getPixelsPhysicalSizeX(0).unit()), 0);
    omeMD.setPixelsPhysicalSizeY(FormatTools.createLength(omeMD.getPixelsPhysicalSizeY(0).value().doubleValue() / magnification, omeMD.getPixelsPhysicalSizeY(0).unit()), 0);
    // Time interval
    if (Double.valueOf(readFrameInterval(msDocument)) != null) {
        omeMD.setPixelsTimeIncrement(new Time(Double.valueOf(readFrameInterval(msDocument)), UNITS.SECOND), 0);
    }
    /*
     * Channels
     */
    final Element channelsEl = getChild(msRoot, "Channels");
    final List<Element> channelEls = getChildren(channelsEl, "Channel");
    channelInfos = new ArrayList<ChannelInfo>();
    for (final Element channelEl : channelEls) {
        final boolean isEnabled = Boolean.parseBoolean(getChildText(channelEl, "IsEnabled"));
        if (!isEnabled) {
            continue;
        }
        final ChannelInfo ci = readChannel(channelEl);
        channelInfos.add(ci);
    }
    /*
     * Fix missing IDs.
     *
     * Some IDs are missing in the malformed OME.XML file. We must put them
     * back manually. Some are fixed here
     */
    omeMD.setProjectID(MetadataTools.createLSID("Project", 0), 0);
    omeMD.setScreenID(MetadataTools.createLSID("Screen", 0), 0);
    omeMD.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    omeMD.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
    // Read pixel sizes from OME metadata.
    final double pixelWidth = omeMD.getPixelsPhysicalSizeX(0).value().doubleValue();
    final double pixelHeight = omeMD.getPixelsPhysicalSizeY(0).value().doubleValue();
    /*
     * Read tile size from channel info. This is weird, but it's like that.
     * Since we build a multi-C image, we have to assume that all channels
     * have the same dimension, even if the file format allows for changing
     * the size, binning, etc. from channel to channel. Failure to load
     * datasets that have this exoticity is to be sought here.
     */
    final int tileWidth = channelInfos.get(0).tileWidth;
    final int tileHeight = channelInfos.get(0).tileHeight;
    /*
     * Handle multiple wells.
     *
     * The same kind of remark apply: We assume that a channel setting can
     * be applied to ALL wells. So this file reader will fail for dataset
     * that have one well that has a different dimension that of others.
     */
    /*
     * First remark: there can be two modes to store Areas in the xml file:
     * Either we define different areas for each well, and in that case, the
     * areas are found as a child element of the well element. Either the
     * definition of areas is common to all wells, and in that case they
     * area defined in a separate element.
     */
    final boolean sameAreaPerWell = Boolean.parseBoolean(getChildText(msRoot, "UsesSameAreaParWell"));
    List<AreaInfo> areas = null;
    if (sameAreaPerWell) {
        final Element areasEl = getChild(msRoot, new String[] { "SameAreaUsingWell", "Areas" });
        final List<Element> areaEls = getChildren(areasEl, "Area");
        int areaIndex = 0;
        areas = new ArrayList<AreaInfo>(areaEls.size());
        int fieldIndex = 1;
        for (final Element areaEl : areaEls) {
            final AreaInfo area = readArea(areaEl, fieldIndex, pixelWidth, pixelHeight, tileWidth, tileHeight);
            area.index = areaIndex++;
            areas.add(area);
            // Continue incrementing field index across areas.
            fieldIndex = area.fields.get(area.fields.size() - 1).index + 1;
        }
    }
    final Element wellsEl = getChild(msRoot, "Wells");
    final List<Element> wellEls = getChildren(wellsEl, "Well");
    wells = new ArrayList<WellInfo>();
    for (final Element wellEl : wellEls) {
        final boolean isWellEnabled = Boolean.parseBoolean(getChild(wellEl, "IsEnabled").getTextContent());
        if (isWellEnabled) {
            final WellInfo wi = readWellInfo(wellEl, pixelWidth, pixelHeight, tileWidth, tileHeight);
            if (sameAreaPerWell) {
                wi.areas = areas;
            }
            wells.add(wi);
        }
    }
    /*
     * Z range.
     *
     * In this file format, the Z range appears to be general: it applies to
     * all fields of all wells.
