Examples with IniParser loci.common.IniParser used on opensource projects

Example 11 with IniParser

use of loci.common.IniParser in project bioformats by openmicroscopy.

the class MetaSupportAutogen method main.

// -- Main method --
public static void main(String[] args) throws Exception {
    if (args.length == 0) {
        System.out.println("Usage: java MetaSupportAutogen ome-xml-version");
        System.out.println("    E.g.: java MetaSupportAutogen 2012-06");
        System.exit(1);
    }
    String version = args[0];
    // create needed directories
    File doc = new File("doc");
    if (!doc.exists()) {
        boolean success = doc.mkdir();
        if (!success) {
            throw new IOException("Could not create " + doc.getAbsolutePath());
        }
    }
    File docMeta = new File(doc, "meta");
    if (!docMeta.exists()) {
        boolean success = docMeta.mkdir();
        if (!success) {
            throw new IOException("Could not create " + docMeta.getAbsolutePath());
        }
    }
    // initialize Velocity
    VelocityEngine ve = VelocityTools.createEngine();
    VelocityContext context = VelocityTools.createContext();
    // parse supported properties list
    MetaSupportList supportList = new MetaSupportList(version);
    context.put("q", supportList);
    // retrieve the table of format page names
    IniParser parser = new IniParser();
    parser.setCommentDelimiter(null);
    IniList data = parser.parseINI(FORMAT_PAGES, MetaSupportAutogen.class);
    for (String handler : supportList.handlers()) {
        supportList.setHandler(handler);
        supportList.setPageName("metadata/" + handler);
    }
    // generate master table of metadata properties
    VelocityTools.processTemplate(ve, context, "doc/meta-summary.vm", "../../docs/sphinx/metadata-summary.rst");
    // generate metadata property support documentation for each handler
    for (String handler : supportList.handlers()) {
        supportList.setHandler(handler);
        String pagename = supportList.getPageName();
        if (pagename != null) {
            VelocityTools.processTemplate(ve, context, "doc/MetadataSupport.vm", "../../docs/sphinx/" + pagename + ".rst");
        }
    }
}

Example 12 with IniParser

use of loci.common.IniParser in project bioformats by openmicroscopy.

the class FakeReader method initFile.

