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Tifffile is a Python library to (1) store numpy arrays in TIFF (Tagged Image File Format) files, and (2) read image and metadata from TIFF-like files used in bioimaging. Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, SGI, NIHImage, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI), NDPI, and GeoTIFF files. Image data can be read as numpy arrays or zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels. Numpy arrays can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form. A subset of the TIFF specification is supported, mainly 8, 16, 32 and 64-bit integer, 16, 32 and 64-bit float, grayscale and multi-sample images. Specifically, CCITT and OJPEG compression, chroma subsampling without JPEG compression, color space transformations, samples with differing types, or IPTC, ICC, and XMP metadata are not implemented. TIFF, the Tagged Image File Format, was created by the Aldus Corporation and Adobe Systems Incorporated. BigTIFF allows for files larger than 4 GB. STK, LSM, FluoView, SGI, SEQ, GEL, QPTIFF, NDPI, SCN, SVS, ZIF, BIF, and OME-TIFF, are custom extensions defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics, Molecular Dynamics, PerkinElmer, Hamamatsu, Leica, ObjectivePathology, Roche Digital Pathology, and the Open Microscopy Environment consortium, respectively. For command line usage run ``python -m tifffile --help`` :Author: `Christoph Gohlke `_ :Organization: Laboratory for Fluorescence Dynamics, University of California, Irvine :License: BSD 3-Clause :Version: 2021.11.2 Requirements ------------ This release has been tested with the following requirements and dependencies (other versions may work): * `CPython 3.7.9, 3.8.10, 3.9.7, 3.10.0, 64-bit `_ * `Numpy 1.21.3 `_ * `Imagecodecs 2021.8.26 `_ (required only for encoding or decoding LZW, JPEG, etc.) * `Matplotlib 3.4.3 `_ (required only for plotting) * `Lxml 4.6.3 `_ (required only for validating and printing XML) * `Zarr 2.10.3 `_ (required only for opening zarr storage) Revisions --------- 2021.11.2 Pass 4731 tests. Lazy-load non-essential tag values (breaking). Warn when reading from closed file. Support ImageJ 'prop' metadata type (#103). Support writing indexed ImageJ format. Fix multi-threaded access of multi-page Zarr stores with chunkmode 2. Raise error if truncate is used with compression, packints, or tile. Read STK metadata without UIC2tag. Improve log and warning messages (WIP). Improve string representation of large tag values. 2021.10.12 Revert renaming of 'file' parameter in FileSequence.asarray (breaking). Deprecate 'file' parameter in FileSequence.asarray. 2021.10.10 Disallow letters as indices in FileSequence; use categories (breaking). Do not warn of missing files in FileSequence; use files_missing property. Support predictors in ZarrTiffStore.write_fsspec. Add option to specify zarr group name in write_fsspec. Add option to specify categories for FileSequence patterns (#76). Add option to specify chunk shape and dtype for ZarrFileSequenceStore. Add option to tile ZarrFileSequenceStore and FileSequence.asarray. Add option to pass additional zattrs to Zarr stores. Detect Roche BIF files. 2021.8.30 Fix horizontal differencing with non-native byte order. Fix multi-threaded access of memory-mappable, multi-page Zarr stores (#67). 2021.8.8 Fix tag offset and valueoffset for NDPI > 4 GB (#96). 2021.7.30 Deprecate first parameter to TiffTag.overwrite (no longer required). TiffTag init API change (breaking). Detect Ventana BIF series and warn that tiles are not stitched. Enable reading PreviewImage from RAW formats (#93, #94). Work around numpy.ndarray.tofile is very slow for non-contiguous arrays. Fix issues with PackBits compression (requires imagecodecs 2021.7.30). 2021.7.2 Decode complex integer images found in SAR GeoTIFF. Support reading NDPI with JPEG-XR compression. Deprecate TiffWriter RGB auto-detection, except for RGB24/48 and RGBA32/64. 2021.6.14 Set stacklevel for deprecation warnings (#89). Fix svs_description_metadata for SVS with double header (#88, breaking). Fix reading JPEG compressed CMYK images. Support ALT_JPEG and JPEG_2000_LOSSY compression found in Bio-Formats. Log warning if TiffWriter auto-detects RGB mode (specify photometric). 2021.6.6 Fix TIFF.COMPESSOR typo (#85). Round resolution numbers that do not fit in 64-bit rationals (#81). Add support for JPEG XL compression. Add numcodecs compatible TIFF codec. Rename ZarrFileStore to ZarrFileSequenceStore (breaking). Add method to export fsspec ReferenceFileSystem from ZarrFileStore. Fix fsspec ReferenceFileSystem v1 for multifile series. Fix creating OME-TIFF with micron character in OME-XML. 2021.4.8 Fix reading OJPEG with wrong photometric or samplesperpixel tags (#75). Fix fsspec ReferenceFileSystem v1 and JPEG compression. Use TiffTagRegistry for NDPI_TAGS, EXIF_TAGS, GPS_TAGS, IOP_TAGS constants. Make TIFF.GEO_KEYS an Enum (breaking). 2021.3.31 Use JPEG restart markers as tile offsets in NDPI. Support version 1 and more codecs in fsspec ReferenceFileSystem (untested). 2021.3.17 Fix regression reading multi-file OME-TIFF with missing files (#72). Fix fsspec ReferenceFileSystem with non-native byte order (#56). 2021.3.16 TIFF is no longer a defended trademark. Add method to export fsspec ReferenceFileSystem from ZarrTiffStore (#56). 2021.3.5 Preliminary support for EER format (#68). Do not warn about unknown compression (#68). 2021.3.4 Fix reading multi-file, multi-series OME-TIFF (#67). Detect ScanImage 2021 files (#46). Shape new version ScanImage series according to metadata (breaking). Remove Description key from TiffFile.scanimage_metadata dict (breaking). Also return ScanImage version from read_scanimage_metadata (breaking). Fix docstrings. 2021.2.26 Squeeze axes of LSM series by default (breaking). Add option to preserve single dimensions when reading from series (WIP). Do not allow appending to OME-TIFF files. Fix reading STK files without name attribute in metadata. Make TIFF constants multi-thread safe and pickleable (#64). Add detection of NDTiffStorage MajorVersion to read_micromanager_metadata. Support ScanImage v4 files in read_scanimage_metadata. 2021.2.1 Fix multi-threaded access of ZarrTiffStores using same TiffFile instance. Use fallback zlib and lzma codecs with imagecodecs lite builds. Open Olympus and Panasonic RAW files for parsing, albeit not supported. Support X2 and X4 differencing found in DNG. Support reading JPEG_LOSSY compression found in DNG. 2021.1.14 Try ImageJ series if OME series fails (#54) Add option to use pages as chunks in ZarrFileStore (experimental). Fix reading from file objects with no readinto function. 2021.1.11 Fix test errors on PyPy. Fix decoding bitorder with imagecodecs >= 2021.1.11. 2021.1.8 Decode float24 using imagecodecs >= 2021.1.8. Consolidate reading of segments if possible. 2020.12.8 Fix corrupted ImageDescription in multi shaped series if buffer too small. Fix libtiff warning that ImageDescription contains null byte in value. Fix reading invalid files using JPEG compression with palette colorspace. 2020.12.4 Fix reading some JPEG compressed CFA images. Make index of SubIFDs a tuple. Pass through FileSequence.imread arguments in imread. Do not apply regex flags to FileSequence axes patterns (breaking). 2020.11.26 Add option to pass axes metadata to ImageJ writer. Pad incomplete tiles passed to TiffWriter.write (#38). Split TiffTag constructor (breaking). Change TiffTag.dtype to TIFF.DATATYPES (breaking). Add TiffTag.overwrite method. Add script to change ImageDescription in files. Add TiffWriter.overwrite_description method (WIP). 2020.11.18 Support writing SEPARATED color space (#37). Use imagecodecs.deflate codec if available. Fix SCN and NDPI series with Z dimensions. Add TiffReader alias for TiffFile. TiffPage.is_volumetric returns True if ImageDepth > 1. Zarr store getitem returns numpy arrays instead of bytes. 2020.10.1 Formally deprecate unused TiffFile parameters (scikit-image #4996). 2020.9.30 Allow to pass additional arguments to compression codecs. Deprecate TiffWriter.save method (use TiffWriter.write). Deprecate TiffWriter.save compress parameter (use compression). Remove multifile parameter from TiffFile (breaking). Pass all is_flag arguments from imread to TiffFile. Do not byte-swap JPEG2000, WEBP, PNG, JPEGXR segments in TiffPage.decode. 2020.9.29 Fix reading files produced by ScanImage > 2015 (#29). 2020.9.28 Derive ZarrStore from MutableMapping. Support zero shape ZarrTiffStore. Fix ZarrFileStore with non-TIFF files. Fix ZarrFileStore with missing files. Cache one chunk in ZarrFileStore. Keep track of already opened files in FileCache. Change parse_filenames function to return zero-based indices. Remove reopen parameter from asarray (breaking). Rename FileSequence.fromfile to imread (breaking). 2020.9.22 Add experimental zarr storage interface (WIP). Remove unused first dimension from TiffPage.shaped (breaking). Move reading of STK planes to series interface (breaking). Always use virtual frames for ScanImage files. Use DimensionOrder to determine axes order in OmeXml. Enable writing striped volumetric images. Keep complete dataoffsets and databytecounts for TiffFrames. Return full size tiles from Tiffpage.segments. Rename TiffPage.is_sgi property to is_volumetric (breaking). Rename TiffPageSeries.is_pyramid to is_pyramidal (breaking). Fix TypeError when passing jpegtables to non-JPEG decode method (#25). 2020.9.3 Do not write contiguous series by default (breaking). Allow to write to SubIFDs (WIP). Fix writing F-contiguous numpy arrays (#24). 2020.8.25 Do not convert EPICS timeStamp to datetime object. Read incompletely written Micro-Manager image file stack header (#23). Remove tag 51123 values from TiffFile.micromanager_metadata (breaking). 2020.8.13 Use tifffile metadata over OME and ImageJ for TiffFile.series (breaking). Fix writing iterable of pages with compression (#20). Expand error checking of TiffWriter data, dtype, shape, and tile arguments. 2020.7.24 Parse nested OmeXml metadata argument (WIP). Do not lazy load TiffFrame JPEGTables. Fix conditionally skipping some tests. 2020.7.22 Do not auto-enable OME-TIFF if description is passed to TiffWriter.save. Raise error writing empty bilevel or tiled images. Allow to write tiled bilevel images. Allow to write multi-page TIFF from iterable of single page images (WIP). Add function to validate OME-XML. Correct Philips slide width and length. 2020.7.17 Initial support for writing OME-TIFF (WIP). Return samples as separate dimension in OME series (breaking). Fix modulo dimensions for multiple OME series. Fix some test errors on big endian systems (#18). Fix BytesWarning. Allow to pass TIFF.PREDICTOR values to TiffWriter.save. 2020.7.4 Deprecate support for Python 3.6 (NEP 29). Move pyramidal subresolution series to TiffPageSeries.levels (breaking). Add parser for SVS, SCN, NDPI, and QPI pyramidal series. Read single-file OME-TIFF pyramids. Read NDPI files > 4 GB (#15). Include SubIFDs in generic series. Preliminary support for writing packed integer arrays (#11, WIP). Read more LSM info subrecords. Fix missing ReferenceBlackWhite tag for YCbCr photometrics. Fix reading lossless JPEG compressed DNG files. 2020.6.3 ... Refer to the CHANGES file for older revisions. Notes ----- The API is not stable yet and might change between revisions. Tested on little-endian platforms only. Python 32-bit versions are deprecated. Python <= 3.7 are no longer supported. Tifffile relies on the `imagecodecs `_ package for encoding and decoding LZW, JPEG, and other compressed image segments. Several TIFF-like formats do not strictly adhere to the TIFF6 specification, some of which allow file or data sizes to exceed the 4 GB limit: * *BigTIFF* is identified by version number 43 and uses different file header, IFD, and tag structures with 64-bit offsets. It adds more data types. Tifffile can read and write BigTIFF files. * *ImageJ* hyperstacks store all image data, which may exceed 4 GB, contiguously after the first IFD. Files > 4 GB contain one IFD only. The size (shape and dtype) of the up to 6-dimensional image data can be determined from the ImageDescription tag of the first IFD, which is Latin-1 encoded. Tifffile can read and write ImageJ hyperstacks. * *OME-TIFF* stores up to 8-dimensional data in one or multiple TIFF of BigTIFF files. The 8-bit UTF-8 encoded OME-XML metadata found in the ImageDescription tag of the first IFD defines the position of TIFF IFDs in the high dimensional data. Tifffile can read OME-TIFF files, except when the OME-XML metadata are stored in a separate file. Tifffile can write numpy arrays to single-file OME-TIFF. * *LSM* stores all IFDs below 4 GB but wraps around 32-bit StripOffsets. The StripOffsets of each series and position require separate unwrapping. The StripByteCounts tag contains the number of bytes for the uncompressed data. Tifffile can read large LSM files. * *STK* (MetaMorph Stack) contains additional image planes stored contiguously after the image data of the first page. The total number of planes is equal to the counts of the UIC2tag. Tifffile can read STK files. * *NDPI* uses some 64-bit offsets in the file header, IFD, and tag structures. Tag values/offsets can be corrected using high bits stored after IFD structures. Tifffile can read NDPI files > 4 GB. JPEG compressed segments with dimensions >65530 or missing restart markers are not decodable with libjpeg. Tifffile works around this limitation by separately decoding the MCUs between restart markers. BitsPerSample, SamplesPerPixel, and PhotometricInterpretation tags may contain wrong values, which can be corrected using the value of tag 65441. * *Philips* TIFF slides store wrong ImageWidth and ImageLength tag values for tiled pages. The values can be corrected using the DICOM_PIXEL_SPACING attributes of the XML formatted description of the first page. Tifffile can read Philips slides. * *Ventana/Roche BIF* slides store tiles and metadata in a BigTIFF container. Tiles may overlap and require stitching based on the TileJointInfo elements in the XMP tag. Volumetric scans are stored using the ImageDepth extension. Tifffile can read BIF and decode individual tiles, but does not perform stitching. * *ScanImage* optionally allows corrupted non-BigTIFF files > 2 GB. The values of StripOffsets and StripByteCounts can be recovered using the constant differences of the offsets of IFD and tag values throughout the file. Tifffile can read such files if the image data are stored contiguously in each page. * *GeoTIFF* sparse files allow strip or tile offsets and byte counts to be 0. Such segments are implicitly set to 0 or the NODATA value on reading. Tifffile can read GeoTIFF sparse files. Other libraries for reading scientific TIFF files from Python: * `Python-bioformats `_ * `Imread `_ * `GDAL `_ * `OpenSlide-python `_ * `Slideio `_ * `PyLibTiff `_ * `SimpleITK `_ * `PyLSM `_ * `PyMca.TiffIO.py `_ (same as fabio.TiffIO) * `BioImageXD.Readers `_ * `CellCognition `_ * `pymimage `_ * `pytiff `_ * `ScanImageTiffReaderPython `_ * `bigtiff `_ * `Large Image `_ Some libraries are using tifffile to write OME-TIFF files: * `Zeiss Apeer OME-TIFF library `_ * `Allen Institute for Cell Science imageio `_ * `xtiff `_ Other tools for inspecting and manipulating TIFF files: * `tifftools `_ * `Tyf `_ References ---------- * TIFF 6.0 Specification and Supplements. Adobe Systems Incorporated. https://www.adobe.io/open/standards/TIFF.html * TIFF File Format FAQ. https://www.awaresystems.be/imaging/tiff/faq.html * The BigTIFF File Format. https://www.awaresystems.be/imaging/tiff/bigtiff.html * MetaMorph Stack (STK) Image File Format. http://mdc.custhelp.com/app/answers/detail/a_id/18862 * Image File Format Description LSM 5/7 Release 6.0 (ZEN 2010). Carl Zeiss MicroImaging GmbH. BioSciences. May 10, 2011 * The OME-TIFF format. https://docs.openmicroscopy.org/ome-model/latest/ * UltraQuant(r) Version 6.0 for Windows Start-Up Guide. http://www.ultralum.com/images%20ultralum/pdf/UQStart%20Up%20Guide.pdf * Micro-Manager File Formats. https://micro-manager.org/wiki/Micro-Manager_File_Formats * ScanImage BigTiff Specification - ScanImage 2019. http://scanimage.vidriotechnologies.com/display/SI2019/ ScanImage+BigTiff+Specification * ZIF, the Zoomable Image File format. http://zif.photo/ * GeoTIFF File Format https://gdal.org/drivers/raster/gtiff.html * Cloud optimized GeoTIFF. https://github.com/cogeotiff/cog-spec/blob/master/spec.md * Tags for TIFF and Related Specifications. Digital Preservation. https://www.loc.gov/preservation/digital/formats/content/tiff_tags.shtml * CIPA DC-008-2016: Exchangeable image file format for digital still cameras: Exif Version 2.31. http://www.cipa.jp/std/documents/e/DC-008-Translation-2016-E.pdf * The EER (Electron Event Representation) file format. https://github.com/fei-company/EerReaderLib * Digital Negative (DNG) Specification. Version 1.5.0.0, June 2012. https://www.adobe.com/content/dam/acom/en/products/photoshop/pdfs/ dng_spec_1.5.0.0.pdf * Roche Digital Pathology. BIF image file format for digital pathology. https://diagnostics.roche.com/content/dam/diagnostics/Blueprint/en/pdf/rmd/ Roche-Digital-Pathology-BIF-Whitepaper.pdf Examples -------- Write a numpy array to a single-page RGB TIFF file: >>> data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8') >>> imwrite('temp.tif', data, photometric='rgb') Read the image from the TIFF file as numpy array: >>> image = imread('temp.tif') >>> image.shape (256, 256, 3) Write a 3D numpy array to a multi-page, 16-bit grayscale TIFF file: >>> data = numpy.random.randint(0, 2**12, (64, 301, 219), 'uint16') >>> imwrite('temp.tif', data, photometric='minisblack') Read the whole image stack from the TIFF file as numpy array: >>> image_stack = imread('temp.tif') >>> image_stack.shape (64, 301, 219) >>> image_stack.dtype dtype('uint16') Read the image from the first page in the TIFF file as numpy array: >>> image = imread('temp.tif', key=0) >>> image.shape (301, 219) Read images from a selected range of pages: >>> images = imread('temp.tif', key=range(4, 40, 2)) >>> images.shape (18, 301, 219) Iterate over all pages in the TIFF file and successively read images: >>> with TiffFile('temp.tif') as tif: ... for page in tif.pages: ... image = page.asarray() Get information about the image stack in the TIFF file without reading the image data: >>> tif = TiffFile('temp.tif') >>> len(tif.pages) # number of pages in the file 64 >>> page = tif.pages[0] # get shape and dtype of the image in the first page >>> page.shape (301, 219) >>> page.dtype dtype('uint16') >>> page.axes 'YX' >>> series = tif.series[0] # get shape and dtype of the first image series >>> series.shape (64, 301, 219) >>> series.dtype dtype('uint16') >>> series.axes 'QYX' >>> tif.close() Inspect the "XResolution" tag from the first page in the TIFF file: >>> with TiffFile('temp.tif') as tif: ... tag = tif.pages[0].tags['XResolution'] >>> tag.value (1, 1) >>> tag.name 'XResolution' >>> tag.code 282 >>> tag.count 1 >>> tag.dtype Iterate over all tags in the TIFF file: >>> with TiffFile('temp.tif') as tif: ... for page in tif.pages: ... for tag in page.tags: ... tag_name, tag_value = tag.name, tag.value Overwrite the value of an existing tag, e.g. XResolution: >>> with TiffFile('temp.tif', mode='r+b') as tif: ... _ = tif.pages[0].tags['XResolution'].overwrite((96000, 1000)) Write a floating-point ndarray and metadata using BigTIFF format, tiling, compression, and planar storage: >>> data = numpy.random.rand(2, 5, 3, 301, 219).astype('float32') >>> imwrite('temp.tif', data, bigtiff=True, photometric='minisblack', ... compression='zlib', planarconfig='separate', tile=(32, 32), ... metadata={'axes': 'TZCYX'}) Write a 10 fps time series of volumes with xyz voxel size 2.6755x2.6755x3.9474 micron^3 to an ImageJ hyperstack formatted TIFF file: >>> volume = numpy.random.randn(6, 57, 256, 256).astype('float32') >>> imwrite('temp.tif', volume, imagej=True, resolution=(1./2.6755, 1./2.6755), ... metadata={'spacing': 3.947368, 'unit': 'um', 'finterval': 1/10, ... 'axes': 'TZYX'}) Read the volume and metadata from the ImageJ file: >>> with TiffFile('temp.tif') as tif: ... volume = tif.asarray() ... axes = tif.series[0].axes ... imagej_metadata = tif.imagej_metadata >>> volume.shape (6, 57, 256, 256) >>> axes 'TZYX' >>> imagej_metadata['slices'] 57 >>> imagej_metadata['frames'] 6 Create a TIFF file containing an empty image and write to the memory-mapped numpy array: >>> memmap_image = memmap( ... 'temp.tif', shape=(256, 256, 3), dtype='float32', photometric='rgb' ... ) >>> type(memmap_image) >>> memmap_image[255, 255, 1] = 1.0 >>> memmap_image.flush() >>> del memmap_image Memory-map and read contiguous image data in the TIFF file: >>> memmap_image = memmap('temp.tif') >>> memmap_image.shape (256, 256, 3) >>> memmap_image[255, 255, 1] 1.0 >>> del memmap_image Write two numpy arrays to a multi-series TIFF file: >>> series0 = numpy.random.randint(0, 255, (32, 32, 3), 'uint8') >>> series1 = numpy.random.randint(0, 1023, (4, 256, 256), 'uint16') >>> with TiffWriter('temp.tif') as tif: ... tif.write(series0, photometric='rgb') ... tif.write(series1, photometric='minisblack') Read the second image series from the TIFF file: >>> series1 = imread('temp.tif', series=1) >>> series1.shape (4, 256, 256) Successively write the frames of one contiguous series to a TIFF file: >>> data = numpy.random.randint(0, 255, (30, 301, 219), 'uint8') >>> with TiffWriter('temp.tif') as tif: ... for frame in data: ... tif.write(frame, contiguous=True) Append an image series to the existing TIFF file: >>> data = numpy.random.randint(0, 255, (301, 219, 3), 'uint8') >>> imwrite('temp.tif', data, photometric='rgb', append=True) Create a TIFF file from a generator of tiles: >>> data = numpy.random.randint(0, 2**12, (31, 33, 3), 'uint16') >>> def tiles(data, tileshape): ... for y in range(0, data.shape[0], tileshape[0]): ... for x in range(0, data.shape[1], tileshape[1]): ... yield data[y : y + tileshape[0], x : x + tileshape[1]] >>> imwrite('temp.tif', tiles(data, (16, 16)), tile=(16, 16), ... shape=data.shape, dtype=data.dtype, photometric='rgb') Write two numpy arrays to a multi-series OME-TIFF file: >>> series0 = numpy.random.randint(0, 255, (32, 32, 3), 'uint8') >>> series1 = numpy.random.randint(0, 1023, (4, 256, 256), 'uint16') >>> with TiffWriter('temp.ome.tif') as tif: ... tif.write(series0, photometric='rgb') ... tif.write(series1, photometric='minisblack', ... metadata={'axes': 'ZYX', 'SignificantBits': 10, ... 