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

Example 1 with AxisGuesser

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

the class LeicaReader method parseFilenames.

private void parseFilenames(int seriesIndex) throws IOException {
    int maxPlanes = 0;
    final List<String> f = new ArrayList<String>();
    int tempImages = in.readInt();
    if (((long) tempImages * nameLength) > in.length()) {
        in.order(!isLittleEndian());
        tempImages = in.readInt();
        in.order(isLittleEndian());
    }
    CoreMetadata ms = core.get(seriesIndex);
    ms.sizeX = in.readInt();
    ms.sizeY = in.readInt();
    in.skipBytes(4);
    int samplesPerPixel = in.readInt();
    ms.rgb = samplesPerPixel > 1;
    ms.sizeC = samplesPerPixel;
    boolean tiffsExist = false;
    String dirPrefix = new Location(currentId).getAbsoluteFile().getParent();
    if (!dirPrefix.endsWith(File.separator))
        dirPrefix += File.separator;
    String prefix = "";
    for (int j = 0; j < tempImages; j++) {
        // read in each filename
        prefix = getString(nameLength);
        f.add(dirPrefix + prefix);
        // test to make sure the path is valid
        Location test = new Location(f.get(f.size() - 1)).getAbsoluteFile();
        LOGGER.debug("Expected to find TIFF file {}", test.getAbsolutePath());
        if (!test.exists()) {
            LOGGER.debug("  file does not exist");
        }
        if (!tiffsExist)
            tiffsExist = test.exists();
    }
    if (!tiffsExist) {
        // Strategy for handling renamed files:
        // 1) Assume that files for each series follow a pattern.
        // 2) Assign each file group to the first series with the correct count.
        LOGGER.info("Handling renamed TIFF files");
        String[] listing = getTIFFList();
        // grab the file patterns
        final List<String> filePatterns = new ArrayList<String>();
        for (String q : listing) {
            Location l = new Location(q).getAbsoluteFile();
            if (!l.exists()) {
                l = new Location(dirPrefix, q).getAbsoluteFile();
            }
            FilePattern pattern = new FilePattern(l);
            if (!pattern.isValid())
                continue;
            AxisGuesser guess = new AxisGuesser(pattern, "XYZCT", 1, 1, 1, false);
            String fp = pattern.getPattern();
            if (guess.getAxisCountS() >= 1) {
                String pre = pattern.getPrefix(guess.getAxisCountS());
                final List<String> fileList = new ArrayList<String>();
                for (int n = 0; n < listing.length; n++) {
                    Location p = new Location(dirPrefix, listing[n]);
                    if (p.getAbsolutePath().startsWith(pre)) {
                        fileList.add(listing[n]);
                    }
                }
                fp = FilePattern.findPattern(l.getAbsolutePath(), dirPrefix, fileList.toArray(new String[fileList.size()]));
            }
            if (fp != null && !filePatterns.contains(fp)) {
                filePatterns.add(fp);
            }
        }
        for (String q : filePatterns) {
            String[] pattern = new FilePattern(q).getFiles();
            if (pattern.length == tempImages) {
                // make sure that this pattern hasn't already been used
                boolean validPattern = true;
                for (int n = 0; n < seriesIndex; n++) {
                    if (files[n] == null)
                        continue;
                    if (files[n].contains(pattern[0])) {
                        validPattern = false;
                        break;
                    }
                }
                if (validPattern) {
                    files[seriesIndex] = new ArrayList<String>();
                    files[seriesIndex].addAll(Arrays.asList(pattern));
                }
            }
        }
    } else {
        files[seriesIndex] = f;
        for (int s = 0; s < seriesIndex; s++) {
            if (files[s] != null) {
                if (files[s].get(0).equals(f.get(0))) {
                    valid[s] = false;
                    files[s] = null;
                }
            }
        }
    }
    if (files[seriesIndex] == null)
        valid[seriesIndex] = false;
    else {
        ms.imageCount = files[seriesIndex].size();
        maxPlanes = (int) Math.max(maxPlanes, ms.imageCount);
    }
}

Example 2 with AxisGuesser

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

the class AxisGuesserTest method check.

private void check(// IN
String p, // IN
String order, // IN
int sZ, // IN
int sT, // IN
int sC, // IN
boolean cert, String newOrder, int[] types) {
    // OUT
    FilePattern fp = new FilePattern(p);
    AxisGuesser ag = new AxisGuesser(fp, order, sZ, sT, sC, cert);
    assertEquals(ag.getFilePattern().getPattern(), p);
    assertEquals(ag.getOriginalOrder(), order);
    assertEquals(ag.getAdjustedOrder(), newOrder);
    assertEquals(ag.getAxisTypes(), types);
    checkAxisCount(ag, types);
}

Example 3 with AxisGuesser

use of loci.formats.AxisGuesser 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);
    }
}