Ejz&dZddlmZmZddlZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl Z ddlZddlZddlZddlZddlZddlZddlZddlZddlZddlZddlZdZdZdZdZddZdd ZGd d e Z!Gd d e Z"Gdde Z#Gdde Z$Gdde Z%Gdde Z&Gdde Z'Gdde(Z)Gdde Z*Gdde Z+Gdde Z,Gd d!e Z-Gd"d#e Z.Gd$d%e Z/e/Gd&d'e Z0dd(Z1d)Z2d*Z3d+Z4d,Z5d-Z6d.Z7d/Z8d0Z9d1Z:d2Z;dd3Zd6Z?d7Z@d8ZAd9ZBd:ZCd;ZDd<ZEd=ZFd>ZGd?ZHd@ZIdAZJdBZKdCZLdDZMdEZNdFZOdGZPdHZQdIZR ddJZSddKZTdLZUdMZVddNZWdOZXdPZYdQZZdRZ[dSZ\dTZ]e^ddUfdVZ_dWZ`e_dXdYZae_dZd[Zbe_d\dd]Zcdd^Zde_d_d`ZeddaZfdbZgdcZhddZiddeZjddfZkddgZlddhZmdiZnddjZoddkZpdlZqddmZrdnZsddoZtddpZuddqZvdrZwdsZxdtZyduZzdvZ{ej&jdwfdxZ}ddyZ~dzZd{Zdd|Zdd~ZdZddZdZddZddZdZdZdZddZddZ ddZdZdZddZej"dd}k(r eefZdZddZddZdZGddeZe%Z&neZeefZeZeZddZddZdZedk(rejBeyy)a8Read image and meta data from (bio) TIFF(R) files. Save numpy arrays as TIFF. Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, SGI, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, and GeoTIFF files. Tifffile is not a general-purpose TIFF library. Only a subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 1, 8, 16, 32 and 64 bit integer, 16, 32 and 64-bit float, grayscale and RGB(A) images, which are commonly used in scientific imaging. Specifically, reading slices of image data, image trees defined via SubIFDs, CCITT and OJPEG compression, chroma subsampling without JPEG compression, or IPTC and XMP metadata are not implemented. TIFF(R), the tagged Image File Format, is a trademark and under control of Adobe Systems Incorporated. BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, SGI, SEQ, GEL, and OME-TIFF, are custom extensions defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics, Molecular Dynamics, and the Open Microscopy Environment consortium respectively. For command line usage run C{python -m tifffile --help} :Author: `Christoph Gohlke `_ :Organization: Laboratory for Fluorescence Dynamics, University of California, Irvine :Version: 2018.06.15 Requirements ------------ * `CPython 3.6 64-bit `_ * `Numpy 1.14 `_ * `Matplotlib 2.2 `_ (optional for plotting) * `Tifffile.c 2018.02.10 `_ (recommended for faster decoding of PackBits and LZW encoded strings) * `Tifffile_geodb.py 2018.02.10 `_ (optional enums for GeoTIFF metadata) * Python 2 requires 'futures', 'enum34', 'pathlib'. Revisions --------- 2018.06.15 Pass 2680 tests. Towards reading JPEG and other compressions via imagecodecs package (WIP). Add function to validate TIFF using 'jhove -m TIFF-hul'. Save bool arrays as bilevel TIFF. Accept pathlib.Path as filenames. Move 'software' argument from TiffWriter __init__ to save. Raise DOS limit to 16 TB. Lazy load lzma and zstd compressors and decompressors. Add option to save IJMetadata tags. Return correct number of pages for truncated series (bug fix). Move EXIF tags to TIFF.TAG as per TIFF/EP standard. 2018.02.18 Pass 2293 tests. Always save RowsPerStrip and Resolution tags as required by TIFF standard. Do not use badly typed ImageDescription. Coherce bad ASCII string tags to bytes. Tuning of __str__ functions. Fix reading 'undefined' tag values (bug fix). Read and write ZSTD compressed data. Use hexdump to print byte strings. Determine TIFF byte order from data dtype in imsave. Add option to specify RowsPerStrip for compressed strips. Allow memory map of arrays with non-native byte order. Attempt to handle ScanImage <= 5.1 files. Restore TiffPageSeries.pages sequence interface. Use numpy.frombuffer instead of fromstring to read from binary data. Parse GeoTIFF metadata. Add option to apply horizontal differencing before compression. Towards reading PerkinElmer QPTIFF (no test files). Do not index out of bounds data in tifffile.c unpackbits and decodelzw. 