'Plane': {'PositionZ': [0.0, 1.0, 2.0, 3.0]}}) Write a tiled, multi-resolution, pyramidal, OME-TIFF file using JPEG compression. Sub-resolution images are written to SubIFDs: >>> data = numpy.arange(1024*1024*3, dtype='uint8').reshape((1024, 1024, 3)) >>> with TiffWriter('temp.ome.tif', bigtiff=True) as tif: ... options = dict(tile=(256, 256), photometric='rgb', compression='jpeg') ... tif.write(data, subifds=2, **options) ... # save pyramid levels to the two subifds ... # in production use resampling to generate sub-resolutions ... tif.write(data[::2, ::2], subfiletype=1, **options) ... tif.write(data[::4, ::4], subfiletype=1, **options) Access the image levels in the pyramidal OME-TIFF file: >>> baseimage = imread('temp.ome.tif') >>> second_level = imread('temp.ome.tif', series=0, level=1) >>> with TiffFile('temp.ome.tif') as tif: ... baseimage = tif.series[0].asarray() ... second_level = tif.series[0].levels[1].asarray() Iterate over and decode single JPEG compressed tiles in the TIFF file: >>> with TiffFile('temp.ome.tif') as tif: ... fh = tif.filehandle ... for page in tif.pages: ... for index, (offset, bytecount) in enumerate( ... zip(page.dataoffsets, page.databytecounts) ... ): ... _ = fh.seek(offset) ... data = fh.read(bytecount) ... tile, indices, shape = page.decode( ... data, index, jpegtables=page.jpegtables ... ) Use zarr to read parts of the tiled, pyramidal images in the TIFF file: >>> import zarr >>> store = imread('temp.ome.tif', aszarr=True) >>> z = zarr.open(store, mode='r') >>> z >>> z[0] # base layer >>> z[0][256:512, 512:768].shape # read a tile from the base layer (256, 256, 3) >>> store.close() Read images from a sequence of TIFF files as numpy array: >>> imwrite('temp_C001T001.tif', numpy.random.rand(64, 64)) >>> imwrite('temp_C001T002.tif', numpy.random.rand(64, 64)) >>> image_sequence = imread(['temp_C001T001.tif', 'temp_C001T002.tif']) >>> image_sequence.shape (2, 64, 64) >>> image_sequence.dtype dtype('float64') Read an image stack from a series of TIFF files with a file name pattern as numpy or zarr arrays: >>> image_sequence = TiffSequence('temp_C0*.tif', pattern=r'_(C)(\d+)(T)(\d+)') >>> image_sequence.shape (1, 2) >>> image_sequence.axes 'CT' >>> data = image_sequence.asarray() >>> data.shape (1, 2, 64, 64) >>> with image_sequence.aszarr() as store: ... zarr.open(store, mode='r') >>> image_sequence.close() Write the zarr store to a fsspec ReferenceFileSystem in JSON format: >>> with image_sequence.aszarr() as store: ... store.write_fsspec('temp.json', url='file://') Open the fsspec ReferenceFileSystem as a zarr array: >>> import fsspec >>> import tifffile.numcodecs >>> tifffile.numcodecs.register_codec() >>> mapper = fsspec.get_mapper( ... 'reference://', fo='temp.json', target_protocol='file') >>> zarr.open(mapper, mode='r') z 2021.11.2)5OmeXml OmeXmlErrorTIFFTiffFile TiffFileError TiffFrameTiffPageTiffPageSeries TiffReader TiffSequenceTiffTagTiffTagsTiffTagRegistry TiffWriterZarrFileSequenceStore ZarrStore ZarrTiffStoreimreadimshowimwritelsm2binmemmapread_micromanager_metadataread_scanimage_metadata tiff2fsspec tiffcomment FileCache FileHandle FileSequenceTimeraskopenfilenameastype create_outputenumargenumstr format_sizelazyattr matlabstr2pynatural_sortednullfunc parse_kwargspformatproduct repeat_nd reshape_axes reshape_nd squeeze_axes stripnulltranspose_axes update_kwargsxml2dictimsave _app_showN)IterableMutableMapping)ThreadPoolExecutorFc Kst|ddddddddd f d d |D}t|d d dddd}|dddk r|dddk rftdtjdtdd|d|d<|d ddkrDt|trd|ksd|krt |}|st dt |dst|tt j fst|dkr|d}t|tt j fst |drDt|f| }|r2|jf|S|jf|SQRXt|f|(}|rh|jf||S|jf||SQRXdS)aReturn image data from TIFF file(s) as numpy array or zarr storage. Refer to the TiffFile and TiffSequence classes and their asarray functions for documentation. Parameters ---------- files : str, path-like, binary stream, or sequence File name, seekable binary stream, glob pattern, or sequence of file names. aszarr : bool If True, return file sequences, series, or single pages as zarr storage instead of numpy array (experimental). kwargs : dict Parameters 'name', 'offset', 'size', and 'is_' flags are passed to TiffFile or TiffSequence.imread. Parameters 'imread', 'container', 'sort', 'pattern', 'axesorder', and 'categories' are passed to TiffSequence. Other parameters are passed to the asarray or aszarr functions. The first image series in the file is returned if no arguments are provided. Returns ------- numpy.ndarray or zarr storage Image data from the specified pages. Zarr storage instances must be closed after use. See TiffPage.asarray for operations that are applied (or not) to the raw data stored in the file. nameoffsetsize _multifile _useframesfastijmovie multifilemultifile_closecss"|]}|dddkr|VqdS)Nis_).0keyrErET/home/ankuromar296_gmail_com/.local/lib/python3.7/site-packages/tifffile/tifffile.py Sszimread..r containersortpattern axesorder categoriespagesNrGz8the 'pages' and 'key' parameters cannot be used togetherz^ the 'pages' parameter is deprecated since 2017.9.29. Use the 'key' parameter) stacklevel*?zno files foundseekr6)r)get TypeErrorwarningswarnDeprecationWarningpop isinstancestrglob ValueErrorhasattrosPathLikelenraszarrasarrayr )filesrdkwargsZ kwargs_fileZ kwargs_seqtifZimseqrErErHr$s^     rc Kst|ddddd}|dkr:t|}t||j}|j}n0y|j}|jj}Wntk rhd}d}YnX|dd }d|kr||kr| dd s| d d s| d d s| d d sd|d<d|kr||d<t |f|} | j |||f|} WdQRX| S)aWrite numpy array to TIFF file. Refer to the TiffWriter class and its write function for documentation. A BigTIFF file is created if the data's size is larger than 4 GB minus 32 MB (for metadata), and 'bigtiff' is not specified, and 'imagej' or 'truncate' are not enabled. Parameters ---------- file : str, path-like, or binary stream File name or writable binary stream, such as an open file or BytesIO. data : array-like Input image. The last dimensions are assumed to be image depth, length, width, and samples. If None, an empty array of the specified shape and dtype is saved to file. Unless 'byteorder' is specified in 'kwargs', the TIFF file byte order is determined from the data's dtype or the dtype argument. shape : tuple If 'data' is None, shape of an empty array to save to the file. dtype : numpy.dtype If 'data' is None, datatype of an empty array to save to the file. kwargs : dict Parameters 'append', 'byteorder', 'bigtiff', 'imagej', and 'ome', are passed to TiffWriter(). Other parameters are passed to TiffWriter.write(). Returns ------- offset, bytecount : tuple or None If the 'returnoffset' argument is True and the image data are written contiguously, return offset and bytecount of image data in the file. appendbigtiff byteorderimagejomeNr6bigsizel|Ftruncate compressioncompressT) r)numpydtyper+itemsizerknbytes Exceptionr[rVrwrite) filedatashapersrgZtifargsdatasizerkrnrhresultrErErHrs2$        rr+c Ks|dk rL|dk rL|jd||tjddt|f|}|dkrBtd|d} nt|f|x} |dk r| j|}|jsztd|j\} } |j }|j }n.| j |}|j dkrtd|j }|j }|j } | j |j}WdQRXt|||| |dS)a%Return memory-mapped numpy array stored in TIFF file. Memory-mapping requires data stored in native byte order, without tiling, compression, predictors, etc. If 'shape' and 'dtype' are provided, existing files are overwritten or appended to depending on the 'append' parameter. Otherwise the image data of a specified page or series in an existing file are memory-mapped. By default, the image data of the first series are memory-mapped. Call flush() to write any changes in the array to the file. Raise ValueError if the image data in the file are not memory-mappable. Parameters ---------- filename : str or path-like Name of the TIFF file which stores the array. shape : tuple Shape of the empty array. dtype : numpy.dtype Datatype of the empty array. page : int Index of the page which image data to memory-map. series, level : int Index of the page series and pyramid level which image data to memory-map. mode : {'r+', 'r', 'c'} The file open mode. Default is to open existing file for reading and writing ('r+'). kwargs : dict Additional parameters passed to imwrite() or TiffFile(). Returns ------- numpy.memmap Image data in TIFF file. NT)ryrzrsalign returnoffsetz"image data are not memory-mappabler6C)updaterALLOCATIONGRANULARITYrr_rrOis_memmappable is_contiguousrzrsseriesr;rkcharrrr) filenamerzrspagerlevelmodergr|r;rh_rErErHrs6/      rcs,eZdZdZdZddZfddZZS)r%z\Attribute whose value is computed on first access. Lazyattrs are not thread-safe. )func__dict__cCs*||_|j|_|j|_|j|_|j|_dS)z,Initialize instance from decorated function.N)r__doc__ __module____name__ __qualname__)selfrrErErH__init__&s zlazyattr.__init__c sv|dkr |Sy||}Wn*tk rD}z t|Wdd}~XYnX|tkrbtt|||jjSt||jj||S)N)rAttributeError RuntimeErrorNotImplementedgetattrsuperrsetattr)rinstanceownervalueexc) __class__rErH__get__/szlazyattr.__get__)rrrr __slots__rr __classcell__rErE)rrHr%s r%c@seZdZdZdS)rz-Exception to indicate invalid TIFF structure.N)rrrrrErErErHr=src@seZdZdZdddZeddZddddddddddddddddddddddddid dddfd d Zd d ZddZ ddZ ddZ ddZ ddZ ddZddZdS)raWrite numpy arrays to TIFF file. TiffWriter's main purpose is saving nD numpy array's as TIFF, not to create any possible TIFF format. Specifically, ExifIFD and GPSIFD tags are not supported. TiffWriter instances must be closed using the 'close' method, which is automatically called when using the 'with' context manager. TiffWriter instances are not thread-safe. FNc Csf|ryxt|ddd`}|}zDt|2} |dkr@| js@td| j}| j}| jj|_ WdQRXWd| |XWdQRXWnt t fk rd}YnX|dkrt jd krd nd }n|d krtd ||d kr|rtjntj|_n|rtjntj|_d|_d|_d|_d|_d|_d|_d|_d|_d|_d|_d|_d|_g|_ g|_!d|_"d|_#|rt|ddd|_$|j$ dt%j&nt|ddd|_$|j$'ddd ||r|j$'t()|ddddn|j$'t()|dd|j$|_ |j$'t()|jj*d|dkrdnt+||_,|j,r,dnt+||_-|j-rDd|_,|rb|rbt./|dt0dS)aOpen TIFF file for writing. An empty TIFF file is created if the file does not exist, else the file is overwritten with an empty TIFF file unless 'append' is true. Use 'bigtiff=True' when creating files larger than 4 GB. Parameters ---------- file : path-like, binary stream, or FileHandle File name or writable binary stream, such as an open file or BytesIO. bigtiff : bool (optional) If True, the BigTIFF format is used. byteorder : {'<', '>', '=', '|'} (optional) The endianness of the data in the file. By default, this is the system's native byte order. append : bool (optional) If True and 'file' is an existing standard TIFF file, image data and tags are appended to the file. This does not scale well with the number of pages already in the file. Appending data may corrupt specifically formatted TIFF files such as OME-TIFF, LSM, STK, ImageJ, or FluoView. imagej : bool (optional) If True and not 'ome', write an ImageJ hyperstack compatible file. This format can handle data types uint8, uint16, or float32 and data shapes up to 6 dimensions in TZCYXS order. RGB images (S=3 or S=4) must be uint8. ImageJ's default byte order is big-endian but this implementation uses the system's native byte order by default. ImageJ hyperstacks do not support BigTIFF or compression. The ImageJ file format is undocumented. When using compression, use ImageJ's Bio-Formats import function. ome : bool (optional) If True, write an OME-TIFF compatible file. If None (default), the value is determined from the file name extension, the value of the 'description' parameter in the first call of the write function, and the value of 'imagej'. Refer to the OME model for restrictions of this format. rbr6)rr<forcez)cannot append to file containing metadataNF)N=|little<>)rrzinvalid byteorder zr+bwbsIIsMMZHHH+H*z% writing nonconformant BigTIFF ImageJ)1rtellr is_appendabler_rk is_bigtiffrOnext_page_offset _ifdoffsetrTOSErrorFileNotFoundErrorsysrBIG_LE CLASSIC_LEtiffBIG_BE CLASSIC_BE _truncate _metadata _colormap_tags _datashape _datadtype _dataoffset_databytecounts_dataoffsetstag_descriptiontag_subifds _subifdslevel_subifdsoffsets_nextifdoffsets _ifdindex _storedshape_fhraSEEK_ENDrwstructpack offsetformatbool_ome_imagejrXrY UserWarning) rrxrjrkrirlrmfhposrhrErErHrOsn1    zTiffWriter.__init__cCs|jS)zReturn file handle.)r)rrErErH filehandleszTiffWriter.filehandler6rEcqs$j}jj|dkr}1|dk rDt?t5j6|}|rVt?t5j<|}|rxt|t0sxt0t?t5j@|}|dkrd}2ntd d!tA|D}2|r|}tC|d(k}n d?}t0|}tN| t5jOL|d }8|8}tC|8}9d}:d }| rV|9d(k rVd}|dk rh|/}d}|dk rd};|+}|# r|,}n||0k r|9d k r|dd2k r|-}|"d5k};n||1k r | r|9d(k r|d@d2k r|-}d};n |9d k r|dAd2k r|-}d};n|9d k r6|dd2k r6|-}|0}|"d5k};njj sFj rP|+}d}nP| r||9d(k r||d@d2k r||-}|1}d};n$|9d k r|dAd2k r|-}|1}d};|; r||0k rdB}n|=f}>|d|>k r|0}nD|| rd@ndA|>k r|1}n&|d|| rd@ndAk r|1}n|0}||0k rdK|| rd@ndAd}8|8d}:n&dL|| rd@ndAdd>}8|8d}:|:|=k r|:|=}nZ|t5j6jPk rtC|d k rptdMd}d}dK|ddd>}8n| r tC|| rd(nd k r ||0k rdK|| rd@ndAd}8|8d}:n&dL|| rd@ndAdd>}8|8d}:|:d}nd}x.tC|d k r>|ddk r>|dd} qWtC|d(k rRd}|2dk r|dK|| rjdAnddd>}8n*dK|| rd@ndAd}8|8d}:|:d}|d&@ r|# r|:dk r|dNk stdOt5j6jQ}d}'|#r| dk r| dkrtdP| dQd} n |4dRkrN|!dSkrN| dk rH| dTkrHtdP| dUdT} n| dkrd|!jd } n|!jHdVks||!jd&kr| |!jd krtdP| dW|!nz| d d d;dX|!jkr| |!jd kstdP| dY|!n<|r| |!jd krtdP| dZn| |!jd krd}'tC|8d[kr>tRd\tC|8d]tC|8d^krh|8dd d>|8d d}8|8d dkrt|8dd}?|?d krdn t|&|?}?|?f|8dd}8y|S|8}WntTk rYnX||/kr|:dks|s|8ddks|8ddkrtd_||-kr2|:d kr2td`g|rFda}@db}Andc}@dd}A|A_Ufdedfdԇfdgdh }Bdidj}C|dk r|Bdkd d |ddl|sin|V_"jrtCjjWd krdm}nd}n؈jrl|dkrtXj"dndodpdqdrdsdtdudvdwdxdydzd{d|d}}nt j d~td d xtY|D]}D|B|Dq0WtZ|&|8dd2kjdk fj"}|d7}nB|s||ikrj(rj"j[ddt\|&fj"}|d7}nd}|dk r|]d}|Bdkd d |ddl~|dkrd}|r|Bdd d |ddl|rzt|tEr4tC|dks*|d;dkrhtdn4y|^d}Wn$tTk rf_^d}YnX|Bdd d |ddl|Bdd(d|4|4dkr|Bdd&d d|r|Bdd(d|5|Bdd&d|8d|Bdd&d|8dA|r|Bdd&d|d|Bdd&d|d|r2|Bdd&d|8d@|r2|Bdd&d|d |rF|Bdd&d||sTj'rʈjd krʈj'rpj'}n8yt|_'}Wn$t k rtC|_'}YnX|Bdd&krdnd|d g||#s|!jHdVksdd d(dd|!jH}E|Bdd(|:|Ef|:|dk r|Bdd(|j`||Bdd(d|:|#r4nD|rj|:dkrj|Bdd(d|ja|Bdd(|:| f|:n|Bdd(d| |r|2dk r|tC|2krtd|dtC|2|Bdd(||2n6||-kr|dkr|Bdd(dd n|Bdd(|d||dk r|BddRtC|||4dRkr|dkr||-|.fkr|dkrBd}n|dkrZtd|tb|d }F|r|d|Fs|d|Frtd|F|dkrtd|Bdd(d |t?t5j6|3Ldd}G||3d<|j/|3d<|Gj/|3d<|Bdd(d|Gtcdd!|Dr|Bdd^ddnn|dkr4tdd|d}d}F|Bdd(d|ja||.kr|Bdd(d dtcdd!|Dr|Bdd^dd|dk r|Bdd^d|C|d |Bdd^d|C|dtC|d kr|d }H|Hdkrdn t?t5je|H}Hnjrd}Hnd }H|Bdd(d|Hn2jsB|Bdd^dd|Bdd^dd|Bdd(dd|fdd}I|p^|'p^|# } |rtC|d kr|8d(|d d|d |8d&|dd|df}J| o|8d(|d ko|8d&|dk} n|8d |d d|d |8d(|dd|d|8d&|d d|d f}J| ob|8d |d kob|8d(|dkob|8d&|d k} t|J|8d}Kt||8d|!jg|K}L|I|L}M|B|@|M|K|L|B|A|Kd g|K|M|K}M| s|dk rn tf|||J}n| r| dkr|8d|8d }Nt|8d(d|!jg|N}L|I|L}M|B|@|M|N|L|B|A|Nd g|N|Bdd&d|8dA|M|8d}M| s|dk rzntg|}nRt|8dd|!j}O| dkr|rd|O} n|8dA} | dkr|F} n:| |8dAkr|8dA} n"|r| |Frthi| |F|F} |Bdd&d| |8dA| d| }P|P|8d|8d }Q| |O}R|Rg|Q}L|R|O|P| |8dA8}Rx"tj|Pd|Q|PD]}S|R|L|S<qzW|I|L}M|B|@|M|Q|L|B|A|Qd g|Q|M|Q}M| s|dk rntg|}|dkr| stdx|D]}D|B|DqWtkddd|#r^|4dkr4ddd„}n(|4dkrTt5jl|4|3fdd„}ntmdŃn|rt5jl|4}T|4dkrd|3d<|r|T|3fdd„}n2|r||T|3fdd„}n|3r|T|3fdd„}n|T}n|'r| fdd„}nd}~|,}Ud&ksjs|s|U|%dkrtd̓xtj| r*dn|8d D]}V|U}W|Wd rZ|ndΡ|Wd7}Wjd kr|$jo|n|W|$|W|Vd krd}Xtpq}Y|Yn|)tC|Y,}Z|YndϠrdd!D|Y,}[|Ynd xntsD]`\}\}]|Z|\|*d&}(|]d }^|]d }_|_r|Y,}`|`d rT|YndΡ|`d7}`|Y$|(|Yn|W|`|Y$|`|Yn|_|^|Akr|(|`f}anR|^|@kr|(|`f}bn>|^dkkr|W|Z|\|*jt_u|W|`jt_vn|^dkr\|(|`f}Xnn|^|Akr|(df}anZ|^|@kr|(df}bnF|^dkkrJ|W|Z|\|*jt_ujtjud&jt_vn|^dkr|(df}XqW|Y,}c|cd r|YndΡ|cd7}c|$|ct%jw|,}d| dkrd;} | |d| | }e|$|et%jw|d|e7}d| rP|dkr|-|%n`|dk rBxT|D]@}f|fj|!kr"td|fjdW|!|.|fS|8ddqWn |.|nZ| r|8ddkrj|}gn||8df}gt|g|!j}h|dkr|-|K|hn| r8d}ixtj|8dt|JD]r}jtx|}k|kdkrd |L|j<q|irt|ktyrn$|kjz|hk rt{|k|g|!}kd}i||k}k|n|ktC|k|L|j<qWnbx`tj|8dt|JD]H}jtx|}k|kdk rr|-|h qN|kjz|hk rt{|k|g|!}k|.|k qNWn |!rh|8dA| d| }Qd }ltx|S|8dd}f|fj|!k rtd|fjdW|!x|fD]h}mx`|mD]X}nxPtj|QD]D}S|n|S| |Sd| }o||o}o|n|otC|o|L|l<|ld7}l!qW!qW qWnBtx|S|8dd}f|fj|!k!rtd|fjdW|!|.|f|a\}(}`|Y$|(|`"r|Yn|W|`|Y$|`|d}(x8|LD]}p|Yn|(|(|p7}(!qWn|Yn|d|"rn|b\}(}`|Y$|(|`"rZ|Yn|W|`|Y$|`|Yn|Mf|L|Xdk "r|X\}(}`|`dk "r|Y$|(|Yn|W|`j*||W|`nj*||W|(|,}U|$|W|n|Y}|~jd k#r |W|[_on|$j*j+j|n|Wjd k#rTj)||W|[n2|$j)j+|n|W|W|[j)j+<j+d7_+j+tCj*;_+|$|U|Vd kr4ddӄDq4W|8_!d>|&_|!_|d_|L_| $r_|$r|dt|LfSdS)a.Write numpy ndarray to a series of TIFF pages. The ND image data are written to a series of TIFF pages/IFDs. By default, metadata in JSON, ImageJ, or OME-XML format are written to the ImageDescription tag of the first page to describe the series such that the image data can later be read back as a ndarray of same shape. The data shape's last dimensions are assumed to be image depth, length (height), width, and samples. If a colormap is provided, the data's dtype must be uint8 or uint16 and the data values are indices into the last dimension of the colormap. If 'shape' and 'dtype' are specified instead of 'data', an empty array is written. This option cannot be used with compression, predictors, packed integers, bilevel images, or multiple tiles. If 'shape', 'dtype', and 'tile' are specified, 'data' must be an iterable of all tiles in the image. If 'shape', 'dtype', and 'data' are specified but not 'tile', 'data' must be an iterable of all single planes in the image. Image data are written uncompressed in one strip per plane by default. Dimensions larger than 2 to 4 (depending on photometric mode, planar configuration, and volumetric mode) are flattened and written as separate pages. If the data size is zero, a single page with shape (0, 0) is written. The SampleFormat tag is derived from the data type or dtype. A UserWarning is logged if RGB colorspace is auto-detected. Specify the 'photometric' parameter to avoid the warning. Parameters ---------- data : numpy.ndarray, iterable of numpy.ndarray, or None Input image or iterable of tiles or images. A copy of the image data is made if 'data' is not a C-contiguous numpy array with the same byteorder as the TIFF file. Iterables must yield C-contiguous numpy array of TIFF byteorder. Iterable tiles must match 'dtype' and the shape specified in 'tile'. Incomplete tiles are zero-padded. Iterable images must match 'dtype' and 'shape[1:]'. shape : tuple or None Shape of the empty or iterable data to write. Use only if 'data' is None or an iterable of tiles or images. dtype : numpy.dtype or None Datatype of the empty or iterable data to write. Use only if 'data' is None or an iterable of tiles or images. photometric : {MINISBLACK, MINISWHITE, RGB, PALETTE, SEPARATED, CFA} The color space of the image data according to TIFF.PHOTOMETRIC. By default, this setting is inferred from the data shape, dtype, and the value of colormap. Always specify this parameter to avoid ambiguities. For CFA images, the CFARepeatPatternDim, CFAPattern, and other DNG or TIFF/EP tags must be specified in 'extratags' to produce a valid file. planarconfig : {CONTIG, SEPARATE} Specifies if samples are stored interleaved or in separate planes. By default, this setting is inferred from the data shape. If this parameter is set, extra samples are used to store grayscale images. CONTIG: last dimension contains samples. SEPARATE: third (or fourth) last dimension contains samples. extrasamples : tuple of {UNSPECIFIED, ASSOCALPHA, UNASSALPHA} Defines the interpretation of extra components in pixels. UNSPECIFIED: no transparency information (default). ASSOCALPHA: single, true transparency with pre-multiplied color. UNASSALPHA: independent transparency masks. volumetric : bool If True, the SGI ImageDepth tag is used to write volumetric data in one page. The volumetric format is not officially specified, and few software can read it. OME and ImageJ formats are not compatible with volumetric storage. tile : tuple of int The shape ([depth,] length, width) of image tiles to write. If None (default), image data are written in strips. The tile length and width must be a multiple of 16. If a tile depth is provided, the SGI ImageDepth and TileDepth tags are used to write volumetric data. Tiles cannot be used to write contiguous series, except if tile matches the data shape. contiguous : bool If False (default), write data to a new series. If True and the data and parameters are compatible with previous written ones (same shape, no compression, etc.), the image data are stored contiguously after the previous one. In that case, 'photometric', 'planarconfig', and 'rowsperstrip' are ignored. Metadata such as 'description', 'metadata', 'datetime', and 'extratags' are written to the first page of a contiguous series only. Cannot be used with the OME or ImageJ formats. truncate : bool If True, only write the first page of a contiguous series if possible (uncompressed, contiguous, not tiled). Other TIFF readers will only be able to read part of the data. Cannot be used with the OME or ImageJ formats. align : int Byte boundary on which to align the image data in the file. Default 16. Use mmap.ALLOCATIONGRANULARITY for memory-mapped data. Following contiguous writes are not aligned. rowsperstrip : int The number of rows per strip. By default, strips are ~64 KB if compression is enabled, else rowsperstrip is set to the image length. bitspersample : int Number of bits per sample. By default, this is the number of bits of the data dtype. Different values for different samples are not supported. Unsigned integer data are packed into bytes as tightly as possible. Valid values are 1-8 for uint8, 9-16 for uint16 and 17-32 for uint32. Cannot be used with compression, contiguous series, or empty files. compression : str, (str, int), (str, int, dict) If None (default), data are written uncompressed. If a str, one of TIFF.COMPRESSION, e.g. 