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

Example 1 with IFormatReader

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

the class CropDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    final int seriesCount = process.getSeriesCount();
    final IFormatReader r = process.getReader();
    // construct dialog
    final GenericDialog gd = new GenericDialog("Bio-Formats Crop Options");
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        r.setSeries(s);
        Region region = process.getCropRegion(s);
        gd.addMessage(process.getSeriesLabel(s).replaceAll("_", " "));
        gd.addNumericField("X_Coordinate_" + (s + 1), region.x, 0);
        gd.addNumericField("Y_Coordinate_" + (s + 1), region.y, 0);
        gd.addNumericField("Width_" + (s + 1), region.width, 0);
        gd.addNumericField("Height_" + (s + 1), region.height, 0);
    }
    WindowTools.addScrollBars(gd);
    return gd;
}

Example 2 with IFormatReader

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

the class ImportProcess method initializeStack.

/**
 * Performed following ImportStep.STACK notification.
 */
private void initializeStack() throws FormatException, IOException {
    IFormatReader r = baseReader;
    if (options.isGroupFiles()) {
        r = fileStitcher = new FileStitcher(baseReader);
        // overwrite base filename with file pattern
        String id = options.getId();
        fileStitcher.setId(id);
        fileStitcher.setUsingPatternIds(true);
        fileStitcher.setCanChangePattern(false);
    }
    r.setId(options.getId());
    if (options.isGroupFiles()) {
        options.setId(fileStitcher.getFilePattern().getPattern());
    }
    final byte[][] lut8 = r.get8BitLookupTable();
    final int sizeC = r.getSizeC();
    r = channelFiller = new ChannelFiller(r);
    if (channelFiller.isFilled()) {
        BF.warn(options.isQuiet(), getIdName() + ": index values will be lost");
    }
    r = channelSeparator = new ChannelSeparator(r);
    r = dimensionSwapper = new DimensionSwapper(r);
    if (options.isAutoscale() || FormatTools.isFloatingPoint(r)) {
        r = minMaxCalculator = new MinMaxCalculator(r);
    }
    if (options.doStitchTiles()) {
        r = tileStitcher = new TileStitcher(r);
    }
    r = virtualReader = new VirtualReader(r);
    reader = new ImageProcessorReader(r);
    if (options != null && !options.showROIs()) {
        baseReader.getMetadataOptions().setMetadataLevel(MetadataLevel.NO_OVERLAYS);
    }
    setId();
    computeSeriesLabels(reader);
}

Example 3 with IFormatReader

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

the class MakeDatasetStructureTable method printTable.

/**
 * Write the table to the file specified using setOutputFile(String[])
 */
public void printTable() {
    ImageReader baseReader = new ImageReader();
    IFormatReader[] allReaders = baseReader.getReaders();
    Comparator<IFormatReader> comparator = new Comparator<IFormatReader>() {

        @Override
        public int compare(IFormatReader r1, IFormatReader r2) {
            String s1 = r1.getFormat();
            String s2 = r2.getFormat();
            return s1.compareTo(s2);
        }
    };
    Arrays.sort(allReaders, comparator);
    printHeader();
    for (IFormatReader reader : allReaders) {
        try {
            printFormatEntry(reader);
        } catch (IllegalStateException e) {
        }
    }
    printFooter();
}

Example 4 with IFormatReader

use of loci.formats.IFormatReader 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 5 with IFormatReader

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

the class GetPhysicalMetadata method main.

public static void main(String[] args) throws Exception {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java GetMetadata imageFile [seriesNo]");
        System.exit(1);
    }
    String id = args[0];
    int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
    // create OME-XML metadata store
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    // create format reader
    IFormatReader reader = new ImageReader();
    reader.setMetadataStore(meta);
    // initialize file
    System.out.println("Initializing " + id);
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    if (series < seriesCount)
        reader.setSeries(series);
    series = reader.getSeries();
    System.out.println("\tImage series = " + series + " of " + seriesCount);
    printPixelDimensions(reader);
    printPhysicalDimensions(meta, series);
}