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

Example 1 with IniTable

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

the class FormatPageAutogen method writeFormatTable.

public void writeFormatTable() throws Exception {
    File doc = new File("../../docs/sphinx/");
    if (!doc.exists()) {
        boolean success = doc.mkdir();
        if (!success) {
            throw new IOException("Could not create " + doc.getAbsolutePath());
        }
    }
    VelocityEngine engine = VelocityTools.createEngine();
    VelocityContext context = VelocityTools.createContext();
    IniTable[] sortedTable = new IniTable[data.size()];
    for (int i = 0; i < data.size(); i++) {
        IniTable table = data.get(i);
        table.put("pagename", getPageName(table.get(IniTable.HEADER_KEY), table.get("pagename")));
        sortedTable[i] = table;
    }
    Arrays.sort(sortedTable, new Comparator<IniTable>() {

        @Override
        public int compare(IniTable t1, IniTable t2) {
            String page1 = t1.get("pagename");
            String page2 = t2.get("pagename");
            return page1.compareTo(page2);
        }
    });
    context.put("formats", sortedTable);
    context.put("count", sortedTable.length);
    VelocityTools.processTemplate(engine, context, TABLE_TEMPLATE, "../../docs/sphinx/supported-formats.rst");
}

Example 2 with IniTable

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

the class FEITiffReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    boolean helios = ifds.get(0).containsKey(HELIOS_TAG);
    boolean titan = ifds.get(0).containsKey(TITAN_TAG);
    // Helios etc data might have a stray Titan tag
    if (titan && ifds.get(0).getIFDTextValue(TITAN_TAG).trim().isEmpty()) {
        titan = false;
    }
    // Titan data (always?) has an empty Helios tag as well, so the Titan tag is checked first
    String software = "S-FEG";
    if (titan) {
        software = "Titan";
    } else if (helios) {
        software = "Helios NanoLab";
    }
    addGlobalMeta("Software", software);
    int tagKey = SFEG_TAG;
    if (titan) {
        tagKey = TITAN_TAG;
    } else if (helios) {
        tagKey = HELIOS_TAG;
    }
    String tag = ifds.get(0).getIFDTextValue(tagKey);
    if (tag == null) {
        return;
    }
    tag = tag.trim();
    if (tag.isEmpty()) {
        // fall back to regular reader
        return;
    }
    // store metadata for later conversion to OME-XML
    if (tag.startsWith("<")) {
        XMLTools.parseXML(tag, new FEIHandler());
    } else {
        IniParser parser = new IniParser();
        IniList ini = parser.parseINI(new BufferedReader(new StringReader(tag)));
        detectors = new ArrayList<String>();
        if (helios) {
            IniTable userTable = ini.getTable("User");
            date = userTable.get("Date") + " " + userTable.get("Time");
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                userName = userTable.get("User");
                IniTable systemTable = ini.getTable("System");
                if (systemTable == null) {
                    systemTable = ini.getTable("SYSTEM");
                }
                if (systemTable != null) {
                    microscopeModel = systemTable.get("SystemType");
                }
                IniTable beamTable = ini.getTable("Beam");
                if (beamTable != null) {
                    String beamTableName = beamTable.get("Beam");
                    if (beamTableName != null) {
                        beamTable = ini.getTable(beamTableName);
                    }
                }
                if (beamTable != null) {
                    String beamX = beamTable.get("StageX");
                    String beamY = beamTable.get("StageY");
                    String beamZ = beamTable.get("StageZ");
                    IniTable stageTable = ini.getTable("Stage");
                    if (beamX != null) {
                        final Double number = Double.valueOf(beamX);
                        stageX = new Length(number, UNITS.REFERENCEFRAME);
                    } else if (stageTable != null) {
                        final Double number = Double.valueOf(stageTable.get("StageX"));
                        stageX = new Length(number, UNITS.REFERENCEFRAME);
                    }
                    if (beamY != null) {
                        final Double number = Double.valueOf(beamY);
                        stageY = new Length(number, UNITS.REFERENCEFRAME);
                    } else if (stageTable != null) {
                        final Double number = Double.valueOf(stageTable.get("StageY"));
                        stageY = new Length(number, UNITS.REFERENCEFRAME);
                    }
                    if (beamZ != null) {
                        final Double number = Double.valueOf(beamZ);
                        stageZ = new Length(number, UNITS.REFERENCEFRAME);
                    } else if (stageTable != null) {
                        final Double number = Double.valueOf(stageTable.get("StageZ"));
                        stageZ = new Length(number, UNITS.REFERENCEFRAME);
                    }
                }
                IniTable scanTable = ini.getTable("Scan");
                sizeX = new Double(scanTable.get("PixelWidth"));
                sizeY = new Double(scanTable.get("PixelHeight"));
                timeIncrement = new Double(scanTable.get("FrameTime"));
            }
        } else {
            IniTable dataTable = ini.getTable("DatabarData");
            imageName = dataTable.get("ImageName");
            imageDescription = dataTable.get("szUserText");
            String magnification = ini.getTable("Vector").get("Magnification");
            sizeX = new Double(magnification) * MAG_MULTIPLIER;
            sizeY = new Double(magnification) * MAG_MULTIPLIER;
            IniTable scanTable = ini.getTable("Vector.Sysscan");
            final Double posX = Double.valueOf(scanTable.get("PositionX"));
            final Double posY = Double.valueOf(scanTable.get("PositionY"));
            stageX = new Length(posX, UNITS.REFERENCEFRAME);
            stageY = new Length(posY, UNITS.REFERENCEFRAME);
            IniTable detectorTable = ini.getTable("Vector.Video.Detectors");
            int detectorCount = Integer.parseInt(detectorTable.get("NrDetectorsConnected"));
            for (int i = 0; i < detectorCount; i++) {
                detectors.add(detectorTable.get("Detector_" + i + "_Name"));
            }
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            HashMap<String, String> iniMap = ini.flattenIntoHashMap();
            metadata.putAll(iniMap);
        }
    }
}