'JPEG' or 'ZSTD'. If a tuple, the first item is one of TIFF.COMPRESSION, the second item is the compression level, and the third item is a dict of arguments passed to the compression codec. Compression cannot be used to write contiguous series. Compressors may require certain data shapes, types or value ranges. For example, JPEG requires grayscale or RGB(A), uint8 or 12-bit uint16. JPEG compression is experimental. JPEG markers and TIFF tags may not match. Only a limited set of compression shemes are implemented. predictor : bool or TIFF.PREDICTOR If True, apply horizontal differencing or floating-point predictor before compression. Predictors are disabled for 64-bit integers. subsampling : {(1, 1), (2, 1), (2, 2), (4, 1)} The horizontal and vertical subsampling factors used for the chrominance components of images. The default is (2, 2). Currently applies to JPEG compression of RGB images only. Images are stored in YCbCr color space. Segment widths must be a multiple of 8 times the horizontal factor. Segment lengths and rowsperstrip must be a multiple of 8 times the vertical factor. jpegtables : bytes JPEG quantization and/or Huffman tables. Use for copying pre-compressed JPEG segments. colormap : numpy.ndarray RGB color values for the corresponding data value. Must be of shape (3, 2**(data.itemsize*8)) and dtype uint16. description : str or encoded bytes The subject of the image. Must be 7-bit ASCII. Cannot be used with the ImageJ or OME formats. Written with the first page of a series only. datetime : datetime, str, or bool Date and time of image creation in '%Y:%m:%d %H:%M:%S' format or datetime object. Else if True, the current date and time is used. Written with the first page of a series only. resolution : (float, float[, str]) or ((int, int), (int, int)[, str]) X and Y resolutions in pixels per resolution unit as float or rational numbers. A third, optional parameter specifies the resolution unit, which must be None (default for ImageJ), 'INCH' (default), or 'CENTIMETER'. subfiletype : int Bitfield to indicate the kind of data. Set bit 0 if the image is a reduced-resolution version of another image. Set bit 1 if the image is part of a multi-page image. Set bit 2 if the image is transparency mask for another image (photometric must be MASK, SamplesPerPixel and BitsPerSample must be 1). software : str or bool Name of the software used to create the file. If None (default), 'tifffile.py'. Must be 7-bit ASCII. Written with the first page of a series only. subifds : int Number of child IFDs. If greater than 0, the following 'subifds' number of series are written as child IFDs of the current series. The number of IFDs written for each SubIFD level must match the number of IFDs written for the current series. All pages written to a certain SubIFD level of the current series must have the same hash. SubIFDs cannot be used with truncated or ImageJ files. SubIFDs in OME-TIFF files must be sub-resolutions of the main IFDs. metadata : dict Additional metadata describing the image data, written along with shape information in JSON, OME-XML, or ImageJ formats in ImageDescription or IJMetadata tags. If None, do not write an ImageDescription tag with shape in JSON format. If ImageJ format, values for keys 'Info', 'Labels', 'Ranges', 'LUTs', 'Plot', 'ROI', and 'Overlays' are written in IJMetadata and IJMetadataByteCounts tags. Refer to the imagej_metadata_tag function for valid values. Refer to the OmeXml class for supported keys when writing OME-TIFF. Strings must be 7-bit ASCII. Written with the first page of a series only. extratags : sequence of tuples Additional tags as [(code, dtype, count, value, writeonce)]. code : int The TIFF tag Id. dtype : int or str Data type of items in 'value'. One of TIFF.DATATYPES. count : int Number of data values. Not used for string or bytes values. value : sequence 'Count' values compatible with 'dtype'. Bytes must contain count values of dtype packed as binary data. writeonce : bool If True, the tag is written to the first page of a series only. returnoffset : bool If True and the image data in the file are memory-mappable, return the offset and number of bytes of the image data in the file. Returns ------- offset, bytecount : tuple or None If 'returnoffset' is true and the image data in the file are memory-mappable, return the offset and number of bytes of the image data in the file. N__iter____next__z1generators require 'shape' and 'dtype' parametersrsrz ignoring 'dtype' argumentz ignoring 'shape' argumentzs the 'compress' parameter is deprecated since 2020.9.30. Use the 'compression' parameterrP)rQr6r zinvalid compression level rSrrUFT)Nr6rUNONEnonez8the ImageJ format does not support non-contiguous seriesz,SubIFDs cannot be used with truncated seriesz$SubIFDs in SubIFDs are not supportedz7contiguous cannot be used with compression, tiles, etc.z.ome.tifz.rZLIB) iiiiiiLiuiviQiRiufrCzcannot apply predictor to z$ not writing description to OME-TIFFz$OME-TIFF does not support ImageDepthz' not writing description to ImageJ fileZBHhfz-the ImageJ format does not support data type z-the ImageJ format does not support ImageDepthBaxes)rCrz for RGBz0the ImageJ format does not support planar imagesBHz#invalid data dtype for palette moder)rszinvalid color map shapecss|]}t|VqdS)N)int)rFirErErHrIscss|]}|dkVqdS)rUNrE)rFrrErErHrIszinvalid tile shape)rUrE)zcontiguous samplesz parameter is)zseparate component planesz!and 'planarconfig' parameters arez, data with shape z and dtype 'z' are stored as RGB with zk. Future versions will store such data as MINISBLACK in separate pages by default unless the 'photometric' z specified.znot a z image)rrU)rzinvalid CFA image)r6rUrzinvalid SubfileType MASKzbitspersample z must be 1 for bilevelruint16 z& must be 12 for JPEG compressed uint16uz does not match dtype )rUrPrz out of range of dtype z cannot be used with compression)zlength of storedshape z not in (5, 6)rz#invalid data shape for palette modez#not a RGB image (samplesperpixel=2)iEiDiics$|ddkr|}tj|f|S)Nr6z<>)rr)fmtval)rkrErHrs zTiffWriter.write..packc sTt|tstj|}y|}tj|d}Wnvtk r}zXy*|}|ddkrZ|dd}tj|}Wn(ttfk rtd||YnXWdd}~XYnX~|}|dkrt|t ry| d}Wn,t k r}ztd|Wdd}~XYnXnt|t stdt |dks*|dd kr2|d 7}t |}|d krtdd d|dd_|d }|dkrt|}ntd|d}t||}n|}|f}nrUzunknown dtype rPasciiz TIFF strings must be 7-bit ASCIIiszinvalid packed binary data)r HHzvalue.size != countzvalue.dtype.char != dtype) r\rrTAGS DATA_FORMATSKeyError DATA_DTYPESrWr_r]encodeUnicodeEncodeErrorbytesrcr rfindmaxminrcalcsizerituplelistrrndarrayr<rrsrtobytesjoin) coderscountr writeoncedatatype dataformatrZrawcountrtZifdentryZifdvalue)r offsetsizerrtags valueformatrErHaddtag s    (                    z TiffWriter.write..addtagcSsddlm}y||}Wn&tk r@||d|d}YnXy|\}}Wn,tk r~|d}|j|j}}YnX|dks|dkrdt ||}t ||}t ||}||fS)Nr6)FractionrUll) fractionsr from_floatrWas_integer_ratiorlimit_denominator numerator denominatorrround)argrrrrrrErErHrationalms    z"TiffWriter.write..rationali)r InfoLabelsRangesLUTsPlotROIOverlays PropertiesinfolabelsrangesZlutsZplotZroiZoverlayspropzq the 'ijmetadata' parameter is deprecated since 2020.5.5. Use the 'metadata' parameterz@) truncatedzrz tifffile.pyi1:zinvalid datetime stringz%Y:%m:%d %H:%M:%Si2iiGi)rr6i=iiBiCiiiJ r)rrrciSi@iiizwrong number of extrasamples z != iR)r6i[)rPrP))rUrU)rPrU)rPrP)rrUzinvalid subsampling factors ztile shape not a multiple of z'JPEG subsampling requires RGB(A) imagesi outcolorspace subsampling colorspaceicss|]}|ddkVqdS)r6iNrE)rFetrErErHrI( si) r6rUrUrUr6rUr7rUr6rU)N)rUrUz cannot apply subsampling )rUrUcss|]}|ddkVqdS)r6iNrE)rFr5rErErHrI7 siii(cSsVt|dkrddd|S|d}|r.|d}|dkr:dS|d krFdS|d krRdSdS) NrUIQ)rrr6rirlr)rc) bytecountsrpr< bytecountrErErHbytecount_formatN s z*TiffWriter.write..bytecount_formatiiz&cannot write non-contiguous empty filecSs|dS)Nr6rE)xrErErH rz"TiffWriter.write..)rGcSstj|ddS)Nr)axis)rrpackbitsr)ryrrErErHrq sz"TiffWriter.write..compress)ricSstj|dd}||f|S)Nr)r?)rrr@r)ry compressorrgrErErHrq szcannot compress bilevel imageir?cSs ||f|S)NrE)ryrArgrErErHrq scSs||dd}||f|S)Nr)r?rE)ry predictorrArgrErErHrq s cSs ||f|S)NrE)ryrArgrErErHrq scSst||ddS)Nr)r?)packints_encode)rybpsrErErHrq slz%data too large for standard TIFF filerrcss|]}|dVqdS)rUNrE)rFtrErErHrI' szdtype of iterable cSsg|]}|ds|qS)rrE)rFtagrErErH sz$TiffWriter.write..)F)N)rrrkrrrrs newbyteorderrr`iterrWrerXrYrrzisnativerZr\rintegerr_r+rtrrZ array_equalr_write_remaining_pagesrrraddimagerr_write_image_descriptionrTrarrrrrrr write_empty write_arrayr:rr tagnoformatrtagsizer PHOTOMETRIC MINISBLACK MINISWHITERGBYCBCRPALETTE PLANARCONFIGCONTIGSEPARATEr" PREDICTORsequencerrcdictr]upper COMPRESSIONkind PREDICTORSr imagej_shaperVanyr.PHOTOMETRIC_SAMPLESCFAMASKrreshaperrcopyimagesr)imagej_metadata_tagimagej_descriptionrjson_descriptionrstrftime_nowr<rrall log_warningRESUNIT iter_tiles iter_imagesmathceilrangesorted COMPRESSORSNotImplementedErrorrwrioBytesIOr  enumeraterr; valueoffsetSEEK_CURnextrrupad_tileri getbufferflushrrrsum)qrryrzrs photometric planarconfig extrasamplesZ volumetrictile contiguousror~ rowsperstrip bitspersamplerprBr3 jpegtablescolormap descriptiondatetime resolution subfiletypesoftwaresubifdsmetadataZ extratagsrZ ijmetadatarqrZdataiterZ datashapeZ datadtypeZ datadtypecharZbilevelindexr{Z inputshapeZpackintsr;rQrRrTrUrVrWrXrZr[Z extrasamples_ZcompressionargsZcompressiontagZ predictortagZijrgbZijshape storedshapendimsamplesperpixelZ deprecatemsgZphotometricsamplesZsamples_s0Z tagbytecountsZ tagoffsetsrrrE sampleformatZ maxsamplingr2unitr<tilesZnumtilesdatabytecountsZbytecountformatr ZrowsizeZ numstrips1Z numstripsZ stripsizerrAfhpos pageindexifdpossubifdsoffsetsifd tagoffset ifdoffsettagindexrFr rrdataoffsetsoffsetZdatabytecountsoffsetifdsize dataoffsetskipZpagedataZ tileshapeZtilesizeisbytes tileindexchunk stripindexplanedepthstripr<rE)rkrrrrrrrHrwss                                                          $                     `            "         "                                                                                       zTiffWriter.writecCs4|jdkrtd||jj|ddd|_dS)zOverwrite the value of the last ImageDescription tag. Can be used to write OME-XML after writing the image data. Ends a contiguous series. Nzno ImageDescription tag foundF)erase)rr_rL overwrite)rrrErErHoverwrite_description s  z TiffWriter.overwrite_descriptionc CsR|jr|js|jdkrdS|jd|jdd}|dkrPd|_d|_d|_dS|j}|}|drx|d|d7}t j }|j j }|j j }|j j}|j j}|j} t|j} d} t} | ||t|j| } | ddd|jD| }| ||dx4t|jD]$\}}| |||d }|d}|d}|r| }|drr| d|d7}| |y| ||||WnBtk r|jrt|d td |_dStd YnX| || |||jkr||f}n|d kr>||f} n(||jkr,|df}n|d kr|df} qW| }|drh| d|d7}|dkr|||dkr|jrt|d td |_dStd tt||}|}xt|D]}| | 7} |\}}| ||dk rJ| ||||| || }x:|jD]}| |||||7}q&Wn| ||| | dk r| \}}|j !||dk r|n||j"dkr| dk r| \}}|dk r| || ||||||7}| || |||n||j |j#|j"||||||j"dkr>|j$!||n2||j$|j#|||||||j$|j#<|j#d7_#|j#t|j ;_#||7}|| %qW|||d7}|||||d||||%|j"dkr<|}||j&|||||'|||||_&d|_d|_d|_dS)z(Write outstanding IFDs and tags to file.Nr6rUrPrrcss|]}|dVqdS)rUNrE)rFrErErErHrI) sz4TiffWriter._write_remaining_pages..rz truncating ImageJ fileTz#data too large for non-BigTIFF fileiJrl)(rrrrrrrrrwrrrrrrQrRrr{r|rcr r}rTrvrrXrYrr_rrrwrrirrrrrr)rZpagenorrrrrrQrRrZ pagedatasizerrrrrrFr;r rrrrifdsrrr<rErErHrL s                                  z!TiffWriter._write_remaining_pagescCs|jdks|jdkrd|_dS|jrx|jdkrd|jj|j|j|jddkrNdndd|jf|j|jjdd }n\|jddkrd|_dS|j r|j dk }|jddk}t |j||f|j}nt |jf|j}|jj|dd d|_dS) z'Write metadata to ImageDescription tag.Nr6rUT) declarationr)rCrF)r)rrrrrMrrrtostringrrrrlrmr)rrZ colormappedisrgbrErErHrN s,  z#TiffWriter._write_image_descriptioncCs tjS)zReturn current date and time.)rnow)rrErErHro szTiffWriter._nowcCs$|js|||jdS)z,Write remaining pages and close file handle.N)rrLrNrclose)rrErErHr szTiffWriter.closecCs|S)NrE)rrErErH __enter__ szTiffWriter.__enter__cCs |dS)N)r)rexc_type exc_value tracebackrErErH__exit__ szTiffWriter.__exit__cCsdt|jjddS)Nzd?Z#d@dAZ$dBdCZ%dDdEZ&dFdGZ'ddJdKZ(e dLdMZ)edNdOZ*e dPdQZ+e dRdSZ,edTdUZ-e dVdWZ.edXdYZ/edZd[Z0ed\d]Z1ed^d_Z2e d`daZ3e dbdcZ4e dddeZ5edfdgZ6edhdiZ7edjdkZ8edldmZ9e dndoZ:edpdqZ;edrdsZe dxdyZ?e dzd{Z@e d|d}ZAed~dZBeddZCdS)raoRead image and metadata from TIFF file. TiffFile instances must be closed using the 'close' method, which is automatically called when using the 'with' context manager. TiffFile instances are not thread-safe. Attributes ---------- pages : TiffPages Sequence of TIFF pages in file. series : list of TiffPageSeries Sequences of closely related TIFF pages. These are computed from OME, LSM, ImageJ, etc. metadata or based on similarity of page properties such as shape, dtype, and compression. is_flag : bool If True, file is of a certain format. Flags are: bigtiff, uniform, shaped, ome, imagej, stk, lsm, fluoview, nih, vista, micromanager, metaseries, mdgel, mediacy, tvips, fei, sem, scn, svs, scanimage, andor, epics, ndpi, pilatus, qpi. All attributes are read-only. NTc  Ks\| rx2dD]*} | | kr | | =tjd| dtddq Wd| krHtdx^| D]R\} } | dd d kr| d dtjkr| dk rt|| t| qRtd | qRW|d krt d |t |||||d} | |_ t||_ | j |i|_i|_|dkr|n||_y0| d| d} ydddd| dd}Wn$tk r\td| YnXt|d| ddd}|dkrt|d| d\}}|dks|dkrtd||f|dkrtj|_ntj|_n|dkr0|dkrtj|_n.| dds| j dr&tj|_ntj|_n|dkrd|dkrLtdt|d tj|_n`|d!ks|d"ks|d#krt|d$|d%d&|dkrtj|_ntj|_ntd'|t ||_!|j"r|j#j$d(ks|j!dj%d)ks|j!d)j%d)kr|&n |j'rv|j(svy|j!)Wn@t*k rr}z t|d*|j+j,d+|Wdd}~XYnXn|j-ry |.Wn@t*k r}z t|d,|j+j,d+|Wdd}~XYnXnf|j/r&y |0Wn@t*k r"}z t|d-|j+j,d+|Wdd}~XYnXn|r4d.|j!_1Wn t*k rV| 2YnXdS)/alInitialize instance from file. Parameters ---------- arg : path_like or open file Name of file or open file object. The file objects are closed in TiffFile.close(). mode : str (optional) File open mode in case 'arg' is a file name. Must be 'rb' or 'r+b'. Default is 'rb'. name : str (optional) Optional name of file in case 'arg' is a file handle. offset : int (optional) Optional start position of embedded file. By default, this is the current file position. size : int (optional) Optional size of embedded file. By default, this is the number of bytes from the 'offset' to the end of the file. kwargs : bool (optional) 'is_ome': If False, disable processing of OME-XML metadata. )r?r@rArBz the z argument is ignoredrP)rQrOzwthe 'pages' parameter is no longer supported. Use TiffFile.asarray(key=[...]) to read image data from specific pages. NrCrDzunexpected keyword argument: )Nrzr+bz invalid mode )rr:r;r<r6rrr)sIIsMMsEPznot a TIFF file rrrrzinvalid BigTIFF offset size ris_ndpiFndpii1Nzinvalid NIFF filez NIFF format not supportedUiROiRSz RAW format 0xZ04Xz not supportedzinvalid TIFF version lrUz" _load_virtual_frames failed with z: z! _philips_load_pages failed with z _ndpi_load_pages failed with T)3rXrYrZrWitemsr FILE_FLAGSrrr_rrr=r:_files _decoders_parentrTreadrrrunpackrrrrrVendswithNDPI_LErrq TiffPagesrOis_lsmrr<rp_lsm_load_pages is_scanimager_load_virtual_framesrvrr is_philips_philips_load_pagesr_ndpi_load_pages useframesr)rrrr:r;r<r=r>rrgrGrrheaderrkversionrzerorrErErHr s"   "                     . . . zTiffFile.__init__cCs|jjS)N)rrk)rrErErHrk szTiffFile.byteordercCs|jS)zReturn file handle.)r)rrErErHr szTiffFile.filehandlecCs|jjS)zReturn name of file handle.)rr:)rrErErHr szTiffFile.filenamecCs*yt|jStk r$dSXdS)z3Return status of file handle as stat_result object.N)rafstatrfilenorv)rrErErHr szTiffFile.fstatcCs"x|jD]}|jq WdS)zClose open file handle(s).N)rvaluesrr)rrhrErErHr szTiffFile.closec s|jstgS|dkr$|dkr$d}|dkr4|jn@y|j|}Wnttfk rZYnX|dk rn|j|}|j|dkr~nl|dkr|j|nVt|t tj fr|gn:t|t rĈ|n&t|t rfdd|Dntdst d|dkr|r|jr|j|jj}djr\t|tr\|dkr\||}|j|||j} nF||}|dk r~t|||j}|j|j|jj|t||d} n0td krƈdj||d } nt||d } | dkrdS|dkrj||}y || _Wnft k rfy(t|d | jd |d || _Wn&t k r`d dj| _YnXYnXnhtd kr|dkrd}|rdjndj | _n.|dkrd}d |rĈdjndj | _| S)a' Return image data from selected TIFF page(s) as numpy array. By default, the data from the first series is returned. Parameters ---------- key : int, slice, or sequence of indices Defines which pages to return as array. If None (default), data from a series (default 0) is returned. If not None, data from the specified pages in the whole file (if 'series' is None) or a specified series are returned as a stacked array. Requesting an array from multiple pages that are not compatible wrt. shape, dtype, compression etc. is undefined, i.e. may crash or return incorrect values. series : int or TiffPageSeries Defines which series of pages to return as array. level : int Defines which pyramid level of a series to return as array. squeeze : bool If True, all length-1 dimensions (except X and Y) are squeezed out from the array. If False, single pages are returned as 5D array (TiffPage.shaped). For series, the shape of the returned array also includes singlet dimensions specified in some file formats. E.g. ImageJ series, and most commonly also OME series, are returned in TZCYXS order. If None (default), all but "shaped" series are squeezed. out : numpy.ndarray, str, or file-like object Buffer where image data are saved. If None (default), a new array is created. If numpy.ndarray, a writable array of compatible dtype and shape. If 'memmap', directly memory-map the image data in the TIFF file if possible; else create a memory-mapped array in a temporary file. If str or open file, the file name or file object used to create a memory-map to an array stored in a binary file on disk. maxworkers : int or None Maximum number of threads to concurrently get data from multiple pages or compressed segments. If None (default), up to half the CPU cores are used. If 1, multi-threading is disabled. Reading data from file is limited to a single thread. Using multiple threads can significantly speed up this function if the bottleneck is decoding compressed data, e.g. in case of large LZW compressed LSM files or JPEG compressed tiled slides. If the bottleneck is I/O or pure Python code, using multiple threads might be detrimental. Returns ------- numpy.ndarray Image data from the specified pages. See TiffPage.asarray for operations that are applied (or not) to the raw data stored in the file. Nr6csg|] }|qSrErE)rFk)rOrErHrG sz$TiffFile.asarray..z&key must be an int, slice, or sequencezno pages selectedr)outrU)r maxworkersz asarray failed to reshape z to )rT)!rOrrarrayrrrWlevels_getlistr\rrKslicer7r_r;rkrsrrr] get_shaper memmap_arrayr!rT read_arrayr+rcre stack_pagesrzrqshaped) rrGrrsqueezerrtypecoderzr|rE)rOrHre s@                  zTiffFile.asarrayc Ks|jstd|dkr8|dkr8|jdjfd|i|S|dkrH|j}nJy|j|}Wnttfk rnYnX|dkr|jfd|i|S|j}t|ttj fr||jf|StddS)z=Return image data from selected TIFF page(s) as zarr storage.zempty zarr arrays not supportedNr6rzkey must be an integer index) rOrzrrdrrWr\rrrrK)rrGrrrgrOrErErHrdP s zTiffFile.aszarrcCs|js gS|jj}|jjj}g}xLdD]D}t|d|dr&t|d|}|sh|dkrh|jrh|jq&Pq&W||j_||j_|s|}xt|D]\}}||_qW|S)zReturn related pages as TiffPageSeries. Side effect: after calling this function, TiffFile.pages might contain TiffPage and TiffFrame instances. )rlsmrmrlZfluoviewstkZsissvsscnqpirbifZ scanimageZmdgeluniformrDFZ_series_rm) rOrkeyframerr is_imagej_clear_series_genericr})rrrrr:rrrErErHrd s(   zTiffFile.seriescCsj|jd}|jp|j }|jj|d}t|f|j}d|j}|j}|jrRd}nd}t|||||dgS)z+Return all images in file as single series.r6)validater8ZNIHImageZUniform)ra) rOris_nihrrcrzrrsr)rrrrOrzrrsrarErErH_series_uniform s  zTiffFile._series_uniformc sn|j}|dd|_|jr$|g}gifdd}x|D]}|||jdk rDxt|jD]z\}}|dkrxqfy |j|t ||j |f}Wn>t k r}z t |d|j jd|Wdd}~XYqfX||qfWqDWxjD]b} | }|d}t|f|j} d |j} d | kr6| d 7} | d 7} |t|| |j| d d qWt|dk|_t||S)zgReturn image series in file. A series is a sequence of TiffPages with the same hash. Fcs`|js dS|j}|krHxB|D]}|j|jkr"Pq"W||n||g|<dS)N)rzhashr;ri)rrGp)keys seriesdictrErHaddpage s  z)TiffFile._series_generic..addpageNrz generic series failed with z: r6r8S)rUGeneric)rarU)rOrrcache_loadrr}rrTrrrvrqrrrcrzrrirrs is_uniformpyramidize_series) rrOrrrrr;subifdrrGrzrrE)rrrHr sF    ,   zTiffFile._series_genericcs\fddd fdd dj_jg}|dkr>dSt|dk_t|dd |S) z%Return image series in "shaped" file.c s|d}|s:|j}|j}t|dkr:t|f|}d|}t|}t|} |jr| |kr| |dkr|dkrpd}d|}| |f|}yt|||}|}Wn>tk r} z td| jj d| Wdd} ~ XYnX| t |||j ||d|dd dS) Nr6rUr9Tz shaped series failed with z: ZShapedF)r:rar*r) rzrrcr+rr-r_rqrrrirrs) rrOrrzrhr:r*rr<resizer)rrErHri s<  ,z'TiffFile._series_shaped..appendFc st|}d}}}}}d} x| |kr.P|r<|d}n | |_|j}|js`tddSd}d}t|j} | dd}| d}|jdkrdnd} | d| } d| kr| d}t|t|kr|}nd}td |g} t|} | dkr t| t|j \}}nd }d}|r*td dSd |krF|| krnn| |j j 9} | rbd }nn|j r|j | || d j kr|jdkrd} n:d} x4t| d | |D]}||}||_| |qW|| ||||| | |7} |jr$xt|jD]\}}|d krqg}xt| D]\}}yJj|j||dkr^t|j|f}|}nt|j|f|d }Wn@tk r}z td|jjd|dSd}~XYnX||q"W|r||d}|dkrdSqWq$W|S)Nr6z1 invalid shaped series metadata or corrupted filer:rrzFr*rz& shaped series axes do not match shaperUz. shaped series shape does not match page shaper)rz shaped series failed with z: T)rcr is_shapedrqjson_description_metadatarVrr+divmodrz_dtypertis_finalr;rwrir}rrTrrrrvrr)rOrZ issubifdslenpagesrrrzrhr:rrr*Zspagesr<npagesmodjrrr;rrZ keysubifdr)ri detect_seriesrrErHrs                z.TiffFile._series_shaped..detect_seriesTNrU) isreduced)F)rOrrcrr)rrrE)rirrrH_series_shaped s %f  zTiffFile._series_shapedc s jd_d_djfdd}y |}Wn&ttfk rbtddSX|rpgn dddt}dd }d d }d d }|||f}d }|t |} | d krtd | f|}d|}j dd krVj d|kr0td|dj d|ddj }|j d d7}nJj d|kr|d kr||d fj }|j 7}n|j 7}|j 7}d|kr|d7}|d7}|otjd