2017.09.29 (tentative) Many backwards incompatible changes improving speed and resource usage: Pass 2268 tests. Add detail argument to __str__ function. Remove info functions. Fix potential issue correcting offsets of large LSM files with positions. Remove TiffFile sequence interface; use TiffFile.pages instead. Do not make tag values available as TiffPage attributes. Use str (not bytes) type for tag and metadata strings (WIP). Use documented standard tag and value names (WIP). Use enums for some documented TIFF tag values. Remove 'memmap' and 'tmpfile' options; use out='memmap' instead. Add option to specify output in asarray functions. Add option to concurrently decode image strips or tiles using threads. Add TiffPage.asrgb function (WIP). Do not apply colormap in asarray. Remove 'colormapped', 'rgbonly', and 'scale_mdgel' options from asarray. Consolidate metadata in TiffFile _metadata functions. Remove non-tag metadata properties from TiffPage. Add function to convert LSM to tiled BIN files. Align image data in file. Make TiffPage.dtype a numpy.dtype. Add 'ndim' and 'size' properties to TiffPage and TiffPageSeries. Allow imsave to write non-BigTIFF files up to ~4 GB. Only read one page for shaped series if possible. Add memmap function to create memory-mapped array stored in TIFF file. Add option to save empty arrays to TIFF files. Add option to save truncated TIFF files. Allow single tile images to be saved contiguously. Add optional movie mode for files with uniform pages. Lazy load pages. Use lightweight TiffFrame for IFDs sharing properties with key TiffPage. Move module constants to 'TIFF' namespace (speed up module import). Remove 'fastij' option from TiffFile. Remove 'pages' parameter from TiffFile. Remove TIFFfile alias. Deprecate Python 2. Require enum34 and futures packages on Python 2.7. Remove Record class and return all metadata as dict instead. Add functions to parse STK, MetaSeries, ScanImage, SVS, Pilatus metadata. Read tags from EXIF and GPS IFDs. Use pformat for tag and metadata values. Fix reading some UIC tags (bug fix). Do not modify input array in imshow (bug fix). Fix Python implementation of unpack_ints. 2017.05.23 Pass 1961 tests. Write correct number of SampleFormat values (bug fix). Use Adobe deflate code to write ZIP compressed files. Add option to pass tag values as packed binary data for writing. Defer tag validation to attribute access. Use property instead of lazyattr decorator for simple expressions. 2017.03.17 Write IFDs and tag values on word boundaries. Read ScanImage metadata. Remove is_rgb and is_indexed attributes from TiffFile. Create files used by doctests. 2017.01.12 Read Zeiss SEM metadata. Read OME-TIFF with invalid references to external files. Rewrite C LZW decoder (5x faster). Read corrupted LSM files missing EOI code in LZW stream. 2017.01.01 Add option to append images to existing TIFF files. Read files without pages. Read S-FEG and Helios NanoLab tags created by FEI software. Allow saving Color Filter Array (CFA) images. Add info functions returning more information about TiffFile and TiffPage. Add option to read specific pages only. Remove maxpages argument (backwards incompatible). Remove test_tifffile function. 2016.10.28 Pass 1944 tests. Improve detection of ImageJ hyperstacks. Read TVIPS metadata created by EM-MENU (by Marco Oster). Add option to disable using OME-XML metadata. Allow non-integer range attributes in modulo tags (by Stuart Berg). 2016.06.21 Do not always memmap contiguous data in page series. 2016.05.13 Add option to specify resolution unit. Write grayscale images with extra samples when planarconfig is specified. Do not write RGB color images with 2 samples. Reorder TiffWriter.save keyword arguments (backwards incompatible). 2016.04.18 Pass 1932 tests. TiffWriter, imread, and imsave accept open binary file streams. 2016.04.13 Correctly handle reversed fill order in 2 and 4 bps images (bug fix). Implement reverse_bitorder in C. 2016.03.18 Fix saving additional ImageJ metadata. 2016.02.22 Pass 1920 tests. Write 8 bytes double tag values using offset if necessary (bug fix). Add option to disable writing second image description tag. Detect tags with incorrect counts. Disable color mapping for LSM. 2015.11.13 Read LSM 6 mosaics. Add option to specify directory of memory-mapped files. Add command line options to specify vmin and vmax values for colormapping. 