Example 3 with IniTable

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

the class HitachiReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "txt")) {
        String base = id;
        if (base.indexOf('.') >= 0) {
            base = base.substring(0, base.lastIndexOf("."));
        }
        id = base + ".txt";
        initFile(id);
        return;
    }
    super.initFile(id);
    String data = DataTools.readFile(id);
    IniParser parser = new IniParser();
    parser.setBackslashContinuesLine(false);
    IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
    IniTable image = ini.getTable("SemImageFile");
    if (image == null) {
        throw new FormatException("Could not find 'SemImageFile' table.");
    }
    for (String key : image.keySet()) {
        addGlobalMeta(key, image.get(key));
    }
    String imageName = image.get("SampleName");
    String pixelsFile = image.get("ImageName");
    String date = image.get("Date");
    String time = image.get("Time");
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    pixelsFile = new Location(parent, pixelsFile).getAbsolutePath();
    ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses();
    Class<? extends IFormatReader>[] classArray = classes.getClasses();
    ClassList<IFormatReader> newClasses = new ClassList<IFormatReader>(IFormatReader.class);
    for (Class<? extends IFormatReader> c : classArray) {
        if (!c.equals(HitachiReader.class)) {
            newClasses.addClass(c);
        }
    }
    helperReader = new ImageReader(newClasses);
    helperReader.setId(pixelsFile);
    core = new ArrayList<CoreMetadata>(helperReader.getCoreMetadataList());
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM);
    store.setImageName(imageName, 0);
    date = DateTools.formatDate(date + " " + time, DATE_FORMAT);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    populateOMEMetadata(image, store);
}

