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Example 16 with Location

use of loci.common.Location 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);
}
Also used : IniParser(loci.common.IniParser) IFormatReader(loci.formats.IFormatReader) IniList(loci.common.IniList) ClassList(loci.formats.ClassList) CoreMetadata(loci.formats.CoreMetadata) Timestamp(ome.xml.model.primitives.Timestamp) FormatException(loci.formats.FormatException) MetadataStore(loci.formats.meta.MetadataStore) IniTable(loci.common.IniTable) BufferedReader(java.io.BufferedReader) StringReader(java.io.StringReader) ImageReader(loci.formats.ImageReader) Location(loci.common.Location)

Example 17 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class HitachiReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
    if (!open) {
        return false;
    }
    String base = name;
    if (base.indexOf('.') >= 0) {
        base = base.substring(0, base.lastIndexOf("."));
    }
    if (checkSuffix(name, "txt")) {
        Location bmp = new Location(base + ".bmp");
        Location jpg = new Location(base + ".jpg");
        Location tif = new Location(base + ".tif");
        if (!bmp.exists() && !jpg.exists() && !tif.exists()) {
            return false;
        }
        return super.isThisType(name, open);
    }
    String textFile = base + ".txt";
    return new Location(textFile).exists() && isThisType(textFile, open);
}
Also used : Location(loci.common.Location)

Example 18 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class ImarisHDFReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        netcdf = factory.getInstance(NetCDFService.class);
        netcdf.setFile(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(NetCDFServiceImpl.NO_NETCDF_MSG, e);
    }
    pixelSizeX = pixelSizeY = pixelSizeZ = 1;
    emWave = new ArrayList<String>();
    exWave = new ArrayList<String>();
    channelMin = new ArrayList<String>();
    channelMax = new ArrayList<String>();
    gain = new ArrayList<String>();
    pinhole = new ArrayList<String>();
    channelName = new ArrayList<String>();
    microscopyMode = new ArrayList<String>();
    colors = new ArrayList<double[]>();
    seriesCount = 0;
    // read all of the metadata key/value pairs
    parseAttributes();
    CoreMetadata ms0 = core.get(0);
    if (seriesCount > 1) {
        for (int i = 1; i < seriesCount; i++) {
            core.add(new CoreMetadata());
        }
        for (int i = 1; i < seriesCount; i++) {
            CoreMetadata ms = core.get(i);
            String groupPath = "DataSet/ResolutionLevel_" + i + "/TimePoint_0/Channel_0";
            ms.sizeX = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeX"));
            ms.sizeY = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeY"));
            ms.sizeZ = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeZ"));
            ms.imageCount = ms.sizeZ * getSizeC() * getSizeT();
            ms.sizeC = getSizeC();
            ms.sizeT = getSizeT();
            ms.thumbnail = true;
            if (ms.sizeZ == ms0.sizeZ && ms.sizeC == ms0.sizeC && ms.sizeT == ms0.sizeT) {
                // do not assume that all series will have the same dimensions
                // if the Z, C or T size is different, then it cannot
                // be a subresolution
                ms0.resolutionCount++;
            }
        }
    }
    ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
    ms0.thumbnail = false;
    ms0.dimensionOrder = "XYZCT";
    // determine pixel type - this isn't stored in the metadata, so we need
    // to check the pixels themselves
    int type = -1;
    Object pix = getImageData(0, 0, 0, 1, 1);
    if (pix instanceof byte[][])
        type = FormatTools.UINT8;
    else if (pix instanceof short[][])
        type = FormatTools.UINT16;
    else if (pix instanceof int[][])
        type = FormatTools.UINT32;
    else if (pix instanceof float[][])
        type = FormatTools.FLOAT;
    else if (pix instanceof double[][])
        type = FormatTools.DOUBLE;
    else {
        throw new FormatException("Unknown pixel type: " + pix);
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        ms.pixelType = type;
        ms.dimensionOrder = "XYZCT";
        ms.rgb = false;
        ms.thumbSizeX = 128;
        ms.thumbSizeY = 128;
        ms.orderCertain = true;
        ms.littleEndian = true;
        ms.interleaved = false;
        ms.indexed = colors.size() >= getSizeC();
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String imageName = new Location(getCurrentFile()).getName();
    for (int s = 0; s < getSeriesCount(); s++) {
        store.setImageName(imageName + " Resolution Level " + (s + 1), s);
    }
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
        return;
    }
    int cIndex = 0;
    for (int s = 0; s < getSeriesCount(); s++) {
        setSeries(s);
        double px = pixelSizeX, py = pixelSizeY, pz = pixelSizeZ;
        if (px == 1)
            px = (maxX - minX) / getSizeX();
        if (py == 1)
            py = (maxY - minY) / getSizeY();
        if (pz == 1)
            pz = (maxZ - minZ) / getSizeZ();
        Length sizeX = FormatTools.getPhysicalSizeX(px);
        Length sizeY = FormatTools.getPhysicalSizeY(py);
        Length sizeZ = FormatTools.getPhysicalSizeZ(pz);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, s);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, s);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, s);
        }
        for (int i = 0; i < getSizeC(); i++, cIndex++) {
            Float gainValue = null;
            Integer pinholeValue = null, emWaveValue = null, exWaveValue;
            if (cIndex < gain.size()) {
                try {
                    gainValue = new Float(gain.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < pinhole.size()) {
                try {
                    pinholeValue = new Integer(pinhole.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < emWave.size()) {
                try {
                    emWaveValue = new Integer(emWave.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < exWave.size()) {
                try {
                    exWaveValue = new Integer(exWave.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            Double minValue = null, maxValue = null;
            if (cIndex < channelMin.size()) {
                try {
                    minValue = new Double(channelMin.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < channelMax.size()) {
                try {
                    maxValue = new Double(channelMax.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (i < colors.size()) {
                double[] color = colors.get(i);
                Color realColor = new Color((int) (color[0] * 255), (int) (color[1] * 255), (int) (color[2] * 255), 255);
                store.setChannelColor(realColor, s, i);
            }
        }
    }
    setSeries(0);
}
Also used : ServiceFactory(loci.common.services.ServiceFactory) Color(ome.xml.model.primitives.Color) DependencyException(loci.common.services.DependencyException) CoreMetadata(loci.formats.CoreMetadata) FormatException(loci.formats.FormatException) MetadataStore(loci.formats.meta.MetadataStore) Length(ome.units.quantity.Length) MissingLibraryException(loci.formats.MissingLibraryException) NetCDFService(loci.formats.services.NetCDFService) Location(loci.common.Location)

