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

Example 1 with FormatException

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

the class Colorizer method applyDisplayRanges.

// -- Helper methods --
private void applyDisplayRanges(ImagePlus imp, int series) {
    if (imp instanceof VirtualImagePlus) {
        // virtual stacks handle their own display ranges
        return;
    }
    final ImporterOptions options = process.getOptions();
    final ImageProcessorReader reader = process.getReader();
    final int pixelType = reader.getPixelType();
    final boolean autoscale = options.isAutoscale() || // always autoscale float data
    FormatTools.isFloatingPoint(pixelType);
    final int cSize = imp.getNChannels();
    final double[] cMin = new double[cSize];
    final double[] cMax = new double[cSize];
    Arrays.fill(cMin, Double.NaN);
    Arrays.fill(cMax, Double.NaN);
    if (autoscale) {
        // extract display ranges for autoscaling
        final MinMaxCalculator minMaxCalc = process.getMinMaxCalculator();
        final int cBegin = process.getCBegin(series);
        final int cStep = process.getCStep(series);
        for (int c = 0; c < cSize; c++) {
            final int cIndex = cBegin + c * cStep;
            Double cMinVal = null, cMaxVal = null;
            try {
                cMinVal = minMaxCalc.getChannelGlobalMinimum(cIndex);
                cMaxVal = minMaxCalc.getChannelGlobalMaximum(cIndex);
                if (cMinVal == null) {
                    cMinVal = minMaxCalc.getChannelKnownMinimum(cIndex);
                }
                if (cMaxVal == null) {
                    cMaxVal = minMaxCalc.getChannelKnownMaximum(cIndex);
                }
            } catch (FormatException exc) {
            } catch (IOException exc) {
            }
            if (cMinVal != null)
                cMin[c] = cMinVal;
            if (cMaxVal != null)
                cMax[c] = cMaxVal;
        }
    }
    // for calibrated data, the offset from zero
    final double zeroOffset = getZeroOffset(imp);
    // fill in default display ranges as appropriate
    final double min, max;
    if (FormatTools.isFloatingPoint(pixelType)) {
        // no defined min and max values for floating point data
        min = max = Double.NaN;
    } else {
        final int bitDepth = reader.getBitsPerPixel();
        final double halfPow = Math.pow(2, bitDepth - 1);
        final double fullPow = 2 * halfPow;
        final boolean signed = FormatTools.isSigned(pixelType);
        if (signed) {
            // signed data is centered at 0
            min = -halfPow;
            max = halfPow - 1;
        } else {
            // unsigned data begins at 0
            min = 0;
            max = fullPow - 1;
        }
        for (int c = 0; c < cSize; c++) {
            if (Double.isNaN(cMin[c]))
                cMin[c] = min;
            if (Double.isNaN(cMax[c]))
                cMax[c] = max;
        }
    }
    // apply display ranges
    if (imp instanceof CompositeImage) {
        // apply channel display ranges
        final CompositeImage compImage = (CompositeImage) imp;
        for (int c = 0; c < cSize; c++) {
            LUT lut = compImage.getChannelLut(c + 1);
            // NB: Uncalibrate values before assigning to LUT min/max.
            lut.min = cMin[c] - zeroOffset;
            lut.max = cMax[c] - zeroOffset;
        }
    } else {
        // compute global display range from channel display ranges
        double globalMin = Double.POSITIVE_INFINITY;
        double globalMax = Double.NEGATIVE_INFINITY;
        for (int c = 0; c < cSize; c++) {
            if (cMin[c] < globalMin)
                globalMin = cMin[c];
            if (cMax[c] > globalMax)
                globalMax = cMax[c];
        }
        // NB: Uncalibrate values before assigning to display range min/max.
        globalMin -= zeroOffset;
        globalMax -= zeroOffset;
        // apply global display range
        ImageProcessor proc = imp.getProcessor();
        if (proc instanceof ColorProcessor) {
            // NB: Should never occur. ;-)
            final ColorProcessor colorProc = (ColorProcessor) proc;
            colorProc.setMinAndMax(globalMin, globalMax, 3);
        } else {
            ColorModel model = proc.getColorModel();
            proc.setMinAndMax(globalMin, globalMax);
            proc.setColorModel(model);
            imp.setDisplayRange(globalMin, globalMax);
        }
    }
}

