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

Example 11 with IFormatReader

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

the class FormatReaderTest method testIsThisType.

@Test(groups = { "all", "fast", "automated" })
public void testIsThisType() {
    String testName = "testIsThisType";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        IFormatReader r = reader;
        // unwrap reader
        while (true) {
            if (r instanceof ReaderWrapper) {
                r = ((ReaderWrapper) r).getReader();
            } else if (r instanceof FileStitcher) {
                r = ((FileStitcher) r).getReader();
            } else
                break;
        }
        if (r instanceof ImageReader) {
            ImageReader ir = (ImageReader) r;
            r = ir.getReader();
            IFormatReader[] readers = ir.getReaders();
            String[] used = reader.getUsedFiles();
            for (int i = 0; i < used.length && success; i++) {
                // and only one reader, identifies the dataset as its own
                for (int j = 0; j < readers.length; j++) {
                    boolean result = readers[j].isThisType(used[i]);
                    // TIFF reader is allowed to redundantly green-light files
                    if (result && readers[j] instanceof TiffDelegateReader)
                        continue;
                    // green-light PIC files from NRRD datasets
                    if (result && r instanceof NRRDReader && readers[j] instanceof BioRadReader) {
                        String low = used[i].toLowerCase();
                        boolean isPic = low.endsWith(".pic") || low.endsWith(".pic.gz");
                        if (isPic)
                            continue;
                    }
                    // Analyze reader is allowed to redundantly accept NIfTI files
                    if (result && r instanceof NiftiReader && readers[j] instanceof AnalyzeReader) {
                        continue;
                    }
                    if (result && r instanceof MetamorphReader && readers[j] instanceof MetamorphTiffReader) {
                        continue;
                    }
                    if (result && (readers[j] instanceof L2DReader) || ((r instanceof L2DReader) && (readers[j] instanceof GelReader) || readers[j] instanceof L2DReader)) {
                        continue;
                    }
                    // ND2Reader is allowed to accept JPEG-2000 files
                    if (result && r instanceof JPEG2000Reader && readers[j] instanceof ND2Reader) {
                        continue;
                    }
                    if ((result && r instanceof APLReader && readers[j] instanceof SISReader) || (!result && r instanceof APLReader && readers[j] instanceof APLReader)) {
                        continue;
                    }
                    // reader to pick up TIFFs from a Prairie dataset
                    if (result && r instanceof PrairieReader && readers[j] instanceof OMETiffReader) {
                        continue;
                    }
                    // extra metadata files
                    if (result && r instanceof ColumbusReader && readers[j] instanceof OMETiffReader) {
                        continue;
                    }
                    // with an extra metadata file
                    if (result && r instanceof MicromanagerReader && readers[j] instanceof OMETiffReader) {
                        continue;
                    }
                    if (!result && r instanceof MicromanagerReader && readers[j] instanceof MicromanagerReader && (used[i].toLowerCase().endsWith(".ome.tif") || used[i].toLowerCase().endsWith(".ome.tiff"))) {
                        continue;
                    }
                    if (result && r instanceof TrestleReader && (readers[j] instanceof JPEGReader || readers[j] instanceof PGMReader || readers[j] instanceof TiffDelegateReader)) {
                        continue;
                    }
                    if (result && ((r instanceof HitachiReader) || (readers[j] instanceof HitachiReader && (r instanceof TiffDelegateReader || r instanceof JPEGReader || r instanceof BMPReader)))) {
                        continue;
                    }
                    if (result && r instanceof BDReader && readers[j] instanceof BMPReader) {
                        continue;
                    }
                    if (!result && readers[j] instanceof BDReader && (used[i].endsWith(".bmp") || used[i].endsWith(".adf") || used[i].endsWith(".txt") || used[i].endsWith(".roi"))) {
                        continue;
                    }
                    if (!result && r instanceof VolocityReader && readers[j] instanceof VolocityReader) {
                        continue;
                    }
                    if (!result && r instanceof InCellReader && readers[j] instanceof InCellReader && !used[i].toLowerCase().endsWith(".xdce")) {
                        continue;
                    }
                    if (!result && r instanceof BrukerReader && readers[j] instanceof BrukerReader && !used[i].toLowerCase().equals("acqp") && !used[i].toLowerCase().equals("fid")) {
                        continue;
                    }
                    // Volocity reader is allowed to accept files of other formats
                    if (result && r instanceof VolocityReader) {
                        continue;
                    }
                    if (result && r instanceof NikonReader && readers[j] instanceof DNGReader) {
                        continue;
                    }
                    // DICOM reader is not expected to pick up companion files
                    if (!result && r instanceof DicomReader && readers[j] instanceof DicomReader) {
                        continue;
                    }
                    // AFI reader is not expected to pick up .svs files
                    if (r instanceof AFIReader && (readers[j] instanceof AFIReader || readers[j] instanceof SVSReader)) {
                        continue;
                    }
                    if (!result && readers[j] instanceof MIASReader) {
                        continue;
                    }
                    if ((readers[j] instanceof NDPISReader || r instanceof NDPISReader) && used[i].toLowerCase().endsWith(".ndpi")) {
                        continue;
                    }
                    // Hamamatsu VMS dataset
                    if (readers[j] instanceof JPEGReader && r instanceof HamamatsuVMSReader && used[i].toLowerCase().endsWith(".jpg")) {
                        continue;
                    }
                    // the Hamamatsu VMS reader only picks up its .vms file
                    if (!result && !used[i].toLowerCase().endsWith(".vms") && r instanceof HamamatsuVMSReader) {
                        continue;
                    }
                    // QuickTime reader doesn't pick up resource forks
                    if (!result && i > 0 && r instanceof QTReader) {
                        continue;
                    }
                    if (r instanceof CellVoyagerReader && (!result || readers[j] instanceof OMEXMLReader) && used[i].toLowerCase().endsWith(".ome.xml")) {
                        continue;
                    }
                    // the pattern reader only picks up pattern files
                    if (!used[i].toLowerCase().endsWith(".pattern") && r instanceof FilePatternReader) {
                        continue;
                    }
                    // ignore companion files for Leica LIF
                    if (!used[i].toLowerCase().endsWith(".lif") && r instanceof LIFReader) {
                        continue;
                    }
                    boolean expected = r == readers[j];
                    if (result != expected) {
                        success = false;
                        if (result) {
                            msg = TestTools.shortClassName(readers[j]) + " flagged \"" + used[i] + "\" but so did " + TestTools.shortClassName(r);
                        } else {
                            msg = TestTools.shortClassName(readers[j]) + " skipped \"" + used[i] + "\"";
                        }
                        break;
                    }
                }
            }
        } else {
            success = false;
            msg = "Reader " + r.getClass().getName() + " is not an ImageReader";
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 12 with IFormatReader