     */
    final int nZSlices = Integer.parseInt(getChildText(msRoot, new String[] { "ZStackConditions", "NumberOfSlices" }));
    /*
     * Time points. They are general as well. Which just makes sense.
     */
    timePoints = readTimePoints(msDocument);
    /*
     * Populate CORE metadata for each area.
     *
     * This reader takes to convention that state that 1 area = 1 series. So
     * if you have 10 wells with 2 areas in each well, and each area is made
     * of 20 fields, you will get 20 series, and each series will be
     * stitched from 20 fields.
     */
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omeMD.getRoot();
    Image firstImage = root.getImage(0);
    core.clear();
    for (final WellInfo well : wells) {
        for (final AreaInfo area : well.areas) {
            final CoreMetadata ms = new CoreMetadata();
            core.add(ms);
            if (core.size() > 1) {
                root.addImage(firstImage);
            }
            ms.sizeX = area.width;
            ms.sizeY = area.height;
            ms.sizeZ = nZSlices;
            ms.sizeC = channelInfos.size();
            ms.sizeT = timePoints.size();
            ms.dimensionOrder = "XYCZT";
            ms.rgb = false;
            ms.imageCount = nZSlices * channelInfos.size() * timePoints.size();
            // Bit depth.
            switch(omeMD.getPixelsType(0)) {
                case UINT8:
                    ms.pixelType = FormatTools.UINT8;
                    ms.bitsPerPixel = 8;
                    break;
                case UINT16:
                    ms.pixelType = FormatTools.UINT16;
                    ms.bitsPerPixel = 16;
                    break;
                case UINT32:
                    ms.pixelType = FormatTools.UINT32;
                    ms.bitsPerPixel = 32;
                    break;
                default:
                    throw new FormatException("Cannot read image with pixel type = " + omeMD.getPixelsType(0));
            }
            // Determined manually on sample data. Check here is the image
            // you get is weird.
            ms.littleEndian = true;
        }
    }
    omeMD.setRoot(root);
    /*
     * Populate the MetadataStore.
     */
    final MetadataStore store = makeFilterMetadata();
    MetadataConverter.convertMetadata(omeMD, store);
    MetadataTools.populatePixels(store, this, true);
    /*
     * Pinhole disk
     */
    final double pinholeSize = Double.parseDouble(getChildText(msRoot, new String[] { "PinholeDisk", "PinholeSize_um" }));
    /*
     * MicroPlate specific stuff
     */
    final Element containerEl = getChild(msRoot, new String[] { "Attachment", "HolderInfoList", "HolderInfo", "MountedSampleContainer" });
    final String type = containerEl.getAttribute("xsi:type");
    boolean plateMetadata = false;
    if (type.equals("WellPlate")) {
        plateMetadata = true;
        final int nrows = Integer.parseInt(getChildText(containerEl, "RowCount"));
        final int ncols = Integer.parseInt(getChildText(containerEl, "ColumnCount"));
        store.setPlateRows(new PositiveInteger(nrows), 0);
        store.setPlateColumns(new PositiveInteger(ncols), 0);
        final String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
        store.setPlateAcquisitionID(plateAcqID, 0, 0);
        final Element dimInfoEl = getChild(msRoot, "DimensionsInfo");
        final int maxNFields = Integer.parseInt(getChild(dimInfoEl, "F").getAttribute("Max"));
        final PositiveInteger fieldCount = FormatTools.getMaxFieldCount(maxNFields);
        if (fieldCount != null) {
            store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
        }
        // Plate acquisition time
        final String beginTime = getChildText(msRoot, "BeginTime");
        final String endTime = getChildText(msRoot, "EndTime");
        store.setPlateAcquisitionStartTime(new Timestamp(beginTime), 0, 0);
        store.setPlateAcquisitionEndTime(new Timestamp(endTime), 0, 0);
        store.setPlateName(beginTime, 0);
    } else if (!type.equals("PreparedSlide")) {
        LOGGER.warn("Unexpected acquisition type: {}", type);
    }
    // Wells position on the plate