Example 4 with IniTable

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

the class HamamatsuVMSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    IniParser parser = new IniParser();
    IniList layout = parser.parseINI(new BufferedReader(new InputStreamReader(in, Constants.ENCODING)));
    IniTable slideInfo = layout.getTable("Virtual Microscope Specimen");
    int nLayers = Integer.parseInt(slideInfo.get("NoLayers"));
    nRows = Integer.parseInt(slideInfo.get("NoJpegRows"));
    nCols = Integer.parseInt(slideInfo.get("NoJpegColumns"));
    String imageFile = slideInfo.get("ImageFile");
    mapFile = slideInfo.get("MapFile");
    String optimisationFile = slideInfo.get("OptimisationFile");
    macroFile = slideInfo.get("MacroImage");
    Double physicalWidth = new Double(slideInfo.get("PhysicalWidth"));
    Double physicalHeight = new Double(slideInfo.get("PhysicalHeight"));
    Double magnification = new Double(slideInfo.get("SourceLens"));
    Double macroWidth = new Double(slideInfo.get("PhysicalMacroWidth"));
    Double macroHeight = new Double(slideInfo.get("PhysicalMacroHeight"));
    for (String key : slideInfo.keySet()) {
        addGlobalMeta(key, slideInfo.get(key));
    }
    Location dir = new Location(id).getAbsoluteFile().getParentFile();
    if (imageFile != null) {
        imageFile = new Location(dir, imageFile).getAbsolutePath();
        files.add(imageFile);
    }
    tileFiles = new String[nLayers][nRows][nCols];
    tileFiles[0][0][0] = imageFile;
    for (int layer = 0; layer < nLayers; layer++) {
        for (int row = 0; row < nRows; row++) {
            for (int col = 0; col < nCols; col++) {
                String f = slideInfo.get("ImageFile(" + col + "," + row + ")");
                if (f != null) {
                    f = new Location(dir, f).getAbsolutePath();
                    tileFiles[layer][row][col] = f;
                    files.add(f);
                }
            }
        }
    }
    if (mapFile != null) {
        mapFile = new Location(dir, mapFile).getAbsolutePath();
        files.add(mapFile);
    }
    if (optimisationFile != null) {
        optimisationFile = new Location(dir, optimisationFile).getAbsolutePath();
        files.add(optimisationFile);
    }
    if (macroFile != null) {
        macroFile = new Location(dir, macroFile).getAbsolutePath();
        files.add(macroFile);
    }
    int seriesCount = 3;
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        String file = null;
        switch(i) {
            case 0:
                file = tileFiles[0][nRows - 1][nCols - 1];
                break;
            case 1:
                file = macroFile;
                break;
            case 2:
                file = mapFile;
                break;
        }
        int[] dims;
        try (RandomAccessInputStream s = new RandomAccessInputStream(file);
            JPEGTileDecoder decoder = new JPEGTileDecoder()) {
            dims = decoder.preprocess(s);
        }
        CoreMetadata m = new CoreMetadata();
        if (i == 0) {
            m.sizeX = (MAX_JPEG_SIZE * (nCols - 1)) + dims[0];
            m.sizeY = (MAX_JPEG_SIZE * (nRows - 1)) + dims[1];
        } else {
            m.sizeX = dims[0];
            m.sizeY = dims[1];
        }
        m.sizeZ = 1;
        m.sizeC = 3;
        m.sizeT = 1;
        m.rgb = true;
        m.imageCount = 1;
        m.dimensionOrder = "XYCZT";
        m.pixelType = FormatTools.UINT8;
        m.interleaved = m.sizeX > MAX_SIZE && m.sizeY > MAX_SIZE;
        m.thumbnail = i > 0;
        core.add(m);
    }
    CoreMetadata ms0 = core.get(0);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String path = new Location(currentId).getAbsoluteFile().getName();
    store.setImageName(path + " full resolution", 0);
    store.setImageName(path + " macro", 1);
    store.setImageName(path + " map", 2);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth / ms0.sizeX);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight / ms0.sizeY);
        Length macroSizeX = FormatTools.getPhysicalSizeX(macroWidth / core.get(1).sizeX);
        Length macroSizeY = FormatTools.getPhysicalSizeY(macroHeight / core.get(1).sizeY);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (macroSizeX != null) {
            store.setPixelsPhysicalSizeX(macroSizeX, 1);
        }
        if (macroSizeY != null) {
            store.setPixelsPhysicalSizeY(macroSizeY, 1);
        }
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveNominalMagnification(magnification, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
    }
}