Example 2 with FormatException

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

the class ImagePlusReader method readPlanes.

private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts, boolean thumbnail) throws FormatException, IOException {
    final ImageProcessorReader reader = process.getReader();
    reader.setSeries(s);
    final int zCount = process.getZCount(s);
    final int cCount = process.getCCount(s);
    final int tCount = process.getTCount(s);
    final IMetadata meta = process.getOMEMetadata();
    // get list of planes to load
    final boolean[] load = getPlanesToLoad(s);
    int current = 0, total = 0;
    for (int j = 0; j < load.length; j++) if (load[j])
        total++;
    final List<ImageProcessor> procs = new ArrayList<ImageProcessor>();
    final List<String> labels = new ArrayList<String>();
    // read applicable image planes
    final Region region = process.getCropRegion(s);
    for (int i = 0; i < load.length; i++) {
        if (!load[i])
            continue;
        // limit message update rate
        updateTiming(s, current, current++, total);
        // get image processor for ith plane
        final ImageProcessor[] p = readProcessors(process, i, region, thumbnail);
        if (p == null || p.length == 0) {
            throw new FormatException("Cannot read plane #" + i);
        }
        // generate a label for ith plane
        String label = constructSliceLabel(i, reader, meta, s, zCount, cCount, tCount);
        for (ImageProcessor ip : p) {
            procs.add(ip);
            labels.add(label);
        }
    }
    return createStack(procs, labels, luts);
}

Example 3 with FormatException

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

the class Slicer method makeStack.

/**
 * Returns a new ImageStack using the given ImageStack as a template.
 */
private ImageStack makeStack(ImageStack stack) {
    if (!(stack instanceof BFVirtualStack)) {
        return new ImageStack(stack.getWidth(), stack.getHeight());
    }
    BFVirtualStack virtualStack = (BFVirtualStack) stack;
    String path = virtualStack.getPath();
    ImageProcessorReader reader = virtualStack.getReader();
    try {
        return new BFVirtualStack(path, reader, false, false, false);
    } catch (FormatException e) {
        WindowTools.reportException(e);
    } catch (IOException e) {
        WindowTools.reportException(e);
    }
    return null;
}

Example 4 with FormatException

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

the class LegacyND2Reader 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 {
        openFile(id);
        int numSeries = getNumSeries();
        core.clear();
        for (int i = 0; i < numSeries; i++) {
            CoreMetadata ms = new CoreMetadata();
            core.add(ms);
            ms.sizeX = getWidth(i);
            if (ms.sizeX % 2 != 0)
                ms.sizeX++;
            ms.sizeY = getHeight(i);
            ms.sizeZ = getZSlices(i);
            ms.sizeT = getTFrames(i);
            ms.sizeC = getChannels(i);
            int bytes = getBytesPerPixel(i);
            if (bytes % 3 == 0) {
                ms.sizeC *= 3;
                bytes /= 3;
                ms.rgb = true;
            } else
                ms.rgb = false;
            ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, true);
            ms.imageCount = ms.sizeZ * ms.sizeT;
            if (!ms.rgb)
                ms.imageCount *= ms.sizeC;
            ms.interleaved = true;
            ms.littleEndian = true;
            ms.dimensionOrder = "XYCZT";
            ms.indexed = false;
            ms.falseColor = false;
        }
    } catch (UnsatisfiedLinkError e) {
        throw new MissingLibraryException(NO_NIKON_MSG, e);
    } catch (Exception e) {
        throw new MissingLibraryException(NO_NIKON_MSG, e);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName("Series " + (i + 1), i);
    }
}

