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

Example 11 with FilePattern

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

the class BioRadReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // always initialize a PIC file, even if we were given something else
    if (!checkSuffix(id, PIC_SUFFIX)) {
        Location dir = new Location(id).getAbsoluteFile().getParentFile();
        String[] list = dir.list(true);
        for (int i = 0; i < list.length; i++) {
            if (checkSuffix(list[i], PIC_SUFFIX)) {
                id = new Location(dir.getAbsolutePath(), list[i]).getAbsolutePath();
            }
        }
        if (!checkSuffix(id, PIC_SUFFIX)) {
            throw new FormatException("No .pic files found - invalid dataset.");
        }
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    in.order(true);
    offset = new ArrayList<Double>();
    gain = new ArrayList<Double>();
    used = new ArrayList<String>();
    used.add(new Location(currentId).getAbsolutePath());
    LOGGER.info("Reading image dimensions");
    noteStrings = new ArrayList<Note>();
    // read header
    CoreMetadata m = core.get(0);
    m.sizeX = in.readShort();
    m.sizeY = in.readShort();
    int npic = in.readShort();
    m.imageCount = npic;
    int ramp1min = in.readShort();
    int ramp1max = in.readShort();
    boolean notes = in.readInt() != 0;
    m.pixelType = in.readShort() == 0 ? FormatTools.UINT16 : FormatTools.UINT8;
    int imageNumber = in.readShort();
    String name = in.readString(32);
    for (int i = 0; i < name.length(); i++) {
        if (name.charAt(i) == 0) {
            name = name.substring(0, i);
            break;
        }
    }
    float magFactor = 1f;
    int lens = 0;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        int merged = in.readShort();
        int color1 = in.readShort();
        int fileId = in.readShort();
        int ramp2min = in.readShort();
        int ramp2max = in.readShort();
        int color2 = in.readShort();
        int edited = in.readShort();
        lens = in.readShort();
        magFactor = in.readFloat();
        // check validity of header
        if (fileId != PIC_FILE_ID) {
            throw new FormatException("Invalid file header : " + fileId);
        }
        // populate metadata fields
        addGlobalMeta("nx", getSizeX());
        addGlobalMeta("ny", getSizeY());
        addGlobalMeta("npic", getImageCount());
        addGlobalMeta("ramp1_min", ramp1min);
        addGlobalMeta("ramp1_max", ramp1max);
        addGlobalMeta("notes", notes);
        addGlobalMeta("image_number", imageNumber);
        addGlobalMeta("name", name);
        addGlobalMeta("merged", MERGE_NAMES[merged]);
        addGlobalMeta("color1", color1);
        addGlobalMeta("file_id", fileId);
        addGlobalMeta("ramp2_min", ramp2min);
        addGlobalMeta("ramp2_max", ramp2max);
        addGlobalMeta("color2", color2);
        addGlobalMeta("edited", edited);
        addGlobalMeta("lens", lens);
        addGlobalMeta("mag_factor", magFactor);
    } else
        in.skipBytes(20);
    // skip image data
    int imageLen = getSizeX() * getSizeY();
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    in.skipBytes(bpp * getImageCount() * imageLen + 6);
    m.sizeZ = getImageCount();
    m.sizeC = 1;
    m.sizeT = 1;
    m.orderCertain = false;
    m.rgb = false;
    m.interleaved = false;
    m.littleEndian = LITTLE_ENDIAN;
    m.metadataComplete = true;
    m.falseColor = true;
    LOGGER.info("Reading notes");
    MetadataStore store = makeFilterMetadata();
    // read notes
    readNotes(in, true);
    LOGGER.info("Populating metadata");
    // look for companion metadata files
    final List<String> pics = new ArrayList<String>();
    if (isGroupFiles()) {
        Location parent = new Location(currentId).getAbsoluteFile().getParentFile();
        String parentPath = parent.getAbsolutePath();
        String[] list = parent.list(true);
        Arrays.sort(list);
        for (int i = 0; i < list.length; i++) {
            if (list[i].endsWith("lse.xml")) {
