-
Notifications
You must be signed in to change notification settings - Fork 19
/
_file_extensions_bioformatsv7.0.0.txt
348 lines (348 loc) · 16.4 KB
/
_file_extensions_bioformatsv7.0.0.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
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<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;
}