    int seriesIndex = -1;
    int wellIndex = -1;
    for (final WellInfo well : wells) {
        wellIndex++;
        final int wellNumber = well.number;
        if (plateMetadata) {
            store.setWellID(MetadataTools.createLSID("Well", 0, wellIndex), 0, wellIndex);
            store.setWellRow(new NonNegativeInteger(well.row), 0, wellIndex);
            store.setWellColumn(new NonNegativeInteger(well.col), 0, wellIndex);
        }
        int areaIndex = -1;
        for (final AreaInfo area : well.areas) {
            seriesIndex++;
            areaIndex++;
            String imageID = MetadataTools.createLSID("Image", seriesIndex);
            store.setImageID(imageID, seriesIndex);
            final String imageName = "Well " + wellNumber + " (UID=" + well.UID + ", r=" + well.row + ", c=" + well.col + ") - Area " + areaIndex;
            store.setImageName(imageName, seriesIndex);
            if (plateMetadata) {
                Length posX = new Length(Double.valueOf(well.centerX), UNITS.REFERENCEFRAME);
                Length posY = new Length(Double.valueOf(well.centerY), UNITS.REFERENCEFRAME);
                String wellSample = MetadataTools.createLSID("WellSample", 0, wellIndex, areaIndex);
                store.setWellSampleID(wellSample, 0, wellIndex, areaIndex);
                store.setWellSampleImageRef(imageID, 0, wellIndex, areaIndex);
                store.setWellSampleIndex(new NonNegativeInteger(area.index), 0, wellIndex, areaIndex);
                store.setWellSamplePositionX(posX, 0, wellIndex, areaIndex);
                store.setWellSamplePositionY(posY, 0, wellIndex, areaIndex);
                store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, seriesIndex);
            }
            store.setImageInstrumentRef(MetadataTools.createLSID("Instrument", 0), seriesIndex);
            for (int i = 0; i < channelInfos.size(); i++) {
                store.setChannelPinholeSize(new Length(pinholeSize, UNITS.MICROMETER), seriesIndex, i);
                store.setChannelName(channelInfos.get(i).name, seriesIndex, i);
                store.setChannelColor(channelInfos.get(i).color, seriesIndex, i);
            }
        }
    }
}

Example 33 with ServiceException

use of loci.common.services.ServiceException in project bioformats by openmicroscopy.

the class CellWorxReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "htd")) {
        LOGGER.info("Searching for .htd file");
        String base = new Location(id).getAbsolutePath();
        base = base.substring(0, base.lastIndexOf("_"));
        id = base + ".HTD";
        if (!new Location(id).exists()) {
            Location parent = new Location(id).getAbsoluteFile().getParentFile();
            directoryList = parent.list(true);
            for (String f : directoryList) {
                if (checkSuffix(f, "htd")) {
                    id = new Location(parent, f).getAbsolutePath();
                    LOGGER.info("Found .htd file {}", f);
                    break;
                }
            }
        }
    }
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    String plateData = DataTools.readFile(id);
    String[] lines = plateData.split("\n");
    int xWells = 0, yWells = 0;
    int xFields = 0, yFields = 0;
    String[] wavelengths = null;
    int nTimepoints = 1;
    // determine dataset dimensions
    for (String line : lines) {
        int split = line.indexOf("\",");
        if (split < 1)
            continue;
        String key = line.substring(1, split).trim();
        String value = line.substring(split + 2).trim();
        if (key.equals("XWells")) {
            xWells = Integer.parseInt(value);
        } else if (key.equals("YWells")) {
            yWells = Integer.parseInt(value);
            wellFiles = new String[yWells][xWells][];
            logFiles = new String[yWells][xWells];
        } else if (key.startsWith("WellsSelection")) {
            int row = Integer.parseInt(key.substring(14)) - 1;
            String[] mapping = value.split(",");
            for (int col = 0; col < xWells; col++) {
                if (new Boolean(mapping[col].trim()).booleanValue()) {