@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "fake")) {
        if (checkSuffix(id, "fake.ini")) {
            id = id.substring(0, id.lastIndexOf("."));
        }
        Location file = new Location(id).getAbsoluteFile();
        if (!file.exists()) {
            Location dir = file.getParentFile();
            String[] list = dir.list(true);
            String name = file.getName();
            name = name.substring(0, name.lastIndexOf("."));
            for (String f : list) {
                if (checkSuffix(f, "fake") && f.startsWith(name)) {
                    id = new Location(dir, f).getAbsolutePath();
                    break;
                }
            }
        }
    }
    // Logic copied from deltavision. This should probably be refactored into
    // a helper method "replaceBySuffix" or something.
    super.initFile(id);
    findLogFiles();
    String path = id;
    Location location = new Location(id);
    String[] tokens = null;
    if (location.exists()) {
        path = location.getAbsoluteFile().getName();
        if (path.startsWith("Field")) {
            Location root = location.getAbsoluteFile().getParentFile();
            if (root != null) {
                root = root.getParentFile();
                if (root != null) {
                    root = root.getParentFile();
                    if (root != null) {
                        root = root.getParentFile();
                        if (isSPWStructure(root.getAbsolutePath())) {
                            tokens = extractTokensFromFakeSeries(root.getAbsolutePath());
                            // makes sure that getSeriesUsedFiles returns correctly
                            currentId = root.getAbsolutePath();
                        }
                    }
                }
            }
        }
    }
    if (location.isDirectory() && isSPWStructure(location.getAbsolutePath())) {
        tokens = extractTokensFromFakeSeries(location.getAbsolutePath());
    } else if (tokens == null) {
        String noExt = path.substring(0, path.lastIndexOf("."));
        tokens = noExt.split(TOKEN_SEPARATOR);
    }
    String name = null;
    // default
    int thumbSizeX = 0;
    // default
    int thumbSizeY = 0;
    int pixelType = DEFAULT_PIXEL_TYPE;
    // default
    int bitsPerPixel = 0;
    int rgb = DEFAULT_RGB_CHANNEL_COUNT;
    String dimOrder = DEFAULT_DIMENSION_ORDER;
    boolean orderCertain = true;
    boolean little = true;
    boolean interleaved = false;
    boolean indexed = false;
    boolean falseColor = false;
    boolean metadataComplete = true;
    boolean thumbnail = false;
    boolean withMicrobeam = false;
    int seriesCount = 1;
    int lutLength = 3;
    String acquisitionDate = null;
    int screens = 0;
    int plates = 0;
    int plateRows = 0;
    int plateCols = 0;
    int fields = 0;
    int plateAcqs = 0;
    Integer defaultColor = null;
    ArrayList<Integer> color = new ArrayList<Integer>();
    ArrayList<IniTable> seriesTables = new ArrayList<IniTable>();
    // add properties file values to list of tokens.
    if (iniFile != null) {
        IniParser parser = new IniParser();
        IniList list = parser.parseINI(new File(iniFile));
        List<String> newTokens = new ArrayList<String>();
        // Unclear what to do with other headers...
        IniTable table = list.getTable(IniTable.DEFAULT_HEADER);
        if (table != null) {
            for (Map.Entry<String, String> entry : table.entrySet()) {
                newTokens.add(entry.getKey() + "=" + entry.getValue());
            }
        }
        table = list.getTable("GlobalMetadata");
        if (table != null) {
            for (Map.Entry<String, String> entry : table.entrySet()) {
                addGlobalMeta(entry.getKey(), entry.getValue());
            }
        }
        String[] newTokArr = newTokens.toArray(new String[0]);
        String[] oldTokArr = tokens;
        tokens = new String[newTokArr.length + oldTokArr.length];
        System.arraycopy(oldTokArr, 0, tokens, 0, oldTokArr.length);
        System.arraycopy(newTokArr, 0, tokens, oldTokArr.length, newTokArr.length);
        // Properties overrides file name values
        int seriesIndex = 0;
        while (list.getTable("series_" + seriesIndex) != null) {
            seriesTables.add(list.getTable("series_" + seriesIndex));
            seriesIndex++;
        }
    }
    // parse tokens from filename
    for (String token : tokens) {
        if (name == null) {
            // first token is the image name
            name = token;
            continue;
        }
        int equals = token.indexOf('=');
        if (equals < 0) {
            LOGGER.warn("ignoring token: {}", token);
            continue;
        }
        String key = token.substring(0, equals);
        String value = token.substring(equals + 1);
        boolean boolValue = value.equals("true");
        double doubleValue;
        try {
            doubleValue = Double.parseDouble(value);