2015.10.06 New helper function to apply colormaps. Renamed is_palette attributes to is_indexed (backwards incompatible). Color-mapped samples are now contiguous (backwards incompatible). Do not color-map ImageJ hyperstacks (backwards incompatible). Towards reading Leica SCN. 2015.09.25 Read images with reversed bit order (FillOrder is LSB2MSB). 2015.09.21 Read RGB OME-TIFF. Warn about malformed OME-XML. 2015.09.16 Detect some corrupted ImageJ metadata. Better axes labels for 'shaped' files. Do not create TiffTag for default values. Chroma subsampling is not supported. Memory-map data in TiffPageSeries if possible (optional). 2015.08.17 Pass 1906 tests. Write ImageJ hyperstacks (optional). Read and write LZMA compressed data. Specify datetime when saving (optional). Save tiled and color-mapped images (optional). Ignore void bytecounts and offsets if possible. Ignore bogus image_depth tag created by ISS Vista software. Decode floating point horizontal differencing (not tiled). Save image data contiguously if possible. Only read first IFD from ImageJ files if possible. Read ImageJ 'raw' format (files larger than 4 GB). TiffPageSeries class for pages with compatible shape and data type. Try to read incomplete tiles. Open file dialog if no filename is passed on command line. Ignore errors when decoding OME-XML. Rename decoder functions (backwards incompatible). 2014.08.24 TiffWriter class for incremental writing images. Simplify examples. 2014.08.19 Add memmap function to FileHandle. Add function to determine if image data in TiffPage is memory-mappable. Do not close files if multifile_close parameter is False. 2014.08.10 Pass 1730 tests. Return all extrasamples by default (backwards incompatible). Read data from series of pages into memory-mapped array (optional). Squeeze OME dimensions (backwards incompatible). Workaround missing EOI code in strips. Support image and tile depth tags (SGI extension). Better handling of STK/UIC tags (backwards incompatible). Disable color mapping for STK. Julian to datetime converter. TIFF ASCII type may be NULL separated. Unwrap strip offsets for LSM files greater than 4 GB. Correct strip byte counts in compressed LSM files. Skip missing files in OME series. Read embedded TIFF files. 2014.02.05 Save rational numbers as type 5 (bug fix). 2013.12.20 Keep other files in OME multi-file series closed. FileHandle class to abstract binary file handle. Disable color mapping for bad OME-TIFF produced by bio-formats. Read bad OME-XML produced by ImageJ when cropping. 2013.11.03 Allow zlib compress data in imsave function (optional). Memory-map contiguous image data (optional). 2013.10.28 Read MicroManager metadata and little-endian ImageJ tag. Save extra tags in imsave function. Save tags in ascending order by code (bug fix). 2012.10.18 Accept file like objects (read from OIB files). 2012.08.21 Rename TIFFfile to TiffFile and TIFFpage to TiffPage. TiffSequence class for reading sequence of TIFF files. Read UltraQuant tags. Allow float numbers as resolution in imsave function. 2012.08.03 Read MD GEL tags and NIH Image header. 2012.07.25 Read ImageJ tags. ... Notes ----- The API is not stable yet and might change between revisions. Tested on little-endian platforms only. Other Python packages and modules for reading (bio) scientific TIFF files: * `python-bioformats `_ * `Imread `_ * `PyLibTiff `_ * `ITK `_ * `PyLSM `_ * `PyMca.TiffIO.py `_ (same as fabio.TiffIO) * `BioImageXD.Readers `_ * `Cellcognition.io `_ * `pymimage `_ * `pytiff `_ Acknowledgements ---------------- * Egor Zindy, University of Manchester, for lsm_scan_info specifics. * Wim Lewis for a bug fix and some LSM functions. * Hadrien Mary for help on reading MicroManager files. * Christian Kliche for help writing tiled and color-mapped files. References ---------- 1) TIFF 6.0 Specification and Supplements. Adobe Systems Incorporated. http://partners.adobe.com/public/developer/tiff/ 2) TIFF File Format FAQ. http://www.awaresystems.be/imaging/tiff/faq.html 3) MetaMorph Stack (STK) Image File Format. http://support.meta.moleculardevices.com/docs/t10243.pdf 4) Image File Format Description LSM 5/7 Release 6.0 (ZEN 2010). Carl Zeiss MicroImaging GmbH. BioSciences. May 10, 2011 5) The OME-TIFF format. http://www.openmicroscopy.org/site/support/file-formats/ome-tiff 