                    wellFiles[row][col] = new String[1];
                }
            }
        } else if (key.equals("XSites")) {
            xFields = Integer.parseInt(value);
        } else if (key.equals("YSites")) {
            yFields = Integer.parseInt(value);
            fieldMap = new boolean[yFields][xFields];
        } else if (key.equals("TimePoints")) {
            nTimepoints = Integer.parseInt(value);
        } else if (key.startsWith("SiteSelection")) {
            int row = Integer.parseInt(key.substring(13)) - 1;
            String[] mapping = value.split(",");
            for (int col = 0; col < xFields; col++) {
                fieldMap[row][col] = new Boolean(mapping[col].trim()).booleanValue();
            }
        } else if (key.equals("Waves")) {
            doChannels = new Boolean(value.toLowerCase());
        } else if (key.equals("NWavelengths")) {
            wavelengths = new String[Integer.parseInt(value)];
        } else if (key.startsWith("WaveName")) {
            int index = Integer.parseInt(key.substring(8)) - 1;
            wavelengths[index] = value.replaceAll("\"", "");
        }
    }
    for (int row = 0; row < fieldMap.length; row++) {
        for (int col = 0; col < fieldMap[row].length; col++) {
            if (fieldMap[row][col])
                fieldCount++;
        }
    }
    // find pixels files
    String plateName = new Location(id).getAbsolutePath();
    plateName = plateName.substring(0, plateName.lastIndexOf(".")) + "_";
    int wellCount = 0;
    for (int row = 0; row < wellFiles.length; row++) {
        for (int col = 0; col < wellFiles[row].length; col++) {
            if (wellFiles[row][col] != null) {
                wellCount++;
                char rowLetter = (char) (row + 'A');
                String base = plateName + rowLetter + String.format("%02d", col + 1);
                wellFiles[row][col][0] = base + ".pnl";
                logFiles[row][col] = base + "_scan.log";
                if (!new Location(wellFiles[row][col][0]).exists()) {
                    // using TIFF files instead
                    wellFiles[row][col] = getTiffFiles(plateName, rowLetter, col, wavelengths.length, nTimepoints);
                }
            }
        }
    }
    plateLogFile = plateName + "scan.log";
    String serialNumber = null;
    if (new Location(plateLogFile).exists()) {
        String[] f = DataTools.readFile(plateLogFile).split("\n");
        for (String line : f) {
            if (line.trim().startsWith("Z Map File")) {
                String file = line.substring(line.indexOf(':') + 1);
                file = file.substring(file.lastIndexOf("/") + 1).trim();
                String parent = new Location(id).getAbsoluteFile().getParent();
                zMapFile = new Location(parent, file).getAbsolutePath();
            } else if (line.trim().startsWith("Scanner SN")) {
                serialNumber = line.substring(line.indexOf(':') + 1).trim();
            }
        }
    }
    int seriesCount = fieldCount * wellCount;
    int planeIndex = 0;
    int seriesIndex = 0;
    String file = getFile(seriesIndex, planeIndex);
    while (!new Location(file).exists()) {
        if (planeIndex < nTimepoints * wavelengths.length) {
            planeIndex++;
        } else if (seriesIndex < seriesCount - 1) {
            planeIndex = 0;
            seriesIndex++;
        } else {
            break;
        }
        file = getFile(seriesIndex, planeIndex);
    }
    IFormatReader pnl = getReader(file, true);
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        setSeries(i);
        ms.littleEndian = pnl.isLittleEndian();
        ms.sizeX = pnl.getSizeX();
        ms.sizeY = pnl.getSizeY();
        ms.pixelType = pnl.getPixelType();
        ms.sizeZ = 1;
        ms.sizeT = nTimepoints;
        ms.sizeC = wavelengths.length;
        ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
        ms.dimensionOrder = "XYCZT";
        ms.rgb = false;
        ms.interleaved = pnl.isInterleaved();
    }
    OMEXMLMetadata readerMetadata = (OMEXMLMetadata) pnl.getMetadataStore();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) readerMetadata.getRoot();