Example 5 with IniTable

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

the class TillVisionReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "vws")) {
        Location pst = new Location(id).getAbsoluteFile();
        String name = pst.getParentFile().getName();
        Location parent = pst.getParentFile().getParentFile();
        Location vwsFile = new Location(parent, name.replaceAll(".pst", ".vws"));
        if (vwsFile.exists() && !vwsFile.isDirectory()) {
            id = vwsFile.getAbsolutePath();
        } else if (vwsFile.isDirectory()) {
            parent = pst.getParentFile();
            String[] list = parent.list(true);
            boolean foundVWS = false;
            for (String f : list) {
                if (checkSuffix(f, "vws")) {
                    id = new Location(parent, f).getAbsolutePath();
                    foundVWS = true;
                    break;
                }
            }
            if (!foundVWS) {
                throw new FormatException("Could not find .vws file.");
            }
        } else
            throw new FormatException("Could not find .vws file.");
    }
    super.initFile(id);
    exposureTimes = new HashMap<Integer, Double>();
    POIService poi = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        poi = factory.getInstance(POIService.class);
    } catch (DependencyException de) {
        throw new FormatException("POI library not found", de);
    }
    poi.initialize(id);
    Vector<String> documents = poi.getDocumentList();
    int nImages = 0;
    final Hashtable<String, Object> tmpSeriesMetadata = new Hashtable<String, Object>();
    for (String name : documents) {
        LOGGER.debug("Reading {}", name);
        if (name.equals("Root Entry" + File.separator + "Contents")) {
            RandomAccessInputStream s = poi.getDocumentStream(name);
            s.order(true);
            boolean specialCImage = false;
            int nFound = 0;
            Long[] cimages = null;
            Location dir = new Location(id).getAbsoluteFile().getParentFile();
            String[] list = dir.list(true);
            boolean hasPST = false;
            for (String f : list) {
                if (checkSuffix(f, "pst")) {
                    hasPST = true;
                    break;
                }
            }
            if (!hasPST) {
                cimages = findImages(s);
                nFound = cimages.length;
                if (nFound == 0) {
                    s.seek(13);
                    int len = s.readShort();
                    String type = s.readString(len);
                    if (type.equals("CImage")) {
                        nFound = 1;
                        cimages = new Long[] { s.getFilePointer() + 6 };
                        specialCImage = true;
                    }
                }
                embeddedImages = nFound > 0;
            }
            LOGGER.debug("Images are {}embedded", embeddedImages ? "" : "not ");
            if (embeddedImages) {
                core.clear();
                embeddedOffset = new long[nFound];
                for (int i = 0; i < nFound; i++) {
                    CoreMetadata ms = new CoreMetadata();
                    core.add(ms);
                    s.seek(cimages[i]);
                    int len = s.read();
                    String imageName = s.readString(len);
                    imageNames.add(imageName);
                    if (specialCImage) {
                        s.seek(1280);
                    } else {
                        while (true) {
                            if (s.readString(2).equals("sB")) {
                                break;
                            } else
                                s.seek(s.getFilePointer() - 1);
                        }
                    }
                    s.skipBytes(20);
                    ms.sizeX = s.readInt();
                    ms.sizeY = s.readInt();
                    ms.sizeZ = s.readInt();
                    ms.sizeC = s.readInt();
                    ms.sizeT = s.readInt();
                    ms.pixelType = convertPixelType(s.readInt());
                    if (specialCImage) {
                        embeddedOffset[i] = s.getFilePointer() + 27;
                    } else {
                        embeddedOffset[i] = s.getFilePointer() + 31;
                    }
                }
                if (in != null)
                    in.close();
                in = poi.getDocumentStream(name);
                s.close();
                break;
            }
            s.seek(0);
            int lowerBound = 0;
            int upperBound = 0x1000;
            while (s.getFilePointer() < s.length() - 2) {
                LOGGER.debug("  Looking for image at {}", s.getFilePointer());
                s.order(false);
                int nextOffset = findNextOffset(s);
                if (nextOffset < 0 || nextOffset >= s.length())
                    break;
                s.seek(nextOffset);
                s.skipBytes(3);
                int len = s.readShort();
                if (len <= 0)
                    continue;
                imageNames.add(s.readString(len));
                if (s.getFilePointer() + 8 >= s.length())
                    break;
                s.skipBytes(6);
                s.order(true);
                len = s.readShort();
                if (nImages == 0 && len > upperBound * 2 && len < upperBound * 4) {
                    lowerBound = 512;
                    upperBound = 0x4000;
                }
                if (len < lowerBound || len > upperBound)
                    continue;
                String description = s.readString(len);
                LOGGER.debug("Description: {}", description);
                // parse key/value pairs from description
                String dateTime = "";
                String[] lines = description.split("[\r\n]");
                for (String line : lines) {
                    line = line.trim();
                    int colon = line.indexOf(':');