koj d t |jdk} d_t|j|d| dgS)z#Return image series in ImageJ file.Tr6csjs dSdd}|dkr"dSj\}}|tjjdksX|||jjkr\tt dkr|||dj krdSdS)NFrjr6rUrT) r rVrr+rzrrr<r_rcr;)rjr;r )metarrOrrErH is_virtuals  "z+TiffFile._series_imagej..is_virtualz1 ImageJ series metadata invalid or corrupted fileNrjframesrUsliceschannelsTZCz. ImageJ series contains unidentified dimensionr8z" ImageJ series number of channels z! does not match separate samples rr)rUrImageJ)rar*)rOrrimagej_metadatar_rrqrVrcr+rrzrrrrrrs) rrZ isvirtualrjrrrrzrZremainr*rE)rrrOrrH_series_imagej|sj              zTiffFile._series_imagejc Csn|jjdd}|d}|j}d}|jdi}d|kr6y|d}y t|}Wntk rjt|}YnXd}yt|d}Wn8tk rd}t||rt d t||}YnX|dkrt t|||d}|||f|j }d |j } Wn@tk r4} z t |d | jjd | Wdd} ~ XYnX|dkrZt|f|j }d |j } t|||| ddgS)z&Return image series in ScanImage file.F)rr6N FrameDatazSI.hChannels.channelSavezSI.hStackManager.framesPerSlicerUz"unable to determine framesPerSliceZZTCz ScanImage series failed withz: r8Z ScanImage)ra)rOrrsscanimage_metadatarVrcrWrrvr_rrzrrqrrr) rrOrrsrz framedatarrrrrrErErH_series_scanimages>   ,  zTiffFile._series_scanimagecCsp|jjdd}|j}tt|d}ddd|D}tdd|D}d|_t|||d j ||d d d gS) z%Return image series in FluoView file.F)r Dimensionsrcss$|]}tj|ddVqdS)r6r9N)r MM_DIMENSIONSrVr_)rFrrErErHrIsz,TiffFile._series_fluoview..css|]}t|dVqdS)rUN)r)rFrrErErHrIsTr6 ImageNameZFluoView)r:ra) rOrfluoview_metadatarreversedr rrrrs)rrOmmZmmhdrrzrErErH_series_fluoviewszTiffFile._series_fluoviewcsd|j_d|j_|j}|ddkrltd}|ddd|ddkr^fd d }qpfd d }nd }|jd}d|_t|g|j||j |d dgS)z#Return image series in MD Gel file.Fr6ZFileTag)rPr7float32Z ScalePixelrUrPcs|ddS)Nr(rP)r )a)scalerErH transform6sz)TiffFile._series_mdgel..transformcs|dS)Nr()r )r))r*rErHr+;sNZMDGel)r+ra) rOrrmdgel_metadatarrrsrrrzr)rmdrsr+rrE)r*rH _series_mdgel*s(    zTiffFile._series_mdgelcCs|}x|D]}d|_|jddkr:d|jdd|_|jrf|jdjd}|dkr^dn||_q|jdjd }|dk r|d krd |_q|d krd |_qW|S)z+Return pyramidal image series in NDPI file.ZNDPIr6r8ZrUNiBaselineigMacrogZMap)rrar is_pyramidalrOrvalueofr:)rrrr:magrErErH _series_ndpiMs   zTiffFile._series_ndpicCs|jjdd}|d}t|}|j}d|krRd|krR|d|j}|d|j}n|f|j}d|j}d|_t|||j|dd gS) z(Return image series in Olympus SIS file.F)rr6rzrr8TZSIS)ra) rOrrc sis_metadatarzrrrrs)rrOrr r-rzrrErErH _series_sis`s  zTiffFile._series_sisc CsHg}|j}d|_d|_d|_|g}d}d|dj}|dj}|dj}x6|t|kr||}|j|krpP| ||d7}qPWt|f|} | t || ||ddd|t|kr||}| t |g|j|j|jd dd|d7}|dj rx|t|kr|dd |dd f|d d }g}x<|t|krl||}|j|krVP| ||d7}q2Wt|t|djkrPt|f|} |dj t || ||d ddqW|dj r>|t|kr>||}| t |g|j|j|jd dd|d7}|t|kr>||}| t |g|j|j|jdddd|_|S)z,Return image series in PerkinElmer QPI file.TFr6rrUr0ZQPI)r:ra ThumbnailrPN Resolutionr1Label)rOrrrrrrsrzrcriris_tiledrr2r) rrrOrrrrsZpshaperrzrErErH _series_qpios        $     zTiffFile._series_qpic Csr|jdjsdSg}d|_d|j_d|j_d|j_|jd}|j|}|t|g|j |j |j ddd|d7}|t |jkr|S|j|}|t|g|j |j |j d dd|d7}x\|t |jkr|j|}|jr|j rP|djt|g|j |j |j d dd|d7}qWxTd D]L}|t |jkr4P|j|}|t|g|j |j |j |dd|d7}qW|S) z'Return image series in Aperio SVS file.r6NFTr0SVS)r:rarUr8r9)r:r1)rOr;rrrrrrirrzrsrrc is_reducedr)rrrrr:rErErH _series_svsst              zTiffFile._series_svscCsddlm}|jdj}||}g}d|_d|j_d|j_d|j_|j xp|D]f}|j dsjqVxP|D]F}|j dsqr|j dd}x"|D]}|j d sqi} x|D]} | j d sqt|j d d d krtd t| j d} t| j d} t| j dd} t| j dd}t| j dd}t| j d}|| kr| |}| |dkrt| |d<||dkr||d<||d| |f<q| | g| || |f|id| |<qW| sqg}xt| D]\}}|dd |dd f}d}dgt|}x||||(d8d9~qWqWxt?| |D]\}-}||k r qrt@|-Ad#|-Bd#}x||CD]p\}\}}|3|}%t*|}#|%|#k r|D||d}n2|%|#<E|%d|#|D|||d} qW|-F| qrWx| D]~}-|-j}&|&jGdk rX qt,t*|&jGD]*}.d}&g}x|-jD]}+|+dk r||-jL|d>|.dd8d? qW q.ImageZ AnnotationRefNamePixelsDimensionOrdercsg|]}td|qS)Size)r)rFax)attrrErHrGsChannelFSamplesPerPixelcs,g|]$\}}|dkr |n|qS)rrE)rFrrd)rzspprErHrGsz2OME series cannot handle differing SamplesPerPixelZTiffDataIFDZ NumPlanesZ PlaneCountcs g|]}td|dqS)ZFirstr6)rrV)rFrd)rerErHrG.srz+ OME series contains invalid TiffData indexZFileName)rz OME series failed to read z' OME series contains index out of rangecss|]}|dkVqdS)NrE)rFrrErErHrItsz'TiffFile._series_ome..rz OME series expected z frames, got z: OME series cannot handle discontiguous storage (%s != %s)OME)rIr:rAraz+ OME series cannot read multi-file pyramidsz no keyframeXYzlevel )rIr:ra)QrJr@rOrrK ParseErrorrqrrdecoderrvrrrrrLrVrrdirnamerFrr AXES_LABELSfloatrraranger r%rr}r_ravel_multi_indexr]r=rrapathrrrMrcrrw IndexErrorrprIrclosedopenrrrr+r<r/rzrr:rirrsziprrget_axesrreplacerSset_shape_axesrrTrrrr imagewidth imagelengthrr)0rrNomexmlrOrZ root_uuidroZ modulorefrYrelementannotrrZmodulZalongr?Znewaxisstepstartstopr' annotationrefr:rDrrfirstryrnumidxuuidfnamerhr<rOrrisclosedrAZsqueezedZ keyframesrrZserierrdrE)rerzrhrH _series_omes          $                                               "zTiffFile._series_omec Cs|jd}|j}|d}|dd}|dkrBd|j}d|j}npt|ddkrl|f|j}d |j}nFtt|d dkr|f|j}d |j}n|f|j}d|j}d |_t |g||j |||dkd d}|gS)zReturn series in STK file.r6 NumberPlanesr`rrU)rUr8 ZDistancer/ TimeCreatedTTZSTK)r:r*ra) rO stk_metadatarVrzrrrrpdiffrrrs)rrrplanesr:rzrrrErErH _series_stk"s2          zTiffFile._series_stkc s|jtjd}|jdjdkr8|dddd}dddkrP|d 7}d ddkrh|d 7}|d d d }tfdd|D}dd}|jjt dd ddd}|dj }t |||||ddg}|jd}|j r|jjt dd ddd}|j }d}d} x:|t |krB| t |dkrB||| 9}| d7} q W|d | |j}|d | d}|t |||||ddd|_|S)z-Return main and thumbnail series in LSM file.ScanTyper6rPrrXYZXYC DimensionPP DimensionMMNrc3s |]}ttj|VqdS)N)rrCZ_LSMINFO_DIMENSIONS)rFr)lsmirErHrILsz'TiffFile._series_lsm..r`F)rZLSM)r:rarUSYXZ LSMreduced) lsm_metadatarCZ_LSMINFO_SCANTYPErOrrzrVrrrrsrr>rcrzrir) rrrzr:rOrsrrcprrE)rrH _series_lsmAs<   " zTiffFile._series_lsmcCs|j}d|_d|_d|_d|_|jdd|||d}x|dddD] }||_qRW|d}x|dddD] }||_qxWdS)z%Load and fix all pages from LSM file.TrUr6N)rrP)rOrrrr_lsm_fix_strip_offsets_lsm_fix_strip_bytecounts)rrOrrrErErHris  zTiffFile._lsm_load_pagescCs|jjdkrdS|j}t|}|jd}|j}d}x(dD] }|j|dkr8||j|9}q8W|dkrd}x$dD]}||dkrn|j|}PqnW|rt|d ||\}} | dkrtd |||d f} t t |  | } t | dd} nt | d d } |djd|djdkr*| d ddd f} d} d} x`| jD]V}|t|}g}x4|jD]*}|| krl| d7} ||| |} qVWt||_q:WdS) zUnwrap strip offsets for LSM files greater than 4 GB. Each series and position require separate unwrapping (undocumented). lNr6rU)r6rUZPM)rUrPrrPzmod != 0r.)rr<rOrcrrrzr rrrrrr+rhZmoveaxis dataoffsetsflatrrir)rrOrrrZ positionsrZntimesdivrrzindiceswrapZpreviousoffsetrrZ currentoffsetrErErHrsJ            zTiffFile._lsm_fix_strip_offsetsc Cs|j}|djdkrdSt|ddd}t|d}xt|D]\}}|jdrRq>|j}|j}||krz||djd}nt|dd|d|j j }t |}x0t t|dD]}||d||||<qW||d|d<t ||_q>WdS) zSet databytecounts to size of compressed data. The StripByteCounts tag in LSM files contains the number of bytes for the uncompressed data. r6rUNcSs |jdS)Nr6)r)rrErErHr>rz4TiffFile._lsm_fix_strip_bytecounts..)rGrPr)rOrprxrcr}rrrrrr<rrwr) rrOrrroffsetsr:Z lastoffsetrrErErHrs&  z"TiffFile._lsm_fix_strip_bytecountscCs|j}|djd}|dks&|dkr*dSd|_d|_|x|D]}|jd}|dksd|dkrDtjj|_ d|_ d|_ d |_ t d |_|_|jd dkrD|jdd |_|jdd |_|jdd d |_qDWdS) aLoad and fix pages from NDPI slide file if CaptureMode > 6. If the value of the CaptureMode tag is greater than 6, change the attributes of the TiffPages that are part of the pyramid to match 16-bit grayscale data. TiffTags are not corrected. r6iNrTFirUrrr)rU)rOrr3rrrrrSrTrrrrrrrsr rrrz)rrOZ capturemoderr4rErErHrs&   zTiffFile._ndpi_load_pagesc Csddlm}|j}d|_d|_|t|}||dj}|dj }|dj }d}x| D]}|j dks`|j ddd krq`d d |jd dD\} } |dkr|| 9}|| 9}g}q`|tt|| tt|| fq`Wd} x|D]\}}x,| |kr,|| jdkr,| d 7} qqW| |kr:P|| } || _ || _ | jdd krr||| jdf| _n.| jdd kr| jd||f| _n ||f| _| jdd||f| jdd| _| d 7} qWdS)zLoad and fix all pages from Philips slide file. The imagewidth and imagelength values of all tiled pages are corrected using the DICOM_PIXEL_SPACING attributes of the XML formatted description of the first page. r6)r@TFN Attributer`rZDICOM_PIXEL_SPACINGcss|]}t|VqdS)N)rq)rFvrErErHrIsz/TiffFile._philips_load_pages.."rUrrP)rJr@rOrrrrcrKrr|r}rIrFrLrVr]rzsplitrirrurv tilewidthrrz) rrNrOrrOr|r}sizeselemwhrrrErErHrsN        &zTiffFile._philips_load_pagescCsZ|ddtjkr@|jsdStt|jd|}t||||St|jjd|dS)z,Return 'is_flag' attributes from first page.rCNFr6z object has no attribute ) rrrOrrrrrr)rr:rrErErH __getattr__1s zTiffFile.__getattr__cCs|S)NrE)rrErErHr=szTiffFile.__enter__cCs |dS)N)r)rrrrrErErHr@szTiffFile.__exit__cCsdt|jjddS)Nz.rUz Pagesz Seriesz Filesz z z rrPr6 css|]}t|VqdS)N)r])rFrrErErHrIisrCN)detailwidthc3s,|]$}|jjjjstj|jdVqdS))rrN)rrIrrvr__str__)rFr)rrrErHrIusrz{}_METADATA {})rheightz z )r$rr<byteorder_isnativerkrrir flagsrcrOrrrzformatrr:rrrrMrxr`rr_r*)rrrr&rrr:mrE)rrrHrFs\    "        zTiffFile.__str__csfddttjDS)zsz!TiffFile.flags..)rxrr)rrE)rrHrs zTiffFile.flagscCs |jjdkS)z"Return if file has BigTIFF format.r)rr)rrErErHrszTiffFile.is_bigtiffcCsFy,|jdjp|jjdddj}|r*d|_|Stk r@dSXdS)z!Return if file has MD Gel format.r6rUT)rFN)rOis_mdgelrVrru)rZismdgelrErErHrs zTiffFile.is_mdgelcCs|j}|d}|jrdS|js$|jr(dSzTy:|j}d|_|j}x"dD]}||j|krDdSqDWWntk rxdSXWd||_XdS)z2Return if file contains a uniform series of pages.r6FT)rUrrN)rOrrrrraspageru)rrOrrrrrErErHrs"    zTiffFile.is_uniformcCs&|jp"|jp"|jp"|jp"|jp"|j S)z;Return if pages can be appended to file without corrupting.)is_omeris_stkr is_fluoviewis_micromanager)rrErErHrs zTiffFile.is_appendablecCs|js dStdd|jDS)z9Return tifffile metadata from JSON descriptions as dicts.Ncss,|]$}|jdkrt|jdjVqdS)rr6N)rarr rOr)rFrrErErHrIsz+TiffFile.shaped_metadata..)rrr)rrErErHshaped_metadatas zTiffFile.shaped_metadatacCs|js dS|jdjS)zReturn OME XML.Nr6)rrOr)rrErErH ome_metadataszTiffFile.ome_metadatacCs|js dS|jdjS)zReturn Leica SCN XML.Nr6)is_scnrOr)rrErErH scn_metadataszTiffFile.scn_metadatacCs|js dS|jdjS)zReturn Philips DP XML.Nr6)rrOr)rrErErHphilips_metadataszTiffFile.philips_metadatacCs|js dS|jdjdS)z0Return LSM metadata from CZ_LSMINFO tag as dict.Nr6il)rrOrr3)rrErErHrszTiffFile.lsm_metadatac Cs~|js dS|jd}|j}i}|jr4|jd|d<|d}|dkrJdn|j|d<|d}|dk rp|||d }|dk r|||d }|dk r|||d}|dk rz|d |d <|d |d <|d |d <yXt j ddt |d|d Ddd|d<t j ddt |d|d Ddd|d<Wn@t k rx}z t |d|jjd|Wdd}~XYnX|S)z*Return STK metadata from UIC tags as dict.Nr6ZPlaneDescriptionsi]rUri\i^i_rr TimeModifiedcSsg|] }t|qSrE)julian_datetime)rFdtrErErHrGsz)TiffFile.stk_metadata.. DateCreatedzdatetime64[ns])rsZDatetimeCreatedcSsg|] }t|qSrE)r)rFrrErErHrGs DateModifiedZDatetimeModifiedz STK metadata failed with z: )rrOrrrrVr r3rrrrrxr_rqrr)rrrr|rFrZuic2tagrrErErHrsL              ,zTiffFile.stk_metadatacCsZ|js dS|jd}t|j}|jd}|dk rVy||Wntk rTYnX|S)z,Return consolidated ImageJ metadata as dict.Nr6i)rrOimagej_description_metadatarr3rrv)rrr|rrErErHr)s   zTiffFile.imagej_metadatacCsV|js dSi}|jd}|jd}|dk r6|||jd}|dk rR||d<|S)z.Return consolidated FluoView metadata as dict.Nr6i9i:ZStamp)rrOrr3r)rr|rrrErErHr$8s     zTiffFile.fluoview_metadatacCs|js dS|jdjdS)z:Return NIH Image metadata from NIHImageHeader tag as dict.Nr6i2)rrOrr3)rrErErH nih_metadataRszTiffFile.nih_metadatacCs(|js dS|jdj}|d|dS)z5Return FEI metadata from SFEG or HELIOS tags as dict.Nr6ixiz)is_feirOrr3)rrrErErH fei_metadataYs zTiffFile.fei_metadatacCs|js dS|jdjdS)z,Return SEM metadata from CZ_SEM tag as dict.Nr6iF)is_semrOrr3)rrErErH sem_metadataaszTiffFile.sem_metadatacCsr|js dS|jdj}i}y||dWntk rBYnXy||dWntk rlYnX|S)z:Return Olympus SIS metadata from SIS and INI tags as dict.Nr6ii)is_sisrOrrr3rv)rrr|rErErHr6hs zTiffFile.sis_metadatacCstx,|jddD]}d|jkr|j}PqWdSi}xtj|}||||dd<q>W|S)z6Return consolidated metadata from MD GEL tags as dict.NrPii)rOrrwrrr3)rrrr|r r:rErErHr,ys  zTiffFile.mdgel_metadatacCs |jdjS)zReturn Andor tags as dict.r6)rO andor_tags)rrErErHandor_metadataszTiffFile.andor_metadatacCs |jdjS)z'Return EPICS areaDetector tags as dict.r6)rO epics_tags)rrErErHepics_metadataszTiffFile.epics_metadatacCs|js dS|jdjdS)zReturn TVIPS tag as dict.Nr6iJ)is_tvipsrOrr3)rrErErHtvips_metadataszTiffFile.tvips_metadatacCs|js dSt|jdjS)z:Return MetaSeries metadata from image description as dict.Nr6) is_metaseriesmetaseries_description_metadatarOr)rrErErHmetaseries_metadataszTiffFile.metaseries_metadatacCs|js dSt|jdjS)z7Return Pilatus metadata from image description as dict.Nr6) is_pilatuspilatus_description_metadatarOr)rrErErHpilatus_metadataszTiffFile.pilatus_metadatacCs|js dSt|jS)z8Return MicroManager non-TIFF settings from file as dict.N)rrr)rrErErHmicromanager_metadataszTiffFile.micromanager_metadatacCsV|js dSi}y.t|j\}}}||d<||d<||Wntk rPYnX|S)zReturn ScanImage non-varying frame and ROI metadata as dict. The returned dict may be empty or contain 'FrameData', 'RoiGroups', and 'version' keys. The varying frame data can be found in the ImageDescription tags. Nrr)rrrrr_)rr|rZroidatarrErErHrs zTiffFile.scanimage_metadatacCs|js dS|jdjS)z0Return GeoTIFF metadata from first page as dict.Nr6) is_geotiffrO geotiff_tags)rrErErHgeotiff_metadataszTiffFile.geotiff_metadatacCs0|js dS|jdjd}|dkr(dS|S)z+Return EER metadata from first page as XML.Nr6i)is_eerrOrr3rn)rrrErErH eer_metadataszTiffFile.eer_metadata)NNNNTNN)NNNNNN)NNN)r6r)Drrrrrrrkrrr%rrrerdrrrrrr r'r.r5r7r<r?rQrTrrrrrrrrrrrrrrrrrrrrrrrrrr$rrrr6r,rrrrrrrrrrErErErHr s        4@e5#_MUIk(6>  D        6               rc@seZdZdZd*ddZeddZejddZedd Zejd d Zed d Z e jd d Z eddZ d+ddZ d,ddZ ddZ d-ddZd.ddZd/ddZd0ddZd d!Zd"d#Zd$d%Zd&d'Zd(d)ZdS)1rzSequence of TIFF image file directories (IFD chain). Instances of TiffPages have a state (cache, keyframe, etc.) and are not thread-safe. NcCsd|_g|_d|_d|_t|_d|_d|_d|_d|_ t |t t j frTt |f|_n|dkrdd|_n t||_t |tr||_|jj}||_ t|jjj||jjjd}|dkrt|dd|_dSn^d|jkr(|j|_|jj}|jdj}|d}|dkr2t|dd|_dSn d|_dS||_||jkr`t|d|d|_dS|jdkrpdn|jd }||t|j|d }|j|||_|j dkr|j|d dd|_d|_dS) zInitialize instance and read first TiffPage from file. If arg is a TiffFile, the file position must be at an offset to an offset to a TiffPage. If arg is a TiffPage, page offsets are read from the SubIFDs tag. NFr6z contains no pagesTiJz contains invalid SubIFDsz invalid offset to first page )r6)rrU) rIrO_indexed_cachedr _tiffpage _keyframe_cache_offset_nextpageoffsetr\rrrrK_indexrrrrrrrrrrrqrrr<rTrirM)rrrrr;rrrrErErHrsf          zTiffPages.__init__cCs|jS)z2Return if pages/frames are currently being cached.)r)rrErErHr%szTiffPages.cachecCs$t|}|jr|s|||_dS)z@Enable or disable caching of pages/frames. Clear cache if False.N)rrr)rrrErErHr*s cCs|jtkottk S)z?Return if currently using TiffFrame (True) or TiffPage (False).)rrr)rrErErHr2szTiffPages.useframescCs|rtnt|_dS)z0Set to use TiffFrame (True) or TiffPage (False).N)rrr)rrrErErHr7scCs|jS)zReturn current keyframe.)r)rrErErHr<szTiffPages.keyframecCst|}|dkr|t|;}|jj|kr,dS|dkrD|jd|_dS|jsX|t|jkr|j|}t|trv||_dSt|tr|j |j|<|j }t|_ z| ||_Wd||_ X|j|j|<dS)z;Set current keyframe. Load TiffPage from file if necessary.r6N) rrcrrrOrr\rrr;r_getitem)rrrtiffpagerErErHrAs*       cCs|js|d|jS)z7Return offset where offset to a new page can be stored.r)r_seekr)rrErErHr^s zTiffPages.next_page_offsetFTcCs6y|j||||dStk r0|dkr,YnX|S)z)Return specified page from cache or file.)rrrN)rru)rrGdefaultrrrrErErHrVesz TiffPages.getcCs|jr dS|j}|sdS|js(|d|js2dS|jj}|dk rH|j}xbt|D]V\}}t |t t j frR|j dkrx|n |j |f}|||j|j||d}|||<qRWd|_dS)z#Read all remaining pages from file.Nr)rrT)rrOrrrrIrrr}r\rrrrKrrTr)rrrOrrrrrErErHrps(   zTiffPages._loadc s|j}yrt|dkrtd|d}|js4td|d|d|d}|d|d|ksv|d|d|kr~td|jd|jd }|jd|j}|dks||krtd||g}|j j j |}xt t |j|||D]x\}}|d} | |tfd d |jD} |d kr"|nd }|jd k r>|j| f} |t|j | || |j|dqW||_d|_d|_d|_WnRtk r} z2|j j j dkrt|d| jjd| dWd d } ~ XYnXd S)zCalculate virtual TiffFrames.rUzpages already loadedr6zdata not contiguousrrPrCzpage offsets not equidistant)rc3s|]}|VqdS)NrE)rFr)drErHrIsz1TiffPages._load_virtual_frames..iN)rIrr;rr:rTlz# _load_virtual_frames failed with (z: ))rOrcr_rrrrrr;rIrr<r}rwrrrirrrrrrvrqrr) rrOrdeltaZpage1Z offsetoffsetfilesizerr;rrrrE)rrHrsR  (   zTiffPages._load_virtual_framescCs|j}|sdS|d|_|r^x|t|ddD]*\}}t|ts.|jdk r.|j||d<q.Wn.)rrrIrwrcr\r7rrrrrOrrrrrKrWrrrrrS) rrGrrr>rrrrrOrE)rrrHr!s@        zTiffPages._getlistc Cs:t|}|j}|dkr$|t|;}n,|jrP|t|krPtd|dt|d|rXtn|j}|t|kr||}|jr|st|tt j fs|r||j krt d|Sn(t|t|fr|r||j krt d|S|j dkr|n |j |f}||||j||jd}|r ||j kr t d|js.|r6|||<|S)z)Return specified page from cache or file.r6zindex z out of range(rzpage hash mismatchN)rr)rrOrcrrurrrr\rrrKrrrrrIr) rrGrrrrOrrrrErErHrRs4   zTiffPages._getitemcs|j}|jt|ttjfr4|dkr,||S|St|tr|d\}}}|jspt ||t |krp| dfddt |t |DSt|t rfdd|DStddS) zReturn specified page(s).r6ircsg|] }|qSrErE)rFr)rrErHrGsz)TiffPages.__getitem__..csg|] }|qSrErE)rFr)rrErHrGsz*key must be an integer, slice, or iterableN)rOrr\rrrrKrrrrrcrrwr7rW)rrGrOrrrrE)rrH __getitem__ss    zTiffPages.__getitem__ccsJd}x4y||V|d7}Wqtk r4PYqXqW|jrFd|_dS)zReturn iterator over all pages.r6rUTN)rrurr)rrrErErHrs   zTiffPages.__iter__cCst|jdkS)z'Return True if file contains any pages.r6)rcrO)rrErErH__bool__szTiffPages.__bool__cCs|js|dt|jS)zReturn number of pages in file.r)rrrcrO)rrErErH__len__s zTiffPages.__len__cCsd|jdS)Nzd?Z9ed@dAZ:edBdCZ;edDdEZe'dJdKZ?e'dLdMZ@e'dNdOZAe'dPdQZBe'dRdSZCedTdUZDedVdWZEe'dXdYZFe'dZd[ZGe'd\d]ZHe'd^d_ZIe'd`daZJe'dbdcZKe'dddeZLe'dfdgZMe'dhdiZNe'djdkZOe'dldmZPe'dndoZQe'dpdqZRe'drdsZSe'dtduZTe'dvdwZUe'dxdyZVe'dzd{ZWe'd|d}ZXe'd~dZYe'ddZZe'ddZ[e'ddZ\e'ddZ]e'ddZ^e'ddZ_e'ddZ`e'ddZadS)razTIFF image file directory (IFD). Attributes ---------- index : int or tuple of int Index of the page in file. dtype : numpy.dtype or None Data type (native byte order) of the image in IFD. shape : tuple of int Dimensions of the image in IFD, as returned by asarray. axes : str Axes label codes for each dimension in shape: 'S' sample, 'X' width, 'Y' length, 'Z' depth, tags : TiffTags Multidict like interface to tags in IFD. colormap : numpy.ndarray Color look up table, if exists. shaped : tuple of int Normalized 5-dimensional shape of the image in IFD: 0 : separate samplesperpixel or 1. 1 : imagedepth Z or 1. 2 : imagelength Y. 3 : imagewidth X. 4 : contig samplesperpixel or 1. All attributes are read-only. r6rUlrENrc s ||_||_d|_d|_d|_d|_d|_t|_}d|_ d|_ |j }|j }| |_y4t|j||jd}|dkrtd|Wn4tk r}ztd|j|Wdd}~XYnX|j|j} |j} } || |t| |krtd|jd krT|jd krTd } |d tj|d |d fddt|D| } xt|D]~} | | 7} | | | }yt !|| | | |}Wn:tk r}zt"|d|wdWdd}~XYnX|#|qdW|sdSx`t$j%&D]R\}}|'|dkrq|dks0|dkr@t(t)s@qt*||qW|j'dddrl|_+|j,dkr|'ddkrd|_,ndkrd|_,|'d|_ |j dkr|'d|_ |j dkr|'d|_ |j dkrd|_ t"|d|'d|_ |j dkr<|'d|_ |j dkr<|'d|_ |j-dkr |j.dkr |j r |j r y6||j dt/|t0|j dd\}}}}Wntk rYnlX||_.||_-||_1d|kr|d krd nd |_2d |kr|dkrd!|_3d"|kr d!|_4d#|kr||_5nx|j4d!krd |kr>d!|_3n|j3dkrPd!|_3d|kr`d |_2d$|kr|j3d%kr~d|_1n|j3d&krd|_1n|j6s|jdkr|jj6r|d7|j4dkr|j8dkrd|_8n|j9s|jdkr|jj9rd|_:n|j;r|||j?|j|j@d|d'j@|_AWn@tk r}z t"|d)|jBjCd*|Wdd}~XYnX|d|||df|_|dkrR||f|_d7|_n|||f|_d8|_|j stJ|j|j2d f|_ |j4dkrt"|d9| rn|j5 rn|j6 sntKtLM||j5d|j5|j:}|jIdkr||j19}|t|j k r.t"|d:t|j d;|d<|j d||_ |t|j k rnt"|d=t|j d;|d<|j d||_ |'d>dk ry tN|NdO}||_PWntk rYnX|'d?}|dk r|jQ r|'d@}|dk r|RdA}|dBK}|RdA}||7}||j d||d}ytS|\|_T|_U|_VWn@tk r}z t"|dC|jBjCd*|Wdd}~XYnLX|dd|ddDW|j dtK|dDg|_ ||j dW|_ dS)EzlInitialize instance from file. The file handle position must be at offset to a valid IFD. rENrr6izsuspicious number of tags zcorrup tag list at offset zcorrupted IFD structurerrrrrc3s>|]6}|d|dd|d|ddVqdS)rrNrE)rFr)ryextrErHrI sz$TiffPage.__init__..rii1rU)rr6rPrCiDiiz missing data offset tagiEiiiiriii)rPr)r6rUi]i\z read_uic1tag failed with z: iiz imagej_metadata failed with c3s|]}|dVqdS)r6NrE)rFr)rrErHrIsiSc3s|]}|dVqdS)r6NrE)rFr)rrErHrIsiBiYXSZZYXSrZSZYXYXZZYXz missing ByteCounts tagz" incorrect StripByteCounts count (z != rz incorrect StripOffsets count (iiiuint64rz ndpi_jpeg_tile failed with r)XrIrrzrrsr rr rrrrrrr;rrrQrrr_rvrrRrcrrrTrarr rwr fromfilerqaddrTAG_ATTRIBUTESrr3r\r]r description1rr|r} jpeg_shaperrrrrprr_fix_lsm_bitspersamplerBis_vista imagedepthrrVr~ read_uic1tagrkr rrrrrdr SAMPLE_DTYPESrrrr+rrufloortypeitemnodatarr ndpi_jpeg_tile tilelengthr jpegheadertolist)rrIrrrrrrrrrRZtagsize_rrZtagdatarFr r: precisionr}r|rrsrZ maxstripsZpytype mcustartshighrrE)ryrrrHrs                          &               ,  ,                              ,zTiffPage.__init__c s( j jjjkr jjj jS fdd} jdkrJ fdd}||Sd jkrddd}||Sy jdkrvdn tj jWn@t k r}z"t |dd d d d}||Sd}~XYnXy j dkrdn tj j WnBt k r(}z"t |dd d d d}||Sd}~XYnX j d dk r j d jdkrtfddjDrfdd}||S jr jdks jdkrdd}||S jr̈ j j jdgnd j jdg jdkr jd <t\ jdd\ jrdd d fdd fdd jfdd nBd  fdddd jffdd jdkrb jdkrt dr t dd j kr$t d!t j j j!\}}ddd" j"||f fd#d }||S jd$krĈ jdkrt d% jrt d& jd: fd'd }||St# jj$ j%j& j'd(krFdk rt(d)t# jj$d* j"d+t# jj$d,j)dfd-d.n j"d/kr j" d0rnt*d1 j d2krt# j%j& fd3d.nlt+ j"tr fd4d.nN j"d5krj&d,krdk rt(d6 jj$fd7d.n fd8d.d; fd9d }||S).cacheNcstdjdjddS)Nz&data type not supported (SampleFormat z, z-bit))r_rr)argsrg)rrErHrnszTiffPage.decode..decoder6c_s tddS)Nz empty image)r_)rrgrErErHrnsrUr)rc_st|dS)N)r_)rrrgrErErHrnsc_st|dS)N)r_)rrrgrErErHrnsiSc3s|]}|jdVqdS)r6N)r)rFr)rFrErHrIsz"TiffPage.decode..cstdjdS)Nzsample formats do not match )r_r)rrg)rFrErHrns)rrrPc_s tddS)Nz chroma subsampling not supported)rz)rrgrErErHrnscsB||||dffS)Nr6rE)r)rlengthstdepthstlengthstshapestwidthrrErHrs  z TiffPage.decode..indicescs|dkr |S|d|d|d|d}|j|krHd|_|d|}|j|kr^||}nyL|t|d|dt|d|dt|d|df}Wndtk rtd|jd|t||j}t|j|}|d||d|<||}YnX|S)Nr6rUrPrCrz+ incomplete tile r) r<rzrhrr_rqrrzerosrs)ryrrzr<rE)imdepthimlengthimwidthsamplesrErHrhs,       z TiffPage.decode..reshapecSsJ|dks|j|kr||fSddt||jD}tj|||d}||jfS)NcSsg|]\}}d||fqS)r6rE)rFrrrErErHrGsz0TiffPage.decode..pad..)constant_values)rzrxrrpad)ryrzrpadwidthrErErHr(s zTiffPage.decode..padcsL|||ddf}t|df}||fS)Nr6rP)r)rrrz)r#r$rr&rrr!rErHr s  cSsx|dkr |S|d|d|d|d}|j|krHd|_|d|}|j|krZ||_n|dd|d|df|_|S)Nr6rUrPrCr)r<rz)ryrrzr<rErErHrhs    csf|d|d|df}|dks*|j|kr2||fSdd|jdfddg}tj|||d}||jfS)Nr6rPrC)r6r6rU)r')rzrrr()ryrzrr))rrErHr(0s)rriLiz disabling LSB2MSB for JPEGz disabling predictor for JPEGipz@ SonyRawFileType might need additional unpacking (see issue #95)Fc sx|\}} |dkr0|r&|| \}} ||| fStj||||||| ddd}||| }|rn|| \}} ||| fS)NrUrC)rtablesrr4r2rz) imagecodecs jpeg_decode) ry segmentindexrr _fullsizerr4r2rrz)rr(rhrErHrnNs"   ) iiiiiuiviRXiQiRz# disabling LSB2MSB for compression z% disabling predictor for compression cs`|\}}|dkr0|r&||\}}|||fS|}|||}|rV||\}}|||fS)NrE)ryr-rr.rrz) decompressrr(rhrErHrns   rz+unpredicting complex integers not supportedrrrcst|}|S)N)rr frombufferr view)ry)rsftypeityperErHrs zTiffPage.decode..unpack)rrr@r7rzdata and sample size mismatchrCcsPy t|Stk rJjd}t|||}t|d|SXdS)Nr)rrr0r_rrc)ryrDr<)rsrrErHrs   cst|jS)N) unpack_rgbr)ry)rsrrErHrsrz"unpredicting float24 not supportedcSs t||S)N)float24_decode)ryrkrErErHrscst|jS)N)packints_decoder)ry)rsr&rr!rErHrscs|\}}|dkr0|r&||\}}|||fSjdkrBt|}dk r||d|d|d|d}||jd}|}|||}|dj}dk r|d|d}|rȈ||\}}|||fS) NrPr6rUrC)rrr)r?r) fillorderbitorder_decodertr r)ryr-rr.rrzr<)r/rsrr(rhrr unpredictrErHrns$     )NF)NF),rrIrrrsrrpr DECOMPRESSORSrr]rB UNPREDICTORSrrVr rdr is_subsampledrr; tiledepthrrrr|rrrr8rqjpeg_decode_colorspacerrrrrrkr rrrzrtr_r\)rrrnrr4r2rE)r/rrsr2r#r$r%rr3rr(rhr&rrrr r!rFrr:rrHrnWs       &     %             zTiffPage.decodeFc cs|j}|jj}|dkr|j}|dkr*|j}dt|i}|jdkrT|j|d<|j|d<|dkrl||fdd} n|||fdd} |dks|d kr|j }|d krxt|j |j |j ||d d D]} | | VqWnHt |:} x2|j |j |j ||d d D]} | | | EdHqWWdQRXdS)zpReturn iterator over decoded segments in TiffPage. See the decode function for return values. Nr.)rriLirrcSs |j||S)N)rn)r decodeargsrrErErHrnsz!TiffPage.segments..decodecSs||j||S)N)rn)rr@rrrErErHrn srUrPT)lockrKrF)rrIrrAr;rrprrr read_segmentsrrr9map) rrArrrKr.rrr@rnsegmentexecutorsegmentsrErErHrFs>       zTiffPage.segmentsTc s|j}|jrt|jdkrdSt|jdkr4td|jj}|dkrJ|j}|*|j }|rtt |dt | WdQRXt|tr|dkr|jr|*|j|jj|jj|j|jddWdQRXn|jr|jrtd|dk rt||j|j}|8||jd|j|jj|jjt|j|dWdQRX|jd krVtd|jd krtj|j}|jd kr|d d n|d d }|dd<n|j dk rD||krDd |j!krD|j"rD|j#dkrD|j$dkrD|2||j!d j%d|&|j!dj%d} WdQRXtj'|j(} | | |j)|d~ nHt||j|j|j*||ffdd } x|j+| ||dddD]} qW|j_,|ry |j,_,Wn2t-k rt.