6) UltraQuant(r) Version 6.0 for Windows Start-Up Guide. http://www.ultralum.com/images%20ultralum/pdf/UQStart%20Up%20Guide.pdf 7) Micro-Manager File Formats. http://www.micro-manager.org/wiki/Micro-Manager_File_Formats 8) Tags for TIFF and Related Specifications. Digital Preservation. http://www.digitalpreservation.gov/formats/content/tiff_tags.shtml 9) ScanImage BigTiff Specification - ScanImage 2016. http://scanimage.vidriotechnologies.com/display/SI2016/ ScanImage+BigTiff+Specification 10) 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 Examples -------- >>> # write numpy array to TIFF file >>> data = numpy.random.rand(4, 301, 219) >>> imsave('temp.tif', data, photometric='minisblack') >>> # read numpy array from TIFF file >>> image = imread('temp.tif') >>> numpy.testing.assert_array_equal(image, data) >>> # iterate over pages and tags in TIFF file >>> with TiffFile('temp.tif') as tif: ... images = tif.asarray() ... for page in tif.pages: ... for tag in page.tags.values(): ... _ = tag.name, tag.value ... image = page.asarray() )divisionprint_functionNz 2018.06.15zrestructuredtext en)imsaveimreadimshowmemmapTiffFile TiffWriter TiffSequence FileHandlelazyattrnatural_sorted decode_lzw stripnull create_output repeat_nd format_sizeproductxml2dictc t|dd}t|d}ttr)tfddDrt js t dt dstdk(rd tts t dr(tfi|5}|jd i|cd d d Stfi|5}|jd i|cd d d S#1swYy xYw#1swYy xYw) aReturn image data from TIFF file(s) as numpy array. Refer to the TiffFile class and member functions for documentation. Parameters ---------- files : str, binary stream, or sequence File name, seekable binary stream, glob pattern, or sequence of file names. kwargs : dict Parameters 'multifile' and 'is_ome' are passed to the TiffFile class. The 'pattern' parameter is passed to the TiffSequence class. Other parameters are passed to the asarray functions. The first image series is returned if no arguments are provided. Examples -------- >>> # get image from first page >>> imsave('temp.tif', numpy.random.rand(3, 4, 301, 219)) >>> im = imread('temp.tif', key=0) >>> im.shape (4, 301, 219) >>> # get images from sequence of files >>> ims = imread(['temp.tif', 'temp.tif']) >>> ims.shape (2, 3, 4, 301, 219) multifileis_omepatternc3&K|]}|v ywN).0ifiless W/root/workspace/ytshorts/venv/lib/python3.12/site-packages/imageio/plugins/_tifffile.py zimread..s,FAQ%Z,F?*no files foundseekrNr) parse_kwargs isinstance basestringanyglob ValueErrorhasattrlenr asarrayr )rkwargs kwargs_file kwargs_seqtifimseqs` r rrs<v{H=Kfi0J%$,F,F)F %  )** 5& !c%jAoa%$v(> e +{ + )s3;;(( ) )% .: . +% 5==*6* + + ) ) + +s(C,C8,C58Dc t|dddd}|Kt|tj|jz}tj|j }n# |j }|jj }||kDr-d|vr)|jdds|jddsd |d<d|vr||d<t|fi|5} | j|||fi|cdddS#t$rd}d}YuwxYw#1swYyxYw) a Write numpy array to TIFF file. Refer to the TiffWriter class and member functions for documentation. Parameters ---------- file : str 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, height, 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, data-type of an empty array to save to the file. bigsize : int Create a BigTIFF file if the size of data in bytes is larger than this threshold and 'imagej' or 'truncate' are not enabled. By default, the threshold is 4 GB minus 32 MB reserved for metadata. Use the 'bigtiff' parameter to explicitly specify the type of file created. kwargs : dict Parameters 'append', 'byteorder', 'bigtiff', and 'imagej', are passed to TiffWriter(). Other parameters are passed to TiffWriter.save(). Returns ------- If the image data are written contiguously, return offset and bytecount of image data in the file. Examples -------- >>> # save a RGB image >>> data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8') >>> imsave('temp.tif', data, photometric='rgb') >>> # save a random array and metadata, using compression >>> data = numpy.random.rand(2, 5, 3, 301, 219) >>> imsave('temp.tif', data, compress=6, metadata={'axes': 'TZCYX'}) appendbigtiff byteorderimagejNrFtruncateT) r'rnumpydtypeitemsizer8nbytes Exceptiongetr save) filedatashaper<bigsizer0tifargssizer8r3s r rrs \68Y XNG |u~ E 2 ; ;;KK&00  ;;D ,,I w W $Xu-Z1O! '!