    Instrument instrument = root.getInstrument(0);
    List<Image> images = root.copyImageList();
    OMEXMLMetadataRoot convertRoot = new OMEXMLMetadataRoot();
    convertRoot.addInstrument(instrument);
    for (int i = 0; i < core.size() / images.size(); i++) {
        for (Image img : images) {
            convertRoot.addImage(img);
        }
    }
    OMEXMLMetadata convertMetadata;
    try {
        convertMetadata = service.createOMEXMLMetadata();
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    convertMetadata.setRoot(convertRoot);
    pnl.close();
    MetadataStore store = makeFilterMetadata();
    MetadataConverter.convertMetadata(convertMetadata, store);
    MetadataTools.populatePixels(store, this);
    String plateID = MetadataTools.createLSID("Plate", 0);
    Location plate = new Location(id).getAbsoluteFile();
    store.setPlateID(plateID, 0);
    plateName = plate.getName();
    if (plateName.indexOf('.') > 0) {
        plateName = plateName.substring(0, plateName.lastIndexOf('.'));
    }
    store.setPlateName(plateName, 0);
    store.setPlateRows(new PositiveInteger(wellFiles.length), 0);
    store.setPlateColumns(new PositiveInteger(wellFiles[0].length), 0);
    for (int i = 0; i < core.size(); i++) {
        store.setImageID(MetadataTools.createLSID("Image", i), i);
    }
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger fieldCount = FormatTools.getMaxFieldCount(fieldMap.length * fieldMap[0].length);
    if (fieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(fieldCount, 0, 0);
    }
    int nextImage = 0;
    for (int row = 0; row < wellFiles.length; row++) {
        for (int col = 0; col < wellFiles[row].length; col++) {
            int wellIndex = row * wellFiles[row].length + col;
            String wellID = MetadataTools.createLSID("Well", 0, wellIndex);
            store.setWellID(wellID, 0, wellIndex);
            store.setWellColumn(new NonNegativeInteger(col), 0, wellIndex);
            store.setWellRow(new NonNegativeInteger(row), 0, wellIndex);
            int fieldIndex = 0;
            for (int fieldRow = 0; fieldRow < fieldMap.length; fieldRow++) {
                for (int fieldCol = 0; fieldCol < fieldMap[fieldRow].length; fieldCol++) {
                    if (fieldMap[fieldRow][fieldCol] && wellFiles[row][col] != null) {
                        String wellSampleID = MetadataTools.createLSID("WellSample", 0, wellIndex, fieldIndex);
                        store.setWellSampleID(wellSampleID, 0, wellIndex, fieldIndex);
                        String imageID = MetadataTools.createLSID("Image", nextImage);
                        store.setWellSampleImageRef(imageID, 0, wellIndex, fieldIndex);
                        store.setWellSampleIndex(new NonNegativeInteger(nextImage), 0, wellIndex, fieldIndex);
                        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, nextImage);
                        String well = (char) (row + 'A') + String.format("%02d", col + 1);
                        store.setImageName("Well " + well + " Field #" + (fieldIndex + 1), nextImage);
                        nextImage++;
                        fieldIndex++;
                    }
                }
            }
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (serialNumber != null) {
            store.setMicroscopeSerialNumber(serialNumber, 0);
        }
        for (int well = 0; well < wellCount; well++) {
            parseWellLogFile(well, store);
        }
        if (timestamps.size() > 0) {
            store.setPlateAcquisitionStartTime(timestamps.get(0), 0, 0);
            store.setPlateAcquisitionEndTime(timestamps.get(timestamps.size() - 1), 0, 0);
        }
        for (int i = 0; i < core.size(); i++) {
            for (int c = 0; c < getSizeC(); c++) {
                if (c < wavelengths.length && wavelengths[c] != null) {
                    store.setChannelName(wavelengths[c], i, c);
                }
            }
        }
    }
}

Example 34 with ServiceException

use of loci.common.services.ServiceException in project bioformats by openmicroscopy.

the class PlugInBioFormatsImporter method readImage.