|dj,d|j,YnX|r|/S)aRead image data from file and return as numpy array. Raise ValueError if format is not supported. Parameters ---------- out : numpy.ndarray, str, or file-like object Buffer where image data are saved. If None (default), a new array is created. If numpy.ndarray, a writable array of compatible dtype and shape. If 'memmap', directly memory-map the image data in the TIFF file if possible; else create a memory-mapped array in a temporary file. If str or open file, the file name or file object used to create a memory-map to an array stored in a binary file on disk. squeeze : bool If True (default), all length-1 dimensions (except X and Y) are squeezed out from the array. If False, the shape of the returned array is the normalized 5-dimensional shape (TiffPage.shaped). lock : {RLock, NullContext} A reentrant lock used to synchronize seeks and reads from file. If None (default), the lock of the parent's filehandle is used. maxworkers : int or None Maximum number of threads to concurrently decode strips or tiles. If None (default), up to half the CPU cores are used. See remarks in TiffFile.asarray. Returns ------- numpy.ndarray Numpy array of decompressed, unpredicted, and unpacked image data read from Strip/Tile Offsets/ByteCounts, formatted according to shape and dtype metadata found in tags and parameters. Photometric conversion, pre-multiplied alpha, orientation, and colorimetry corrections are not applied. Specifically, CMYK images are not converted to RGB, MinIsWhite images are not inverted, and color palettes are not applied. Exception are YCbCr JPEG compressed images, which are converted to RGB. r6Nzmissing data offsetz reading array from closed filer)r;z chroma subsampling not supported)rrPrUr)r?riii)rrc s|\}\}}}}}} |dkr$|j}n,|d|j|d|j|d|j|f}||||| d||| d||| df<dS)Nr6rUrP)rrr}r|) Z decoderesultrrrDrrlrrrz)r|rErHrs  zTiffPage.asarray..funcTF)rrArrKr.z failed to reshape z to )0rrr+rcrrrIrrArvrXrYrrwr\r]rrrkr rrr=rzr!rTrr8r9rBrr<rrr;r|r}rrr;rprrnrFrzr_rqr) rrrrArrrrvr:ryr/rrrE)r|rHre)s)                zTiffPage.asarraycKs t|f|S)z"Return image data as zarr storage.)r)rrgrErErHrdszTiffPage.aszarrc Ks|jf|}|j}|jtjjkr|j}|jdd|jksF|j j dkrNt d|rp| dkrf|dL}| d}d|jkr|jdkr|d n|d }t||}n|jtjjkrb|jr.|d krtj}xt|jD]T\} } | |kr|jdkr |d d ddd | gf}n|d d d ddd | gf}PqWn2|jdkrL|d d d f}n|d d d d f}nF|jtjjkrxtn0|jtjjkrtn|jtjjkrtnt|S)zAReturn image data as RGB(A). Work in progress. rUrPrzcannot apply colormapr6ruint8r).r6r6N.rC)rerrrrSrXrrzrrsrr_rr rrapply_colormaprVrrr}rTrzrU SEPARATED) rrHalpharZdminZdmaxrgryrrexsrErErHasrgbsF       zTiffPage.asrgbcsfdd|jDS)zReturn list of (code, TiffTag).cs(g|] }dks|jkr|j|fqS)N)r )rFrF)codesrErHrGsz%TiffPage._gettags..)r)rrNrArE)rNrH_gettags s zTiffPage._gettagscCsl|jj}|jj}||jt|j||j d}||j|j ||j t|j ||j dS)z$Return offset to next IFD from file.r6) rIrrrTr;rrrQrrrRrr)rrrrrErErH_nextifds  zTiffPage._nextifdcCs|S)z Return self.rE)rrErErHrszTiffPage.aspagecCs|S)zReturn keyframe, self.rE)rrErErHr"szTiffPage.keyframecCsdS)zSet keyframe, NOP.NrE)rrrErErHr'scCs t|jS)z"Return number of array dimensions.)rcrz)rrErErHr,sz TiffPage.ndimcCs t|jS)z#Return number of elements in array.)r+rz)rrErErHr<1sz TiffPage.sizecCst|j|jjS)z Return number of bytes in array.)r+rzrsrt)rrErErHru6szTiffPage.nbytescCs |jdS)zReturn colormap as numpy array.i@)rr3)rrErErHr;szTiffPage.colormapcCs |jdS)z'Return transferfunction as numpy array.i-)rr3)rrErErHtransferfunction@szTiffPage.transferfunctioncCsng}|jdkr||j|jr4||j|jfn||j|jf|jdkrf|j dkrf||j t |S)z!Return shape of tiles or stripes.rU) r>rir;rMrrrr|rrr)rrzrErErHchunksEs   zTiffPage.chunkscCsg}|jdkr$|jdkr$||j|jr|jdkrP||j|jd|j||j|jd|j||j|j d|j n<|jdkr||j||j|j d|j |d|jdkr|jdkr|dt |S)zReturn shape of chunked image.rPrU) rrrir;rr>r}rr|rrr)rrzrErErHchunkedSs&      zTiffPage.chunkedcCsDt|j|jj|j|j|j|j|j|j |j |j |j |j |j|jf S)zReturn checksum to identify pages in same series. Pages with the same hash can use the same decode function. )rrrIrkrrr>rrrr8rBrrrrp)rrErErHrosz TiffPage.hashcCsd|jkrdSt||jdS)z&Return sequence of sub-pages, SubIFDs.iJrE)r)rrr)rrErErHrOs zTiffPage.pagescCs|js|jdkrdS|jdkr0ttjt|jSt|j |jj }|dkrNdS|jdksl|j dksl|j dkr|jdkr|dkrdSt|jdkrdS|jdks|j dks|j dkrt dk rttjt|jSd S) zReturn maximum number of threads for decoding segments. Return 0 to disable multi-threading also for stacking pages. Nr6) rriiiiiiLiuiviRXiQiRirUri@rrP)rrsrprr MAXWORKERSrcrr+rRrtr8rBr+)rr;rErErHrs"zTiffPage.maxworkerscs|jdkrdS|jdks"|jdkr&dSd|jkr|j|jks\|j|js\|jds\|jdr`dSd|jkrd|jkr|j|jks|j|j rdS|j |j t d krdSt dkrȈd d fS|j s|jrd tfStfd d tt dDrd tfSdS) zlReturn offset and size of contiguous data, else None. Excludes prediction and fill_order. rNrU)rrrr4iBriir6c3s6|].}|dko,|||dkVqdS)r6rUNrE)rFr)r:rrErHrIsz)TiffPage.is_contiguous..)rrprrr|rr}rrr>rrrcrrrrprw)rrE)r:rrHrs8              zTiffPage.is_contiguouscCs"|jo |jdko |jdko |j S)z`Return if page's image data are stored in final form. Excludes byte-swapping. rU)rr8rBr=)rrErErHr s  zTiffPage.is_finalcCs&|jjjo$|jo$|jd|jjdkS)z9Return if page's image data in file can be memory-mapped.r6)rIris_filer rrsrt)rrErErHrs zTiffPage.is_memmappablecCsd|jd|jdS)Nzt|}yt|d}Wntk r,dSX||kr:|SdS)Nr:r)rr)r:robjr)rrErHtostr s zTiffPage.__str__..tostrz css|]}|r|VqdS)N)r)rFrrErErHrIsz#TiffPage.__str__..r=css|]}t|VqdS)N)r])rFrrErErHrIsz{}{}rcss|]}|r|VqdS)NrE)rFrrErErHrIs ZREDUCEDrgZTILEDrprrBr8css|]}|VqdS)N)r_)rFrrErErHrI)sz TiffPage z @r6)r)rrFz{} {}r)rrrCzDATA {}z )rU)rrrrr_r rzrr SAMPLEFORMATrr:rrSrr>is_maskr;rrrr;rrir*rerv)rrrrer:rYr&rE)rrHrsN     t     zTiffPage.__str__csfddttjDS)zReturn set of flags.cs"h|]}td|r|qS)rD)rr)rFr:)rrErHrMsz!TiffPage.flags..)rxrr)rrE)rrHrJs zTiffPage.flagscCsx|js dSd|jdji}xX|jD]N}|j}d|kr@dksDq"q"|j}t|dkrb|ddn|}|j||<q"W|S)z5Return consolidated metadata from Andor tags as dict.NZIdiir)is_andorrrr r:rc)rr|rFr r:rErErHrSs zTiffPage.andor_tagscCs|js dSi}x|jD]}|j}d|kr4dks8qq|j}|dkrTt||d<q|dkrjt||d<q|dkrt||d<q|d krt||d <q|d d \}}t|||<qW|S) zReturn consolidated metadata from EPICS areaDetector tags as dict. Use epics_datetime() to get a datetime object from the epicsTSSec and epicsTSNsec tags. NiiZ timeStampiZuniqueIDiZ epicsTSSeciZ epicsTSNsecr,rU)is_epicsrr rrqrrr )rr|rFr rrGrErErHrcs& zTiffPage.epics_tagscCs|js dS|j}i}xdD]}||j||<qWx,tjD]\}}||kr<||j||<qszTiffPage.is_reducedcCs |jd@S)z!Page is part of multi-page image.rP)r)rrErErH is_multipageszTiffPage.is_multipagecCs |jd@S)z,Page is transparency mask for another image.r)r)rrErErHr[ szTiffPage.is_maskcCs |jd@S)z%Page is part of Mixed Raster Content.r)r)rrErErHis_mrc%szTiffPage.is_mrccCs |jdkS)zPage contains tiled image.r6)r)rrErErHr;*szTiffPage.is_tiledcCs2|jdk r|jdkS|jdko0|jdko0|jdkS)z&Page contains chroma subsampled image.N)rUrUrrU)rPr)r3rprr)rrErErHr=/s     zTiffPage.is_subsampledcCs6x0|j|jfD] }|sdS|dddkr|SqWdS)z/Return ImageJ description if exists, else None.NrzImageJ=)rr )rrrErErHr:s zTiffPage.is_imagejcCsZxT|j|jfD]D}|rd|kr"dS|dddkr>d|kr>|S|dddkr|SqWdS)z?Return description containing array shape if exists, else None.z"mibi.NrU{z"shape":rzshape=)rr )rrrErErHrDs zTiffPage.is_shapedcCs d|jkS)zPage contains MDFileTag tag.i)r)rrErErHrPszTiffPage.is_mdgelcCs@|jd}y|dk o&|jdddkStk r:dSXdS)z'Page contains Media Cybernetics Id tag.ipNrsMC TIFFF)rrVrrv)rrFrErErH is_mediacyUs  zTiffPage.is_mediacycCs d|jkS)zPage contains UIC1Tag tag.i\)r)rrErErHr^szTiffPage.is_stkcCs d|jkS)zPage contains CZ_LSMINFO tag.il)r)rrErErHrcszTiffPage.is_lsmcCs d|jkS)z$Page contains FluoView MM_STAMP tag.i:)r)rrErErHrhszTiffPage.is_fluoviewcCs d|jkS)z!Page contains NIHImageHeader tag.i2)r)rrErErHrmszTiffPage.is_nihcCs |jdkS)z0Page contains SGI ImageDepth tag with value > 1.rU)r)rrErErH is_volumetricrszTiffPage.is_volumetriccCs |jdkS)zSoftware tag is 'ISS Vista'.z ISS Vista)r)rrErErHr wszTiffPage.is_vistacCs2|jdks|jdkrdS|j}|do0|dS)z>Page contains MDS MetaSeries metadata in ImageDescription tag.r6Z MetaSeriesFz z )rrr startswithr)rrrErErHr|szTiffPage.is_metaseriescCs&|jdks|jsdS|jdddkS)z.Page contains OME-XML in ImageDescription tag.r6FrNzOME>)rr)rrErErHrszTiffPage.is_omecCs&|jdks|jsdS|jdddkS)z4Page contains Leica SCN XML in ImageDescription tag.r6FiNz)rr)rrErErHrszTiffPage.is_scncCs d|jkS)z'Page contains MicroManagerMetadata tag.i)r)rrErErHrszTiffPage.is_micromanagercCs d|jkS)z.Page contains Andor Technology tags 4864-5030.i)r)rrErErHr\szTiffPage.is_andorcCs$|jdddko"|jdddkS)zPage contains Pilatus tags.NrzTVX TIFFrPz# )rr)rrErErHrszTiffPage.is_pilatuscCs|jdkp|jdkS)z&Page contains EPICS areaDetector tags.zEPICS areaDetector)rr)rrErErHr]s zTiffPage.is_epicscCs d|jkS)zPage contains TVIPS metadata.iJ)r)rrErErHrszTiffPage.is_tvipscCsd|jkpd|jkS)z*Page contains FEI_SFEG or FEI_HELIOS tags.ixiz)r)rrErErHrszTiffPage.is_feicCs d|jkS)zPage contains CZ_SEM tag.iF)r)rrErErHrszTiffPage.is_semcCs|jdddkS)zPage contains Aperio metadata.NrzAperio )r)rrErErHis_svsszTiffPage.is_svscCs^yDd|jkoDd|jkpD|jdddkpD|jdkpD|jdkpD|jdkStk rXd SXdS) zPage contains Ventana metadata.iZVentanaNZScanOutputManagerz Label ImageZ Label_ImageZProbability_ImageF)rrrrv)rrErErHis_bifs     zTiffPage.is_bifcCs6|jdddkp4|jdddkp4d|jddkS)z!Page contains ScanImage metadata.NrCzSI.rzstate.z scanimage.SIi)rr)rrErErHrszTiffPage.is_scanimagecCs|jdddkS)z1Page contains PerkinElmer tissue images metadata.NzPerkinElmer-QPI)r)rrErErHis_qpiszTiffPage.is_qpicCs d|jkS)zPage contains GeoTIFF metadata.i)r)rrErErHrszTiffPage.is_geotiffcCs d|jkS)zPage contains TIFF/EP metadata.i)r)rrErErH is_tiffepszTiffPage.is_tiffepcCsd|jkpd|jkS)z#Page contains Olympus SIS metadata.ii)r)rrErErHrszTiffPage.is_siscCsd|jkod|jkS)zPage contains NDPI metadata.ii)r)rrErErHrszTiffPage.is_ndpicCs$|jdddko"|jdddkS)z"Page contains Philips DP metadata.Nrz Philips DPiz )rr)rrErErHrszTiffPage.is_philipscCs|jjo|jdkod|jkS)zPage contains EER metadata.)iii)rIrrpr)rrErErHrs zTiffPage.is_eer)N)NNNFN)NTNN)FNNNN)NN)r6r)brrrrrr|r}rrrr>rrrrrprr8rrBrr3rrrrrr rrr%rnrFrerdrMrOrPrrrrrr<rurrQrRrSrrOrrr rrrrrrrdrr>rkr[rlr;r=rrrrnrrrrror rrrrr\rr]rrrrqrsrrurrvrrrrrErErErHrs {  8 % 6             ) +   J   z                              rc@seZdZdZdZdZdZd'ddZd(dd Zd d Z d d Z ddZ ddZ ddZ ddZeddZejddZeddZeddZeddZdd Zd!d"Zd)d%d&ZdS)*ra\Lightweight TIFF image file directory (IFD). Only a limited number of tag values are read from file. Other tag values are assumed to be identical with a specified TiffPage instance, the keyframe. TiffFrame is intended to reduce resource usage and speed up reading image data from file, not for introspection of metadata. )rrIr;rrrrrFrENc Csnd|_||_||_||_d|_d|_d|_d|_|dk rN||_||_||_dS|dkrf|jj |_n|jj ||dkrddddddh}n.|j rd dddh}|j|_nd ddddddh}x| |D]\}} |dks|dkr| j |_q|dks|dkr| j |_q|dkr| j |_q|dkr.| j |_q|d kr|j| j krtd qW|jsdt|d ||_dS) z{Initialize TiffFrame from file or values. The file handle position must be at the offset to a valid IFD. NrEiiiDiEiJi[r-zincompatible keyframez is missing required tags)rrIrr;rrrrrrrTrrOrr|rrqr) rrIrr;rrr:rr rFrErErHrsH         zTiffFrame.__init__c Cs|jj}|jj}tj}|dkr$tn|}g}|X||jy2||j| |j d}|dkrpt d|Wn,t k r}zt d|Wdd}~XYnX|j|j } |j } | } |jdd} | | |} xt|D]}| | 7} || | | | dd}|r||krqy$t|j| | | | | | }Wn8t k rr}zt|d|wWdd}~XYnX|||fqWWdQRX|S)z)Return list of (code, TiffTag) from file.Nr6izsuspicious number of tags zcorrupted tag listrPr)rIrrrr NullContextrTr;rQrrrrvrR tagformat1rwr rrqri)rrNrArrrrrrrrRrZ codeformatZtagbytesrr rFrErErHrO[sB  zTiffFrame._gettagscCs t|S)z$Return offset to next IFD from file.)rrP)rrErErHrPszTiffFrame._nextifdcCsr|jdkrtd|jj}|j}|r>t|dt|z | |jt |j|j d}Wd|rl| X|S)zReturn TiffPage from file.Nz#cannot return virtual frame as pagez" reading TiffPage from closed file)r) r;r_rIrrvrXrYrrwrTrrr)rrrvrrErErHrs   zTiffFrame.aspagecOstj|f||S)z4Read image data from file and return as numpy array.)rre)rrrgrErErHreszTiffFrame.asarraycKstj|f|S)z"Return image data as zarr storage.)rrd)rrgrErErHrdszTiffFrame.aszarrcOstj|f||S)z>Read image data from file and return RGB image as numpy array.)rrM)rrrgrErErHrMszTiffFrame.asrgbcOstj|f||S)z3Return iterator over decoded segments in TiffFrame.)rrF)rrrgrErErHrFszTiffFrame.segmentscCs|jS)zReturn keyframe.)r)rrErErHrszTiffFrame.keyframecCsT|j|krdS|jdk r tdt|jt|jkr.r=css|]}t|VqdS)N)r])rFrrErErHrIsrR)rrCr)rrr0z Keyframe z Offsets z Bytecounts z TiffFrame z @) rr rzr]rsrrr*rrrr;)rrrr&ZkfZofbcrErErHrs zTiffFrame.__str__)NNNN)NN)r6r)rrrrrrrOrrOrPrrerdrMrFrrrrrrrrrrErErErHrs.   6 )    rc@seZdZdZdZddZed$ddZed d Z ed d Z e d dZ e j ddZ e ddZe ddZe ddZe ddZddZd%ddZddZddZd&d"d#ZdS)'r a+TIFF tag structure. Attributes ---------- name : string Name of tag, TIFF.TAGS[code]. code : int Decimal code of tag. dtype : int Datatype of tag data. One of TIFF.DATATYPES. count : int Number of values. value : various types Tag data as Python object. valueoffset : int Location of value in file. offset : int Location of tag structure in file. parent : TiffFile or TiffWriter Reference to parent TIFF file. All attributes are read-only. )rIr;r rsr _valuer~cCsd||_t||_t||_t||_||_||_yt||_ Wnt k r^t||_ YnXdS)z(Initialize TiffTag instance from values.N) rIrr;r r r{r~r DATATYPESrsr_)rrIr;r rsr rr~rErErHrs   zTiffTag.__init__NTc Cs|j}|dkr>|dkr"|j}n |j||j|j}n|dkrP|j}||j|j}t|j |dd\}}t|j |dd\} } yt j |} WnNt k rd|d|d|} |rt| t| |||||| ddSX| t| } | |jks|t jkrt|j| d}|rR|t jkrRt||||| |} nt|dksn|| |jjkrd|d|d|} |rt| t| d} n&|t jkrt||||| |} nd} n|d ks|d ks|d kr| d| } n|jd krJ|jdkrJ| d krJ|dks*|d krJ| dddkrJtd| } n4d|j| t| d| d }t|| d| } t| |||} |||||| | |S)z'Return TiffTag instance read from file.Nrz invalid data type r6rz> invalid value offset rUrPrrr0sz invalid data type Nrz> invalid value offset rUrPrz> could not read all valuesiz{}{}{}r6)rrrrrrrrr<rTrrkrrrcrq TAG_TUPLE read_numpyrrr) rIr;r rsr r~rrrrreadfuncrrrErErHr{s:    zTiffTag._read_valuec s |dks2|dks2|dks2|tjks2t|tttfs6|S|dkrytt|dd}Wn*t k rt d|d|d YnX|S|tj krtj |ytfd d |D}WnDt k r}z&|d krt d|d|d |Wdd}~XYnXt |dkr|tjkr|d}|S)zProcess tag value. .NrUrrPF)rz coercing invalid ASCII to bytesc3s|]}|VqdS)NrE)rFr)rErErHrIsz)TiffTag._process_value..)ii=z> r6)rrr\rr]r bytes2strr0rUnicodeDecodeErrorrqTAG_ENUMr_rcr)rr rsr;rrE)rErHrs.   ,zTiffTag._process_valuec Cs|jdkr|jj}|j^|j}|r>t|dt|z$t |j|j |j |j |j|j}Wd|rp|XWdQRXt ||j |j |j |_|jS)z1Return value of tag. Load from file if necessary.Nz reading value from closed file)r{rIrrArvrXrYrrwr rr;r rsr r~rr)rrrvrrErErHrs0   z TiffTag.valuecCs ||_dS)N)r{)rrrErErHrscCs*y|jjStk r$d|jSXdS)NTYPE)rsr:r)rrErErH dtype_nameszTiffTag.dtype_namecCstj|jt|jS)z+Return name of tag from TIFF.TAGS registry.)rrrVr r])rrErErHr: sz TiffTag.namecCs tj|jS)z)Return data type as Python struct format.)rrrs)rrErErHr szTiffTag.dataformatcCs|jttj|jS)zReturn size of value in file.)r rrrrrs)rrErErHvaluebytecount szTiffTag.valuebytecountcCst|jtr|j}ntj|j}|jt|d}d|j j j ||d}y.|dkrdt ||j}nt j |f|j}Wnntk r|j j }|jdkr|jdkrtd|j j}|}||j|t |}||YnX|j|jj|j|fS)zvReturn tag code, dtype, count, and encoded value. The encoded value is read from file if necessary. r6z{}{}{}rUrrz"cannot read from NDPI > 4 GB files)r\rrrrrsr rrrIrrkrrrvrrrzrrrTr~rrr )rrrr rrrrrErErH_astuple s*   zTiffTag._astuplec Cs2|jdks|jdkr&td|jdt|drD|}tjdtdd|jj}|jj }|j dkrp|j dkrpt d |d kr|d }|d kr|j }ytj|}Wntk r}zby2|d d }|d dkr|dd }tj|}Wn*ttfk rtd||YnXWd d }~XYnX|dkrt|trry|d}Wn.tk rn}ztd|Wd d }~XYnXnt|tstdt|d ks|d dkr|d7}t|} |f}nnt|trt|} t|| rtdt|| } |f}n.y t|} Wn tk r&|f}d} YnX|dkrV| dksF| drNtd| d} tjd|j| t|d |df|} t| } |jttj|j } |j}| }zX||j kr|!|jd|"t|jd|| |j#kr| |j#kr(|!|jd|"t|j$| | nl|!d t%j&| }|drZ|"d|d7}|"| |!|jd|"t|j$| t|j'|np| |j#kr|jd|j }|!|jd|"t|j$| | |r|!|j|"d| n | | ks|j| |j(kr||!|jd|"t|j'| |!|j|"| |r| | d kr|"d| | n|r|!|j|"d| |!d t%j&| }|dr|"d|d7}|"| |!|jd|"t|j$| t|j'|Wd |!|Xt)|j|j|j*|| ||S)aRWrite new tag value to file and return new TiffTag instance. The value must be compatible with the struct.pack formats in TIFF.DATA_FORMATS. The new packed value is appended to the file if it is longer than the old value. The old value is zeroed. The file position is left where it was. rzcannot rewrite tag at offset z < 8rzn passing a TiffFile instance is deprecated and no longer required since 2021.7.30.rP)rQrzcannot patch NDPI > 4 GB filesNrrr6z<>rUzunknown dtype rz TIFF strings must be 7-bit ASCIIrzinvalid packed binary data)rrzinvalid RATIONAL valuez{}{}{}rr)+r;r~r_r`rXrYrZrIrrrrrzrsrrrrrWr\r]rrrrcrrrrrkrr rrTrwr}r~rarrr<r r )rrZ_argrsrrrrrr ZdtsizeZ packedvaluenewsizeZoldsizer~rrErErHr6 s     (                        zTiffTag.overwritecCst|jdks|jdkrdSt|dtjd |j}td|d|_|jj |jtd|jj d|_dS) zCorrect LSM bitspersample tag. Old LSM writers may use a separate region for two 16-bit values, although they fit into the tag value element of the tag. irPNz! correcting LSM bitspersample tag.)rrr)rr r rrgetallr r;r~rrr#r*rrv)rrrrrsr:linerrErErHr s2        zTiffTag.__str__)NNT)NNT)r6r)rrrrrr classmethodr staticmethodrrrrrrr:rrrrr rrrErErErHr s&   O 5 % &    ! *r c@seZdZdZdZddZddZddZd d Zd d Z d&ddZ d'ddZ d(ddZ ddZ ddZddZddZddZddZd d!Zd)d$d%Zd S)*r aGMultidict like interface to TiffTag instances in TiffPage. 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The file handles of TiffPages or TiffFrames may not be open. keyframe : TiffPage A key frame of the series. dtype : numpy.dtype Data type (native byte order) of the image array in series. shape : tuple Dimensions of the image array in series. axes : str Labels of axes in shape. See TIFF.AXES_LABELS. offset : int or None Position of image data in file if memory-mappable, else None. levels : list of TiffPageSeries Pyramid levels. levels[0] is 'self'. NFTc Cs"d|_||_|g|_|dkr&|dj}|dkr8|dj}|dkrJ|dj}|||| t||_|rl|nd|_|rz|nd|_ ||_ t dd|D|_ t | |_|r||_n|r|j j|_nd|_| st|dkrt|dj} | dkrtt|j| |_n t||_n t||_dS)zInitialize instance.r6Nrcss|]}|dk r|jVqdS)N)r)rFrrErErHrIy"sz*TiffPageSeries.__init__..rU)r_pagesrrzrrsr{rrrar:r+rrr is_multifilerIrcr+r_len) rrOrzrsrrIr:r+rar*rArrrErErHrZ"s6        zTiffPageSeries.__init__cCsXt|}d|}||_||_t||\|_|_|r:|jn|j|_|rL|jn|j|_dS)zSet shape and axes.rN) rr _shape_expanded_axes_expandedr/_shape_squeezed_axes_squeezedrzr)rrzrrrErErHr{"s zTiffPageSeries.set_shape_axescCs|dkr|jS|r|jS|jS)z,Return default, squeezed, or expanded shape.N)rzrr)rrrErErHr"szTiffPageSeries.get_shapecCs|dkr|jS|r|jS|jS)z+Return default, squeezed, or expanded axes.N)rrr)rrrErErHry"szTiffPageSeries.get_axescKsR|dk r|j|jf|S|jrN|jjfd|i|}|jdk rJ||}|SdS)z;Return image data from series of TIFF pages as numpy array.Nr)rrerIr+)rrrgr|rErErHre"s  zTiffPageSeries.asarraycKs|jrt|fd|i|SdS)z|jkr`nn|jdj}|jj||S|j|S)z3Return specified page of series from cache or file.r6rU)rrrcrrrIrOr)rrGrrErErHr"s ( zTiffPageSeries._getitemcsjt|ttjfr|St|trBfddt|jDSt|t r^fdd|DSt ddS)zReturn specified page(s).csg|]}|qSrE)r)rFr)rrErHrG"sz.TiffPageSeries.__getitem__..csg|]}|qSrE)r)rFr)rrErHrG"sz*key must be an integer, slice, or iterableN) r\rrrrKrrrwrrr7rW)rrGrE)rrHr"s   zTiffPageSeries.__getitem__ccsXt|j|jkr|jEdHn6|jj}|jdj}x t|jD]}|||Vq>WdS)z%Return iterator over pages in series.Nr6)rcrrrIrOrrw)rrOrrrErErHr"s  zTiffPageSeries.__iter__cCs|jS)z!Return number of pages in series.)r)rrErErHr#szTiffPageSeries.__len__cCsd|jdS)Nz.rr=css|]}t|VqdS)N)r])rFrrErErHrI#sz Levelsz Pages@zTiffPageSeries ) r r:rrzr]rsrrar2rcrr;r)rrrErErHr #s zTiffPageSeries.__str__) NNNNNNNFFT)T)N)N)N)N)rrrrrr{rryrerdr%r;rr2rr<rOrrrrrrrErErErHrB"s6 %           rc@seZdZdZd1ddZddZddZd d Zd d Zd dZ ddZ ddZ ddZ ddZ ddZddZddZddZdd Zd!d"Zd#d$Zed%d&Zed'd(Zed)d*Zed+d,Zed-d.Zed/d0ZdS)2raZarr storage base class. ZarrStore instances must be closed using the 'close' method, which is automatically called when using the 'with' context manager. https://zarr.readthedocs.io/en/stable/spec/v2.html https://forum.image.sc/t/multiscale-arrays-v0-1/37930 NcCs@i|_|dkrdn||_|dkr.td|_nttj||_dS)zInitialize ZarrStore.Nr6)_store _fillvaluer CHUNKMODE _chunkmoder")r fillvalue chunkmoderErErHr+#s zZarrStore.__init__cCs|S)NrE)rrErErHr4#szZarrStore.__enter__cCs |dS)N)r)rrrrrErErHr7#szZarrStore.__exit__cCs |dS)N)r)rrErErH__del__:#szZarrStore.