diff --git a/_file_extensions_bioformatsv7.0.0.txt b/_file_extensions_bioformatsv7.0.0.txt new file mode 100644 index 0000000..28a2293 --- /dev/null +++ b/_file_extensions_bioformatsv7.0.0.txt @@ -0,0 +1,348 @@ + domains = new String[] {FormatTools.LM_DOMAIN}; + super("SlideBook 7 SLD (native)", new String[] {"sldy"}); + CompressionType.J2K.getCompression()}; + CompressionType.UNCOMPRESSED.getCompression()}; + super("Vaa3d", new String[]{"v3draw"}); + "ano", "cfg", "csv", "htm", "rec", "tim", "zpo", "tif"}); + "dic", "dcm", "dicom", "jp2", "j2ki", "j2kr", "raw", "ima"}); + AWTImageTools.makeColorSpace(nChannels), nChannels == 4, false, + COMPRESSION_UNCOMPRESSED, + ColorModel.TRANSLUCENT, dataType); + CompressionType.UNCOMPRESSED.getCompression(), + FormatTools.UNKNOWN_DOMAIN}; + new String[] {"cr2", "crw", "jpg", "thm", "wav", "tif", "tiff"}); + new String[] {"dv", "r3d", "r3d_d3d", "dv.log", "r3d.log"}); + new String[] {"mvd2", "aisf", "aiix", "dat", "atsf"}); + new String[] {"ome.tif", "ome.tiff", "ome.tf2", "ome.tf8", "ome.btf"}); + new String[] {"pbm", "pgm", "ppm"}); + new String[] {"xdce", "xml", "tiff", "tif", "xlog"}); + new String[] {CompressionType.UNCOMPRESSED.getCompression(), + new String[] {FormatTools.ASTRONOMY_DOMAIN, FormatTools.UNKNOWN_DOMAIN}; + null, path); + suffixNecessary = false; + suffixSufficient = false; + super("JPEG", new String[] {"jpg", "jpeg", "jpe"}); + super(name, recType, offset, recLength); + super(name, type, offset, length); + "dic", "dcm", "dicom", "j2ki", "j2kr" + /** + // call getStatistics() to ensure that single-slice stacks have the + // correct pixel type + // remove unavailable stack formats + ClassList classes = ImageReader.getDefaultReaderClasses(); + LMSFileReader.log = LOGGER; + bankData = dataArray; + bankData = new byte[1][]; + bankData = new int[1][]; + bankData[0] = dataArray; + canSeparateSeries = false; + compressionTypes = new String[] {CompressionType.J2K_LOSSY.getCompression(), + datasetDescription = "One .hed file plus one similarly-named .img file"; + datasetDescription = "One .htd file plus one or more .tif files"; + datasetDescription = "One .ndpis file and at least one .ndpi file"; + datasetDescription = "One .omp2info file and at least one .oir or .vsi file"; + datasetDescription = "One .vms file plus several .jpg files"; + datasetDescription = "One or more .c01 files"; + domains = FormatTools.NON_GRAPHICS_DOMAINS; + domains = new String[] {FormatTools.ASTRONOMY_DOMAIN}; + domains = new String[] {FormatTools.EM_DOMAIN}; + domains = new String[] {FormatTools.FLIM_DOMAIN}; + domains = new String[] {FormatTools.GEL_DOMAIN}; + domains = new String[] {FormatTools.GRAPHICS_DOMAIN}; + domains = new String[] {FormatTools.HCS_DOMAIN}; + domains = new String[] {FormatTools.HISTOLOGY_DOMAIN, FormatTools.LM_DOMAIN}; + domains = new String[] {FormatTools.HISTOLOGY_DOMAIN}; + domains = new String[] {FormatTools.LM_DOMAIN, FormatTools.FLIM_DOMAIN, + domains = new String[] {FormatTools.LM_DOMAIN, FormatTools.HCS_DOMAIN}; + domains = new String[] {FormatTools.LM_DOMAIN, FormatTools.HISTOLOGY_DOMAIN}; + domains = new String[] {FormatTools.LM_DOMAIN}; + domains = new String[] {FormatTools.MEDICAL_DOMAIN, + domains = new String[] {FormatTools.MEDICAL_DOMAIN, FormatTools.LM_DOMAIN}; + domains = new String[] {FormatTools.MEDICAL_DOMAIN}; + domains = new String[] {FormatTools.SEM_DOMAIN}; + domains = new String[] {FormatTools.SPM_DOMAIN}; + domains = new