        } catch (NumberFormatException exc) {
            doubleValue = Double.NaN;
        }
        int intValue = Double.isNaN(doubleValue) ? -1 : (int) doubleValue;
        if (key.equals("sizeX"))
            sizeX = intValue;
        else if (key.equals("sizeY"))
            sizeY = intValue;
        else if (key.equals("sizeZ"))
            sizeZ = intValue;
        else if (key.equals("sizeC"))
            sizeC = intValue;
        else if (key.equals("sizeT"))
            sizeT = intValue;
        else if (key.equals("thumbSizeX"))
            thumbSizeX = intValue;
        else if (key.equals("thumbSizeY"))
            thumbSizeY = intValue;
        else if (key.equals("pixelType")) {
            pixelType = FormatTools.pixelTypeFromString(value);
        } else if (key.equals("bitsPerPixel"))
            bitsPerPixel = intValue;
        else if (key.equals("rgb"))
            rgb = intValue;
        else if (key.equals("dimOrder"))
            dimOrder = value.toUpperCase();
        else if (key.equals("orderCertain"))
            orderCertain = boolValue;
        else if (key.equals("little"))
            little = boolValue;
        else if (key.equals("interleaved"))
            interleaved = boolValue;
        else if (key.equals("indexed"))
            indexed = boolValue;
        else if (key.equals("falseColor"))
            falseColor = boolValue;
        else if (key.equals("metadataComplete"))
            metadataComplete = boolValue;
        else if (key.equals("thumbnail"))
            thumbnail = boolValue;
        else if (key.equals("series"))
            seriesCount = intValue;
        else if (key.equals("lutLength"))
            lutLength = intValue;
        else if (key.equals("scaleFactor"))
            scaleFactor = doubleValue;
        else if (key.equals("exposureTime"))
            exposureTime = new Time((float) doubleValue, UNITS.SECOND);
        else if (key.equals("acquisitionDate"))
            acquisitionDate = value;
        else if (key.equals("screens"))
            screens = intValue;
        else if (key.equals("plates"))
            plates = intValue;
        else if (key.equals("plateRows"))
            plateRows = intValue;
        else if (key.equals("plateCols"))
            plateCols = intValue;
        else if (key.equals("fields"))
            fields = intValue;
        else if (key.equals("plateAcqs"))
            plateAcqs = intValue;
        else if (key.equals("withMicrobeam"))
            withMicrobeam = boolValue;
        else if (key.equals("annLong"))
            annLong = intValue;
        else if (key.equals("annDouble"))
            annDouble = intValue;
        else if (key.equals("annMap"))
            annMap = intValue;
        else if (key.equals("annComment"))
            annComment = intValue;
        else if (key.equals("annBool"))
            annBool = intValue;
        else if (key.equals("annTime"))
            annTime = intValue;
        else if (key.equals("annTag"))
            annTag = intValue;
        else if (key.equals("annTerm"))
            annTerm = intValue;
        else if (key.equals("annXml"))
            annXml = intValue;
        else if (key.equals("ellipses"))
            ellipses = intValue;
        else if (key.equals("labels"))
            labels = intValue;
        else if (key.equals("lines"))
            lines = intValue;
        else if (key.equals("masks"))
            masks = intValue;
        else if (key.equals("points"))
            points = intValue;
        else if (key.equals("polygons"))
            polygons = intValue;
        else if (key.equals("polylines"))
            polylines = intValue;
        else if (key.equals("rectangles"))
            rectangles = intValue;
        else if (key.equals("physicalSizeX"))
            physicalSizeX = parseLength(value, getPhysicalSizeXUnitXsdDefault());
        else if (key.equals("physicalSizeY"))
            physicalSizeY = parseLength(value, getPhysicalSizeYUnitXsdDefault());
        else if (key.equals("physicalSizeZ"))
            physicalSizeZ = parseLength(value, getPhysicalSizeZUnitXsdDefault());
        else if (key.equals("color")) {
            defaultColor = parseColor(value);
        } else if (key.startsWith("color_")) {
            // 'color' and 'color_x' can be used together, but 'color_x' takes
            // precedence.  'color' will in that case be used for any missing
            // or invalid 'color_x' values.
            int index = Integer.parseInt(key.substring(key.indexOf('_') + 1));
            while (index >= color.size()) {
                color.add(null);
            }
            color.set(index, parseColor(value));
        }
    }
    // do some sanity checks
    if (sizeX < 1)
        throw new FormatException("Invalid sizeX: " + sizeX);
    if (sizeY < 1)
        throw new FormatException("Invalid sizeY: " + sizeY);
    if (sizeZ < 1)
        throw new FormatException("Invalid sizeZ: " + sizeZ);