use of loci.formats.IFormatReader 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 13 with IFormatReader

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

the class BioFormatsExtensionPrinter method main.

public static void main(String[] args) throws IOException {
    System.out.println("Generating list of Bio-Formats supported suffixes...");
    try (IFormatReader reader = new ImageReader()) {
        String[] suffixes = reader.getSuffixes();
        PrintWriter fo = null;
        fo = new PrintWriter(new File("BioFormatsSuffixes.txt"), Constants.ENCODING);
        for (String s : suffixes) fo.println("*." + s);
        fo.close();
        System.out.println(suffixes.length + " suffixes discovered.");
    }
}

Example 14 with IFormatReader

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

the class PrintFormatTable method printSupportedFormats.

public static void printSupportedFormats(String[] args) {
    PrintStyles printStyle = PrintStyles.TXT;
    boolean usage = false;
    if (args != null) {
        for (int i = 0; i < args.length; i++) {
            if (args[i].equals("-help"))
                usage = true;
            else if (args[i].equals("-xml"))
                printStyle = PrintStyles.XML;
            else if (args[i].equals("-html"))
                printStyle = PrintStyles.HTML;
            else if (args[i].equals("-txt"))
                printStyle = PrintStyles.TXT;
            else {
                LOGGER.warn("unknown flag: {}; try -help for options", args[i]);
            }
        }
    }
    if (usage) {
        LOGGER.info("Usage: formatlist [-html] [-txt] [-xml]");
        LOGGER.info("  -html: show formats in an HTML table");
        LOGGER.info("   -txt: show formats in plaintext (default)");
        LOGGER.info("   -xml: show formats as XML data");
        return;
    }
    LOGGER.info(getHeader(printStyle));
    // retrieve all of the file format readers and writers
    ImageReader baseReader = new ImageReader();
    IFormatReader[] readers = baseReader.getReaders();
    ImageWriter baseWriter = new ImageWriter();
    IFormatWriter[] writers = baseWriter.getWriters();
    for (int i = 0; i < readers.length; i++) {
        String readerFormatName = readers[i].getFormat();
        boolean read = true;
        boolean write = false;
        boolean wmp = false;
        // check if there is a corresponding writer
        IFormatWriter writer = null;
        for (int j = 0; j < writers.length; j++) {
            if (writers[j].getFormat().equals(readerFormatName)) {
                writer = writers[j];
            }
        }
        if (writer != null) {
            write = true;
            // written to a single file
            if (writer.canDoStacks())
                wmp = true;
        }
        String[] extensions = readers[i].getSuffixes();
        StringBuilder ext = new StringBuilder();
        for (int j = 0; j < extensions.length; j++) {
            ext.append(extensions[j]);
            if (j < extensions.length - 1) {
                ext.append(", ");
            }
        }
        // display information about the format
        LOGGER.info(getFormatLine(printStyle, readerFormatName, read, write, wmp, ext.toString()));
    }
    LOGGER.info(getFooter(printStyle));
}

Example 15 with IFormatReader

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

the class ImageConverterTest method checkImage.

public void checkImage() throws FormatException, IOException {
    IFormatReader r = new ImageReader();
    r.setId(outFile.getAbsolutePath());
    assertEquals(r.getSizeX(), 512);
    r.close();
}