String[] {FormatTools.UNKNOWN_DOMAIN}; + domains = new String[]{FormatTools.FLIM_DOMAIN}; + handle = new ByteArrayHandle(INITIAL_CAPACITY); + hasCompanionFiles = true; + helper = new DataBufferShort(data, size); + helper = new DataBufferShort(data, size, offset); + helper = new DataBufferShort(data, size, offsets); + helper = new DataBufferShort(size); + helper = new DataBufferShort(size, numbanks); + ifds = new IFDList(); + imageFormat = checkImageFormat(); + imageFormat = xlif.getImageFormat(); + index = -1; + initChildren(); + initImagePaths(); + inputOrder = dimensionOrder; + legacyReader = new TiffJAIReader(); + legacyReader = new TileJPEGReader(); + nativeReader = new DefaultJPEGReader(); + nativeReader = new TiffReader(); + new String[] {"apl", "tnb", "mtb" }; + new String[] {"tif", "tiff", "im"}; + new String[] {"xml", "xlog"}; + new String[] {FLEX_SUFFIX, MEA_SUFFIX, RES_SUFFIX}; + new String[] {MEA_SUFFIX, RES_SUFFIX}; + noSubresolutions = true; + panel = getTextPanel(); + reader = new ImageProcessorReader(r); + suffixNecessary = false; + suffixNecessary = false; // allow extensionless IPLab files + suffixNecessary = true; + suffixSufficient = false; + suffixSufficient = true; + super( "CellVoyager", new String[] { "tif", "xml" } ); + super("AIM", "aim"); + super("ARF", "arf"); + super("Adobe Photoshop TIFF", new String[] {"tif", "tiff"}); + super("Adobe Photoshop", "psd"); + super("Alicona AL3D", "al3d"); + super("Amersham Biosciences GEL", new String[] {"gel"}); + super("Amira", new String[] {"am", "amiramesh", "grey", "hx", "labels"}); + super("Analyze 7.5", new String[] {"img", "hdr"}); + super("Andor SIF", "sif"); + super("Animated PNG", "png"); + super("Aperio AFI", "afi"); + super("Aperio SVS", new String[] {"svs"}); + super("Audio Video Interleave", "avi"); + super("BD Pathway", new String[] {"exp", "tif"}); + super("BDV", new String[] {"xml", "h5"}); + super("Bio-Rad GEL", "1sc"); + super("Bio-Rad PIC", new String[] {"pic", "xml", "raw"}); + super("Bio-Rad SCN", "scn"); + super("Bitplane Imaris 3 (TIFF)", "ims"); + super("Bitplane Imaris 5.5 (HDF)", "ims"); + super("Bitplane Imaris", "ims"); + super("Bruker", ""); + super("Burleigh", "img"); + super("Canon RAW", new String[] {"cr2", "crw", "jpg", "thm", "wav"}); + super("CellH5 (HDF)", "ch5"); + super("CellSens VSI", new String[] {"vsi", "ets"}); + super("CellWorx", new String[] {"pnl", "htd", "log"}); + super("Cellomics C01", new String[] {"c01", "dib"}); + super("Compix Simple-PCI", "cxd"); + super("DICOM", "dcm"); + super("DNG", + super("Deltavision", + super("ECAT7", "v"); + super("Encapsulated PostScript", new String[] {"eps", "epsi", "ps"}); + super("Encapsulated PostScript", new String[] {"eps", "epsi"}); + super("Evotec Flex", SUFFIXES); + super("Extended leica file", "xlef"); + super("FEI TIFF", new String[] {"tif", "tiff"}); + super("FEI/Philips", "img"); + super("File pattern", new String[] {"pattern"}); + super("Flexible Image Transport System", new String[] {"fits", "fts"}); + super("FlowSight", "cif"); + super("Fuji LAS 3000", new String[] {"img", "inf"}); + super("Gatan DM2", "dm2"); + super("Gatan Digital Micrograph", new String[] {"dm3", "dm4"}); + super("Graphics Interchange Format", "gif"); + super("Hamamatsu Aquacosmos", "naf"); + super("Hamamatsu HIS", "his"); + super("Hamamatsu NDPI", new String[] {"ndpi"}); + super("Hamamatsu NDPIS", "ndpis"); + super("Hamamatsu VMS", "vms"); + super("Hitachi", "txt"); + super("I2I", new