                String path = new Location(parentPath, list[i]).getAbsolutePath();
                used.add(path);
                DefaultHandler handler = new BioRadHandler();
                RandomAccessInputStream xml = new RandomAccessInputStream(path);
                XMLTools.parseXML(xml, handler);
                xml.close();
                used.remove(currentId);
                for (int q = 0; q < list.length; q++) {
                    if (checkSuffix(list[q], PIC_SUFFIX)) {
                        path = new Location(parentPath, list[q]).getAbsolutePath();
                        pics.add(path);
                        if (!used.contains(path))
                            used.add(path);
                    }
                }
            } else if (list[i].endsWith("data.raw")) {
                used.add(new Location(parentPath, list[i]).getAbsolutePath());
            }
        }
    }
    // populate Pixels
    m.dimensionOrder = "XYCTZ";
    boolean multipleFiles = parseNotes(store);
    if (multipleFiles && isGroupFiles() && pics.isEmpty()) {
        // do file grouping
        used.remove(currentId);
        long length = new Location(currentId).length();
        FilePattern pattern = new FilePattern(new Location(id).getAbsoluteFile());
        String[] patternFiles = pattern.getFiles();
        for (String file : patternFiles) {
            Location f = new Location(file);
            if (f.length() == length) {
                pics.add(file);
                if (!used.contains(f.getAbsolutePath())) {
                    used.add(f.getAbsolutePath());
                }
            }
        }
        if (pics.size() == 1)
            m.sizeC = 1;
    }
    picFiles = pics.toArray(new String[pics.size()]);
    Arrays.sort(picFiles);
    if (picFiles.length > 0) {
        if (getSizeC() == 0)
            m.sizeC = 1;
        m.imageCount = npic * picFiles.length;
        if (multipleFiles) {
            m.sizeT = getImageCount() / (getSizeZ() * getSizeC());
        } else
            m.sizeC = getImageCount() / (getSizeZ() * getSizeT());
    } else
        picFiles = null;
    if (getEffectiveSizeC() != getSizeC() && !isRGB()) {
        m.sizeC = 1;
    }
    LOGGER.info("Reading lookup tables");
    lut = new byte[getEffectiveSizeC()][][];
    for (int channel = 0; channel < lut.length; channel++) {
        int plane = getIndex(0, channel, 0);
        String file = picFiles == null ? currentId : picFiles[plane % picFiles.length];
        LOGGER.trace("reading table for C = {} from {}", channel, file);
        RandomAccessInputStream s = new RandomAccessInputStream(file);
        s.order(true);
        readLookupTables(s);
        s.close();
        if (lut == null)
            break;
    }
    m.indexed = lut != null;
    MetadataTools.populatePixels(store, this);
    store.setImageName(name, 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // link Instrument and Image
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        // link Objective to Image using ObjectiveSettings
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
        store.setObjectiveLensNA(new Double(lens), 0, 0);
        store.setObjectiveNominalMagnification(new Double(magFactor), 0, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        // link Detector to Image
        for (int i = 0; i < getEffectiveSizeC(); i++) {
            Double detectorOffset = i < offset.size() ? offset.get(i) : null;
            Double detectorGain = i < gain.size() ? gain.get(i) : null;
            if (detectorOffset != null || detectorGain != null) {
                String detectorID = MetadataTools.createLSID("Detector", 0, i);
                store.setDetectorSettingsID(detectorID, 0, i);
                store.setDetectorID(detectorID, 0, i);
                store.setDetectorType(getDetectorType("Other"), 0, i);
            }
            if (detectorOffset != null) {
                store.setDetectorSettingsOffset(detectorOffset, 0, i);
            }
            if (detectorGain != null) {
                store.setDetectorSettingsGain(detectorGain, 0, i);
            }
        }
    }
}