Example 19 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class InCellReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    int[] coordinates = getZCTCoords(no);
    int well = getWellFromSeries(getSeries());
    int field = getFieldFromSeries(getSeries());
    int timepoint = oneTimepointPerSeries ? getSeries() % channelsPerTimepoint.size() : coordinates[2];
    int image = getIndex(coordinates[0], coordinates[1], 0);
    if (imageFiles[well][field][timepoint][image] == null)
        return buf;
    String filename = imageFiles[well][field][timepoint][image].filename;
    if (filename == null || !(new Location(filename).exists()))
        return buf;
    if (imageFiles[well][field][timepoint][image].isTiff) {
        try {
            tiffReader.setId(filename);
            return tiffReader.openBytes(0, buf, x, y, w, h);
        } catch (FormatException e) {
            LOGGER.debug("", e);
        } catch (IOException e) {
            LOGGER.debug("", e);
        }
        return buf;
    }
    // pixels are stored in .im files
    RandomAccessInputStream s = new RandomAccessInputStream(filename);
    if (s.length() > FormatTools.getPlaneSize(this)) {
        s.seek(128);
        readPlane(s, x, y, w, h, buf);
    }
    s.close();
    return buf;
}
Also used : IOException(java.io.IOException) RandomAccessInputStream(loci.common.RandomAccessInputStream) FormatException(loci.formats.FormatException) Location(loci.common.Location)

Example 20 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class InCellReader method getSeriesUsedFiles.

/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
    FormatTools.assertId(currentId, true, 1);
    final List<String> files = new ArrayList<String>();
    files.add(currentId);
    files.addAll(metadataFiles);
    if (!noPixels && imageFiles != null) {
        int well = getWellFromSeries(getSeries());
        int field = getFieldFromSeries(getSeries());
        for (Image[] timepoints : imageFiles[well][field]) {
            for (Image plane : timepoints) {
                if (plane != null && plane.filename != null) {
                    if (new Location(plane.filename).exists()) {
                        files.add(plane.filename);
                    }
                    if (plane.thumbnailFile != null && new Location(plane.thumbnailFile).exists()) {
                        files.add(plane.thumbnailFile);
                    }
                }
            }
        }
    }
    return files.toArray(new String[files.size()]);
}
Also used : ArrayList(java.util.ArrayList) Location(loci.common.Location)

Aggregations

Location (loci.common.Location)185 CoreMetadata (loci.formats.CoreMetadata)55 MetadataStore (loci.formats.meta.MetadataStore)51 FormatException (loci.formats.FormatException)49 ArrayList (java.util.ArrayList)47 RandomAccessInputStream (loci.common.RandomAccessInputStream)47 Length (ome.units.quantity.Length)34 IOException (java.io.IOException)28 Timestamp (ome.xml.model.primitives.Timestamp)28 Time (ome.units.quantity.Time)20 IFD (loci.formats.tiff.IFD)15 TiffParser (loci.formats.tiff.TiffParser)15 NonNegativeInteger (ome.xml.model.primitives.NonNegativeInteger)15 PositiveInteger (ome.xml.model.primitives.PositiveInteger)15 DependencyException (loci.common.services.DependencyException)13 ServiceException (loci.common.services.ServiceException)12 File (java.io.File)11 ServiceFactory (loci.common.services.ServiceFactory)11 IniList (loci.common.IniList)10 FilePattern (loci.formats.FilePattern)10