Example 5 with FormatException

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

the class LeicaReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    close();
    String leiFile = findLEIFile(id);
    if (leiFile == null || leiFile.trim().length() == 0 || new Location(leiFile).isDirectory()) {
        if (checkSuffix(id, TiffReader.TIFF_SUFFIXES)) {
            super.initFile(id);
            TiffReader r = new TiffReader();
            r.setMetadataStore(getMetadataStore());
            r.setId(id);
            core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
            metadataStore = r.getMetadataStore();
            final Map<String, Object> globalMetadata = r.getGlobalMetadata();
            for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
                addGlobalMeta(entry.getKey(), entry.getValue());
            }
            r.close();
            files = new List[] { new ArrayList<String>() };
            files[0].add(id);
            tiff = new MinimalTiffReader();
            return;
        } else {
            throw new FormatException("LEI file not found.");
        }
    }
    // parse the LEI file
    super.initFile(leiFile);
    leiFilename = new File(leiFile).exists() ? new Location(leiFile).getAbsolutePath() : id;
    in = new RandomAccessInputStream(leiFile);
    byte[] data = null;
    try {
        data = new byte[(int) in.length()];
        in.read(data);
    } finally {
        in.close();
    }
    in = new RandomAccessInputStream(data);
    MetadataLevel metadataLevel = metadataOptions.getMetadataLevel();
    seriesNames = new ArrayList<String>();
    byte[] fourBytes = new byte[4];
    in.read(fourBytes);
    core.get(0).littleEndian = (fourBytes[0] == TiffConstants.LITTLE && fourBytes[1] == TiffConstants.LITTLE && fourBytes[2] == TiffConstants.LITTLE && fourBytes[3] == TiffConstants.LITTLE);
    boolean realLittleEndian = isLittleEndian();
    in.order(isLittleEndian());
    LOGGER.info("Reading metadata blocks");
    in.skipBytes(8);
    int addr = in.readInt();
    headerIFDs = new IFDList();
    while (addr != 0) {
        IFD ifd = new IFD();
        headerIFDs.add(ifd);
        in.seek(addr + 4);
        int tag = in.readInt();
        while (tag != 0) {
            // create the IFD structure
            int offset = in.readInt();
            long pos = in.getFilePointer();
            in.seek(offset + 12);
            int size = in.readInt();
            ifd.putIFDValue(tag, in.getFilePointer());
            in.seek(pos);
            tag = in.readInt();
        }
        addr = in.readInt();
    }
    numSeries = headerIFDs.size();
    tileWidth = new int[numSeries];
    tileHeight = new int[numSeries];
    core.clear();
    for (int i = 0; i < numSeries; i++) {
        core.add(new CoreMetadata());
    }
    files = new List[numSeries];
    channelNames = new List[getSeriesCount()];
    emWaves = new List[getSeriesCount()];
    exWaves = new List[getSeriesCount()];
    cutInPopulated = new boolean[getSeriesCount()][];
    cutOutPopulated = new boolean[getSeriesCount()][];
    filterRefPopulated = new boolean[getSeriesCount()][];
    for (int i = 0; i < getSeriesCount(); i++) {
        channelNames[i] = new ArrayList();
        emWaves[i] = new ArrayList();
        exWaves[i] = new ArrayList();
    }
    // determine the length of a filename
    LOGGER.info("Parsing metadata blocks");
    core.get(0).littleEndian = !isLittleEndian();
    int seriesIndex = 0;
    int invalidCount = 0;
    valid = new boolean[numSeries];
    timestamps = new String[headerIFDs.size()][];
    for (int i = 0; i < headerIFDs.size(); i++) {
        IFD ifd = headerIFDs.get(i);
        valid[i] = true;
        if (ifd.get(SERIES) != null) {
            long offset = ((Long) ifd.get(SERIES)).longValue();
            in.seek(offset + 8);
            nameLength = in.readInt() * 2;
        }
        in.seek(((Long) ifd.get(IMAGES)).longValue());
        parseFilenames(i);
        if (!valid[i])
            invalidCount++;
    }