Example 12 with FilePattern

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

the class FilePatternTest method testFindPattern.

@Test(dataProvider = "booleanStates")
public void testFindPattern(Boolean createFiles) throws IOException {
    int minZ = 1, maxZ = 2;
    int minT = 1, maxT = 12;
    int minC = 9, maxC = 11;
    // 2nd prefix empty to test sub-block detection
    String[] prefixes = { "foo_", "", "c" };
    String[] formats = { "%d", "%02d", "%d" };
    String[] blocks = { String.format("<%d-%d>", minZ, maxZ), String.format("<%02d-%02d>", minT, maxT), String.format("<%d-%d>", minC, maxC) };
    String suffix = ".ext";
    String pattern = mkPattern(prefixes, blocks, suffix);
    List<String> names = new ArrayList<String>();
    names.add("outlier.ext");
    for (int z = minZ; z <= maxZ; z++) {
        for (int t = minT; t <= maxT; t++) {
            for (int c = minC; c <= maxC; c++) {
                names.add(mkPattern(prefixes, new String[] { String.format(formats[0], z), String.format(formats[1], t), String.format(formats[2], c) }, suffix));
            }
        }
    }
    String[] namesA = names.toArray(new String[names.size()]);
    if (!createFiles) {
        assertEquals(FilePattern.findPattern(namesA[1], null, namesA), pattern);
        // test excludeAxes
        String[] minCBlocks = new String[] { blocks[0], blocks[1], Integer.toString(minC) };
        int[] excl = new int[] { AxisGuesser.C_AXIS };
        assertEquals(FilePattern.findPattern(namesA[1], null, namesA, excl), mkPattern(prefixes, minCBlocks, suffix));
        return;
    }
    Path wd = Files.createTempDirectory("");
    wd.toFile().deleteOnExit();
    String absPattern = resolveToString(wd, pattern);
    String[] fullNames = mkFiles(wd, namesA);
    assertEquals(FilePattern.findPattern(fullNames[1]), absPattern);
    assertEquals(FilePattern.findPattern(namesA[1], wd.toString()), absPattern);
    assertEquals(FilePattern.findPattern(new File(fullNames[1])), absPattern);
    assertEquals(FilePattern.findPattern(new Location(fullNames[1])), absPattern);
    // test constructors that use findPattern
    FilePattern fp = new FilePattern(new Location(fullNames[1]));
    assertEquals(fp.getPattern(), absPattern);
    fp = new FilePattern(namesA[1], wd.toString());
    assertEquals(fp.getPattern(), absPattern);
}

Example 13 with FilePattern

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

the class FilePatternTest method testSingleFile.

@Test
public void testSingleFile() {
    String pattern = "test.fake";
    FilePattern fp = new FilePattern(pattern);
    assertTrue(fp.isValid());
    assertTrue(fp.isRegex());
    assertEquals(fp.getPattern(), pattern);
    assertEquals(fp.getFiles(), new String[] { pattern });
}

Example 14 with FilePattern

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

the class FilePatternTest method testBadPatterns.

@Test(dataProvider = "badPatterns")
public void testBadPatterns(String pattern) {
    FilePattern fp = new FilePattern(pattern);
    assertFalse(fp.isValid());
    assertNotNull(fp.getErrorMessage());
}