    if (sizeC < 1)
        throw new FormatException("Invalid sizeC: " + sizeC);
    if (sizeT < 1)
        throw new FormatException("Invalid sizeT: " + sizeT);
    if (thumbSizeX < 0) {
        throw new FormatException("Invalid thumbSizeX: " + thumbSizeX);
    }
    if (thumbSizeY < 0) {
        throw new FormatException("Invalid thumbSizeY: " + thumbSizeY);
    }
    if (rgb < 1 || rgb > sizeC || sizeC % rgb != 0) {
        throw new FormatException("Invalid sizeC/rgb combination: " + sizeC + "/" + rgb);
    }
    getDimensionOrder(dimOrder);
    if (falseColor && !indexed) {
        throw new FormatException("False color images must be indexed");
    }
    if (seriesCount < 1) {
        throw new FormatException("Invalid seriesCount: " + seriesCount);
    }
    if (lutLength < 1) {
        throw new FormatException("Invalid lutLength: " + lutLength);
    }
    // populate SPW metadata
    MetadataStore store = makeFilterMetadata();
    boolean hasSPW = screens > 0 || plates > 0 || plateRows > 0 || plateCols > 0 || fields > 0 || plateAcqs > 0;
    if (hasSPW) {
        if (screens < 0)
            screens = 0;
        if (plates <= 0)
            plates = 1;
        if (plateRows <= 0)
            plateRows = 1;
        if (plateCols <= 0)
            plateCols = 1;
        if (fields <= 0)
            fields = 1;
        if (plateAcqs <= 0)
            plateAcqs = 1;
        // generate SPW metadata and override series count to match
        int imageCount = populateSPW(store, screens, plates, plateRows, plateCols, fields, plateAcqs, withMicrobeam);
        if (imageCount > 0)
            seriesCount = imageCount;
        else
            // failed to generate SPW metadata
            hasSPW = false;
    }
    // populate core metadata
    int effSizeC = sizeC / rgb;
    core.clear();
    for (int s = 0; s < seriesCount; s++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeX = sizeX;
        ms.sizeY = sizeY;
        ms.sizeZ = sizeZ;
        ms.sizeC = sizeC;
        ms.sizeT = sizeT;
        ms.thumbSizeX = thumbSizeX;
        ms.thumbSizeY = thumbSizeY;
        ms.pixelType = pixelType;
        ms.bitsPerPixel = bitsPerPixel;
        ms.imageCount = sizeZ * effSizeC * sizeT;
        ms.rgb = rgb > 1;
        ms.dimensionOrder = dimOrder;
        ms.orderCertain = orderCertain;
        ms.littleEndian = little;
        ms.interleaved = interleaved;
        ms.indexed = indexed;
        ms.falseColor = falseColor;
        ms.metadataComplete = metadataComplete;
        ms.thumbnail = thumbnail;
    }
    // populate OME metadata
    boolean planeInfo = (exposureTime != null) || seriesTables.size() > 0;
    MetadataTools.populatePixels(store, this, planeInfo);
    fillExposureTime(store);
    fillPhysicalSizes(store);
    for (int currentImageIndex = 0; currentImageIndex < seriesCount; currentImageIndex++) {
        if (currentImageIndex < seriesTables.size()) {
            parseSeriesTable(seriesTables.get(currentImageIndex), store, currentImageIndex);
        }
        String imageName = currentImageIndex > 0 ? name + " " + (currentImageIndex + 1) : name;
        store.setImageName(imageName, currentImageIndex);
        fillAcquisitionDate(store, acquisitionDate, currentImageIndex);
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            Color channel = defaultColor == null ? null : new Color(defaultColor);
            if (c < color.size() && color.get(c) != null) {
                channel = new Color(color.get(c));
            }
            if (channel != null) {
                store.setChannelColor(channel, currentImageIndex, c);
            }
        }
        fillAnnotations(store, currentImageIndex);
        fillRegions(store, currentImageIndex);
    }
    // for indexed color images, create lookup tables
    if (indexed) {
        if (pixelType == FormatTools.UINT8) {
            // create 8-bit LUTs
            final int num = 256;
            createIndexMap(num);
            lut8 = new byte[sizeC][lutLength][num];
            // linear ramp
            for (int c = 0; c < sizeC; c++) {
                for (int i = 0; i < lutLength; i++) {
                    for (int index = 0; index < num; index++) {
                        lut8[c][i][index] = (byte) indexToValue[c][index];
                    }
                }
            }
        } else if (pixelType == FormatTools.UINT16) {
            // create 16-bit LUTs
            final int num = 65536;
            createIndexMap(num);
            lut16 = new short[sizeC][lutLength][num];
            // linear ramp
            for (int c = 0; c < sizeC; c++) {
                for (int i = 0; i < lutLength; i++) {
                    for (int index = 0; index < num; index++) {
                        lut16[c][i][index] = (short) indexToValue[c][index];
                    }
                }
            }
        }
    // NB: Other pixel types will have null LUTs.
    }
}