    numSeries -= invalidCount;
    if (numSeries <= 0) {
        throw new FormatException("TIFF files not found");
    }
    int[] count = new int[getSeriesCount()];
    for (int i = 0; i < getSeriesCount(); i++) {
        count[i] = core.get(i).imageCount;
    }
    final List<String>[] tempFiles = files;
    IFDList tempIFDs = headerIFDs;
    core = new ArrayList<CoreMetadata>(numSeries);
    files = new List[numSeries];
    headerIFDs = new IFDList();
    int index = 0;
    core.clear();
    for (int i = 0; i < numSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        while (index < valid.length && !valid[index]) index++;
        if (index >= valid.length) {
            break;
        }
        ms.imageCount = count[index];
        files[i] = tempFiles[index];
        Collections.sort(files[i]);
        headerIFDs.add(tempIFDs.get(index));
        index++;
        core.add(ms);
    }
    tiff = new MinimalTiffReader();
    LOGGER.info("Populating metadata");
    if (headerIFDs == null)
        headerIFDs = ifds;
    seriesDescriptions = new ArrayList<String>();
    physicalSizes = new double[headerIFDs.size()][5];
    pinhole = new double[headerIFDs.size()];
    exposureTime = new double[headerIFDs.size()];
    channelColor = new Color[headerIFDs.size()][];
    for (int i = 0; i < headerIFDs.size(); i++) {
        IFD ifd = headerIFDs.get(i);
        CoreMetadata ms = core.get(i);
        ms.littleEndian = isLittleEndian();
        setSeries(i);
        Integer[] keys = ifd.keySet().toArray(new Integer[ifd.size()]);
        Arrays.sort(keys);
        for (Integer key : keys) {
            long offset = ((Long) ifd.get(key)).longValue();
            in.seek(offset);
            if (key.equals(SERIES)) {
                parseSeriesTag();
            } else if (key.equals(IMAGES)) {
                parseImageTag(i);
            } else if (key.equals(DIMDESCR)) {
                parseDimensionTag(i);
            } else if (key.equals(TIMEINFO) && metadataLevel != MetadataLevel.MINIMUM) {
                parseTimeTag(i);
            } else if (key.equals(EXPERIMENT) && metadataLevel != MetadataLevel.MINIMUM) {
                parseExperimentTag();
            } else if (key.equals(LUTDESC)) {
                parseLUT(i);
            } else if (key.equals(CHANDESC) && metadataLevel != MetadataLevel.MINIMUM) {
                parseChannelTag();
            }
        }
        ms.orderCertain = true;
        ms.littleEndian = isLittleEndian();
        ms.falseColor = true;
        ms.metadataComplete = true;
        ms.interleaved = false;
        String filename = (String) files[i].get(0);
        if (checkSuffix(filename, TiffReader.TIFF_SUFFIXES)) {
            RandomAccessInputStream s = new RandomAccessInputStream(filename, 16);
            try {
                TiffParser parser = new TiffParser(s);
                parser.setDoCaching(false);
                IFD firstIFD = parser.getFirstIFD();
                parser.fillInIFD(firstIFD);
                ms.sizeX = (int) firstIFD.getImageWidth();
                ms.sizeY = (int) firstIFD.getImageLength();
                // override the .lei pixel type, in case a TIFF file was overwritten
                ms.pixelType = firstIFD.getPixelType();
                // won't affect the pixel data
                if (FormatTools.getBytesPerPixel(ms.pixelType) > 1) {
                    ms.littleEndian = firstIFD.isLittleEndian();
                } else {
                    ms.littleEndian = realLittleEndian;
                }
                tileWidth[i] = (int) firstIFD.getTileWidth();
                tileHeight[i] = (int) firstIFD.getTileLength();
            } finally {
                s.close();
            }
        } else {
            ms.littleEndian = realLittleEndian;
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        setSeries(i);
        CoreMetadata ms = core.get(i);
        if (getSizeZ() == 0)
            ms.sizeZ = 1;
        if (getSizeT() == 0)
            ms.sizeT = 1;
        if (getSizeC() == 0)
