Examples with PhotoInterp loci.formats.tiff.PhotoInterp used on opensource projects

Example 16 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class IonpathMIBITiffReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    int seriesIndex;
    String imageType = null;
    core.clear();
    for (int i = 0; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        Object description = ifd.get(IFD.IMAGE_DESCRIPTION);
        if (description == null) {
            throw new FormatException("Image description is mandatory.");
        }
        String imageDescription = null;
        if (description instanceof TiffIFDEntry) {
            Object value = tiffParser.getIFDValue((TiffIFDEntry) description);
            if (value != null) {
                imageDescription = value.toString();
            }
        } else if (description instanceof String) {
            imageDescription = (String) description;
        }
        JSONObject jsonDescription;
        try {
            jsonDescription = new JSONObject(imageDescription);
            imageType = jsonDescription.getString("image.type");
            if (imageType.equals("SIMS")) {
                String mass = jsonDescription.getString("channel.mass");
                if (mass == null) {
                    throw new FormatException("Channel masses are mandatory.");
                }
                String target = jsonDescription.getString("channel.target");
                channelIDs.add(mass);
                channelNames.add(target != null && target != "null" ? target : mass);
            }
        } catch (JSONException e) {
            throw new FormatException("Unexpected format in SIMS description JSON.");
        }
        if (seriesTypes.containsKey(imageType)) {
            if (!imageType.equals("SIMS")) {
                throw new FormatException("Only type 'SIMS' can have >1 image per file.");
            }
            seriesIndex = seriesTypes.get(imageType);
            CoreMetadata ms = core.get(seriesIndex);
            ms.sizeC += 1;
            ms.imageCount += 1;
        } else {
            seriesIndex = seriesTypes.size();
            seriesTypes.put(imageType, seriesIndex);
            seriesIFDs.add(i);
            core.add(new CoreMetadata());
            setSeries(seriesIndex);
            tiffParser.setDoCaching(true);
            tiffParser.fillInIFD(ifd);
            if (imageType.equals("SIMS")) {
                try {
                    Iterator<?> keySet = jsonDescription.keys();
                    while (keySet.hasNext()) {
                        String key = (String) keySet.next();
                        if (key.startsWith("mibi.")) {
                            simsDescription.put(key, jsonDescription.getString(key));
                        }
                    }
                } catch (JSONException e) {
                    throw new FormatException("Unexpected format in SIMS description JSON.");
                }
            }
            CoreMetadata ms = core.get(seriesIndex);
            PhotoInterp p = ifd.getPhotometricInterpretation();
            int samples = ifd.getSamplesPerPixel();
            ms.rgb = samples > 1 || p == PhotoInterp.RGB;
            ms.sizeX = (int) ifd.getImageWidth();
            ms.sizeY = (int) ifd.getImageLength();
            ms.sizeZ = 1;
            ms.sizeT = 1;
            ms.sizeC = ms.rgb ? samples : 1;
            ms.littleEndian = ifd.isLittleEndian();
            ms.indexed = p == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
            ms.imageCount = 1;
            ms.pixelType = ifd.getPixelType();
            ms.metadataComplete = true;
            ms.interleaved = false;
            ms.falseColor = false;
            ms.dimensionOrder = "XYCZT";
            ms.thumbnail = false;
            ms.imageCount = 1;
            if (imageType.equals("SIMS")) {
                ms.seriesMetadata = simsDescription;
            }
        }
    }
}

