Examples with ClassList loci.formats.ClassList used on opensource projects

Example 1 with ClassList

use of loci.formats.ClassList 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 2 with ClassList

use of loci.formats.ClassList in project bioformats by openmicroscopy.

the class LociPrefs method makeImageReader.

// -- Utility methods --
/**
 * Creates an image reader according to the current configuration settings,
 * including which format readers are currently enabled, as well as
 * format-specific configuration settings.
 */
public static ImageReader makeImageReader() {
    ClassList<IFormatReader> defaultClasses = ImageReader.getDefaultReaderClasses();
    Class<? extends IFormatReader>[] c = defaultClasses.getClasses();
    // include only enabled classes
    ClassList<IFormatReader> enabledClasses = new ClassList<IFormatReader>(IFormatReader.class);
    for (int i = 0; i < c.length; i++) {
        boolean on = LociPrefs.isReaderEnabled(c[i]);
        if (on)
            enabledClasses.addClass(c[i]);
    }
    ImageReader reader = new ImageReader(enabledClasses);
    MetadataOptions options = reader.getMetadataOptions();
    if (options instanceof DynamicMetadataOptions) {
        ((DynamicMetadataOptions) options).setBoolean(ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY, allowCZIAutostitch());
        ((DynamicMetadataOptions) options).setBoolean(ZeissCZIReader.INCLUDE_ATTACHMENTS_KEY, includeCZIAttachments());
        ((DynamicMetadataOptions) options).setBoolean(NativeND2Reader.USE_CHUNKMAP_KEY, useND2Chunkmap());
        ((DynamicMetadataOptions) options).setBoolean(LIFReader.OLD_PHYSICAL_SIZE_KEY, isLeicaLIFPhysicalSizeBackwardsCompatible());
        ((DynamicMetadataOptions) options).setBoolean(CellSensReader.FAIL_ON_MISSING_KEY, isCellsensFailOnMissing());
        reader.setMetadataOptions(options);
    }
    // toggle reader-specific options
    boolean nd2Nikon = LociPrefs.isND2Nikon();
    boolean pictQTJava = LociPrefs.isPictQTJava();
    boolean qtQTJava = LociPrefs.isQTQTJava();
    boolean sdtIntensity = LociPrefs.isSDTIntensity();
    boolean tiffImageIO = LociPrefs.isTiffImageIO();
    IFormatReader[] r = reader.getReaders();
    for (int i = 0; i < r.length; i++) {
        if (r[i] instanceof ND2Reader) {
            ND2Reader nd2 = (ND2Reader) r[i];
            nd2.setLegacy(nd2Nikon);
        } else if (r[i] instanceof PictReader) {
            PictReader pict = (PictReader) r[i];
            pict.setLegacy(pictQTJava);
        } else if (r[i] instanceof QTReader) {
            QTReader qt = (QTReader) r[i];
            qt.setLegacy(qtQTJava);
        } else if (r[i] instanceof SDTReader) {
            SDTReader sdt = (SDTReader) r[i];
            sdt.setIntensity(sdtIntensity);
        } else if (r[i] instanceof TiffDelegateReader) {
            TiffDelegateReader tiff = (TiffDelegateReader) r[i];
            tiff.setLegacy(tiffImageIO);
        }
    }
    return reader;
}

Example 3 with ClassList

use of loci.formats.ClassList in project bioformats by openmicroscopy.