public void readImage() {
    final ViewUserInterface mipav = ViewUserInterface.getReference();
    // prompt user to choose a file
    if (chooser == null) {
        chooser = GUITools.buildFileChooser(reader);
        chooser.setCurrentDirectory(new File(Preferences.getImageDirectory()));
    }
    JFrame parent = mipav.getMainFrame();
    int rval = chooser.showOpenDialog(parent);
    // user canceled
    if (rval != JFileChooser.APPROVE_OPTION)
        return;
    final File file = chooser.getSelectedFile();
    // load the image in a separate thread
    Thread importerThread = new Thread("BioFormats-Importer") {

        public void run() {
            String name = file.getName();
            String dir = file.getParent();
            // open file using Bio-Formats
            setMessage(mipav, "Importing " + name + "...", true);
            String id = file.getPath();
            try {
                long tic = System.currentTimeMillis();
                IMetadata store;
                try {
                    ServiceFactory factory = new ServiceFactory();
                    OMEXMLService service = factory.getInstance(OMEXMLService.class);
                    store = service.createOMEXMLMetadata();
                } catch (DependencyException exc) {
                    throw new FormatException("Could not create OME-XML store.", exc);
                } catch (ServiceException exc) {
                    throw new FormatException("Could not create OME-XML store.", exc);
                }
                reader.setMetadataStore(store);
                reader.setId(id);
                // MIPAV assumes 4-D data in XYZT order
                reader.setOutputOrder("XYZTC");
                // harvest some core metadata
                int imageCount = reader.getImageCount();
                boolean little = reader.isLittleEndian();
                int pixelType = reader.getPixelType();
                int bpp = FormatTools.getBytesPerPixel(pixelType);
                boolean floating = FormatTools.isFloatingPoint(pixelType);
                int sizeX = reader.getSizeX();
                int sizeY = reader.getSizeY();
                int sizeZ = reader.getSizeZ();
                int sizeT = reader.getSizeT();
                int sizeC = reader.getSizeC();
                String imageName = store.getImageName(0);
                if (sizeC > 1) {
                    throw new FormatException("Multichannel data is unsupported at the moment");
                }
                // compute MIPAV buffer type
                int mipavType;
                switch(pixelType) {
                    case FormatTools.INT8:
                        mipavType = ModelStorageBase.BYTE;
                        break;
                    case FormatTools.UINT8:
                        mipavType = ModelStorageBase.UBYTE;
                        break;
                    case FormatTools.INT16:
                        mipavType = ModelStorageBase.SHORT;
                        break;
                    case FormatTools.UINT16:
                        mipavType = ModelStorageBase.USHORT;
                        break;
                    case FormatTools.INT32:
                        mipavType = ModelStorageBase.INTEGER;
                        break;
                    case FormatTools.UINT32:
                        mipavType = ModelStorageBase.UINTEGER;
                        break;
                    case FormatTools.FLOAT:
                        mipavType = ModelStorageBase.FLOAT;
                        break;
                    case FormatTools.DOUBLE:
                        mipavType = ModelStorageBase.DOUBLE;
                        break;
                    default:
                        throw new FormatException("Unsupported pixel type: " + pixelType);
                }
                // harvest physical resolution
                Length dimPhysSizeX = store.getPixelsPhysicalSizeX(0);
                Length dimPhysSizeY = store.getPixelsPhysicalSizeY(0);
                Length dimPhysSizeZ = store.getPixelsPhysicalSizeZ(0);
                Time dimTimeInc = store.getPixelsTimeIncrement(0);
                float physSizeX = dimPhysSizeX == null ? 1.0f : dimPhysSizeX.value(UNITS.MICROMETER).floatValue();
                float physSizeY = dimPhysSizeY == null ? 1.0f : dimPhysSizeY.value(UNITS.MICROMETER).floatValue();
                float physSizeZ = dimPhysSizeZ == null ? 1.0f : dimPhysSizeZ.value(UNITS.MICROMETER).floatValue();
                float timeInc = dimTimeInc == null ? 1.0f : dimTimeInc.value(UNITS.SECOND).floatValue();
                // compute dimensional extents
                int[] dimExtents = { sizeX, sizeY, sizeZ, sizeT };
                float[] res = { physSizeX, physSizeY, physSizeZ, timeInc };
                int[] units = { FileInfoBase.MICROMETERS, FileInfoBase.MICROMETERS, FileInfoBase.MICROMETERS, FileInfoBase.SECONDS };
                // create MIPAV image object
                ModelImage modelImage = new ModelImage(mipavType, dimExtents, imageName);
                // import planes into MIPAV image
                byte[] buf = new byte[bpp * sizeX * sizeY];