Example 17 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class ImaconReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    core.clear();
    for (int i = 0; i < ifds.size(); i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.imageCount = 1;
        IFD ifd = ifds.get(i);
        ifd.remove(PIXELS_TAG);
        tiffParser.fillInIFD(ifd);
        PhotoInterp photo = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        ms.rgb = samples > 1 || photo == PhotoInterp.RGB || photo == PhotoInterp.CFA_ARRAY;
        if (photo == PhotoInterp.CFA_ARRAY)
            samples = 3;
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = 1;
        ms.sizeC = isRGB() ? samples : 1;
        ms.sizeT = 1;
        ms.pixelType = ifd.getPixelType();
        ms.indexed = photo == PhotoInterp.RGB_PALETTE;
        ms.dimensionOrder = "XYCZT";
        ms.interleaved = false;
    }
    IFD firstIFD = ifds.get(0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String xml = firstIFD.getIFDTextValue(XML_TAG).trim();
        xml = xml.substring(xml.indexOf('<'));
        XMLTools.parseXML(xml, new ImaconHandler());
    }
    String[] creationInfo = firstIFD.getIFDTextValue(CREATOR_TAG).split("\n");
    if (creationInfo.length > 4) {
        experimenterName = creationInfo[4].trim();
    }
    if (creationInfo.length > 6) {
        imageName = creationInfo[6].trim();
    }
    if (creationInfo.length > 8) {
        creationDate = creationInfo[8].trim();
    }
    if (creationInfo.length > 10) {
        creationDate += " " + creationInfo[10].trim();
    }
}

Example 18 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class LeicaSCNReader method initCoreMetadata.

// -- Internal BaseTiffReader API methods --
protected void initCoreMetadata(int s, int resolution) throws FormatException, IOException {
    ImageCollection c = handler.collection;
    Image i = handler.imageMap.get(s);
    if (c == null || i == null) {
        throw new FormatException("Error setting core metadata for image number " + s);
    }
    CoreMetadata ms = core.get(s);
    if (resolution == 0) {
        ms.resolutionCount = i.pixels.sizeR;
    }
    Dimension dimension = i.pixels.lookupDimension(0, 0, resolution);
    if (dimension == null) {
        throw new FormatException("No dimension information for subresolution=" + resolution);
    }
    IFD ifd = ifds.get(dimension.ifd);
    PhotoInterp pi = ifd.getPhotometricInterpretation();
    int samples = ifd.getSamplesPerPixel();
    ms.rgb = samples > 1 || pi == PhotoInterp.RGB;
    ms.sizeX = (int) dimension.sizeX;
    ms.sizeY = (int) dimension.sizeY;
    ms.sizeZ = (int) i.pixels.sizeZ;
    ms.sizeT = 1;
    ms.sizeC = ms.rgb ? samples : i.pixels.sizeC;
    if ((ifd.getImageWidth() != ms.sizeX) || (ifd.getImageLength() != ms.sizeY)) {
        throw new FormatException("IFD dimensions do not match XML dimensions for image " + s + ": x=" + ifd.getImageWidth() + ", " + ms.sizeX + ", y=" + ifd.getImageLength() + ", " + ms.sizeY);
    }
    ms.orderCertain = true;
    ms.littleEndian = ifd.isLittleEndian();
    ms.indexed = pi == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
    ms.imageCount = i.pixels.sizeZ * i.pixels.sizeC;
    ms.pixelType = ifd.getPixelType();
    ms.metadataComplete = true;
    ms.interleaved = false;
    ms.falseColor = false;
    ms.dimensionOrder = "XYCZT";
    ms.thumbnail = i.imageThumbnail == resolution;
}

Example 19 with PhotoInterp

use of loci.formats.tiff.PhotoInterp in project bioformats by openmicroscopy.

the class JPKReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    // repopulate core metadata
    int seriesCount = ifds.size() > 1 ? 2 : 1;
    core.clear();
    for (int s = 0; s < seriesCount; s++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        IFD ifd = ifds.get(s);
        tiffParser.fillInIFD(ifd);
        PhotoInterp p = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        ms.rgb = samples > 1 || p == PhotoInterp.RGB;
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = 1;
        ms.sizeT = s == 0 ? 1 : ifds.size() - 1;
        ms.sizeC = ms.rgb ? samples : 1;
        ms.littleEndian = ifd.isLittleEndian();
        ms.indexed = p == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
        ms.imageCount = s == 0 ? 1 : ifds.size() - 1;
        ms.pixelType = ifd.getPixelType();
        ms.metadataComplete = true;
        ms.interleaved = false;
        ms.falseColor = false;
        ms.dimensionOrder = "XYCZT";
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            setSeries(s);
            for (Integer key : ifds.get(s).keySet()) {
                if (key >= 32848) {
                    addSeriesMeta("Tag " + key, ifds.get(s).get(key));
                }
            }
        }
    }
    setSeries(0);
}