(  D $G $6sxxeU5f566 DI 66s"C&C9& C65C69Dc l|E|C|jd||dtjt|fi|}| t d|d}nt |fi|5} |N| j |}|js t d|j\}} |j}|j}nJ| j|}|j t d|j}|j}|j}| j|jz}dddtj ||||dS#1swY#xYw)aTReturn memory-mapped numpy array stored in TIFF file. Memory-mapping requires data stored in native byte order, without tiling, compression, predictors, etc. If 'shape' and 'dtype' are provided, existing files will be overwritten or appended to depending on the 'append' parameter. Otherwise the image data of a specified page or series in an existing file will be memory-mapped. By default, the image data of the first page series is memory-mapped. Call flush() to write any changes in the array to the file. Raise ValueError if the image data in the file is not memory-mappable. Parameters ---------- filename : str Name of the TIFF file which stores the array. shape : tuple Shape of the empty array. dtype : numpy.dtype Data-type of the empty array. page : int Index of the page which image data to memory-map. series : int Index of the page series which image data to memory-map. mode : {'r+', 'r', 'c'}, optional The file open mode. Default is to open existing file for reading and writing ('r+'). kwargs : dict Additional parameters passed to imsave() or TiffFile(). Examples -------- >>> # create an empty TIFF file and write to memory-mapped image >>> im = memmap('temp.tif', shape=(256, 256), dtype='float32') >>> im[255, 255] = 1.0 >>> im.flush() >>> im.shape, im.dtype ((256, 256), dtype('float32')) >>> del im >>> # memory-map image data in a TIFF file >>> im = memmap('temp.tif', page=0) >>> im[255, 255] 1.0 NT)rCrDr< returnoffsetalignz"image data are not memory-mappablerC)updateTIFFALLOCATIONGRANULARITYrr,r pagesis_memmappable is_contiguousrDr<seriesoffsetr8charr;r) filenamerDr<pagerRmoder0resultrSr3_s r rrs<^ U. ,,  +F+ >AB Bh )& ) /Syy**$%IJJ ..   F+==($%IJJ  MMEJJ.E / <<%vuc BB! / /s B4D**D3c,eZdZdZdZdZfdZxZS)r z2Attribute whose value is computed on first access.funcc||_yrr[)selfr\s r __init__zlazyattr.__init__ms  c||S |j|}|tur*t t |||jj St||jj ||S#t$r}t|d}~wwxYwr)r\AttributeError RuntimeErrorNotImplementedgetattrsuper__name__setattr)r^instanceownervaluee __class__s r __get__zlazyattr.__get__ss  K "IIh'E N "514993E3EF F$)),,e4  "q/ ! "sA-- B6 BB)rg __module__ __qualname____doc__ __slots__r_rn __classcell__)rms@r r r gs<I  r`r cneZdZdZddZddddddddddddddddddidd fd Zd Zd Zd ZdZ dZ dZ y)r aWrite numpy arrays to TIFF file. TiffWriter instances must be closed using the 'close' method, which is automatically called when using the 'with' context manager. TiffWriter's main purpose is saving nD numpy array's as TIFF, not to create any possible TIFF format. Specifically, JPEG compression, SubIFDs, ExifIFD, or GPSIFD tags are not supported. Examples -------- >>> # successively append images to BigTIFF file >>> data = numpy.random.rand(2, 5, 3, 301, 219) >>> with TiffWriter('temp.tif', bigtiff=True) as tif: ... for i in range(data.shape[0]): ... tif.save(data[i], compress=6, photometric='minisblack') FNc |r t|dd5}|j} t|5 |dk7rt fddDr t d j } j } jj|_ ddd|j| ddd|d vrtj d k(rd nd}n|dvrt d|z|r|rt!j"d||_t'||_d |_d|_d|_d|_d|_d|_d|_d|_d|_d|_d|_d|_ d|_!|r+d|_"d|_#d|_$d|_%d|_&d|_'n*d |_"d|_#d|_$d|_%d|_&d|_'|r0t|dd|_(|jPjddyt|dd|_(|jPjSdd d||r5|jPjStUjV|d!zd"ddn2|jPjStUjV|dzd#|jPj|_ |jPjStUjV||jLzdy#1swY_xYw#t$r}t d t|zd}~wwxYw#|j|wxYw#1swYxYw#ttf$rd }YwxYw)$aOpen a 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 : str, binary stream, or FileHandle File name or writable binary stream, such as an open file or BytesIO. bigtiff : bool If True, the BigTIFF format is used. byteorder : {'<', '>', '=', '|'} The endianness of the data in the file. By default, this is the system's native byte order. append : bool If True and 'file' is an existing standard TIFF file, image data and tags are appended to the file. Appending data may corrupt specifically formatted TIFF files such as LSM, STK, ImageJ, NIH, or FluoView. imagej : bool If True, 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 does not support BigTIFF format or LZMA compression. The ImageJ file format is undocumented. rbr)rWrGforcec3<K|]}td|zywis_N)re)rar3s r r!z&TiffWriter.