Example 13 with IniParser

use of loci.common.IniParser in project bioformats by openmicroscopy.

the class SISReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    IFD ifd = ifds.get(0);
    CoreMetadata m = core.get(0);
    String iniMetadata = ifd.getIFDTextValue(SIS_INI_TAG);
    if (iniMetadata != null) {
        IniParser parser = new IniParser();
        IniList ini = parser.parseINI(new BufferedReader(new StringReader(iniMetadata)));
        IniTable dimensions = ini.getTable("Dimension");
        int z = Integer.parseInt(dimensions.get("Z"));
        int c = Integer.parseInt(dimensions.get("Band"));
        int t = Integer.parseInt(dimensions.get("Time"));
        if (z * c * t == ifds.size()) {
            m.sizeZ = z;
            m.sizeT = t;
            m.sizeC *= c;
        }
    // TODO : parse more metadata from the INI tables
    }
    if (!ifd.containsKey(SIS_TAG)) {
        // TODO: parse this metadata more thoroughly
        in.seek(ifd.getIFDLongValue(SIS_TAG_2, 0));
        while (!in.readString(2).equals("IS")) {
            in.seek(in.getFilePointer() - 1);
        }
        in.skipBytes(28);
        in.seek(in.readLong() - 84);
        physicalSizeX = in.readDouble() * 1000;
        physicalSizeY = in.readDouble() * 1000;
        return;
    }
    long metadataPointer = ifd.getIFDLongValue(SIS_TAG, 0);
    in.seek(metadataPointer);
    in.skipBytes(4);
    in.skipBytes(6);
    int minute = in.readShort();
    int hour = in.readShort();
    int day = in.readShort();
    int month = in.readShort() + 1;
    int year = 1900 + in.readShort();
    acquisitionDate = year + "-" + month + "-" + day + " " + hour + ":" + minute;
    acquisitionDate = DateTools.formatDate(acquisitionDate, "yyyy-M-d H:m");
    in.skipBytes(6);
    imageName = in.readCString();
    if ((in.getFilePointer() % 2) == 1) {
        in.skipBytes(1);
    }
    short check = in.readShort();
    while (check != 7 && check != 8) {
        check = in.readShort();
        if (check == 0x700 || check == 0x800 || check == 0xa00) {
            in.skipBytes(1);
            break;
        }
    }
    in.skipBytes(4);
    long pos = in.readInt() & 0xffffffffL;
    if (pos >= in.length()) {
        return;
    }
    in.seek(pos);
    in.skipBytes(12);
    physicalSizeX = in.readDouble();
    physicalSizeY = in.readDouble();
    if (Math.abs(physicalSizeX - physicalSizeY) > Constants.EPSILON) {
        // ??
        physicalSizeX = physicalSizeY;
        physicalSizeY = in.readDouble();
    }
    in.skipBytes(8);
    magnification = in.readDouble();
    int cameraNameLength = in.readShort();
    channelName = in.readCString();
    if (channelName.length() > 128) {
        channelName = "";
    }
    int length = (int) Math.min(cameraNameLength, channelName.length());
    if (length > 0) {
        cameraName = channelName.substring(0, length);
    }
    // these are no longer valid
    getGlobalMetadata().remove("XResolution");
    getGlobalMetadata().remove("YResolution");
    addGlobalMeta("Nanometers per pixel (X)", physicalSizeX);
    addGlobalMeta("Nanometers per pixel (Y)", physicalSizeY);
    addGlobalMeta("Magnification", magnification);
    addGlobalMeta("Channel name", channelName);
    addGlobalMeta("Camera name", cameraName);
    addGlobalMeta("Image name", imageName);
    addGlobalMeta("Acquisition date", acquisitionDate);
}