__del__cCsdS)zClose ZarrStore.NrE)rrErErHr=#szZarrStore.closecCs tddS)zFlush ZarrStore.zZarrStore is read-onlyN)PermissionError)rrErErHr@#szZarrStore.flushcCs tddS)zClear ZarrStore.zZarrStore is read-onlyN)r)rrErErHclearD#szZarrStore.clearcCs |jS)zReturn keys in ZarrStore.)rr)rrErErHrH#szZarrStore.keyscCs |jS)zReturn items in ZarrStore.)rr)rrErErHrL#szZarrStore.itemscCs |jS)zReturn values in ZarrStore.)rr)rrErErHrP#szZarrStore.valuescCst|jS)N)rIrr)rrErErHrT#szZarrStore.__iter__cCs t|jS)N)rcr)rrErErHrW#szZarrStore.__len__cCs tddS)NzZarrStore is read-only)r)rrGrErErHrZ#szZarrStore.__delitem__cCs ||jkS)N)r)rrGrErErHr]#szZarrStore.__contains__cCs tddS)NzZarrStore is read-only)r)rrGrrErErHr`#szZarrStore.__setitem__cCs||jkr|j|S||S)N)rr)rrGrErErHrc#s  zZarrStore.__getitem__cCstdS)zReturn chunk from file.N)rz)rrGrErErHrh#szZarrStore._getitemcCsd|jdkS)z#Return if ZarrStore is multiscales.s multiscalesz.zattrs)r)rrErErHis_multiscalesl#szZarrStore.is_multiscalescCs>|dks|dkr"tt||jSt||}||dd<|S)zReturn empty chunk.Nr6)rr+rtrrempty)rzrsrrrErErH _empty_chunkq#s   zZarrStore._empty_chunkcCs2|jdkrd}ndddtj}||jddS)z.Return dtype as string with native byte order.rUrrr)bigrN)rtrrkr])rsrkrErErHr z#s zZarrStore._dtypecCstj|ddddddS)z)Serialize obj to a JSON formatted string.rUT),z: )indent sort_keys ensure_ascii separatorsr)jsondumpsr)rXrErErH_json#szZarrStore._jsoncCs|dkr |S|jdkrt|S|jdkr0t|S|jdkrlt|rHdSt|rVdSt|rddSt|S|jdkrt||}t |j | j j t |j| jj fS|S) z+Return value which is serializable to JSON.NbuirNaNInfinityz -Infinityr1)rarrrrisnanZisposinfZisneginfrqrrr{realrrsimag)rrsrErErHr{#s&        zZarrStore._valueccsZt|t|ksttddt||D}x(t|D]}ddd|DVq8WdS)z-Return iterator over all chunk index strings.css*|]"\}}||||rdndVqdS)rUr6NrE)rFrrrErErHrI#sz%ZarrStore._ndindex...css|]}t|VqdS)N)r])rFrrErErHrI#sN)rcAssertionErrorrrxrrZndindexr )rzrRrSrrErErH_ndindex#s zZarrStore._ndindex)NN)rrrrrrrrrrrrrrrrrrrrrrrrrr rr{rrErErErHr #s0    rcs`eZdZdZdfdd ZddZddd Zd d Zd d ZddZ e ddZ ddZ Z S)rzZarr storage interface to image data in TiffPage or TiffPageSeries. ZarrTiffStore instances are using a TiffFile instance for reading and decoding chunks. Therefore ZarrTiffStore instances cannot be pickled. Nc  sjtj||d|jdkr*t|jd||_|dkr.z0.1)Zdatasetsrr:rz.zattrsr)rrzrRrsrA fill_valueorderfiltersz/.zarrayz.zarray)%rrrrz _maxworkersr_squeezer _transformr_datarrIrrrAr _filecacher^rcrrrrwr:r}rnrrsrrrzrRr_chunksr r{)rrrrrzattrsrArrZ _openfilesrrrzrsrR)rrErHr#s|&             zZarrTiffStore.__init__cCst|dr|jdS)zClose ZarrTiffStore.rN)r`rr)rrErErHr7$s zZarrTiffStore.closeFc%Csdddddddddd d d dd d dd dd d d|dkr8in|}x|jD]}d}|j} | j|krvt| jd|| jdkrt| jd|| jdkrt| jd|| jdkr| jdkrtd| jd||js| js| j | j rtd||jr*| j s*t|jd|| j dk rHt |jdkrHtd|qHW|dkrbd}n|r~|ddkr~|d7}|dkrd}n|r|ddkr|d7}tjdkrdnd} |jdjjj| ks|jdjjjdkrd} t} |dkr|r tdd| d <i| d!<g| d"<i} |jdjrd} x|jdjD]\}|dkrZqH|jjjj}|| krtqHd#| }d$|| |<||| d!|<| d7} qHWn2|jdjjjj}d#}d$|| |<||| d!|<t| d%<}n| }|r|std&d'i|d(<x|jD]\}}d)|krd|krPt|ddnd}|j|j} t |}|| j}|dkr| j }|dk rddl!}|"|}| j#}|dk rddl!}|"|}t$| j%| j&| j'\}}|||| j||d*|d+<n|dk rd,|i|d+<| j(dkr| j(d-kr.d.}nd/}| j(d0krDd}n| j(d1krVd'}nd2}| j&dkrx| j)dkrxd3}nd}||||d4|d5d6g|d7<| dk r| |d5dd|d5<t|}||||<q Wt*|d8r|}n t+|d9}|dkr,|,tj-| dd:.d;ddd;d<}nR|r^|,d=|,tj-| dd:d'd3d>}n |,tj-| dd:dd3d>}x|jD]\}}d)|krt |}|d?}|d4} d|kr|dddnd}xt/|| D]}!||!}|0|\} }}"}#}$|r0|jr0|#dkr0|j1d}#| j2}$|#r|$r| jjj}|dkrZ| |}n ||}|,d=|d@||dA|dB|#dC|$dD qWqW|dkr|,dEn|s|,dFt*|d8s|3dS)GaWrite fsspec ReferenceFileSystem as JSON to file. Url is the remote location of the TIFF file without the file name(s). Raise ValueError if TIFF store can not be represented as ReferenceFileSystem due to features that are not supported by zarr, numcodecs, or imagecodecs: * compressors, e.g. CCITT * filters, e.g. bitorder reversal, packed integers * dtypes, e.g. float24 * JPEGTables in multi-page files * incomplete chunks, e.g. if imagelength % rowsperstrip != 0 Files containing incomplete tiles may fail at runtime. https://github.com/intake/fsspec-reference-maker NzliblzmaZzstdZimagecodecs_lzwimagecodecs_jpegimagecodecs_jpegxrZimagecodecs_packbitsimagecodecs_jpeg2kZimagecodecs_lercimagecodecs_pngimagecodecs_webpimagecodecs_jpegxl)rUriimiPrriRXiiiiiiiGiLiuiviQiRz0 not supported by the fsspec ReferenceFileSystemz isrU)rUrPrCr)rrrr4r7)riiLzBitsPerSample zincomplete chunks arez"JPEGTables in multi-page files arerr/rrrr6zcannot append to version 1r templatesgenrz{{%s}}refsrrPz.zgroupz.zarray)rr*rrcolorspace_jpegcolorspace_datarAr)rPiLiMZimagecodecs_deltaZimagecodecs_floatpredrC)iLiNrrrRrs)rr?distrzrsrrwr)rz}"z z, rrzrz": ["z", z, rz } }z })4rrrpr_r8rrrr;r}rr rrcrOrrkrIrsrtr^rrr:rrrnrrrrrloadsbase64 b64encoderr?rrrrBrr`rwrwrrsplitr _parse_keyrrur)%rrurl groupnameZ compressorsr_appendrZerrormsgrrkrrrrrrGrefzarrrrcodec_idr*rrrrZ filter_idrr?rrrzrR chunkindexrr;r;rErErH write_fsspec<$sV                                    $          6    zZarrTiffStore.write_fsspecc Cs\||\}}}}}|jr"|j}n|j}|dks@|dks@|dkrjt||j|j}|jdk rf||}|S|j j } |jr|dkr|j | |j |j j|jd}|j | |jdk r||}|S|j | ||}ddi} |jdk r|j| d<|jdk r|j| d<|j||f| d}|jdk r0||}|jt|krXt|jdt||S) zReturn chunk from file.Nr6)rArr.Trrz != )rrrzrRrrrsrrrIrrrwrerArrrrrrnr<r+r) rrGrrrr;r;rRrrr@rErErHr<%s>            zZarrTiffStore._getitemc Cszt|jdkr,|d\}}|jt|}n |jd}|j}|||\}}|dkrt|dkr|jdkrrtd|d}|dkr|d|ddfS||j|j j }||j |7}|j r|j|j j } |j|||| fSn|j r"|j j||}WdQRX|dkr|ddddfS|j|dddfS|j j||}WdQRX|dkrV|d|ddfS|j |}|j|} |j|||| fS)z=Return keyframe, page, index, offset, and bytecount from key.rUrr6Nz"truncated series is not contiguous)rcrrrr_indicesr;rr<rsrtrrrrAr) rrGrrrrrrr;r;rErErHri%s<        zZarrTiffStore._parse_keycCs|j}||j}dd|dD}t|t|ks:t|jrPdt|j}n|j}d}xzt |dddD]`\}} || 9}||j krnt||d}|d|} ||d} |d|} t ||d} PqnWt t| t|jkr|} nt| d}t|jd}xn| ||j|kr<||| |<|d8}|d8}n | |dkrT|d8}nt d|d ksp|d kr Pq Wt | t |kstt| d krtt| | }nd }t| d krtt| | }nd }||fS) z5Return page and strile indices from zarr chunk index.cSsg|] }t|qSrE)r)rFrrErErHrG%sz*ZarrTiffStore._indices..r)rUrUNrzshape does not match page shaper6)rrrrrcrrrzrSr}r<rrr+rrrrs)rrGrrrzrrSrrrZframes_indicesZstrile_indicesZframes_chunkedZstrile_chunkedrZ frameindexZ strileindexrErErHr%sT         zZarrTiffStore._indicescCs0t|}|dkrdSd|kr$d|Sg}|d}t|d}x|dkrZ|d|d8}n||dkr||dkr||||d8}|d8}np||||kr|d|d8}|d8}nD||dkr|d|d8}n$||dkr|d|d8}nt|dks|t|kr>Pq>Wt|dddS)z(Return chunks with same length as shape.r6rE)rUrUNr)rcrirr)rRrzrZ newchunksrrrErErHr%s<            zZarrTiffStore._chunkscCsdt|ddS)Nz.rN) rrrrrrVrrrr rrr)rrGrrrrErErHrH&s    zZarrFileSequenceStore._getitemcCs|jdS)zClear chunk cache.N)rr)rrErErHrX&szZarrFileSequenceStore.closeFcCsddlm}|j}|dk r n|jtkr0d}nd|jjkr|jjdksRd|jkrZtd| d} t | t t frz| d} t | r| jd d} d d d d d d ddddddddd| }ntd|dkrd}n|r|ddkr|d7}|dkrd}n|r|ddkr|d7}t} |dkr`|r0tdd| d<d|i| d<g| d<t| d <} d!}n| } |r|std"d#i| d$<xV|jD]H\} } d%| krt| } d&|i|| d'<t| } | | || <qWt|d(r|}n t|d)}|dkr.|tj| dd*d+ddd+d,}nR|r`|d-|tj| dd*d#d.d/}n |tj| dd*dd.d/}t|j}x|jD]\} } d%| krt| } xt|jd0d1d2D]v\}}|||d d3d}|ddkr|dd}d4!d5d6|D}|d-|d7||d8||d9 qWqW|dkr`|d:n|sp|d;t|d(s|"dS)&rz4ZarrFileSequenceStore.write_fsspec..)rG\rcss|]}t|VqdS)N)r])rFrrErErHrI&sz5ZarrFileSequenceStore.write_fsspec..rz": ["z"]z } }z })# urllib.parserrrirrrrr_r[r\rrcallablerr^rrrnrrrrr`rwrwrrrcrrxrrzr r)rrrrrrrrrgrrrrGrrrprefixrrrErErHr\&s                $     .    z"ZarrFileSequenceStore.write_fsspeccCsdt|ddS)Nz#.z chunks: {}css|]}t|VqdS)N)r])rFrrErErHrI&szdtype: z fillvalue: ) r rrrrrzrRr r)rrErErHr&s zZarrFileSequenceStore.__str__)NNNNNN)NNNF) rrrrrrrrrrrrErE)rrHr%sQ wrc@speZdZdZdddZeddZddZd d Zd d Z d dZ ddZ ddZ dddZ ddZddZdS)raSeries of files containing array data of compatible shape and type. Attributes ---------- files : list List of file names. shape : tuple Shape of file series. Excludes shape of chunks in files. axes : str One letter labels of axes in shape. labels : tuple of str Labels of axes in shape. indices : tuple of tuples ND indices of files in shape. Nc s|dkr d}|dkrt}|_|rddl}t|ttjfrPddl}||_nt jdsdt dt|tr| j |}|r||}n:t|tjrt |g}n t|trt|}|r||}dd|D}|st dt |d rt|jst d |fd d }nt|s&t d |r>|fd d }|dkrZ|ddrZt}|ry||f|\} } } }Wn.t k r} zt d| Wdd} ~ XYnXn(d} t|f} tddtt|D} |_|_ddd| D_t| _t| _| _dS)agInitialize instance from multiple files. Parameters ---------- imread : function or class Array read function or class with asarray function returning numpy array from single file. files : str, path-like, or sequence thereof Glob filename pattern or sequence of file names. Default: \*. Binary streams are not supported. container : str or container instance (optional) Name or open instance of ZIP file in which files are stored. sort : function (optional) Sort function used to sort file names when 'files' is a pattern. The default (None) is the natural_sorted function. If False, disable sorting. parse : func (optional) Parse function used to parse the sequence of sorted file names to axes labels, shape, chunk indices, and filtered file names. The default (None) is the parse_filenames function if kwargs contains 'pattern'. kwargs : dict Additional arguments passed to the parse function. NrRr6rwzinvalid containercSsg|]}t|qSrE)rafspath)rFrrErErHrG;'sz)FileSequence.__init__..zno files foundrezinvalid imread functionc s |}|jf|SQRXdS)N)re)rrghandle)_imread_rErHrE's z%FileSequence.__init__..imreadc s>j|(}t|}|f|SQRXWdQRXdS)N)rrwr{r|r)rrgZhandle1Zhandle2)rrrErHrP'srLzfailed to parse file names)r8css|] }|fVqdS)NrE)rFrrErErHrI`'sz(FileSequence.__init__..rcss|]}|dVqdS)r6NrE)rFr^rErErHrId's)r'rfnmatchr\r]rarbzipfileZipFiler`r_filternamelistrr^rrerVparse_filenamesrcrrwrrfr r_rr'rzr) rrrfrJrKparsergrrr'rzrrrE)rrrHr'sf"            zFileSequence.__init__cCst|jt|jS)zReturn number of empty chunks.)r+rzrcrf)rrErErH files_missingi'szFileSequence.files_missingc Cs|jrt|jn|jd}tj|d}d|jj|dt |jd|j dd dd d |j Dd dd d |j DfS) z7Return string with information about file FileSequence.r6rz zfiles: z (z missing)z shape: {}z, css|]}t|VqdS)N)r])rFrrErErHrIw'sz'FileSequence.__str__..z labels: {}css|] }|VqdS)NrE)rFrrErErHrIx's)rr]rfrartrr rrrcr rrzr')rrxrErErHrn'szFileSequence.__str__cCsdt|ddS)Nz the 'file' parameter is deprecated since 2021.10.12.rP)rQrUr6r)rscsj|f|<dS)N)r)rr)rgr|rrErHr'sz"FileSequence.asarray..funcrcs8|dkr dStt|j}j|f}||<dS)N)rrrrsrzr)rrim)rgr|rrErHr's )r)rXrYrZr\rrrrKrrfrcmultiprocessingr cpu_countrrzr!rsrxrrr9rCrh)rrxrZ ioworkersrrgr r tiledrrrrErrzrE)rgr|rrHre'sL$     zFileSequence.asarraycKs t|f|S)z-Return image data from files as zarr storage.)r)rrgrErErHrd'szFileSequence.aszarrcCs4t|jdkr"tj|jd}ntj|j}|S)z8Return longest common sub-path of each file in sequence.rUr6)rcrfrartror)rrrErErHr'szFileSequence.commonpath)NNN)NNrUN)rrrrrrr rrrrrrrerdrrErErErHr&s" c  arcs.eZdZdZdeffdd ZddZZS)r zSeries of TIFF files.Nc s"tj||dkrdn|f|dS)z-Initialize instance from multiple TIFF files.Nz*.tif)rr)rrfrrg)rrErHr(szTiffSequence.__init__cCsdt|ddS)Nz>> ts = TiledSequence((1, 2), (3, 4), {1: 0}) >>> ts.shape (1, 6, 4) >>> ts.chunks (1, 3, 4) Nc CsBt||_t||_t|t||_|rt|}x"|D]\}}||j||<q>Wttt||_ t |j}dg|jt |}t }xR|j D]H\}}||ks||krt d| || |||||9<qWx|j D]\}}||=||=qWt||_t||_n"d|_ |j|_d|jt||_dS)aInitialize from shape of stacked sequence and axes to be tiled. Parameters ---------- stackshape : tuple of int Shape of the stacked sequence excluding chunks. chunkshape : tuple of int Shape of the chunks excluding stack axes. axestiled: dict (optional) Defines the axes to be tiled. Map stacked sequence axis to chunk axis. rUzduplicate axisrE)rUN)rc _stackdims _chunkdimsr _stackshaper^rr%rx _axestiledrsetr_rrzrR) rZ stackshaperrax0ax1rzrRusedrErErHr"(s2        zTiledSequence.__init__ccsdg|j}x|D]}|dkr&dVqt||jkrLtt|d|jt||}x|jD]\}}||||<q`Wx|jD]\}}||=qWt|VqWdS)zReturn iterator over chunk indices of tiled sequence. Parameters ---------- indices : sequence of tuple of int Indices of chunks in the stacked sequence. r6Nz != )rrcrr_rrr)rrrrrrrErErHrM(s    zTiledSequence.indicesccstdg|j}x|D]}|dkr*dVqt||jksd=Zed?d@Z!dS)Hra Binary file handle. A limited, special purpose file handle that can: * handle embedded files (e.g. for LSM within LSM files) * re-open closed files (for multi-file formats, such as OME-TIFF) * read and write numpy arrays and records from file like objects Only 'rb', 'r+b', and 'wb' modes are supported. Concurrently reading and writing of the same stream is untested. When initialized from another file handle, do not use it unless this FileHandle is closed. Attributes ---------- name : str Name of the file. path : str Absolute path to file. size : int Size of file in bytes. is_file : bool If True, file has a fileno and can be memory-mapped. All attributes are read-only. ) r_file_mode_name_dir_lockr_size_closerUNcCsVd|_||_|dkrdn||_||_d|_||_||_d|_d|_t |_ | dS)a Initialize file handle from file name or another file handle. Parameters ---------- file : str, path-like, binary stream, or FileHandle File name or seekable binary stream, such as an open file or BytesIO. mode : str File open mode in case 'file' is a file name. Must be 'rb', 'r+b', or 'wb'. Default is 'rb'. name : str Optional name of file in case 'file' is a binary stream. offset : int Optional start position of embedded file. By default, this is the current file position. size : int Optional size of embedded file. By default, this is the number of bytes from the 'offset' to the end of the file. NrrT) rrrrrrrrrUrwrrw)rrxrr:r;r<rErErHr(szFileHandle.__init__cCs|jdk rdSt|jtjr*t|j|_t|jtrtj|j|_tj |j\|_ |_ t |j|j |_d|_|jdkrd|_nt|jtrB|jj|_|jdkrd|_|j|jj7_d|_|j s |jrtj|jj \}}|d|j||_ n |jj |_ |j r,|j |jj kr,td|jj |_ |jj |_ nt|jdry|jWntk r|tdYnX|j|_|jdkr|j|_d|_|j sytj |jj\|_ |_ Wntk rd |_ YnXy|jj|_ Wntk r YnXntd |jr,|j|j|jdkrl|j}|j|jtj|j|_|j||jdkry|jd|_Wntk rd|_YnXdS) zOpen or re-open file.NTr6FrzFileHandle has wrong moderTzbinary stream is not seekablezUnnamed binary streamzNthe first parameter must be a file name, seekable binary stream, or FileHandle)rr\rrarbrr]rtrealpathrrrrwrrrrsplitextr_r`rrvr:rrrTrrrUr)rr:rrrErErHrw(sv                   zFileHandle.opencCs$|jr |jdk r |jd|_dS)z Close file.N)rrr)rrErErHr)s zFileHandle.closecCs|j|jS)zReturn file's current position.)rrr)rrErErHr )szFileHandle.tellr6cCsh|jrZ|dkr(|j|j|||jS|dkrZ|jdkrZ|j|j|j|d|jS|j||S)zSet file's current position.r6rP)rrrTr)rr;whencerErErHrT$)szFileHandle.seekrcCs |dkr|jr|j}|j|S)z5Read 'size' bytes from file, or until EOF is reached.r6)rrrr)rr<rErErHr2)szFileHandle.readcCs |j|S)z?Read up to len(b) bytes into b and return number of bytes read.)rreadinto)rrrErErHr"8)szFileHandle.readintocCs |j|S)zWrite bytes to file.)rrw)r bytestringrErErHrw<)szFileHandle.writecCs |jS)z"Flush write buffers if applicable.)rr)rrErErHr@)szFileHandle.flushrGrcCs,|jstdtj|j|||j|||dS)z+Return numpy.memmap of data stored in file.z%cannot memory-map file without fileno)rsrr;rzr)rUr_rrrrr)rrsrzr;rrrErErHrD)szFileHandle.memmap_arraycCs.t|}|dkr2|dkr |jn|j}||j}n ||j}|dkrPt||n|}|j|krftdy|j|}Wn<t k rt |j || |j |dd<|}YnX||krtd|d||jjs|js|d|}n|jj|jkr |d|dk r*t|dr*||S)z2Return numpy array from file in native byte order.r6Nz size mismatchzfailed to read z bytes, got Tr)rrrsrrurtrr_rr"rr0rrhrzrJbyteswaprHr`r)rrsr rrur|nrErErHrQ)s4          zFileHandle.read_arrayrUc Cstj}y|j|j|||d}Wnbtk rt|}|dkrL|j|j}tt ||j}|j |}|j ||||d}YnX|dkr|dS|S)zReturn numpy record from file.)rkNrUr6) rrrecrrrvrsrrtr+r]rrK)rrsrzrkr&recordr<ryrErErH read_recordx)s   zFileHandle.read_recordcCs0|dkr dS|j|dtj|jddS)z;Append size bytes to file. Position must be at end of file.rUNr)rrTrarrw)rr<rErErHrO)szFileHandle.write_emptycCs@yt||jWn$tk r:|j|YnXdS)z!Write numpy array to binary file.N)rrascontiguousarraytofilerrvrwr)rryrErErHrP)szFileHandle.write_arrayTc #st}|dkrdS|dkrdkr(dnd} | dkr| dkr|dkrV|j}|$|| |j| } WdQRXnd} |r| | fn| | fgVdS|dkr|j}|dkrd}dkrfddt|D} nfddt|D} |rt| dd d } d } xjt|dD]Z} | | \}}}| | dd}|dks$|dks$|dkrhq$|||kr$d } Pq$W|j}|jj}| rd} x:| |kr| }d}d}xZ||kr| |kr| | \}}}|dkr|dkr|dkr|}||7}| d7} qW|dkr d} n |||||} WdQRXd}d}g}xl|| kr| |\} }}|dkr|dkr||7}|| ||| f|}n|d| f|d7}qNW|r|EdHn|VqWdSd} x| |krg}d}|~xv||krp| |krp| | \} }}|dkrV|dkrV|||||| f||7}n|d| f| d7} qWWdQRX|r|EdHn|VqWdS) aFReturn iterator over segments read from file and their indices. The purpose of this function is to * reduce small or random reads * reduce acquiring reentrant locks * synchronize seeks and reads * limit the size of segments read into memory at once (ThreadPoolExecutor.map is not collecting iterables lazily). Parameters ---------- offsets, bytecounts : sequence of int offsets and bytecounts of the segments to read from file. indices : sequence of int Indices of the segments in the image. Default: range(len(offsets)). sort : bool If True (default), segments are read from file in the order of their offsets. lock: A reentrant lock used to synchronize seeks and reads. buffersize : int Approximate number of bytes to read from file in one pass. Default: 64 MB. flat : bool If True (default), return an iterator over individual (segment, index) tuples. Else return an iterator over a list of (segment, index) tuples that were acquired in one pass. Returns ------- items : (bytes, int) or [(bytes, int)] Iterator over individual or lists of (segment, index) tuples. rUNr6icsg|]}|||fqSrErE)rFr)r:rrErHrG)sz,FileHandle.read_segments..cs"g|]}|||fqSrErE)rFr)r:rrrErHrG)scSs|dS)NrUrE)r=rErErHr>)rz*FileHandle.read_segments..)rGTF)rcrrTrrrwrxri)rrr:rrKrAZ buffersizerrrryrFZiscontigrrr;r;Z nextoffsetrTrrorrrr|r<rE)r:rrrHrB)s.        zFileHandle.read_segmentscCs|S)NrE)rrErErHr0*szFileHandle.__enter__cCs |dS)N)r)rrrrrErErHr3*szFileHandle.__exit__cCs&|jrtd|dtt|j|S)z-Return attribute from underlying file object.z z# not implemented for embedded files)rrXrYrrr)rr:rErErHr6*s  zFileHandle.__getattr__cCsdt|jddS)Nz>> with NullContext(): ... pass rEcCs|S)NrE)rrErErHr*szNullContext.__enter__cCsdS)NrE)rrrrrErErHr*szNullContext.__exit__cCsdS)Nz NullContext()rE)rrErErHr*szNullContext.__repr__N)rrrrZ_NullContext__slotsrrrrErErErHrw*s rwc@sbeZdZdZdZejZdddZdddZ dd d Z dd d Z d dZ ddZ ddZddZdS)rz%Stopwatch for timing execution speed.)startedstoppeddurationNrcCs<|dk rt||ddd|_|dkr,t}||_|_dS)z#Initialize timer and print message.NT)endrr6)printr5rclockr3r4)rmessager6r3rErErHr*s zTimer.__init__cCs2|dk rt||ddd|_t|_|_|jS)z$Start timer and return current time.NT)r6rr6)r7r5rr8r3r4)rr9r6rErErHr*s z Timer.startcCs4t|_|dk r t||dd|j|j|_|jS)z$Return duration of timer till start.NT)r6r)rr8r4r7r3r5)rr9r6rErErHr*s  z Timer.stopcCs.t|}|dk rt|ddt||dddS)z6Print duration from timer start till last stop or now.Nr)r6T)r6r)r]r7)rr9r6rrErErHr7+s z Timer.printcCs|jdkrt|j}n|j}ttj|d}d}x,|t|kr`|||ddkr`|d7}q6W|||ddkr~|d7}||ddS) zAReturn duration from timer start till last stop or now as string.r6)secondsrPz0:0010203040506070809rUr,Nz s)r5rr8r3r]r timedeltarc)rr5rrrErErHr+s " z Timer.__str__cCsd|jdS)NzTimer(started=r)r3)rrErErHr+szTimer.__repr__cCs|S)NrE)rrErErHr+szTimer.__enter__cCs |dS)N)r7)rrrrrErErHr+szTimer.__exit__)NrN)Nr)Nr)NN)rrrrrtime perf_counterr8rrrr7rrrrrErErErHr*s   rc@seZdZdZdS)rz;Exception to indicate invalid OME-XML or unsupported cases.N)rrrrrErErErHr +src@seZdZdZddZdddZddd Zd d Zd d Ze ddZ e dddZ e ddZ e d ddZ e ddZe ddZe ddgfddZdS)!rz OME-TIFF XML.c Ksd|kr|d}d|_g|_g|_g|_d|krF|ddd|_nddlm}t||_tj |ddt d }d }d |d |d |d|jd|d |_ dS)zCreate a new instance. 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UUID : str (optional) Unique identifier. rjr6rWr,r)uuid1ZCreatorz tifffile.py )rz1http://www.openmicroscopy.org/Schemas/OME/2016-06z{declaration}{images}{annotations}{elements}N) rrj annotationselementsrrr>r]r _attribute __version__xml)rrr>ZcreatorZschemarErErHr'+s    zOmeXml.__init__Nc* s4 t|j}|d|}|d|}t|ttfr8||}d|krjd|dkrV|dd=||d|d=y0t|j }ddddd d d d d ddd |}Wn$t k rt d|dYnX|d||krt d|dd|d}|\}} } } } } | dkrt d| dks*| dks*t dtdd|D}t|}|dks\t |dkrdt d|dkr`| dks|dd| | dfkrd}| }n:| dks|d kr|ddd| | fkrd!}| }nd"}t||krd#|krd nd$ksnt |d%|d&d'ddd(}|d#|kr4d nd$|d|}t|t|kstnj|}t|t|krt d)|d"s|dst d*g}xL|D]D}|d+krt d,|d||krt d-|d.||qW|d#|krd/nd0krt d1| dkrp| }|d2kr4t d3|d(d#krJt d4|d(| ksf|d5| krt d6nZ| dkr| }|d2krt d3|dd#krt d4|d| ks|d(| krt d6||d7| ks||d8| krt d6d#|kr$|dt|d#|d8}n|d|d8}td9d|Drbi}gd:d;dd?d@}xt|D]\}}|dAkr||d|}|r|dBkr||||f||<nLxVdBD]:}|kr||kr||||f||<|PqWt dCn |qnWdD}dDdEd|D}dF|dG}dH|dI|dJ}|j|ni}dD}|ddd(}x@|d&d'd'dKdLdMdNdOfD]|krPqWt dP|dgxtD]l}|d#kr֐q||kr|||}nd}|dQkr |}||9}||kr$|||d9}|qWdDdRdtD}d&|kr|d&}dDfdSd|D}||krt dT|xDtD]6\}}|dU|||krt dV|dW|qWdQ|<|t dXdkr t d6g}|dYdD}|rtfdZdd[D}xt|D]x} t|| d\d]d^d_d`dadbdcdd }!tj| dXddedffdgd|D\}"}#}$|dh|"di|#dj|$dk|!dl qBWdD|}g}%xpt|D]d}"dm}&t|dndD|"dodpdqdrdsdtdudvdwdxdydzd{d|}!|%d}|d~|"d|dk|!d|&d qWdD|%}%t|dd}'tj|dod|d}(t|dddddddddd }!