__init__..s$ 9$%!(UQY 7 9s)lsmstkr9nihfluoview micromanagerzfile contains metadataNzcannot append to file: %sF)N=|little<>rrzinvalid byteorder %sz#writing incompatible BigTIFF ImageJTQ8s HI4szr+bwbIIMMHHH+*),r tellr r*r,r8 is_bigtiffrOnext_page_offset _ifdoffsetr?strr%IOErrorFileNotFoundErrorsyswarningswarn _byteorderbool_imagej _truncate _metadata _colormap_descriptionoffset_descriptionlen_descriptionlenoffset_tags_shape _datashape _datadtype _dataoffset_databytecounts _tagoffsets_bigtiff _offsetsize_tagsize _tagnoformat _offsetformat _valueformat_fhwritestructpack) r^rBr7r8r6r9fhposrlr3s @r r_zTiffWriter.__init__sB  4a8%B'')C%%b\IS%0S 9*" 9 6'11I&J J(+ I&)nnG.1ii.H.HDOI& -%4 ( ("}}8cI j (3i?@ @ g MM? @#F| "# %&"  #  DM D DM #D !$D  $D !DM D DM #D !$D  $D  !$U;DH HHMM!Q !$T:DH HHNNU3I> ?v{{9u+X|j@} tBjDjF}!tBjDjH}"tBjDjJ}#tBjDjL}$tBjNjP}%tBjNjR}&|tUtBjD|}|rtUtBjN|}| sd } d}'d } ntW| tXtZfr| \} }(n:tW| t\r(d t]| }(} d|(cxkrdksntd| zd}(| j_} tUtBj`| }'|j0r| dvr td|rtcjddd}d })|dvrtd|z|r||"k(nd}*|dvrd }*tg||*}+|+ddvr|"}|dvrtd|z||!}d}||&k(r td|*r|%nd}| rg(tBjh|'\V}(n!tBjh|'\V},t]|(}(| r$|jjdvrtd|z|(fVfd } n|(fVfd } |\|dvr tdtj|Tdz }|jd!d"|jd zzfk7r td#||_|r^tYd$|dd!D}tm|d!k(})tm|d"ks"|dd%zs|d d%zstod&|Drtd'd(}d })tq|||"k(rd!nd"}|}tm|}-d}.d}/|)r|-d!krd })||$}d}||!}|rtBjDjr}nv||%k(r|-d"kDrl|ddvre|"}nb||&k(r |)r|-d!kDr |d)dvr|"}nL|-d"kDrG|d*dvr@|"}n=|-d"kDr |ddvr|"}n.|j0r|!}n|)r|-d!kDr |d)dvr|"}n|-d"kDr |d*dvr|"}|rtm||)rd!nd"krd}|!}||"k(rtm|d!kr td+tm|d,krd })|,|ddvr|%}n"||)rd)nd*dvr|&}n|d||)rd)nd*kDr|&}n|%}||%k(rd-||)rd)nd*dz}|d}.nd.||)rd)nd*dzd/z}|d}.|.d!kDr|.d!z }/n||#k(r>tm|d"k7r td0d })d}d-|d dzd/z}d1d2|Dvrtd3|rCtm||)rd!nd"kDr1||%k(rd-||)rd)nd*dz}|d}.nd.||)rd)nd*dzd/z}|d}.|.dz }/nSd}tm|d"kDr$|ddk(r|dd}tm|d"kDr |ddk(rtm|d!krd })d-||)rd*nd dzd/z}tm|d4vsJtm|d5k(r|dd"d/z|d"dz}|ddk(r#t|t|ddz}0|0f|ddz}|}||ju|}|r |)s d|d |df}||$k(r"|.dk7s|/s|ddk7s|ddk7r td6||"k(r|.d"k(r td7|r| r td8|r td9|d:vrtd;tw|zt[|}|d d zr|d d zdz|d <n |d d z|d <tY|}|t|k(sJ|.tjx|d <}|d |jd k(sJtzj|dd=k(rt~nd>UgZ|rd?nd@}1tBj|1dAz}2tBj|1dBz}3|3|_ATfdCYduUWXYZ[fdD }4dvdE}5|r |4dFdGd|dHI|sin|j|_C|j0r*t||ddv|j&dufi|j}nH|s|ik(r?|jr|jjdHJt|fi|j}nd}|r.t|dK}|dLz }tm||_H|4dFdGd|dHI|r |4dMdGd|dHI||j}|4dNdGd|jdOdHI|4dPdd|'| r |4dQddd"|4dRdSd|d |4dTdSd|d*|r@|4dUdSd|d|4dVdSd|d |ddkDr|4dWdSd|d)|4dXdSd|d|4dYdSdd|s#dd"d!dZd[|jj}6|4d\d|.|6f|.z|4d]dd|j||4d^d|j||4d_dd|.|rnQ|r7|.dkDr2|4d`dd|j|4dad|.|jd zf|.zn|4dadd|jd z|/r$||"k(r|/dk(r |4dbdddn|4dbd|/dc|/z|w|4ddded|5|d|4dfded|5|dtm|d"kDr$|d"}7|7dntUtBj|7}7n|j0rd}7nd"}7|4dgdd|7n-|j0s!|4dddeddh|4dfdeddh|4dgddd|rt|TD]}8|4|8 | }|r|d"|dzdz |dz|d!|dzdz |dz|d,|d"zdz |d"zf}9t|9|dz}:t||dz|jzg|:z};|4|2W|:|;|4|3W|:dg|:z|xrt|9dk(}|s tj||dfz| }|>|dz}>dg|>z};|4|2W|>dg|>z|4|3W|>dg|>z| |s tdk|D]}8|4|8 tZdlmZ|js-|j0s!|j3|zdnkDr tdot|rdn|dD]k}?|j3}@|@d"zr|jdp@dz }@|j|j|jYW@|j|@|jY|tmZ|j3}A|jdqjdrZD|j3|_T|jYWdtZD]\}B}C|Cd"s |j3}@|@d"zr|jdp@dz }@|jAB| zzXzd,z|jYW@|j|@Cd|3k(r@}Dn>Cd|2k(r@}En3Cddsk(r+Cd"jdtr@|_AB| zzd,z|_|jCd"|j3}F| |F| zz }G|j|Gd|F|Gz }F|r(||j5|n|j7|n|r]||j5:|;dznd}H||?D]6}It9dD]!}Jt|9dD] }Kt|9d"D]}Lt|d|d"J|dzz }Mt|d|d!K|dzz }Nt|d"|d,|L|d"zz }Od<|Md|Nd|Odf<I|J|dz|J|dz|Mz|K|dz|K|dz|Nz|L|d"z|L|d"z|Ozf|d}H||?D]P}It|>D]@}PId|P| z|Pdz| zf}Q| |Q}Q|j|Qtm|Q|;H<|Hdz }HBR|j3}@tZD]\}B}C|Cd|3k(rsCd"r8|jDF}R|;D]}S|jYWR|R|Sz }R!K|jAB| zzXzd,z|jYWFCd|2k(s| rnCd"r1|jE|;D]}S|jYW|Sn8|jAB| zzXzd,z|jYW|;dn|j@|j|?dk(sVZDCcgc] }C|Cdr C c}CZn||_Zd/|z|_||_F|_[|;|_\|rZ|_|r Ft|;fSyycc}Cw)waWrite numpy array and tags to TIFF file. The data shape's last dimensions are assumed to be image depth, height (length), 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, an empty array is saved. This option cannot be used with compression or multiple tiles. 