the class NRRDReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // make sure we actually have the .nrrd/.nhdr file
    if (!checkSuffix(id, "nhdr") && !checkSuffix(id, "nrrd")) {
        id += ".nhdr";
        if (!new Location(id).exists()) {
            id = id.substring(0, id.lastIndexOf("."));
            id = id.substring(0, id.lastIndexOf("."));
            id += ".nhdr";
        }
        id = new Location(id).getAbsolutePath();
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    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(NRRDReader.class)) {
            newClasses.addClass(c);
        }
    }
    helper = new ImageReader(newClasses);
    helper.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM));
    String key, v;
    String[] pixelSizeUnits = null;
    int numDimensions = 0;
    CoreMetadata m = core.get(0);
    m.sizeX = 1;
    m.sizeY = 1;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.dimensionOrder = "XYCZT";
    String line = in.readLine();
    while (line != null && line.length() > 0) {
        if (!line.startsWith("#") && !line.startsWith("NRRD")) {
            // parse key/value pair
            key = line.substring(0, line.indexOf(':')).trim();
            v = line.substring(line.indexOf(':') + 1).trim();
            addGlobalMeta(key, v);
            if (key.equals("type")) {
                if (v.indexOf("char") != -1 || v.indexOf('8') != -1) {
                    m.pixelType = FormatTools.UINT8;
                } else if (v.indexOf("short") != -1 || v.indexOf("16") != -1) {
                    m.pixelType = FormatTools.UINT16;
                } else if (v.equals("int") || v.equals("signed int") || v.equals("int32") || v.equals("int32_t") || v.equals("uint") || v.equals("unsigned int") || v.equals("uint32") || v.equals("uint32_t")) {
                    m.pixelType = FormatTools.UINT32;
                } else if (v.equals("float"))
                    m.pixelType = FormatTools.FLOAT;
                else if (v.equals("double"))
                    m.pixelType = FormatTools.DOUBLE;
                else
                    throw new FormatException("Unsupported data type: " + v);
            } else if (key.equals("dimension")) {
                numDimensions = Integer.parseInt(v);
            } else if (key.equals("sizes")) {
                String[] tokens = v.split(" ");
                for (int i = 0; i < numDimensions; i++) {
                    int size = Integer.parseInt(tokens[i]);
                    if (numDimensions >= 3 && i == 0 && size > 1 && size <= 16) {
                        m.sizeC = size;
                    } else if (i == 0 || (getSizeC() > 1 && i == 1)) {
                        m.sizeX = size;
                    } else if (i == 1 || (getSizeC() > 1 && i == 2)) {
                        m.sizeY = size;
                    } else if (i == 2 || (getSizeC() > 1 && i == 3)) {
                        m.sizeZ = size;
                    } else if (i == 3 || (getSizeC() > 1 && i == 4)) {
                        m.sizeT = size;
                    }
                }
            } else if (key.equals("data file") || key.equals("datafile")) {
                dataFile = v;
            } else if (key.equals("encoding"))
                encoding = v;
            else if (key.equals("endian")) {
                m.littleEndian = v.equals("little");
            } else if (key.equals("spacings") || key.equals("space directions")) {
                pixelSizes = v.split(" ");
            } else if (key.equals("space units")) {
                pixelSizeUnits = v.split(" ");
            } else if (key.equals("byte skip")) {
                offset = Long.parseLong(v);
            }
        }
        line = in.readLine();
        if (line != null)
            line = line.trim();
    }
    if (dataFile == null)
        offset = in.getFilePointer();
    else {
        Location f = new Location(currentId).getAbsoluteFile();
        Location parent = f.getParentFile();
        if (f.exists() && parent != null) {
            dataFile = dataFile.substring(dataFile.indexOf(File.separator) + 1);
            dataFile = new Location(parent, dataFile).getAbsolutePath();
        }
        initializeHelper = !encoding.equals("raw");
    }
    m.rgb = getSizeC() > 1;
    m.interleaved = true;
    m.imageCount = getSizeZ() * getSizeT();
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (pixelSizes != null) {
            for (int i = 0; i < pixelSizes.length; i++) {
                if (pixelSizes[i] == null)
                    continue;
                try {
                    Double d = parsePixelSize(i);
                    String unit = pixelSizeUnits == null || i >= pixelSizeUnits.length ? null : pixelSizeUnits[i].replaceAll("\"", "");
                    if (i == 0) {
                        Length x = FormatTools.getPhysicalSizeX(d, unit);
                        if (x != null) {
                            store.setPixelsPhysicalSizeX(x, 0);
                        }
                    } else if (i == 1) {
                        Length y = FormatTools.getPhysicalSizeY(d, unit);
                        if (y != null) {
                            store.setPixelsPhysicalSizeY(y, 0);
                        }
                    } else if (i == 2) {
                        Length z = FormatTools.getPhysicalSizeZ(d, unit);
                        if (z != null) {
                            store.setPixelsPhysicalSizeZ(z, 0);
                        }
                    }
                } catch (NumberFormatException e) {
                }
            }
        }
    }
}

Example 4 with ClassList

use of loci.formats.ClassList in project bioformats by openmicroscopy.

the class ImportProcess method createBaseReader.

/**
 * Initializes an {@link loci.formats.IFormatReader}
 * according to the current configuration.
 */
private void createBaseReader() throws FormatException, IOException {
    if (options.isLocal() || options.isHTTP()) {
        BF.status(options.isQuiet(), "Identifying " + idName);
        imageReader = LociPrefs.makeImageReader();
        baseReader = imageReader.getReader(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId());
    } else if (options.isOMERO()) {
        BF.status(options.isQuiet(), "Establishing server connection");
        try {
            ReflectedUniverse r = new ReflectedUniverse();
            r.exec("import loci.ome.io.OmeroReader");
            r.exec("baseReader = new OmeroReader()");
            ClassList<IFormatReader> classes = new ClassList<IFormatReader>(IFormatReader.class);
            r.setVar("classes", classes);
            r.exec("class = baseReader.getClass()");
            r.exec("classes.addClass(class)");
            imageReader = new ImageReader(classes);
            baseReader = imageReader.getReader(options.getId());
        } catch (Exception exc) {
            WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem communicating with the server.");
            cancel();
            return;
        }
    } else {
        WindowTools.reportException(null, options.isQuiet(), "Sorry, there has been an internal error: unknown data source");
        cancel();
        return;
    }
    // attach OME-XML metadata store
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        omeXML = null;
    } catch (DependencyException de) {
        exc = de;
    } catch (ServiceException se) {
        exc = se;
    }
    if (exc != null) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem constructing the OME-XML metadata store");
        throw new FormatException(exc);
    }
    baseReader.setMetadataStore(meta);
    BF.status(options.isQuiet(), "");
    DebugTools.enableIJLogging(IJ.debugMode);
}