| dks| dkr| dkrdnd})d|)dk})ndD})|jd|dk|(d|'d|dd|dk||)|!d|%d|j d|dG|d|d|j |7_ dS)a*Add image to OME-XML. The OME model can handle up to 9 dimensional images for selected axes orders. Refer to the OME-XML specification for details. Non-TZCYXS (modulo) dimensions must be after a TZC dimension or require an unused TZC dimension. Parameters ---------- dtype : numpy.dtype Data type of image array. shape : tuple Shape of image array. storedshape: tuple Normalized shape describing how the image array is stored in TIFF: (pages, separate_samples, depth, length, width, contig_samples). axes : str (optional) Axes labels for each dimension in shape. By default, axes are matched to the shape in reverse order of TZC(S)YX(S) based on storedshape. The following axes codes are supported: 'S' sample, 'X' width, 'Y' length, 'Z' depth, 'C' channel, 'T' time, 'A' angle, 'P' phase, 'R' tile, 'H' lifetime, 'E' lambda, 'Q' other. metadata : miscellaneous (optional) Additional OME-XML attributes or elements to be stored. Image/Pixels: Name, AcquisitionDate, Description, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, TimeIncrement, TimeIncrementUnit. Per Plane: DeltaTUnit, ExposureTime, ExposureTimeUnit, PositionX, PositionXUnit, PositionY, PositionYUnit, PositionZ, PositionZUnit. Per Channel: Name, AcquisitionMode, Color, ContrastMethod, EmissionWavelength, EmissionWavelengthUnit, ExcitationWavelength, ExcitationWavelengthUnit, Fluor, IlluminationType, NDFilter, PinholeSize, PinholeSizeUnit, PockelCellSetting. rjr_rarZint8int16int32rHruint32rqdoublecomplexzdouble-complexbit) rDrErFrHrrGr(float64Z complex64Z complex128rz data type z not supportedr[zmetadata Pixels Type z does not match array dtype rUzImageDepth not supportedzinvalid stored shapecss|]}t|VqdS)N)r)rFrrErErHrI+sz"OmeXml.addimage..r6zempty arrays not supportedNrrrrrrrz dimensions not supportedrbXYCZTrzaxes do not match shapez"dimensions must end with YX or YXSZ TZCYXSAPRHEQz dimension z multiple z dimensionsrrz$more than 8 dimensions not supportedrCz$dimensions do not match stored shapezaxes do not match stored shaperz!shape does not match stored shaperkrlcss|]}|dkVqdS)APRHEQNrE)rFrdrErErHrI+sanglephaserlifetimelambdar\)ArRrEr9rMrzmore than 3 modulo dimensionsrcss2|]*\}\}}d|d|d|ddVqdS)z NrE)rFrdZaxtyper<rErErHrI,szzz!XYZCTXYZTCXYCTZXYTCZZXYTZCzdimension order rcss$|]\}}d|d|dVqdS)z Sizez="rNrE)rFrdr<rErErHrIA,sc3s$|]}|dkr|VqdS)rUN)r)rFrd)dimorderdimsizesrErHrIH,sz'metadata DimensionOrder does not match rcz metadata Sizez does not match rPZPlanec3s |]}dd|VqdS)rPN)r)rFrd)rYrErHrI],sZCZTZ DeltaTUnit ExposureTimeZExposureTimeUnitZ PositionXZ PositionXUnitZ PositionYZ PositionYUnitZ PositionZZ PositionZUnitF)rc3s|]}t|VqdS)N)r)rFr) unraveledrErHrIm,sz d}nd}|jj||||d}|S)zReturn OME-XML string.rzzz&)rrjr?r@)r r@rjr?rCr)rrr@rjr?rCrErErHr,s    zOmeXml.tostringcCsdt|ddS)Nzddlm}|jdd}|||}|j|dddd}WnPtk r}z td|j j d|t Wd d }~XYnt k rYnX|S) zReturn OME-XML string.r6)rNT)Zremove_blank_textzutf-8)encoding pretty_printxml_declarationz z: N) rlxmlrN XMLParserrKrnrvrXrYrrr ImportError)rrCrNparsertreerrErErHr,s   zOmeXml.__str__cCsXt|tst|}nd|ks,d|ks,d|kr0|S|dd}|dd}|dd}|S)zReturn escaped string of value.z&z>z<&rr)r\r]rz)rrErErH_escape,s     zOmeXml._escapecCs6|||}|dkrdSd|dt|d|dS)z1Return XML formatted element if name in metadata.Nrrz.css|]}|r|VqdS)NrE)rFerErErHrI-s)r )rnamesr@rE)rrHrc-szOmeXml._elementscCsl|||}|dkrdS|dk rTt|ttfr8||}n|dkrTtt|jdd|dt|dS)z3Return XML formatted attribute if name in metadata.Nr6z is not a list or tuplerz="r) rVr\rrrWrrrrq)rr:rrrrErErHrA -s  zOmeXml._attributecssdSdkr$fdd|D}nHtttfrNfdd|D}nttrlfdd|D}ddd|DS)z Return XML formatted attributes.rNc3s|]}t|VqdS)N)rrA)rFr:)rrErHrI-sz%OmeXml._attributes..c3s|]}t|VqdS)N)rrA)rFr:)rrErHrI!-sc3s|]}t|VqdS)N)rrA)rFr:)index_rrErHrI$-scss|]}|r|VqdS)NrE)rFr)rErErHrI&-s)r\rrr^r )rrurtrgrE)rurrHrb-s zOmeXml._attributescCsR||d}|dkrdSy |d}Wntk r8YnXd|dt|dS)z'Return XML formatted reference element.NrrZrz ID="z"/>)rVrrrq)rr:rrErErH _reference(-s  zOmeXml._referenceTc Cs>ddlm}|s|dkrtjtjtd}tj|rZt|d}| }WdQRXn(ddl }|j d}| }WdQRX| dr|dd d }y||||Wntk r|dYnX|r:|ddk r:| d r |d d d }||}|r,|d|d S|d|SdS)zReturn if OME-XML is valid according to XMLSchema. 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Flat_fieldZ Trim_fileZ Image_pathr Z Energy_rangeZDetector_distanceZDetector_VoffsetZBeam_xyZFluxZFilter_transmissionZ Start_angleZAngle_incrementZDetector_2thetaZ PolarizationAlphaKappaPhiZ Phi_incrementChiZ Chi_incrementZOscillation_axisZN_oscillationsZStart_positionZPosition_incrementZ Shutter_timeOmegaZOmega_increment)rr]rqrrErErErHPILATUS_HEADER7sL    zTIFF.PILATUS_HEADERcCsddl}|jS)Nr6)mmapr)r^rErErHr7szTIFF.ALLOCATIONGRANULARITYcCsddl}t|ddS)Nr6rPrU)r rr)r rErErHrT7szTIFF.MAXWORKERScCsGdddtj}|S)Nc@seZdZdZdZdZdZdS)z!TIFF.CHUNKMODE..CHUNKMODEr6rUrPrCN)rrrrZPLANErFILErErErErHr7sr)rr)rrErErHr7szTIFF.CHUNKMODEN)Lrrrrrrrrrrrrrr rrrr`rSrerrrrYrrrrrr\rrZr|rrrrbr<ryr;ryrrrrrprcr r r rhrirr"rrr#r$r%r'r*r-r.r?r@rArBrCrFrOrRr"rVr]rrTrrErErErHr-s*B  A     \99IQ2&   A     I  3 /;#K-rc! s|dkr2|d}d}|d}d} |d} |d} n:|dkrd|d }d}|d }d } |d} |d } ntd |d krxi}|d krd}g} tj} |}xt| |kry.| |||d}|dkrtd|Wn<tk r}ztd|d|dPWd d }~XYnXi}|| |}|}d}x"t |D]}| | |||d\}}| | ||d|| \}}|| 7}| |t |}yt j |}Wn*tk rtd|d|YnX|t|}||ks||kr| ||d}|dks|||jkr,td|d|||||kr^||d}||||||}n|dks||dks||dkr||}t||krtd|nJ||krd||t|d|d}| |||}nt|||||}n\|dks|dks|dkr|d |}n0d||t|d|d}| ||d |}||koh|t jkoh|dk} | r|dkrytt|dd}Wn$tk rtd|YnXn|t jkr.t j|ytfdd |D}WnBtk r,}z"|d!krtd"|d#|Wd d }~XYnX| rJt|dkrJ|d}|||<q>W| |||| |||d}|dkrP||jkrtd$|P||qW| r|dkr| d} | S)%zRead tags from chain of IFDs and return as list of dicts. The file handle position must be at a valid IFD header. Does not work with NDPI. rr8rPrrrZI4srr9rZQ8szinvalid offset sizeNlr6izsuspicious number of tags z) corrupted tag list @z (rzinvalid data type z for tag #zinvalid value offset rUrz8 could not read all values for tag #z{}{}{}F)rz> coercing invalid ASCII to bytes for tag #c3s|]}|VqdS)NrE)rFr)rErErHrI:8szread_tags..)ii=z% failed for tag #z: z. invalid next page offset )r_rrrrcrrrvrqrwrVr]rrrrr<rTrrrrrr0rrrrri)!rrkrZtagnamesZ customtagsmaxifdsrrrQrRrxr~r|rr;rrrryrrrr rsr rr:rrr~rrprocessrE)rErH read_tags7s             $     rbc Cst|||tjdd}x6dD].}yt||||<Wqtk rFYqXqWd|kr|ddd}yH|dkrt|ddd|d<n"|dkr|dddd |d<Wntk rYnX|S) z,Read EXIF tags from file and return as dict.rU)r`)rrrNrsASCIIsUNICODEzutf-16)rbrr rrvrn)rrkrsr rZexifr:ZidcoderErErHrY8s   rcCst|||tjddS)z+Read GPS tags from file and return as dict.rU)r`)rbrr )rrkrsr rrErErHrm8srcCst|||tjddS)z8Read Interoperability tags from file and return as dict.rU)r`)rbrr )rrkrsr rrErErHrr8srcCsb|dkr dn|tj|d}|t|j9}||}t||kr^td|dt|d|S)z,Read tag data from file and return as bytes.rPrrz% failed to read z bytes, got r)rrrrrsrtrrcrq)rrkrsr rryrErErHrw8s  rcCs||S)z5Read tag data from file and return as Unicode string.)rrn)rrkrsr rrErErH read_utf88srccCs*|dkr dn|tj|d}|||S)z2Read tag data from file and return as numpy array.rPrr)rrr)rrkrsr rrErErHr8srcCs0||tj|d|}|ddkr,d|_|S)zCRead ColorMap/TransferFunction from file and return as numpy array.rrCr6)rCr)rrrrz)rrkrsr rcmaprErErHr8s rc Cs\||}ytt|Stk rV}ztd|jjd|Wdd}~XYnXdS)z2Read JSON tag data from file and return as object.z z: N) rrrr0rnr_rqrr)rrkrsr rryrrErErHr8s  *rcCsp|jtj|d}t|}dd|dD|d<|d}t|d|d|d|d t|d f|d<|S) z9Read FluoView mm_header tag from file and return as dict.)rkc Ss>g|]6}t|d|d|d|dt|dfqS)r6rUrPrCr)rr)rFrrErErHrG8sz"read_mm_header..r!rQr6rUrPrCr)r(rrR recarray2dictrr)rrkrsr rZmmhrrErErHr8srcCs||ddS)zARead FluoView mm_stamp tag from file and return as numpy.ndarray.rr)r)rrkrsr rrErErHr8src Cs|dks|dkr"td||i}|dkrl|dd||d}d|ddd f|ddd fi}nXxVt|D]J}td |d d } | d kr|d qvt|| |dd\} } | || <qvW|S)zuRead MetaMorph STK UIC1Tag from file and return as dict. Return empty dictionary if planecount is unknown. )rrrzinvalid UIC1Tag rzPt|||dd\}}|||<qW|S) z8Read MetaMorph STK UIC4Tag from file and return as dict.rrzinvalid UIC4Tagz.read_intZ_TagIdrNrrz/ invalid offset for tag z @rrPr6irrz. invalid string in tag zinvalid string size z%ipzinvalid string size: rz%ir).r6).rU)rU)rrVrurrr]rqrTrrUrrrrr0r_rwrirrzrrc)rrjrdr;rjr:rsrroffrr<rstringrE)rrHri8s         $  $    ricCstd|dd}t|d||ddd}td|d\}}|dkr|td |d }|d|d}n2td|dd}t|d||d}t|||d S) z:Read UIC ImagePropertyEx tag from file and return as dict.rrUr6rNrz invalid LSM TimeStamps blockzRead LSM ChannelColors structure from file and return as dict.F)Monor2 ColorNamesz invalid LSM ChannelColors structurerrrHr)r r2z invalid LSM LookupTables structure$ZLutTypeZAdvancedZNumberChannelsZCurrentChannelZ SubBlocksz invalid LSM SubBlock type )r[Data) rrrrqrr-rwrrhrir.) rr|r<Z nsubblocksZ nchannelsZluttypeZadvancedZcurrentchannelZ subblocksrZsbtyperyZnknotsrErErHr9sN         rc Csbi}|g}tj}td|dddkr6td|S|dx|d|d\}}}|d krvtt||}n@|dkr|d |dd}n"|d kr|d |dd}nd}|tjkr||tj|}g} | ||<| }nn|tj kr||i} || | }nD|tj kr0tj |}|||<n$|d krD| }n||d|d<|sDPqDW|S)z9Read LSM ScanInfo structure from file and return as dict.z invalid LSM ScanInfo structurerz z: N)rrr0olympusini_metadatarvrqrr)rrkrsr rinistrrrErErHr{:s  rc Csi}|jtj|d}x"tjD]\}}||||<qW|ddkr|jtj|d}|dtdkrptdiSxTtjD]J\}}|dr||j dd d } t | d d ||<qx||||<qxWxNd D],} |d| d<|d| d<qWn|j dkrtdiS|S)z.Read TVIPS EM-MENU headers and return as dict.)rkr1rPrNl*UUz: invalid TVIPS v2 magic numberrzutf-16rU)rVr)nullrrEgeAZ PixelSizerUz9 unknown TVIPS header version) r(rrFrrOrrqrprrnr0r) rrkrsr rr|rr:Ztypestrrr?rErErHr:s.    rc Csi}i}tt||}xn|D]b}|}|drPi}|||dd<q$y|d\} } Wntk rxw$YnXt| || <q$W|S)z0Read FEI SFEG/HELIOS headers and return as dict.rrUrr) rr0r splitlinesrrprr_r ) rrkrsr rr|sectionryrrGrrErErHr:s rc Cszddi}d}tt||}xT|D]F}|rB|}q*|rVy|d\} } Wn@tk ry|dd\} } Wntk rw*YnXYnX| } d} y.| \} } t | t t f}|| kr|} | } WnPtk r&t | t t f}|| kr|} | dkrd} n| d kr"d } YnX| | f||<| rP||| f7<d}q*|dt |t t ff7<q*W|S) zRead Zeiss SEM tag and return as dict. See https://sourceforge.net/p/gwyddion/mailman/message/29275000/ for unnamed values. rrENrr,rU)ZNoZOffF)ZYesZOnT) rr0rrisupperrrr_rvrr rrq)rrkrsr rr|rGryrr:rrrrnumberrErErHr:sH       rcCsV|jtj|d}||}t|}|dd|d|d<|dd|d|d<|S)z7Read NIH_IMAGE_HEADER tag from file and return as dict.)rkr>Nr=r8r7)r(rr?rHre)rrkrsr rr)rErErHr:s  rc Cs |dy|td|d\}}|dks2|dkr:td|dtd|d\}}}}|d ksn|d krtd |d |d WnVtk r}ztd|Wdd}~XYn,tk r}ztd|Wdd}~XYnXtt||dd}|dkrt |dd|dni}|||fS)aRead ScanImage BigTIFF v3 or v4 static and ROI metadata from open file. Return non-varying frame data, ROI group data, and version as tuple(dict, dict, int). The settings can be used to read image data and metadata without parsing the TIFF file. Raise ValueError if file does not contain valid ScanImage metadata. Frame data and ROI groups can alternatively be obtained from the Software and Artist tags of any TIFF page. r6z<2sHrsIIrznot a BigTIFF filerztdYnXi}|dt|d|d \}}}}}}} } | d krt||d | d |d <ntd |dkrB||t|d|d\} } | dkr8t|d| |d| } | d d d| dd d| dd d| dd d| dd dd|d<ntdntd|dkr||t|d|d\} } | dkrt||d | d |d<ntdntdd|d<|dkr ||t|d|d\} } | d krt||d | d |d!<ntd"n|d#kr||d<ntd"|S)$zRead MicroManager non-TIFF settings from open file and return as dict. The settings can be used to read image data without parsing the TIFF file. r6rr)sIIsMMrPznot a MicroManager TIFF filerIIIIIIIIri$#NZSummaryzI invalid MicroManager summary headeriCrmi4ZIIIIIrrrUrCr)rfSliceFrameZPositionrPZIndexMapzG invalid MicroManager index headeriidZDisplaySettingszI invalid MicroManager display headerZ MajorVersioni}ie r zJ invalid MicroManager comments headeria)rTrrur_rrrrq)rrkr|Z index_headerZ index_offsetZdisplay_headerZdisplay_offsetZcomments_headerZcomments_offsetZsummary_headerZsummary_lengthrr ryrErErHr;sf  &               rcCstdS)zRead MetaSeries non-TIFF hint catalog from file. Raise ValueError if the file does not contain a valid hint catalog. N)rz)rrErErHread_metaseries_catalog};src Cs|sdSddd|g}dg}g}dd}dd }d d }d d }dd|fdd|fdd|fdd|fdd|fdd|fdd|fdd|ff} x| D]\} } } | |kr| } n | |krq|dkr| ddd } || } t| trd!d"| D} t| }n t| trt| }n | g} d#}|| t|d$|x0| D](}| ||}|||t|q:WqW|stdSd% |}d% |}||}t||d<tj|d$t|f|}d&d#t||d'fd(d)t|d)|d'ffS)*aWReturn IJMetadata and IJMetadataByteCounts tags from metadata dict. The tags can be passed to TiffWriter.write() as extratags. The metadata dict may contain the following keys and values: Info : str Human-readable information as string. Labels : sequence of str Human-readable labels for each channel. Ranges : sequence of doubles Lower and upper values for each channel. LUTs : sequence of (3, 256) uint8 ndarrays Color palettes for each channel. Plot : bytes Undocumented ImageJ internal format. ROI: bytes Undocumented ImageJ internal region of interest format. Overlays : bytes Undocumented ImageJ internal format. Properties : {str: str} Map of key, value items as strings. rEsIJIJsJIJI)rrr6cSs|dddd|S)Nzutf-16bele)rr)r)ryrkrErErH_string;sz$imagej_metadata_tag.._stringcSstj|dt|f|S)Nr)rrrc)ryrkrErErH_doubles;sz%imagej_metadata_tag.._doublescSs|S)N)r)ryrkrErErH_ndarray;sz%imagej_metadata_tag.._ndarraycSs|S)NrE)ryrkrErErH_bytes;sz#imagej_metadata_tag.._bytesrsinforslablr srangr!slutsr"splotr#sroi r$soverr%sproprNrcSsg|]}|D] }t|q qSrE)r])rFrrrErErHrG;sz'imagej_metadata_tag..rUr8riTir) rr\r^rrcrrirrr )rrkrr:bodyrrrrmetadata_typesrGmtyperrr rryrErErHrk;s\             rkc sdd}dd}dd}dd}d |fd |fd |fd |fd |fd|fd|fd|fd}|dd|D|sztd|dddkrtd|d}|dks|dkrtd|dd} t|d| |dd| d} d| d} d} i} xt| ddd| d ddD]\}}g}||t||f\}}xBt|D]6}| d 7} | || }| ||| |||} qDW|d kr|dn|| | <qW| drt ddkrt fd!d"tdt dD| d<| S)#a]Return IJMetadata tag value as dict. The 'Info' string can have multiple formats, e.g. OIF or ScanImage, that might be parsed into dicts using the matlabstr2py or oiffile.SettingsFile functions. 'ROI' and 'Overlays' are returned as bytes, which can be parsed with the ImagejRoi.frombytes() function of the roifile package. cSs|dddd|S)Nzutf-16rr)rr)rn)ryrkrErErHr;sz imagej_metadata.._stringcSst|dt|d|S)Nrr)rrrc)ryrkrErErHr;sz!imagej_metadata.._doublescSst|dddS)NrHrr-)rrr0rh)ryrkrErErH_lut;szimagej_metadata.._lutcSs|S)NrE)ryrkrErErHr;szimagej_metadata.._bytesrrr r!r"r#r$r%)sinfoslablsrangslutssplotsroi soverspropcSs i|]\}}||dddqS)NrrE)rFrrrErErHr<sz#imagej_metadata..zno ImageJ metadataNr)sIJIJsJIJIzinvalid ImageJ metadatar6ri$z#invalid ImageJ metadata header sizerZ4sIrPrUc3s|]}||dVqdS)rPNrE)rFr)r)rErHrI"<sz"imagej_metadata..) rrr_rrrxrVrrwrirrcr^)ryr:rkrrrrrZ header_sizeZntypesrrcounterr|rr rr:rrZpos1rE)r)rHr;sP     (  $ $rc Csdd}i}x|D]~}y|d\}}Wntk rBwYnX|}|}x6tt|fD](}y||}PWq`tk rYq`Xq`W|||<qWd|krtd|S)a8Return metatata from ImageJ image description as dict. Raise ValueError if not a valid ImageJ description. >>> description = 'ImageJ=1.11a\nimages=510\nhyperstack=true\n' >>> imagej_description_metadata(description) # doctest: +SKIP {'ImageJ': '1.11a', 'images': 510, 'hyperstack': True} cSsddd|S)NTF)rar`)r)rrErErH_bool2<sz*imagej_description_metadata.._boolrrznot an ImageJ image description)rrrvrrrqr_)rrr|rrGrrsrErErHr'<s&   rc Ks|r d}d}|dkr |dd}|dd}t|||d}|ddk}g} d |g} | d t|dd |dkrd }| d n| dt||ddkr| d|d|dkr|s|sd}|r|r| d||ddkr | d|d|ddkrB| d|d|dkrB| d|dk rd| dt|x8|D],\} } | dkrn| | d| qnWd| | dgS)a5Return ImageJ image description from data shape. ImageJ can handle up to 6 dimensions in order TZCYXS. >>> imagej_description((51, 5, 2, 196, 171)) # doctest: +SKIP ImageJ=1.11a images=510 channels=2 slices=5 frames=51 hyperstack=true mode=grayscale loop=false FNrz1.11ar)rgbrr)rCrzImageJ=zimages=rTzhyperstack=truez hyperstack=rPrUz channels=Z grayscalezmode=zslices=r6zframes=z loop=falsezloop=)rjrrrrrr)r[rcrir+rrrr ) rzrZ colormapedrZ hyperstackrlooprgrrir|rGrrErErHrlJ<sB          rlc Cstdd|D}t|}d|kr.dkr:nntd|rt||krRtdd}|}x*|D]"}d|}||krtd |}qdWt|}g}d}xBdD]:}||kr|||kr||||d7}q|dqW|d d krtd t|S|d kr|d dko|dk}|r6|d dkr6td|s\|dkr\|d dkr\td|sp|d dkrdd||Sdd||dS)zReturn shape normalized to 6D ImageJ hyperstack TZCYXS. Raise ValueError if not a valid ImageJ hyperstack shape or axes order. >>> imagej_shape((2, 3, 4, 5, 3), False) (2, 3, 4, 5, 3, 1) css|]}t|VqdS)N)r)rFrrErErHrI<szimagej_shape..rUrz)ImageJ hyperstack must be 2-6 dimensionalz-ImageJ hyperstack shape and axes do not matchr6ZTZCYXSz.ImageJ hyperstack axes must be in TZCYXS orderr)rUrCrz1ImageJ hyperstack must contain 1, 3, or 4 samplesN)rCrrPz$ImageJ hyperstack is not a RGB imagez*ImageJ hyperstack is not a grayscale image)rUr)rrcr_r_rri) rzrrrrrdrZndimsnewshaperErErHrc<sH        rccCs`d}d}|rnJ|dkrd}n<|dkr6|dkrXd}}n"|dkrDd}n|dkrXt|j}||fS)z;Return JPEG and output colorspace for jpeg_decode function.NrrPrUrrrC)rrSr:)rrrr4r2rErErHr?<s  r?cCsd}x|t|krtd|||dd}|d7}|dkr@q|dkrJPd|kr^dkrdqnq|d krnqtd|||dd}|d7}d |krd krnntd |||d S|dkrP||d7}qWtddS)z(Return bitdepth and shape of JPEG image.r6Tz>HrPiiiiiiiz>BHHBrizno SOF marker foundN)rcrrr_)rrmarkerrrErErHr <s(r cCsd}d}d}d}x|t|krtd|||dd}|d7}|dkrPq|dkrZPd|krndkrtqnq|d kr~qtd|||dd}|d7}|d krtd|||dd}n|d kr|d }td |||d\}}} } |d7}d } d } xdt| D]X} td|||d\}}}|d7}|d?| krT|d?} |d@| kr|d@} qW| d9} | d9} |d }n|dkr||d}P||d7}qW|dks|dks|dkrtd| }|| }|d|td||||d|}|||fS)zAReturn tile shape and JPEG header from JPEG with restart markers.r6Tz>HrPiiiiiiirUz>BHHBrz>BBBrCrrtrizmissing required JPEG markersNz>HH)rcrrrwr_r)rZrestartintervalZ sofoffsetZ sosoffsetrrrrr$r%Z ncomponentsZmcuwidthZ mcuheightrZcidfactortablerrrrErErHr<s\    *rcKs|j|dt|S)zReturn JSON image description from data shape and other metadata. Return UTF-8 encoded JSON. >>> json_description((256, 256, 3), axes='YXS') # doctest: +SKIP b'{"shape": [256, 256, 3], "axes": "YXS"}' )rz)rrr)rzrrErErHrm>=s rmcCsr|dddkr:tdd|dddD}t|d S|dd d krd|ddd krdt|Std |dS)aReturn metatata from JSON formated image description as dict. Raise ValuError if description is of unknown format. >>> description = '{"shape": [256, 256, 3], "axes": "YXS"}' >>> json_description_metadata(description) # doctest: +SKIP {'shape': [256, 256, 3], 'axes': 'YXS'} >>> json_description_metadata('shape=(256, 256, 3)') {'shape': (256, 256, 3)} Nrzshape=css|]}t|VqdS)N)r)rFrrErErHrIY=sz,json_description_metadata..rrr)rzrUrm}zinvalid JSON image description)rrr^rrr_)rrzrErErHr K=s     r c Cs|dstd|dkr"ddh}i}|g}d}x~|D]p}|sN|}|sTq<|ddkr(|ddd kr|d =|d }|d d}|rd ||||<|dd dkr>> descr = ('[Intensity Mapping]\nMap Ch0: Range=00000 to 02047\n' ... '[Intensity Mapping End]') >>> fluoview_description_metadata(descr) {'Intensity Mapping': {'Map Ch0: Range': '00000 to 02047'}} rz"invalid FluoView image descriptionNzRegion Info (Fields)zProtocol DescriptionFr6z End]rrUrrzLUT )rs)rrCTrzRGB css|]}t|VqdS)N)r)rFrrErErHrI=sz0fluoview_description_metadata..)rpr_rrr rrrrHrzrirrcrMr ) rZignoresectionsr|sectionscommentrrr:r)rGrrErErHfluoview_description_metadataa=s^       rc sji}|ds|SxdD]}||d}qWx6|dD]&dddkrRq:d}dtjkrytjdd |d <Wq:tk rdd d||<Yq:Xq:tjd\}t |dt r|d}nfd d |D}t kr|ddkrdg}t fdd|D}t krDd|}nt|d krZ|d}|||<q:W|S)aReturn metatata from Pilatus image description as dict. Return metadata from Pilatus pixel array detectors by Dectris, created by camserver or TVX software. >>> pilatus_description_metadata('# Pixel_size 172e-6 m x 172e-6 m') {'Pixel_size': (0.000172, 0.000172)} z# z#:=,()rrNrPz r6z%Y-%m-%dT%H %M %S.%frrUcsg|] }|qSrErE)rFr)rrErHrG=sz0pilatus_description_metadata..notrc3s|]}|VqdS)NrE)rFr)rsrErHrI=sz/pilatus_description_metadata..)rprzrrr]rstrptimer rvr\rrqrr]rc)rr|r1r:rrrE)rsrrHr=s<      rcCsx|dstdi}|d}|d|d<t|dkr<|Sx6|ddD]&}|d\}}t|||<qJW|S) zReturn metatata from Aperio image description as dict. The Aperio image description format is unspecified. Expect failures. >>> svs_description_metadata('Aperio Image Library v1.0') {'Header': 'Aperio Image Library v1.0'} zAperio z invalid Aperio image descriptionrr6HeaderrUNz = )rpr_rrcr r)rr|rrrGrrErErHsvs_description_metadata=s    rc Cs|}|sgSy t|}Wn:tk rV}ztd|jjd|gSd}~XYnXg}x|dD]}i}xz|dD]l}|dd}t|dkr|\}}t|||<q||d}|r|d |kr|d  |q||g|d <q|W| |qhW|S) zReturn metadata from MetaMorph image description as list of dict. The MetaMorph image description format is unspecified. Expect failures. z$ z: Nrz r,rUr6r) rrrrqrrrrcr ri)rrr|rrrr:rrErErHstk_description_metadata=s0    rcsp|dstdddlm}||}ttdddfdd |i}d |krl|d d d |d <|S) z:Return metatata from MetaSeries image description as dict.z z$invalid MetaSeries image descriptionr6)r@cSs t|ddS)Nonrk)asbool)r=rErErHr>>rz1metaseries_description_metadata..)rqrrcspxj|D]b}|j}|s&|i||j<qd|kr|d}|d}|d}|kr`||||<q|||<qW|S)Nrrr)rLrF)rOr|childrLrrEr)r typesrErHr >s  z.metaseries_description_metadata..parser_z r)rpr_rJr@rKrqrrz)rrNrOadictrE)r rrHr >s     rcCst|S)z9Return metatata from ScanImage image description as dict.)r&)rrErErHscanimage_description_metadata/>src CsJy t|Stk rD}ztd|jjd|Wdd}~XYnXdS)z2Return metatata from ScanImage artist tag as dict.z% z: N)rrr_rqrr)ZartistrrErErHscanimage_artist_metadata4>s  (rc Csdd}i}g}d}d}x|D]}|}|dks$|ddkrHq$|ddkr*|dd kr*|d d}i||<}|d krg|d <} g|d <} n|dkrg||<nx|dkrd |krg||d<}nV|dkrd |krg||d<}n4|dkr|d d} ddt| D}|||<d} q$|d\} }|dkrLd}n,d|krptdd|dD}nt|}|d kr||| <| | | |q$|dkr| dkrig||d<n|| \} }||d|| <q$|dkrf| dddkrL|| d}td|}|t |dd t |d dt |ddgn|| \} } ||| | <q$| dddkr|dk r||q$| dd dkr|dk r||q$||| <q$Wd |krFdd!i}g} g} xNt |d |d D]8\}}|d kr| | ||d | |qWd | |d <t| |d <y0t|ddd|d dd"|dd<Wntk rYnXy0t|ddd|d dd#|dd<Wntk rYnXx"|D]}t|dd$|d<qW|S)%zUReturn OlympusSIS metadata from INI string. No documentation is available. cSsFd}t|d}|t|kr>t||dd}|d|}||fS)Nr6 0123456789rU)rcrstripr)rGrrrErErHkeyindexG>s   z%olympusini_metadata..keyindexNrr6;rrrrUZ DimensionrrzZASDr/rrIZTimePosZBandcSsg|] }dgiqS)LUTrE)rFrrErErHrGh>sz'olympusini_metadata..rrcss|]}t|VqdS)N)r )rFrrErErHrIp>sz&olympusini_metadata..ZCountrCrzs                 2       ,, rTc sj|dkr d}dkrdttt|dkrNtfdd|Ds\td|tfddd D}t|j|}t |j t |fj }xt |D]\}}|tt||d d?