                    if (colon != -1 && !line.startsWith(";")) {
                        String key = line.substring(0, colon).trim();
                        String value = line.substring(colon + 1).trim();
                        String metaKey = "Series " + nImages + " " + key;
                        addMeta(metaKey, value, tmpSeriesMetadata);
                        if (key.equals("Start time of experiment")) {
                            // HH:mm:ss aa OR HH:mm:ss.sss aa
                            dateTime += " " + value;
                        } else if (key.equals("Date")) {
                            // mm/dd/yy ?
                            dateTime = value + " " + dateTime;
                        } else if (key.equals("Exposure time [ms]")) {
                            double exp = Double.parseDouble(value) / 1000;
                            exposureTimes.put(nImages, exp);
                        } else if (key.equals("Image type")) {
                            types.add(value);
                        }
                    }
                }
                dateTime = dateTime.trim();
                if (!dateTime.equals("")) {
                    boolean success = false;
                    for (String format : DATE_FORMATS) {
                        try {
                            dateTime = DateTools.formatDate(dateTime, format, ".");
                            success = true;
                        } catch (NullPointerException e) {
                        }
                    }
                    dates.add(success ? dateTime : "");
                }
                nImages++;
            }
            s.close();
        }
    }
    Location directory = new Location(currentId).getAbsoluteFile().getParentFile();
    String[] pixelsFile = new String[nImages];
    if (!embeddedImages) {
        if (nImages == 0) {
            throw new FormatException("No images found.");
        }
        // look for appropriate pixels files
        String[] files = directory.list(true);
        String name = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
        int nextFile = 0;
        for (String f : files) {
            if (checkSuffix(f, "pst")) {
                Location pst = new Location(directory, f);
                if (pst.isDirectory() && f.startsWith(name)) {
                    String[] subfiles = pst.list(true);
                    Arrays.sort(subfiles);
                    for (String q : subfiles) {
                        if (checkSuffix(q, "pst") && nextFile < nImages) {
                            pixelsFile[nextFile++] = f + File.separator + q;
                        }
                    }
                }
            }
        }
        if (nextFile == 0) {
            for (String f : files) {
                if (checkSuffix(f, "pst")) {
                    pixelsFile[nextFile++] = new Location(directory, f).getAbsolutePath();
                }
            }
            if (nextFile == 0)
                throw new FormatException("No image files found.");
        }
    }
    Arrays.sort(pixelsFile);
    int nSeries = core.size();
    if (!embeddedImages) {
        core.clear();
        nSeries = nImages;
    }
    pixelsFiles = new String[nSeries];
    infFiles = new String[nSeries];
    Object[] metadataKeys = tmpSeriesMetadata.keySet().toArray();
    IniParser parser = new IniParser();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms;
        if (!embeddedImages) {
            ms = new CoreMetadata();
            core.add(ms);
            setSeries(i);
            // make sure that pixels file exists
            String file = pixelsFile[i];
            file = file.replace('/', File.separatorChar);
            file = file.replace('\\', File.separatorChar);
            String oldFile = file;
            Location f = new Location(directory, oldFile);
            if (!f.exists()) {
                oldFile = oldFile.substring(oldFile.lastIndexOf(File.separator) + 1);
                f = new Location(directory, oldFile);
                if (!f.exists()) {
                    throw new FormatException("Could not find pixels file '" + file);
                }
            }
            file = f.getAbsolutePath();
            pixelsFiles[i] = file;
            // read key/value pairs from .inf files
            int dot = file.lastIndexOf(".");
            String inf = file.substring(0, dot) + ".inf";
            infFiles[i] = inf;
            BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inf), Constants.ENCODING));
            IniList data = parser.parseINI(reader);
            reader.close();
            IniTable infoTable = data.getTable("Info");
            ms.sizeX = Integer.parseInt(infoTable.get("Width"));
            ms.sizeY = Integer.parseInt(infoTable.get("Height"));
            ms.sizeC = Integer.parseInt(infoTable.get("Bands"));
            ms.sizeZ = Integer.parseInt(infoTable.get("Slices"));
            ms.sizeT = Integer.parseInt(infoTable.get("Frames"));
            int dataType = Integer.parseInt(infoTable.get("Datatype"));
            ms.pixelType = convertPixelType(dataType);
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                HashMap<String, String> iniMap = data.flattenIntoHashMap();
                ms.seriesMetadata.putAll(iniMap);
            }
        } else {
            ms = core.get(i);
            setSeries(i);
        }
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
        ms.rgb = false;
        ms.littleEndian = true;
        ms.dimensionOrder = "XYCZT";
        ms.seriesMetadata = new Hashtable<String, Object>();
        for (Object key : metadataKeys) {
            String keyName = key.toString();
            if (keyName.startsWith("Series " + i + " ")) {
                keyName = keyName.replaceAll("Series " + i + " ", "");
                ms.seriesMetadata.put(keyName, tmpSeriesMetadata.get(key));
            }
        }
    }
    setSeries(0);
    populateMetadataStore();
    poi.close();
    poi = null;
}