                for (int i = 0; i < imageCount; i++) {
                    setMessage(mipav, "Reading plane #" + (i + 1) + "/" + imageCount, false);
                    reader.openBytes(i, buf);
                    // convert byte array to appropriate primitive type
                    int offset = i * buf.length;
                    Object array = DataTools.makeDataArray(buf, bpp, floating, little);
                    // assign data to MIPAV image object
                    switch(mipavType) {
                        case ModelStorageBase.BYTE:
                        case ModelStorageBase.UBYTE:
                            modelImage.importData(offset, (byte[]) array, false);
                            break;
                        case ModelStorageBase.SHORT:
                        case ModelStorageBase.USHORT:
                            modelImage.importData(offset, (short[]) array, false);
                            break;
                        case ModelStorageBase.INTEGER:
                        case ModelStorageBase.UINTEGER:
                            modelImage.importData(offset, (int[]) array, false);
                            break;
                        case ModelStorageBase.FLOAT:
                            modelImage.importData(offset, (float[]) array, false);
                            break;
                        case ModelStorageBase.DOUBLE:
                            modelImage.importData(offset, (double[]) array, false);
                            break;
                        default:
                            throw new FormatException("Unknown buffer type: " + mipavType);
                    }
                }
                setMessage(mipav, "Finishing import...", true);
                // create a FileInfo object for each image plane
                FileInfoBase[] fileInfo = new FileInfoBase[imageCount];
                for (int i = 0; i < imageCount; i++) {
                    // HACK: Use FileInfoImageXML since FileInfoBase is abstract.
                    fileInfo[i] = new FileInfoImageXML(name, dir, FileUtility.XML);
                    fileInfo[i].setExtents(dimExtents);
                    fileInfo[i].setResolutions(res);
                    fileInfo[i].setUnitsOfMeasure(units);
                    fileInfo[i].setDataType(mipavType);
                }
                modelImage.setFileInfo(fileInfo);
                // scale color range and display MIPAV image
                modelImage.calcMinMax();
                new ViewJFrameImage(modelImage);
                long toc = System.currentTimeMillis();
                long time = toc - tic;
                long avg = time / imageCount;
                setMessage(mipav, name + ": Read " + imageCount + " planes in " + (time / 1000f) + " seconds (" + avg + " ms/plane)", true);
            } catch (FormatException exc) {
                exc.printStackTrace();
                MipavUtil.displayError("An error occurred parsing the file: " + exc.getMessage());
            } catch (IOException exc) {
                exc.printStackTrace();
                MipavUtil.displayError("An I/O error occurred reading the file: " + exc.getMessage());
            }
        }
    };
    importerThread.start();
}

Example 35 with ServiceException

use of loci.common.services.ServiceException in project bioformats by openmicroscopy.

the class SixteenBitLosslessJPEG2000Test method testLosslessPixels.

@Test
public void testLosslessPixels() throws Exception {
    int failureCount = 0;
    for (int v = Short.MIN_VALUE; v < Short.MAX_VALUE; v += increment) {
        int index = v + Short.MAX_VALUE + 1;
        byte[] pixels = DataTools.shortToBytes((short) v, false);
        String file = index + ".jp2";
        ByteArrayHandle tmpFile = new ByteArrayHandle(1);
        Location.mapFile(file, tmpFile);
        IMetadata metadata16;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata16 = service.createOMEXMLMetadata();
        } catch (DependencyException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        MetadataTools.populateMetadata(metadata16, 0, "foo", false, "XYCZT", "uint16", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer16 = new JPEG2000Writer();
        writer16.setMetadataRetrieve(metadata16);
        writer16.setId(file);
        writer16.saveBytes(0, pixels);
        writer16.close();
        byte[] buf = tmpFile.getBytes();
        byte[] realData = new byte[(int) tmpFile.length()];
        System.arraycopy(buf, 0, realData, 0, realData.length);
        tmpFile.close();
        tmpFile = new ByteArrayHandle(realData);
        Location.mapFile(file, tmpFile);
        ImageReader reader = new ImageReader();
        reader.setId(file);
        byte[] plane = reader.openBytes(0);
        for (int q = 0; q < plane.length; q++) {
            if (plane[q] != pixels[q]) {
                LOGGER.debug("FAILED on {}", DataTools.bytesToShort(pixels, false));
                failureCount++;
                break;
            }
        }
        reader.close();
        tmpFile.close();
        Location.mapFile(file, null);
    }
    assertEquals(failureCount, 0);
}