}|td d |d M}|rLjd|d |} | |jjdkr|d}|d | d d |d 9}|d | jd}||dd|f<qW|dS)aReturn array from bytes containing packed samples. Use to unpack RGB565 or RGB555 to RGB888 format. Works on little-endian platforms only. Parameters ---------- data : byte str The data to be decoded. Samples in each pixel are stored consecutively. Pixels are aligned to 8, 16, or 32 bit boundaries. dtype : numpy.dtype The sample data type. The byteorder applies also to the data stream. bitspersample : tuple Number of bits for each sample in a pixel. rescale : bool Upscale samples to the number of bits in dtype. Returns ------- numpy.ndarray Flattened array of unpacked samples of native dtype. Examples -------- >>> data = struct.pack('BBBB', 0x21, 0x08, 0xff, 0xff) >>> print(unpack_rgb(data, '>> print(unpack_rgb(data, '>> print(unpack_rgb(data, 'szunpack_rgb..zsample size not supported: c3s&|]}t|jdkr|VqdS)rN)rrrsrt)rFr)bitsrErHrI>sZBHIrU0b1rPrr8r)rrrsrrrpr_rr0rkrr<rcrr}rtr rh) ryrsrZrescalerr|rrDrEr+rE)rrsrHr5>s,"  r5cCs tddS)z"Return float32 array from float24.r6N)rz)ryrkrErErHr6>sr6cCs ddl}|||dkrdn|S)zCompress Zlib DEFLATE.r6Nr)rrq)ryrrrrErErHr>srcCsddl}||S)zDecompress Zlib DEFLATE.r6N)rr/)ryrrrErErHr>srcCsddl}||S)zCompress LZMA.r6N)rrq)ryrrrrErErHr>srcCsddl}||S)zDecompress LZMA.r6N)rr/)ryrrrErErHr?srrrUcCs|dkrtd|dt|ttfrZtj|tjd}tj|dd}t|d|d S|j }|j dkr|| d|j }tj||d}td g|j}d||<tj|d|t||d}|j dkr| |S|S) z Encode Delta.rUzdist z not implemented)rsr6)r?rrN)rzr\r bytearrayrrr0rHrrSrrsrar1rtrrr)ryr?rrrrsrGrErErHr ?s    rcCs|dkrtd|d|dk r,|jjs,d}t|ttfrbtj|tjd}tj |dtj|d S|j j dkr| d |j j}tj |||j d }| |j Stj |||j |dS) z Decode Delta.rUzdist z not implementedN)rsr6)r?rsrrr)r?rs)rzr writeabler\rrrrr0rHZcumsumrrsrar1rt)ryr?rrr1rErErHr?s  rcCs|s(|d|tj|dtjdy"|d}tj|d||d|Stk rh||dStk rt dYnXdS) aReverse bits in each byte of bytes or numpy array. Decode data where pixels with lower column values are stored in the lower-order bits of the bytes (TIFF FillOrder is LSB2MSB). Parameters ---------- data : bytes or ndarray The data to be bit reversed. If bytes, a new bit-reversed bytes is returned. Numpy arrays are bit-reversed in-place. Examples -------- >>> bitorder_decode(b'\x01\x64') b'\x80&' >>> data = numpy.array([1, 666], dtype='uint16') >>> bitorder_decode(data) >>> data array([ 128, 16473], dtype=uint16) s@ `P0pH(hX8xD$dT4t L,l\<|B"bR2r J*jZ:zF&fV6vN.n^>~A!aQ1q I)iY9yE%eU5u M-m]=}C#cS3s K+k[;{G'gW7wO/o_?r6)rsrHrU)rzslices of arrays not supportedN) rirrr0rHr1taker translater_rz)ryrZ _bitorderr1rErErHr90?s r9cCs tddS)zTightly pack integers.rCN)rz)ryrr?rrErErHrCb?srCcCs|dkrbt|d}t|}|drX|d|d|d}|ddd|fd}||S|dkrvt||Std|dt|d dS) aDecompress bytes to array of integers. This implementation only handles itemsizes 1, 8, 16, 32, and 64 bits. Install the imagecodecs package for decoding other integer sizes. Parameters ---------- data : byte str Data to decompress. dtype : numpy.dtype or str A numpy boolean or integer type. bitspersample : int Number of bits per integer. runlen : int Number of consecutive integers, after which to start at next byte. Examples -------- >>> packints_decode(b'a', 'B', 1) array([0, 1, 1, 0, 0, 0, 0, 1], dtype=uint8) rUz|BrrN)rrrr4z unpacking z-bit integers to z not supported)rrr0Z unpackbitsrhr rzrs)ryrsrZrunlenrrErErHr7f?s    r7cCsg}|j}d}y|xvt|||dd}|d7}|dkr`||||dd||d7}q|dkr|||||||7}qWWntk rYnXt|S)awDecompress PackBits encoded byte string. >>> packbits_decode(b'\x80\x80') # NOP b'' >>> packbits_decode(b'\x02123') b'123' >>> packbits_decode( ... b'\xfe\xaa\x02\x80\x00\x2a\xfd\xaa\x03\x80\x00\x2a\x22\xf7\xaa' ... )[:-5] b'\xaa\xaa\xaa\x80\x00*\xaa\xaa\xaa\xaa\x80\x00*"\xaa\xaa\xaa\xaa\xaa' r6rUi)rMrrWr)encodedrZ out_extendrr%rErErHr?s  rcCs2tj||dd}t|d|j}|r.t|}|S)aReturn palette-colored image. The image values are used to index the colormap on axis 1. The returned image is of shape image.shape+colormap.shape[0] and dtype colormap.dtype. Parameters ---------- image : numpy.ndarray Indexes into the colormap. colormap : numpy.ndarray RGB lookup table aka palette of shape (3, 2**bits_per_sample). contig : bool If True, return a contiguous array. Examples -------- >>> image = numpy.arange(256, dtype='uint8') >>> colormap = numpy.vstack([image, image, image]).astype('uint16') * 256 >>> apply_colormap(image, colormap)[-1] array([65280, 65280, 65280], dtype=uint16) rU)r?r6)rrrZrollaxisrr))rBrrerErErHrI?s  rIcs|}dkrr|dk rJt|dks0|dt|krJtdt|fd|dt|ftddtt|D|fStjstd ttrt dkrifd d }d d |D}t|dkrt j |d}n t j |}t|}dg} x|D]} || |d\} dkr| dk rttksjtfddttDrtddn| krtddk rfdd D| qWdkrtntfddDtj| tjd} tj| dd} |dkrDtj| dd} | | 8} | | 8} | d7} t| }n@t| t|ksptddt|| Drtd| d|dd | D} || |fS)aReturn shape and axes from sequence of file names matching pattern. Parameters ---------- files : sequence of str Sequence of file names to parse. pattern : str Regular expression pattern matching axes labels and chunk indices in file names. By default, no pattern matching is performed. Axes labels can be specified by matching groups preceding the index groups in the file name, be provided as group names for the index groups, or be omitted. The predefined 'axes' pattern matches Olympus OIF and Leica TIFF series. axesorder : sequence of int (optional) Indices of axes in pattern. By default axes are returned in the order they appear in pattern. categories : dict of dicts (optional) Map of index group matches to integer indices. {'axislabel': {'category': index}} _shape : tuple of int (optional) Shape of the file sequence. If None (default), the shape is maximum-minimum+1 of the parsed indices for each dimension. Returns ------- labels : tuple of str Axes labels for each dimension. shape : tuple of int Shape of file series. indices : sequence of tuples Index of each file in shape. files : sequence of str Filtered sequence of file names. Examples -------- >>> parse_filenames( ... ['c1001.ext', 'c2002.ext'], r'([^\d])(\d)(?P\d+)\.ext' ... ) (('c', 't'), (2, 2), [(0, 0), (1, 1)], ['c1001.ext', 'c2002.ext']) NrUr6zshape z does not fit provided shape )r8css|] }|fVqdS)NrE)rFrrErErHrI @sz"parse_filenames..zinvalid patternc sg}g}ddjD}|}|s8td|d}xt|D]\}}|dkr\qJ|d|krv||d}n|dr|}qJ|dkrd}y |kr||}t|}Wn2tk r}ztd||Wdd}~XYnX| || |d}qJWt ||fS)NcSsi|]\}}||qSrErE)rFrrrErErHr@sz2parse_filenames..parse..z!pattern does not match file name rUr6r9zinvalid index ) groupindexrsearchr_r}groupsisalpharrvrir) rr'rrmatchrdrrr)rNrLrErHr @s6     "  zparse_filenames..parsecSsg|]}tj|qSrE)rartnormpath)rFrrErErHrG8@sz#parse_filenames..c3s|]}|kVqdS)NrE)rFr)rMrErHrIG@szinvalid axesorder z for z.axes labels do not match within image sequencecsg|] }|qSrErE)rFr)rrErHrGO@sc3s|]}|VqdS)NrE)rFr)r'rErHrIU@s)rs)r?css|]\}}||kVqdS)NrE)rFrrrErErHrIb@sz parsed shape cSsg|] }t|qSrE)r)rFrrErErHrGh@s)rcr_rrwrrrVr\r]recompilerartrorrdrirrrZintprrrrx)rfrLrMrN_shaperzr Z normpathsrrrZlblZ parsedshapeZ startindexrE)rMrNrr'rLrHr ?sn0$             r ccs|EdHdS)z=Return iterator over pages in data array of normalized shape.NrE)ryrErErHrtm@srtc cs|j}tj||df|jd}dt|kr8dksBntdt|dkr@x|D]}x|D]}xt|dD]}xt|dD]}t|d|d||d} t|d|d||d} d|| d | d f<|d||d||d| ||d||d| f|d | d | f<|VqWqrWq`WqVWn|xx|D]n}xd|D]Z}xPt|dD]>} x4t|dD]"}xt|dD]}t|d|d| |d} t|d|d||d} t|d|d||d} d|| d | d | d f<|| |d| |d| ||d||d| ||d||d| f|d | d | d | f<|ddkr|dVn|VqWqWqlWqVWqHWd S) z=Return iterator over tiles in data array of normalized shape.r)rsrUrzinvalid tile shaperPr6rCN)rzrrrrsrcr_rwr) ryrrrzrrrtytxc1c2tzZc0rErErHrsr@sB  06 rscCsL|j|ks|jt||jkr&tdtddt||jD}t ||S)z!Return tile padded to tile shape.zinvalid tile shape or dtypecss|]\}}d||fVqdS)r6NrE)rFrrrErErHrI@szpad_tile..) rsrur+rtr_rrxrzrrr()rrzrsr(rErErHr@srcCsDtj}t||}||jkr|S||jkr@|ddddddfS||jkrh|ddddddddfS||jkr|dddddddddfS||jkrt |ddS||j krt |ddddddddfS||j kr t |ddddddddddfS||j kr@t |dddddddddddfS|S)a+Return reoriented view of image array. Parameters ---------- image : numpy.ndarray Non-squeezed output of asarray() functions. Axes -3 and -2 must be image length and width respectively. orientation : int or str One of TIFF.ORIENTATION names or values. .Nrrr) rrr"rrrrrrrswapaxesrrr)rBZ orientationZorientrErErHreorient@s&         " ( *rcCs|t|}g}g}g}xHt|j|j|D]4\}}}|||f||df|||q(Wtjjj |||dd |S)aReturn read-only view into input array with elements repeated. Zoom nD image by integer factors using nearest neighbor interpolation (box filter). Parameters ---------- a : array-like Input array. repeats : sequence of int The number of repetitions to apply along each dimension of input array. Examples -------- >>> repeat_nd([[1, 2], [3, 4]], (2, 2)) array([[1, 1, 2, 2], [1, 1, 2, 2], [3, 3, 4, 4], [3, 3, 4, 4]]) r6F)r) rrrerxstridesrzrMrilibZ stride_tricksZ as_stridedrh)r)ZrepeatsrhrzrrrrrErErHr,@s r,cCsNt|t}|r|n|j}t||kr(|Sd|t||}|rD|S||S)aReturn image array or shape with at least ndim dimensions. Prepend 1s to image shape as necessary. >>> reshape_nd(numpy.empty(0), 1).shape (0,) >>> reshape_nd(numpy.empty(1), 2).shape (1, 1) >>> reshape_nd(numpy.empty((2, 3)), 3).shape (1, 2, 3) >>> reshape_nd(numpy.empty((3, 4, 5)), 3).shape (3, 4, 5) >>> reshape_nd((2, 3), 3) (1, 2, 3) )rU)r\rrzrcrh)Z data_or_shaperZis_shaperzrErErHr.@s   r.cst|t|krtddkr$dy$tfddt||D\}}Wn,tk rt|dd}|dd}YnXt|d|fS)aReturn shape and axes with single-dimensional entries removed. Remove unused dimensions unless their axes are listed in 'skip'. >>> squeeze_axes((5, 1, 2, 1, 1), 'TZYXC') ((5, 2, 1), 'TYX') >>> squeeze_axes((1,), 'Q') ((1,), 'Q') z)dimensions of axes and shape do not matchNrc3s*|]"}|ddks|dkr|VqdS)r6rUNrE)rFr)rrErHrIAszsqueeze_axes..rr)rcr_rxrr )rzrrZshape_squeezedZ axes_squeezedrE)rrHr/As " r/csx"D]}||krtd|qW|dkr0d}|j}x(t|D]}|kr@|d|}q@W||}|fdd|D}|S)zReturn image with its axes permuted to match specified axes. A view is returned if possible. >>> transpose_axes(numpy.zeros((2, 3, 4, 5)), 'TYXC', asaxes='CTZYX').shape (5, 2, 1, 3, 4) z unknown axis NZCTZYX)rUcsg|]}|qSrE)r)rFrd)rrErHrG3Asz"transpose_axes..)r_rzr%rhZ transpose)rBrZasaxesrdrzrE)rrHr1As   r1c Csbt|}t|}t|t|kr(tdt|}t|}||krTtd|d||r\|s`dStdt|t|}|r|d|}t|d}d}d} g} x|ddd D]} || 9}x(|dkr||dkr| dkr|d8}qW| ||kr(|| ||kr(| ||9} | |||d8}q|r:| |qd }| |qWdt| |dS) zReturn axes matching new shape. By default, unknown dimensions are labelled 'Q'. >>> reshape_axes('YXS', (219, 301, 1), (219, 301)) 'YX' >>> reshape_axes('IYX', (12, 219, 301), (3, 4, 219, 1, 301, 1)) 'QQYQXQ' zaxes do not match shapezcannot reshape z to rr6)rUrUNrr9)rrcr_r+rrir r%) rrzrunknownr<rZlendiffrZprodnsZprodsr|nsrErErHr-7As<        r-rPrc Cs|j|jks|j|jkrdSd}xt|j|j|jD]\}}}|dkr|dkrxpt|D]2}||} | |krtdSt|| |dkr\|}Pq\WdSq||} | |krdSt|| |dkrdSq8||kr8dSq8W|S)z7Return level of subresolution of series or page b vs a.NZxyzg?)rrsrxrrzrwabs) r)rrr%rrdrrrGrrErErH subresolutiongAs,"rc Csd}d}x|t|kr||}d}|d}t|jjtrB|d7}q x|t|kr||}|rn|jjsn|d7}qD|dkrxX|D]"}t|jd||ddkr||}Pq|W|d7}qDn"t|jd||ddkr|d7}qD|j|||=qDW|d7}q WdS)aNPyramidize list of TiffPageSeries in-place. TiffPageSeries that are a subresolution of another TiffPageSeries are appended to the other's TiffPageSeries levels and removed from the list. Levels are to be ordered by size using the same downsampling factor. TiffPageSeries of subifds cannot be pyramid top levels. )rPrCrr6NrUr)r) rcr\rrrr>rrri) rrZsamplingfactorsrr)rrrrrErErHrAs6     rc Kst|}|dkrtd|dkr@||d<|djfd|i|Stdd|D}|f|j}|j}t|||}|dks|dkr|j}t|t j }|dks|dkrd}}n>|d krd}n0|d kr|j dkr|j dkr|j dkrd}nd}n6|dkrd}}n$||ks|jd krd}n|}d}||d<|jj} | j} | sH|dksR|dkrXd | _ttd || jd } || |fdd} |d krxZt|D]\} }| || qWn8|jt|$}x|| |t|D]}qWWdQRX| | sd| _|S)zRead data from sequence of TiffPage/Frame and stack them vertically. Additional parameters are passsed to the TiffPage.asarray function. r6zno pagesrUrrcss|]}|dk r|jVqdS)N)r)rFrrErErHrIAszstack_pages..NrCrPTr)r<rAcSsD|dk r@||jj|jf|j||d|||jjdS)N)rAr)rwrIrrerAr)rrr filecachergrErErHrAszstack_pages..funcF)rcr_rerrzrsr!rrrrTrpr8rBrIrr.rArrr}rnr9rCrwr)rOrrrgrZpage0rzrsZpage_maxworkersrZhaslockrrrrrErrErErHrAs^          rw+c Cs|dkrH|dkrt||S|r>> matlabstr2py('1') 1 >>> matlabstr2py("['x y z' true false; 1 2.0 -3e4; NaN Inf @class]") [['x y z', True, False], [1, 2.0, -30000.0], [nan, inf, '@class']] >>> d = matlabstr2py( ... "SI.hChannels.channelType = {'stripe' 'stripe'}\n" ... "SI.hChannels.channelsActive = 2" ... ) >>> d['SI.hChannels.channelType'] ['stripe', 'stripe'] csdg}xl|\}}|dkrP|dkr2|dn2|dkrF|dn|dkrZ|dn ||||d}qW|d|S)Nrr)rr)rrr)rr)rMri)rtokensrEr) next_tokenrErHlex:Bs      zmatlabstr2py..lexcSs@t|}|dkrdSd}x ||kr8||dkr8|d7}qW||krJd|fS||dkrf|||dfS||dkr|d}x ||kr||dkr|d7}q|W|||d|dfS||dkr|d}x ||kr||dkr|d7}qW|||d|dfS|}x&||kr.||d kr.|d7}q W||||fS) Nr6)Nr6rrUz{[;]}'rrz {[;]})rc)rrrrrErErHrMBs0     z matlabstr2py..next_tokenFcssStdkrBytStk r@|r.value..z ';[]{}rraTrueTr`FalseFrzzeros(cSsg|] }t|qSrE)r)rFrrErErHrGBsz/matlabstr2py..value..rrzones(cSsg|] }t|qSrE)r)rFrrErErHrGBsrrs) rrcrrvr_rdrrr"rrZonesrq)rfailrE)rrHrhBsZ       && zmatlabstr2py..valuecs|}y |ddStk r(YnXg}}|g}x|D]t}|dkr^g}||qB|dkr|}t|dkrt|dttfr|d}|d}||qB||qBWt|dkrt|dttfr|d}|S)NT)rz[{z]}rUr6r)rr_rir[rcr\rr])rr|Zadd2rrEr=)rrrErHr Bs*   zmatlabstr2py..parse rr6%rrUc3s|]}|kVqdS)NrE)rFr1)rrErHrIBszmatlabstr2py..z ';[]{}<>)F)rrrrd)rlr rrrrE)rrrrrHr&#Bs"  0r&rcCsj|r&||}|dkr|S|d|S|d}t|}x"|rT|d8}|||kr8Pq8Wd}|d|dS)a?Return string truncated at first null character. Clean NULL terminated C strings. For Unicode strings use null='\0'. >>> stripnull(b'string\x00\x00') b'string' >>> stripnull(b'string\x00string\x00\x00', first=False) b'string\x00string' >>> stripnull('string\x00', null='\0') 'string' r6NrUr)rrc)rlrrrrErErHr0Bs   r0cCsLt|}x2|r6|d8}d||kr.dkr nq Pq Wd}|d|dS)zReturn string truncated at last byte that is 7-bit ASCII. Clean NULL separated and terminated TIFF strings. >>> stripascii(b'string\x00string\n\x01\x00') b'string\x00string\n' >>> stripascii(b'\x00') b'' rUrrN)rc)rlrrErErH stripasciiBs rcCs|}d}|dkr@t|tr4|dkr.dSd}n |dkr@dS|dkrp|sVt|trd|dkrpdSn |dkrpdS||kr|dS||krdStdS)zReturn string as bool if possible, else raise TypeError. >>> asbool(b' False ') False >>> asbool('ON', ['on'], ['off']) True FNstrueTrasfalser`)rrr\rrW)rrar`rrErErHrBs(  rc CsL|dkrttttf}x2|D]*}y||Sttttfk rBYqXqW|S)zReturn argument as one of types if possible. >>> astype('42') 42 >>> astype('3.14') 3.14 >>> astype('True') True >>> astype(b'Neee-Wom') 'Neee-Wom' N)rrqrrr_rrWr)rrtyprErErHr Cs    r cCsD||kr|dSx,dD]$}|d}||kr|dd|SqWdS)zReturn file size as string from byte size. >>> format_size(1234) '1234 B' >>> format_size(12345678901) '11.50 GiB' z B)KiBMiBGiBTiBPiBg@z.2frZ ginormousrE)r< thresholdrrErErHr$(Cs   r$cOs|S)zOSingle argument identity function. >>> identityfunc('arg') 'arg' rE)rrrgrErErHr:CsrcOsdS)z>> nullfunc('arg', kwarg='kwarg') NrE)rrgrErErHr(DCsr(cCst|ttfr|S|fS)zReturn tuple containing value if value is not a tuple or list. >>> sequence(1) (1,) >>> sequence([1]) [1] >>> sequence('ab') ('ab',) )r\rr)rrErErHr]MCs r]cCsd}x|D] }||9}q W|S)zReturn product of sequence of numbers. Equivalent of functools.reduce(operator.mul, iterable, 1). Multiplying numpy integers might overflow. >>> product([2**8, 2**30]) 274877906944 >>> product([]) 1 rUrE)iterableprodrrErErHr+[Cs   r+cs"fdd}tdt||dS)zReturn human sorted list of strings. E.g. for sorting file names. >>> natural_sorted(['f1', 'f2', 'f10']) ['f1', 'f2', 'f10'] csddt|DS)NcSs g|]}|rt|n|qSrE)isdigitr)rFr1rErErHrGxCsz3natural_sorted..sortkey..)rr)r=)numbersrErHsortkeywCsznatural_sorted..sortkeyz(\d+))rG)rrrx)rrrE)rrHr'mCs  r'cCstj|d|dS)zBReturn datetime object from epicsTSSec and epicsTSNsec tag values.i%geA)r fromtimestamp)secZnsecrErErHepics_datetime~CsrcCs"|dkrtjd}|t|S)zReturn datetime object from timestamp in Excel serial format. Convert LSM time stamps. >>> excel_datetime(40237.029999999795) datetime.datetime(2010, 2, 28, 0, 43, 11, 999982) NiZ )r fromordinalr;) timestampepochrErErHexcel_datetimeCs  rc Cs|dkr dS|d}|dkrBt|dd}|d||d7}||dkrPdnd }t|d d }td |}t||d }||td |}||d krdnd} || dkrdnd} t|d\} }t|d\} }t|d\} }t| | || | | |S)zReturn datetime from days since 1/1/4713 BC and ms since midnight. Convert Julian dates according to MetaMorph. >>> julian_datetime(2451576, 54362783) datetime.datetime(2000, 2, 2, 15, 6, 2, 783) iODNrUi#g@}@g+@r0g@iliki6i`i)rutruncr r)Z juliandayZ milisecondr)rKrr1rrsrrrrrsecondrErErHrCs$ rcCs6|dks|tjkrdSddd}||||tjkS)zcReturn if byteorder matches the system's byteorder. >>> byteorder_isnative('=') True rTrr)rr)rrkrV)rkrrErErHrCs rcCsV||ks|dks|dkrdS|dkr6dddtj}n|dkrNdddtj}||kS)z}Return if byteorders match. >>> byteorder_compare('<', '<') True >>> byteorder_compare('>', '<') False rTrrr)rr)rrk)rkZ byteorder2rErErHbyteorder_compareCs rcCshi}x^t|jj|D]L\}}|dd\}}|ddkrFtt|}n|jdkrX|}|||<qW|S)zReturn numpy.recarray as dict.NrPrUr)rxrsdescrrr0rr)Zrecarrayr|rrr:rsrErErHreCs   recsJddlm}d|r |\ddfdd||S)zReturn XML as dict. >>> xml2dict('1') {'root': {'key': 1, 'attr': 'name'}} >>> xml2dict('3.5322') {'level1': {'level2': 3.5322}} r6)r@rc SsHt|ttfs|Sx0tttfD]"}y||Stk r>YqXqW|S)N)r\r]rrrqrrv)rrErErErHr Cs zxml2dict..astypec s|j}r|ddd}||jr&indi}t|}|rtt}x:t|D],}x&|D]\}}|||q\WqNW|fdd|Di}|jr|| fdd|jD|j r|j }|s|jr|r|||d<n |||<|S) NrrUrcs2i|]*\}}t|dkr$|dn||qS)rUr6)rc)rFrr)r rErHrDsz0xml2dict..etree2dict..c3s"|]\}}||fVqdS)NrE)rFrr)r atrErHrIDsz/xml2dict..etree2dict..r) rFrrLr collections defaultdictrCrrirr]r) rErGrchildrendddcrrr])r r etree2dictsanitizerrErHrCs*  $   zxml2dict..etree2dict)rJr@rK)rCr rrNrE)r rrr rrHr3Cs  r3Krrc s>t|}|dks |dks |dkr$dS|dkr`d}t||t|d||}|dkrZdSd} nbdtd|}t||t|dd||}|dkrdSd|t|d}|d|d} |d ks|dkr|}n0d t|krdkrnntt||}|d kr||7}|dks.| dkrRd |d |fg} d}d}d|}n|d ksf| |krrd |fg} n|d kr|| |} | || d fg} n~||ks|dkr||} d |d | fg} nN||} |||d}d |d | f|| |d f|||||d fg} |d kr(d n|d }g}x| D]\} }|d kr\||q>> hexdump(binascii.unhexlify('49492a00080000000e00fe0004000100')) '49 49 2a 00 08 00 00 00 0e 00 fe 00 04 00 01 00 II*.............' rUrPrrrs%%0%ix: s%xrCNr6s...cp1252s [^\x20-\x7f]. c3s|]}||dVqdS)rPNrE)rFr)rrErHrI_Dszhexdump.. r)rcrrrrurrribinasciihexlifyrsubrwr rn)bytestrrrsnipatrYellipsisr<addrZ bytesperlinenlinesr{rr6end1end2r|ZhexstrZstrstrrrGrE)rrHhexdumpDsv         (  rcCsT|}|sdSy|Stk r,YnXy |Stk rNYnXdS)zReturn if all characters in string are printable. >>> isprintable('abc') True >>> isprintable(b'\01') False TN)r isprintablervrn)rlrErErHrhDs  rcCsd|dddddddddd}|r\|dddd dddddd}|S) z)Return string with compressed whitespace.z rrz  rz z[ r)rzr)rlcompactrErErHclean_whitespace~Ds  rcCsyPddlm}t|ts |}|t|}|j|dd|j j d}t |}Wn2t k rt|trrt |}| dd}YnX| dd d dS) zReturn pretty formatted XML.r6)rNT)rirjrhz> )rrrYzrr6)rrT)rrc3s|]}|dVqdS)NrE)rFr)rrErHrIDszpformat..rPz...c3s|]}|dVqdS)NrE)rFr)rrErHrIDs)rrZget_printoptionsZset_printoptionsr\rrrrrrrr]rr'pprintr*rrrcr )rrrrZnpoptrZarglrE)rrHr*DsH $     &"        0 r*c Cs|dkr d}|dkr(t|tr$d}nd}t|}|}g}x|D]~}|dkr^||qDt|}||krz||qD|} | dks| dkr|} n.dt| krdkrnntt|| } | dkr| |7} | dkrd} |dks||dkr(| dkr||| dn||d|qD| dkrN|||||dqD| |ksf||dkr||d|||qD|||} | | d} | | } ||d| ||| dqDWt|trd |Sd |S) zcReturn string cut to specified length. >>> snipstr('abcdefghijklmnop', 8) 'abc...op' Ng?s...u…rUr6rrPrr) r\rrcrrirrrurr ) rlrrrrprr|rZlinelenrZsplitlenrrrErErHrDsR       &  rcCs|j}|dkrt|}|S)z4Return short string representation of Enum instance.N)r:r])rr:rErErHr# Esr#c CsRy||Stk rLy ||Stk rFtd|YnXYnXdS)zReturn enum member from its name or value. >>> enumarg(TIFF.PHOTOMETRIC, 2) >>> enumarg(TIFF.PHOTOMETRIC, 'RGB') zinvalid argument N)rvr_r_)rrrErErHr"(Es  r"cOsji}x&|D]}||kr ||||<||=q Wx8|D],\}}||krZ||||<||=q6|||<q6W|S)aXReturn dict with keys from keys|keyvals and values from kwargs|keyvals. Existing keys are deleted from kwargs. >>> kwargs = {'one': 1, 'two': 2, 'four': 4} >>> kwargs2 = parse_kwargs(kwargs, 'two', 'three', four=None, five=5) >>> kwargs == {'one': 1} True >>> kwargs2 == {'two': 2, 'four': 4, 'five': 5} True )r)rgr keyvaluesr|rGrrErErHr):Es      r)cKs*x$|D]\}}||kr |||<q WdS)zUpdate dict with keys and values if keys do not already exist. >>> kwargs = {'one': 1, } >>> update_kwargs(kwargs, one=None, two=2) >>> kwargs == {'one': 1, 'two': 2} True N)r)rgr rGrrErErHr2UEs r2cOs$ddl}|tj|f||dS)zLog message with level WARNING.r6N)logging getLoggerrwarning)rrrgr!rErErHrqcEsrqcCsddl}|dkrdg}|dkr"d}|||ddg}d|krxT|D]H}|}|drF|dd}x|D]}||krrPqrWt|PqFWdS) a2Validate TIFF file using jhove -m TIFF-hul. Raise ValueError if jhove outputs an error message unless the message contains one of the strings in 'ignore'. JHOVE does not support bigtiff or more than 50 IFDs. See `JHOVE TIFF-hul Module `_ r6NzMore than 50 IFDsjhovez-mzTIFF-hulsErrorMessage: r) subprocess check_outputrrrprnr_)rr$rUr%rrerrorrrErErHvalidate_jhovejEs   r(c Cs|dkr d}|dkrd}|dkr$dnd}t||dP}|j|j|d}|dkrhtdtj|d|dkrv|jS||WdQRXdS)zDReturn or replace ImageDescription value in first page of TIFF file.Nr6izr+b)rzno z tag found) rrOrrVr_rrrr)rrrr rrhrFrErErHrEsrc CsV|dkr|d}t|4}|j||||d} | j|||dWdQRXWdQRXdS)z5Write fsspec ReferenceFileSystem JSON from TIFF file.Nz.json)rGrrr)r)rrdr) rrrrGrrrrrhstorerErErHrEs  rcCs|rtnt}|dkrd}|dkr&|}n|dkr6d}|rB|d7}|ddddt}t|d}|js~|d |dd td |jd }|d }| d }|j } t || j } |||d ||| t| dd |jdstd|dddd||d|d|d|df} |rD||d|d|d |df}ddt||}tj|dd| d} tj|d|d|d |df| d} t|j}xt|d D]}xt|dD]}xt|dD]}x&t|dD]}t|| |<qWxt| d D]}xt| dD]x}| d||d |d|d ||d|d|df| dd<|r| ||||||f|ddddq WqWqWqWqW||dd WdQRXdS)zConvert [MP]TZCYX LSM file to series of BIN files. One BIN file containing 'ZCYX' data are created for each position, time, and tile. 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N)r-r-rz*_(z%ic%iy%ix%i)_m%%ip%%it%%03iy%%ix%%i.binz Opening LSM file... rT)r6rr)rznot a LSM filer6Fz5Image axes: {} shape: {} dtype: {} size: {}ZTZCYXznot a *TZCYX LSM filez#Copying image from LSM to BIN filesrrrrrU)rUrrC)rsrP.r)r7r(rrrrr_rrryrsr+rtrr$rrrrcrrrrIrOrwrrer*)ZlsmfileZbinfilerverbosetimerrrrzrrsr<rryrrOrrrErFr5r=rErErHrEsh         " (,r`c s|dkr d}| dkrd} |dk}jdkr4djjdkrDd}|rvjd d ksvjd krnjd d ksvd}d }|dkrtd n tdjd krtdd krdd}n|rjd d krt d dt dd nV|sJjd jddkrJjd jd dkrJt d d t dd |o\jd d k}|rjdnd 8|dkrd}nt |t r|}nd}|rdd| d| d| f|r0jd|ksވjd |krd}nd}nFdd| d| f|r0jd |ks&jd|kr,d}nd}|dkr|ryt }Wntk rhd}YnX|dkr|d?dnjjdkr`|rjj dkr|dkryt tt d }Wn"tk rjj d}YnXnt |t tjfsjj d}d |}|rD|dkr>d|>n|dkrT|d?dnjjdkr|rddk<yt }Wntk rd}YnX|rD|d krDjjd!krd|n|nVjjdkrd}nBjjd"krDtyt }Wntk rBd}YnX|rPd}n|dkr^|}|dkr4jjd#krtjj}yt}Wntk rd }YnX||kr4t|k}nhjjdkr0tjj}yt}Wntk rd}YnX||kr4t|k}nd}tjd$dkrֈjd%d&d'dd(j| d)d*d+d,d-yjjj | Wntk rYnX| rt!| "nd}j#d.d d/|d.d0d1d2dd3| dkrd4} $| } | %d5| r2yt&| d6} Wnt'k r"YnXj | d7d8|dkrjjd9krPd:}n"jjd;ksh|dkrnd<}nd=}|d>kr|d?7}j(t)d@f||||dA||s*fdBdC}dDdE}|| _+|_,|_-rt.d@dt/gfdFdGt0D}x|D] }d|_1q0W|ffdHdI ffdJdK ffdLdM }j2dN|x,t3|D] \}}|4|ffdOdP qW| fS)QaPlot n-dimensional images using matplotlib.pyplot. Return figure, subplot, and plot axis. Requires pyplot already imported C{from matplotlib import pyplot}. Parameters ---------- data : nd array The image data. photometric : {'MINISWHITE', 'MINISBLACK', 'RGB', or 'PALETTE'} The color space of the image data. planarconfig : {'CONTIG' or 'SEPARATE'} Defines how components of each pixel are stored. bitspersample : int Number of bits per channel in integer RGB images. interpolation : str The image interpolation method used in matplotlib.imshow. By default, 'nearest' is used for image dimensions <= 512, else 'bilinear'. cmap : str or matplotlib.colors.Colormap The colormap maps non-RGBA scalar data to colors. vmin, vmax : scalar Data range covered by the colormap. 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