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 SGI mode) are flattened and saved as separate pages. The SampleFormat and BitsPerSample tags are derived from the data type. Parameters ---------- data : numpy.ndarray or None Input image array. shape : tuple or None Shape of the empty array to save. Used only if 'data' is None. dtype : numpy.dtype or None Data-type of the empty array to save. Used only if 'data' is None. returnoffset : bool If True and the image data in the file is memory-mappable, return the offset and number of bytes of the image data in the file. photometric : {'MINISBLACK', 'MINISWHITE', 'RGB', 'PALETTE', 'CFA'} The color space of the image data. By default, this setting is inferred from the data shape and the value of colormap. For CFA images, DNG tags must be specified in 'extratags'. planarconfig : {'CONTIG', 'SEPARATE'} Specifies if samples are stored contiguous 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 last dimension contains samples. 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 the tile depth is provided, the SGI ImageDepth and TileDepth tags are used to save volume data. Unless a single tile is used, tiles cannot be used to write contiguous files. Few software can read the SGI format, e.g. MeVisLab. contiguous : bool If True (default) and the data and parameters are compatible with previous ones, if any, the image data are stored contiguously after the previous one. Parameters 'photometric' and 'planarconfig' are ignored. Parameters 'description', datetime', and 'extratags' are written to the first page of a contiguous series only. 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. truncate : bool If True, only write the first page including shape metadata if possible (uncompressed, contiguous, not tiled). Other TIFF readers will only be able to read part of the data. compress : int or 'LZMA', 'ZSTD' Values from 0 to 9 controlling the level of zlib compression. If 0 (default), data are written uncompressed. Compression cannot be used to write contiguous files. If 'LZMA' or 'ZSTD', LZMA or ZSTD compression is used, which is not available on all platforms. rowsperstrip : int The number of rows per strip used for compression. Uncompressed data are written in one strip per plane. predictor : bool If True, apply horizontal differencing to integer type images before compression. 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 The subject of the image. Must be 7-bit ASCII. Cannot be used with the ImageJ format. Saved with the first page only. datetime : datetime Date and time of image creation in '%Y:%m:%d %H:%M:%S' format. If None (default), the current date and time is used. Saved with the first page 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'. software : str Name of the software used to create the file. Must be 7-bit ASCII. Saved with the first page only. metadata : dict Additional meta data to be saved along with shape information in JSON or ImageJ formats in an ImageDescription tag. If None, do not write a second ImageDescription tag. Strings must be 7-bit ASCII. Saved with the first page only. ijmetadata : dict Additional meta data to be saved in application specific IJMetadata and IJMetadataByteCounts tags. Refer to the imagej_metadata_tags function for valid keys and values. Saved with the first page only. extratags : sequence of tuples Additional tags as [(code, dtype, count, value, writeonce)]. code : int The TIFF tag Id. dtype : str Data type of items in 'value' in Python struct format. One of B, s, H, I, 2I, b, h, i, 2i, f, d, Q, or q. count : int Number of data values. Not used for string or byte string values. value : sequence 'Count' values compatible with 'dtype'. Byte strings must contain count values of dtype packed as binary data. writeonce : bool If True, the tag is written to the first page only. Nz!cannot save compressed empty filerKrzcannot save empty array?r&rFz+ImageJ does not support non-contiguous data ADOBE_DEFLATE zinvalid compression level %s)LZMAZSTDz-ImageJ cannot handle LZMA or ZSTD compressionz¬ writing description to ImageJ fileBHhfz$ImageJ does not support data type %sBrz,ImageJ does not support data type %s for RGBz%ImageJ does not support planar imagesiuz!prediction not implemented for %sc tj|d}tj|d|ddddfd}||S)Nraxisr.)r;diffinsert)rClevelr compressors r compressz!TiffWriter.save..compress#s> ::d4D <<ac1airJD%dE22r`c||Srr)rCrrs r rz!TiffWriter.save..compress+s%dE22r`BHz#invalid data dtype for palette moderr<rrzinvalid color map shapec32K|]}t|ywrintrrs