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Merge pull request camicroscope#80 from CGDogan/biofonabstract
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Add note about updating BioFormats
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@birm
birm authored Sep 2, 2023
2 parents f386374 + 0af970a commit 6b6c5c7
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348 changes: 348 additions & 0 deletions _file_extensions_bioformatsv7.0.0.txt
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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<IFormatReader> 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;
}
5 changes: 4 additions & 1 deletion file_extensions.py
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Original file line number Diff line number Diff line change
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# 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
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