String[] {"i2i"}); + super("IMAGIC", new String[] {"hed", "img"}); + super("IMOD", "mod"); + super("INR", "inr"); + super("IPLab", "ipl"); + super("IVision", "ipm"); + super("Imacon", new String[] {"fff"}); + super("Image Cytometry Standard", new String[] {"ics", "ids"}); + super("Image Cytometry Standard", new String[] {"ids", "ics"}); + super("Image-Pro Sequence", new String[] {"seq", "ips"}); + super("Image-Pro Workspace", "ipw"); + super("Improvision TIFF", new String[] {"tif", "tiff"}); + super("InCell 1000/2000", + super("InCell 3000", "frm"); + super("Inveon", new String[] {"hdr"}); + super("Ionpath MIBI", new String[] {"tif, tiff"}); + super("JEOL", new String[] {"dat", "img", "par"}); + super("JPEG", new String[] {"jpg", "jpeg", "jpe"}); + super("JPEG", new String[] {"jpg", "jpeg", "jpe"}, "jpeg"); + super("JPEG-2000", "jp2"); + super("JPEG-2000", new String[] {"jp2", "j2k", "jpf"}); + super("JPK Instruments", "jpk"); + super("JPX", "jpx"); + super("KLB", "klb"); + super("Khoros XV", "xv"); + super("Kodak Molecular Imaging", "bip"); + super("LEO", new String[] {"sxm", "tif", "tiff"}); + super("LI-FLIM", "fli"); + super("Laboratory Imaging", "lim"); + super("Lavision Imspector", "msr"); + super("Leica Image File Format", "lif"); + super("Leica Object Format", "lof"); + super("Leica SCN", new String[] {"scn"}); + super("Leica TCS TIFF", new String[] {"tif", "tiff", "xml"}); + super("Leica", new String[] {"lei", "tif", "tiff", "raw"}); + super("Li-Cor L2D", new String[] {"l2d", "scn", "tif"}); + super("MIAS", new String[] {"tif", "tiff", "txt"}); + super("MINC MRI", "mnc"); + super("Medical Research Council", MRC_SUFFIXES); + super("MetaXpress TIFF", new String[] {"htd", "tif"}); + super("Metamorph STK", new String[] {"stk", "nd", "scan", "tif", "tiff"}); + super("Metamorph TIFF", new String[] {"tif", "tiff"}); + super("Micro-Manager", new String[] {"tif", "tiff", "txt", "xml"}); + super("MicroCT", "vff"); + super("Mikroscan TIFF", new String[] {"tif", "tiff"}); + super("Minolta MRW", "mrw"); + super("Molecular Imaging", "stp"); + super("Multiple images", ".*"); + super("Multiple-image Network Graphics", "mng"); + super("NIfTI", new String[] {"nii", "img", "hdr", "nii.gz"}); + super("NOAA-HRD Gridded Data Format", ""); + super("NRRD", new String[] {"nrrd", "nhdr"}); + super("Nikon Elements TIFF", new String[] {"tif", "tiff"}); + super("Nikon ND2", new String[] {"nd2", "jp2"}); + super("Nikon NEF", new String[] {"nef", "tif", "tiff"}); + super("Nikon TIFF", new String[] {"tif", "tiff"}); + super("OBF", new String[] {"obf", "msr"}); + super("OME-TIFF", + super("OME-TIFF", OME_TIFF_SUFFIXES); + super("OME-XML", new String[] {"ome", "ome.xml"}); + super("Olympus .omp2info", "omp2info"); + super("Olympus APL", new String[] {"apl", "tnb", "mtb", "tif"}); + super("Olympus FV1000", new String[] {"oib", "oif", "pty", "lut"}); + super("Olympus Fluoview/ABD TIFF", new String[] {"tif", "tiff"}); + super("Olympus OIR", "oir"); + super("Olympus SIS TIFF", new String[] {"tif", "tiff"}); + super("Olympus ScanR", new String[] {"dat", "xml", "tif"}); + super("Olympus Slidebook", new String[] {"sld", "spl"}); + super("Openlab LIFF", "liff"); + super("Openlab RAW", "raw"); + super("Oxford Instruments", "top"); + super("PCO-RAW", new String[] {"pcoraw", "rec"}); + super("PCX", "pcx"); + super("PICT", new String[] {"pict", "pct"}); + super("POV-Ray", "df3"); + super("Perkin Elmer Densitometer", new