Example 15 with FilePattern

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

the class TCSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    Location l = new Location(id).getAbsoluteFile();
    Location parent = l.getParentFile();
    String[] list = parent.list();
    Arrays.sort(list);
    boolean isXML = checkSuffix(id, XML_SUFFIX);
    if (list != null) {
        for (String file : list) {
            if (checkSuffix(file, XML_SUFFIX) && !isXML && isGroupFiles()) {
                xmlFile = new Location(parent, file).getAbsolutePath();
                break;
            } else if (checkSuffix(file, TiffReader.TIFF_SUFFIXES) && isXML) {
                initFile(new Location(parent, file).getAbsolutePath());
                return;
            }
        }
    }
    if (isXML)
        xmlFile = l.getAbsolutePath();
    super.initFile(id);
    MetadataStore store = makeFilterMetadata();
    in = new RandomAccessInputStream(id, 16);
    tiffParser = new TiffParser(in);
    tiffs = new ArrayList<String>();
    IFDList ifds = tiffParser.getIFDs();
    String date = ifds.get(0).getIFDStringValue(IFD.DATE_TIME);
    if (date != null) {
        datestamp = DateTools.getTime(date, "yyyy:MM:dd HH:mm:ss");
    }
    groupFiles();
    addGlobalMeta("Number of image files", tiffs.size());
    tiffReaders = new TiffReader[tiffs.size()];
    for (int i = 0; i < tiffReaders.length; i++) {
        tiffReaders[i] = new TiffReader();
    }
    tiffReaders[0].setId(tiffs.get(0));
    int[] ch = new int[ifds.size()];
    int[] idx = new int[ifds.size()];
    long[] stamp = new long[ifds.size()];
    int channelCount = 0;
    CoreMetadata ms0 = core.get(0);
    ms0.sizeZ = 1;
    ms0.sizeC = tiffReaders[0].getSizeC();
    ms0.dimensionOrder = isRGB() ? "XYC" : "XY";
    if (isGroupFiles()) {
        try {
            FilePattern fp = new FilePattern(new Location(currentId).getAbsoluteFile());
            AxisGuesser guesser = new AxisGuesser(fp, "XYTZC", 1, ifds.size(), 1, true);
            int[] axisTypes = guesser.getAxisTypes();
            int[] count = fp.getCount();
            for (int i = axisTypes.length - 1; i >= 0; i--) {
                if (axisTypes[i] == AxisGuesser.Z_AXIS) {
                    if (getDimensionOrder().indexOf('Z') == -1) {
                        ms0.dimensionOrder += 'Z';
                    }
                    ms0.sizeZ *= count[i];
                } else if (axisTypes[i] == AxisGuesser.C_AXIS) {
                    if (getDimensionOrder().indexOf('C') == -1) {
                        ms0.dimensionOrder += 'C';
                    }
                    ms0.sizeC *= count[i];
                }
            }
        } catch (NullPointerException e) {
        }
    }
    for (int i = 0; i < ifds.size(); i++) {
        String document = ifds.get(i).getIFDStringValue(IFD.DOCUMENT_NAME);
        if (document == null)
            continue;
        int index = document.indexOf("INDEX");
        String s = document.substring(8, index).trim();
        ch[i] = Integer.parseInt(s);
        if (ch[i] > channelCount)
            channelCount = ch[i];
        int space = document.indexOf(" ", index + 6);
        if (space < 0)
            continue;
        String n = document.substring(index + 6, space).trim();
        idx[i] = Integer.parseInt(n);
        date = document.substring(space, document.indexOf("FORMAT")).trim();
        stamp[i] = DateTools.getTime(date, DATE_FORMAT, ".");
        addGlobalMetaList("Timestamp for plane", stamp[i]);
    }
    ms0.sizeT = 0;
    // determine the axis sizes and ordering
    boolean unique = true;
    for (int i = 0; i < stamp.length; i++) {
        for (int j = i + 1; j < stamp.length; j++) {
            if (stamp[j] == stamp[i]) {
                unique = false;
                break;
            }
        }
        if (unique) {
            ms0.sizeT++;
            if (getDimensionOrder().indexOf('T') < 0) {
                ms0.dimensionOrder += 'T';
            }
        } else if (i > 0) {
            if ((ch[i] != ch[i - 1]) && getDimensionOrder().indexOf('C') < 0) {
                ms0.dimensionOrder += 'C';
            } else if (getDimensionOrder().indexOf('Z') < 0) {
                ms0.dimensionOrder += 'Z';
            }
        }
        unique = true;
    }
    if (getDimensionOrder().indexOf('Z') < 0)
        ms0.dimensionOrder += 'Z';
    if (getDimensionOrder().indexOf('C') < 0)