            ms.sizeC = 1;
        if (getImageCount() == 0)
            ms.imageCount = 1;
        if (getImageCount() == 1 && getSizeZ() * getSizeT() > 1) {
            ms.sizeZ = 1;
            ms.sizeT = 1;
        }
        if (getSizeY() == 1 || getSizeY() == getSizeZ() || getSizeY() == getSizeT()) {
            // XZ or XT scan
            if (getSizeZ() > 1 && getImageCount() == getSizeC() * getSizeT()) {
                ms.sizeY = getSizeZ();
                ms.sizeZ = 1;
            } else if (getSizeT() > 1 && getImageCount() == getSizeC() * getSizeZ()) {
                ms.sizeY = getSizeT();
                ms.sizeT = 1;
            }
        }
        if (isRGB())
            ms.indexed = false;
        ms.dimensionOrder = MetadataTools.makeSaneDimensionOrder(getDimensionOrder());
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // minimum metadata level.
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName(seriesNames.get(i), i);
    }
    if (metadataLevel == MetadataLevel.MINIMUM)
        return;
    for (int i = 0; i < getSeriesCount(); i++) {
        CoreMetadata ms = core.get(i);
        IFD ifd = headerIFDs.get(i);
        long firstPlane = 0;
        if (i < timestamps.length && timestamps[i] != null && timestamps[i].length > 0) {
            firstPlane = DateTools.getTime(timestamps[i][0], DATE_FORMAT, ":");
            String date = DateTools.formatDate(timestamps[i][0], DATE_FORMAT);
            if (date != null) {
                store.setImageAcquisitionDate(new Timestamp(date), i);
            }
        }
        store.setImageDescription(seriesDescriptions.get(i), i);
        String instrumentID = MetadataTools.createLSID("Instrument", i);
        store.setInstrumentID(instrumentID, i);
        // parse instrument data
        nextDetector = 0;
        nextChannel = 0;
        detectors.clear();
        cutInPopulated[i] = new boolean[ms.sizeC];
        cutOutPopulated[i] = new boolean[ms.sizeC];
        filterRefPopulated[i] = new boolean[ms.sizeC];
        Integer[] keys = ifd.keySet().toArray(new Integer[ifd.size()]);
        Arrays.sort(keys);
        int nextInstrumentBlock = 1;
        sequential = DataTools.indexOf(keys, SEQ_SCANNERSET) != -1;
        for (Integer key : keys) {
            if (key.equals(FILTERSET) || key.equals(SCANNERSET) || key.equals(SEQ_SCANNERSET) || key.equals(SEQ_FILTERSET) || (key > SEQ_SCANNERSET && key < SEQ_SCANNERSET_END) || (key > SEQ_FILTERSET && key < SEQ_FILTERSET_END)) {
                if (sequential && (key.equals(FILTERSET) || key.equals(SCANNERSET))) {
                    continue;
                }
                long offset = ((Long) ifd.get(key)).longValue();
                in.seek(offset);
                setSeries(i);
                parseInstrumentData(store, nextInstrumentBlock++);
            }
        }
        activeChannelIndices.clear();
        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, i);
        Length sizeX = FormatTools.getPhysicalSizeX(physicalSizes[i][0]);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalSizes[i][1]);
        Length sizeZ = FormatTools.getPhysicalSizeZ(physicalSizes[i][2]);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, i);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, i);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        if ((int) physicalSizes[i][4] > 0) {
            store.setPixelsTimeIncrement(new Time(physicalSizes[i][4], UNITS.SECOND), i);
        }
        for (int j = 0; j < ms.imageCount; j++) {
            if (timestamps[i] != null && j < timestamps[i].length) {
                long time = DateTools.getTime(timestamps[i][j], DATE_FORMAT, ":");
                double elapsedTime = (double) (time - firstPlane) / 1000;
                store.setPlaneDeltaT(new Time(elapsedTime, UNITS.SECOND), i, j);
                if (exposureTime[i] > 0) {
                    store.setPlaneExposureTime(new Time(exposureTime[i], UNITS.SECOND), i, j);
                }
            }
        }
    }
    setSeries(0);
}