String[] {"hdr", "img"}); + super("Perkin-Elmer Nuance IM3", "im3"); + super("PerkinElmer Columbus", new String[] {"xml"}); + super("PerkinElmer Operetta", new String[] {"tif", "tiff", "xml"}); + super("PerkinElmer Vectra/QPTIFF", new String[] {"tiff", "tif", "qptiff"}); + super("PicoQuant Bin", "bin"); + super("Portable Any Map", + super("Prairie TIFF", new String[] {"tif", "tiff", "cfg", "env", "xml"}); + super("Princeton Instruments SPE", "spe"); + super("Pyramid TIFF", new String[] {"tif", "tiff"}); + super("Quesant AFM", "afm"); + super("QuickTime", "mov"); + super("RHK Technologies", new String[] {"sm2", "sm3"}); + super("SBIG", ""); + super("SM Camera", ""); + super("SPC FIFO Data", new String[] {"spc", "set"}); + super("SPCImage Data", "sdt"); + super("SPIDER", "spi"); + super("Seiko", new String[] {"xqd", "xqf"}); + super("SimplePCI TIFF", new String[] {"tif", "tiff"}); + super("Simulated data", "fake"); + super("Slidebook TIFF", new String[] {"tif", "tiff"}); + super("Tagged Image File Format", TIFF_SUFFIXES); + super("Tagged Image File Format", TiffReader.TIFF_SUFFIXES); + super("Tecan Spark Cyto", new String[] {"db"}); + super("Text", new String[] {"txt", "csv"}); + super("Tile JPEG", new String[] {"jpg", "jpeg"}); + super("TillVision", new String[] {"vws", "pst", "inf"}); + super("TopoMetrix", new String[] {"tfr", "ffr", "zfr", "zfp", "2fl"}); + super("Trestle", new String[] {"tif"}); + super("Truevision Targa", "tga"); + super("UBM", "pr3"); + super("Unisoku STM", new String[] {"hdr", "dat"}); + super("VG SAM", "dti"); + super("Varian FDF", "fdf"); + super("Veeco", "hdf"); + super("Ventana .bif", new String[] {"bif"}); + super("Visitech XYS", new String[] {"xys", "html"}); + super("Volocity Library Clipping", "acff"); + super("Volocity Library", + super("WA Technology TOP", "wat"); + super("Windows Bitmap", "bmp"); + super("Yokogawa CV7000", new String[] {"wpi"}); + super("Zeiss AxioVision TIFF", TIFF_SUFFIXES); + super("Zeiss CZI", "czi"); + super("Zeiss LMS", "lms"); + super("Zeiss Laser-Scanning Microscopy", new String[] {"lsm", "mdb"}); + super("Zeiss Vision Image (ZVI)", "zvi"); + super("Zip", "zip"); + super("importer-options.txt", ImporterOptions.class); + super(DataBuffer.TYPE_BYTE, size); + super(DataBuffer.TYPE_INT, size); + super(DataBuffer.TYPE_USHORT, size); + super(DataBuffer.TYPE_USHORT, size, 1, offset); + super(DataBuffer.TYPE_USHORT, size, data.length); + super(DataBuffer.TYPE_USHORT, size, data.length, offsets); + super(DataBuffer.TYPE_USHORT, size, numbanks); + super(filepath, null); + super(filepath, parent); + super(format, exts); + super(format, suffix); + super(format, suffixes); + super(getWidth(r, path, r.getSeries()), getHeight(r, path, r.getSeries()), + super(imp, ic); + super(key, save, label, info); + super(message, cause); + super(name, extensions); + super(name, suffix); + super(name, suffixes); + super(pixelBits, makeBitArray(nChannels, pixelBits), + super(r, seriesNo); + super(s, cause); + super(store, filter); + super(title, headings, data, w, h); + super(title, stack); + super(type, components); + super(x, y, w, h); + this.datasetDescription = "Directory with 2 master files 'MeasurementResult.xml' and 'MeasurementResult.ome.xml', used to stitch together several TIF files."; + this.defaultValue = defaultValue; + this.hasCompanionFiles = true; + this.kind = kind; + this.op = op; this.options = options; this.cf = cf; + this.possibleValues = possibleValues; + this.value = defaultValue; + tileCount = xlif.getTileCount(); + {"mrc", "st", "ali", "map", "rec", "mrcs"}; + {"ome.tiff", "ome.tif", "ome.tf2", "ome.tf8", "ome.btf", "companion.ome"}; + {"tif", "tiff", "tf2", "tf8", "btf"}; + } + /** Constructs a format reader with the given name and default suffixes. */ + /** Constructs a format writer with the given name and default suffixes. */ + /** Constructs a new BaseTiffReader. */ + /** TIFF tiles must be of a height and width divisible by 16. */ + // -- Fields -- + // -- IFormatWriter API methods -- + // Private tags present in Prairie TIFF files + private static final String[] BIG_TIFF_SUFFIXES = {"tf2", "tf8", "btf"}; + private static final String[] METADATA_SUFFIXES = new String[] {"dat", "xml"}; + public AVIWriter() { super("Audio Video Interleave", "avi"); } + public BaseTiffReader(String name, String suffix) { super(name, suffix); } + public CacheException(String s, Throwable cause) { super(s, cause); } + public CacheException(Throwable cause) { super(cause); } + public CoreMetadataList(int size1, int size2) { super(size1, size2); } + public FormatException(String s, Throwable cause) { super(s, cause); } + public FormatException(Throwable cause) { super(cause); } + public FormatReader(String format, String suffix) { super(format, suffix); } + public FormatWriter(String format, String suffix) { super(format, suffix); } + public JavaWriter() { super("Java source code", "java"); } + public MissingLibraryException(String s, Throwable cause) { super(s, cause); } + public MissingLibraryException(Throwable cause) { super(cause); } + public SubResolutionFormatReader(String format, String suffix) { super(format, suffix); } + public UnknownFormatException(String s, Throwable cause) { super(s, cause); } + public UnknownFormatException(Throwable cause) { super(cause); } + public UnsupportedCompressionException(Throwable cause) { super(cause); } + public static final String SKIP_MISSING_WELLS = "scanr.skip_missing_wells"; + public static final String XML_NAME = "_meta.xml"; + public static final String[] COMPANION_SUFFIXES = {"xml", "txt"}; + public static final String[] COMPRESSION_SUFFIXES = {"bz2", "gz"}; + public static final String[] FV1000_SUFFIXES = {"oib", "oif"}; + public static final String[] PRAIRIE_SUFFIXES = {"cfg", "env", "xml"}; + public static final String[] TIFF_SUFFIXES = {"tif", "xml"}; + public static final boolean SKIP_MISSING_WELLS_DEFAULT = true; + public static final int IMAGEJ_TAG = 50839; + } diff --git a/file_extensions.py b/file_extensions.py index c060924..bf03b36 100644 --- a/file_extensions.py +++ b/file_extensions.py @@ -1,6 +1,9 @@ +# Updating BioFormats: # Clone github.com/ome/bioformats and run: # grep -r -e "static final String.*\[\].*SUFFIXES" -e "super.*new String\[\]" -e "super(.*," -A 2 -h | grep " .* .* " | grep -v "=$" | grep -v "{$" | sort -u -# then manually copying extensions, keeping them in order +# then save the output to a file and "diff" it with _file_extensions_bioformatsvX.X.X.txt +# then manually copy the new extensions, making an attempt to preserve the order +# then delete the previous _file_extensions_bioformatsvX.X.X.txt and rename the new output # The command says: match 'static final String[] XYZ_SUFFIXES' or 'super("XYZFILES", ".xyz")' # and print next two lines but keep only lines with at least two space and discard those # ending with "=" or "{" (because in this case only the next line(s) are relevant