        ms0.dimensionOrder += 'C';
    if (getDimensionOrder().indexOf('T') < 0)
        ms0.dimensionOrder += 'T';
    if (getSizeC() == 0)
        ms0.sizeC = 1;
    if (getSizeT() == 0)
        ms0.sizeT = 1;
    if (channelCount == 0)
        channelCount = 1;
    if (getSizeZ() <= 1) {
        ms0.sizeZ = ifds.size() / (getSizeT() * channelCount);
    }
    ms0.sizeC *= channelCount;
    ms0.imageCount = getSizeZ() * getSizeT() * getSizeC();
    // cut up comment
    String comment = ifds.get(0).getComment();
    if (comment != null && comment.startsWith("[") && getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String[] lines = comment.split("\n");
        for (String line : lines) {
            if (!line.startsWith("[")) {
                int eq = line.indexOf('=');
                if (eq < 0)
                    continue;
                String key = line.substring(0, eq).trim();
                String value = line.substring(eq + 1).trim();
                if (key.equals("VoxelSizeX")) {
                    try {
                        voxelX = Double.parseDouble(value);
                    } catch (NumberFormatException e) {
                    }
                } else if (key.equals("VoxelSizeY")) {
                    try {
                        voxelY = Double.parseDouble(value);
                    } catch (NumberFormatException e) {
                    }
                } else if (key.equals("VoxelSizeZ")) {
                    try {
                        voxelZ = Double.parseDouble(value);
                    } catch (NumberFormatException e) {
                    }
                }
                addGlobalMeta(key, value);
            }
        }
        metadata.remove("Comment");
    }
    ms0.sizeX = tiffReaders[0].getSizeX();
    ms0.sizeY = tiffReaders[0].getSizeY();
    ms0.rgb = tiffReaders[0].isRGB();
    ms0.pixelType = tiffReaders[0].getPixelType();
    ms0.littleEndian = tiffReaders[0].isLittleEndian();
    ms0.interleaved = tiffReaders[0].isInterleaved();
    ms0.falseColor = true;
    ms0.indexed = tiffReaders[0].isIndexed();
    if (isRGB())
        ms0.imageCount /= (getSizeC() / channelCount);
    if (getSizeZ() * getSizeT() * getEffectiveSizeC() != (ifds.size() * tiffReaders.length)) {
        int c = getEffectiveSizeC();
        if (c == 0)
            c = 1;
        ms0.sizeT = (ifds.size() * tiffReaders.length) / (c * getSizeZ());
        ms0.imageCount = getSizeT() * c * getSizeZ();
        if (getSizeT() == 0) {
            ms0.sizeT = 1;
            ms0.imageCount = ifds.size() * tiffReaders.length;
        }
    }
    if (getImageCount() == ifds.size() * getSizeZ() * getSizeT() && ifds.size() > 1) {
        if (getSizeZ() == 1) {
            ms0.sizeZ = ifds.size();
        } else if (getSizeT() == 1) {
            ms0.sizeT = ifds.size();
        } else
            ms0.sizeZ *= ifds.size();
    }
    if (xmlFile != null) {
        // parse XML metadata
        String xml = DataTools.readFile(xmlFile);
        xml = XMLTools.sanitizeXML(PREFIX + xml + SUFFIX);
        LeicaHandler handler = new LeicaHandler(store, getMetadataOptions().getMetadataLevel());
        XMLTools.parseXML(xml, handler);
        metadata = handler.getGlobalMetadata();
        MetadataTools.merge(handler.getGlobalMetadata(), metadata, "");
        core = handler.getCoreMetadataList();
        for (int i = 0; i < getSeriesCount(); i++) {
            CoreMetadata ms = core.get(i);
            if (tiffs.size() < ms.imageCount) {
                int div = ms.imageCount / ms.sizeC;
                ms.imageCount = tiffs.size();
                if (div >= ms.sizeZ)
                    ms.sizeZ /= div;
                else if (div >= ms.sizeT)
                    ms.sizeT /= div;
            }
            ms.dimensionOrder = getSizeZ() > getSizeT() ? "XYCZT" : "XYCTZ";
            ms.rgb = false;
            ms.interleaved = false;
            ms.indexed = tiffReaders[0].isIndexed();
        }
    }
    MetadataTools.populatePixels(store, this, true);
    Length sizeX = FormatTools.getPhysicalSizeX(voxelX);
    Length sizeY = FormatTools.getPhysicalSizeY(voxelY);
    Length sizeZ = FormatTools.getPhysicalSizeZ(voxelZ);
    if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
    }
    if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
    }
    if (sizeZ != null) {
        store.setPixelsPhysicalSizeZ(sizeZ, 0);
    }
}