r r!z"TiffWriter.save..9s2AQ2rc3&K|] }|dk ywr&Nrrs r r!z"TiffWriter.save..?s+q1u+zinvalid tile shaperznot a RGB(A) imager)rr&rr&zinvalid CFA imagec3&K|] }|d ywrNr)rets r r!z"TiffWriter.save..s7rRU7rz#must specify DNG tags for CFA image)rz#invalid data shape for palette modez#not a RGB image (samplesperpixel=2)z$cannot save compressed bilevel imagezcannot save tiled bilevel imagerr&zcannot save bilevel image as %sr2c>t|tr t|dS|S)Nascii)r(rbytesxs r z!TiffWriter.save..sAs1CE!W-r`TileStrip ByteCountsOffsetsc6tj|zg|Srrrfmtvalr8s r rzTiffWriter.save..pack;;y355 5r`c xttjj||} tj|}|}|dk(r: |dz}t|x}}|jd}|dkr|}n|dz }|f}nLt|tr.addtagst~~))$56D =++E2H|.#&u:- ::g.a<$HMHE5)/u:&$%ABBE f,5zA~U3BZ(b T42Dx4PQHHu%-;eU+OODe$<=aZ!%%u}})EF %aOODd5%6H$IJOODd3u:;M6VPU6V$WX\1 56eU+$Hu}}5 ::... ;;++u444$~~/Ht}5#CJ$6??H#E51H KKsxx18YG Ha = !3e!;<< =s J!!J9cddlm} |j|}|j |}|j |j fS#t$r||d|d}YCwxYw)z> "Return nominator and denominator from float or two integers.rFractionr&) fractionsr from_float TypeErrorlimit_denominator numerator denominator)argmax_denominatorrfs r rationalz!TiffWriter.save..rationalsd * -'',##O4A;; - - -SVSV, -sAAAImageDescriptionrT)r ) truncatedrs@SoftwareDateTimez%Y:%m:%d %H:%M:%S Compression Predictor ImageWidthr ImageLength TileWidth TileLength ImageDepth TileDepthNewSubfileTyper)urr!c SampleFormatPhotometricInterpretationColorMapSamplesPerPixelPlanarConfiguration BitsPerSample ExtraSamplesr XResolution2I YResolutionResolutionUnitr&r& RowsPerStripiz&cannot write non-contiguous empty filec |dSNrrrs r rz!TiffWriter.save..s !A$r`keyz%data too large for standard TIFF filerr`c3&K|] }|d ywrrrts r r!z"TiffWriter.save..s1qad1rsF)i@B)^rrr,r;r< newbyteorderrTr/rGrDisnativerr=rrrrr array_equalr_write_remaining_pages_write_image_descriptionrrrr write_empty write_arrayrrrrrrM PHOTOMETRIC MINISBLACKRGBCFAPALETTE PLANARCONFIGCONTIGSEPARATEenumargr(rrrupper COMPRESSIONrr imagej_shape COMPESSORSkindr.r* reshape_nd MINISWHITEreshaperpackbitsrversionrrrcopyrimagej_descriptionrLjson_description str2bytesr_nowstrftimerkRESUNITimagej_metadata_tagsemptysortedrrangerr%rr enumerateendswithminflushrrrsum)\r^rCrDr<rI photometric planarconfigtile contiguousrJr:r rowsperstrip predictorcolormap descriptiondatetime resolutionsoftwaremetadata ijmetadata extratagsr datashape datadtype datadtypecharbilevelindexdatasizerS input_shape tagnoformattagsizerRrSrTrUrWrX compresstag compresslevelvolumeijrgbijshaperYndimsamplesperpixel extrasampless0 strip_or_tile tagbytecounts tag_offsetsrr" sampleformatunitrGtilesnumtilesstripbytecountschunkrowsize numstrips pageindexr tag_offsettagindextagstripoffsetsoffsetstrip_bytecounts_offset data_offsetskip stripindexplanetztytxc0c1c2rstrip strip_offsetrGr8rrrrrrrs\ @@@@@@@@r rAzTiffWriter.saves`XXOO < !DEEI E*77 BI%NNM==y4::??'BCHDyyA~ !:;; I I JJOOM#: (:(: 3& #B-!+BEy%01H!#Ie,1A55Ie,11y)I,>,>>Hh ????12&)3??i/((4>>B++---/!&*+'-.*"&!%<<$%RSS$(??1#5#9";i"GWWYF|x0t,#%x// '' '' )) %% --%%00 """"""**""))$$--  "!$"2"2K@K "4#4#4lCLHKI(UDM2*2'-Hc**93x=-M.Q.$%Ch%NOO $ ~~'H!$"2"2H=K <<++ !PQQ FG" FF* !G-!WXX*5K3&4EC'"9e4Gr{f$!  +$"$12$( # x' !HII).vD  $,0OOK,H) M $ < A #M 2 >>-$%H9%TUU)63*73  D( !FGG}}XY_EH~~!Q9+=+=+A%B!CC !:;;%DN 2bq22DY!^FD A 8b=8b=+d++ !566DFy{c/A!qI 9~ dQhF  !KL  $K"..99 '!8b V 3"%K)dQh59+>"%KAX%)v"5"%KeBi61! ( D1Hrf)<! eBi61! CJ1A>L$K # 5zA~ !5665zA~#9&#)L2R0F:#+L2YVr!<<#+L#)Lv%#e6Rr,D&EE "+B-!E2R*B$CCdJ "+A,".2 C 5zQ !455FL%*,t3I7Y77 !FGG c%jAQ?v%#e6Rr,D&EE "+B-!E2R*B$CCdJ "+A,*Q.LLe*q.U2Y!^cr e*q.U2Y!^5zA~%v2(@"AADHI9~''' y>Q !"1 ,y}? & 66 I6 Ip .  %sA{d K$, <<,b V#d*.. K R~~%%%5*;I$..IKK $K9K : %K#&{#3D %sA{d K  :sAx4 @  yy{H Q 1 1 12E FRV  }c1k2  ;Q *|S!U2Y/}c1eBi0  ;QR 1 <ab 2Aw{|S!U2Y7{CDG4a+!";INNKL _|o6W  *CK4E4EF   :sHMM8 < #q/:   o1 (#q,2D2D E ##a')O;   ?CI,>,>,B C c!la&7~sAq1~sL$:MN  ! =$8JqM+B C =$8JqM+B C:"!!} LqgdllD.I #S!T 2 =$6 2 =$6 2 #S!Q / )*i@   "\ qDG#a'DG3qDG#a'DG3qDG#a'DG3E u~a0H b )I,>,>>O =,/ J ; hh G#;!(;J DE"I<$7yI #*9QR=#9":U1X"E#*9QR=#9I359 5eBCj)I,>,>>G#$/ a b )$Ry >3< 8r\1A5,FI q !I cIoO =, A3? K ; i!y I < EF F A AJ  d/ BGGI4H94TDE EJqE!H=t .packBrr`r`c3&K|] }|d ywrrrFs r r!z4TiffWriter._write_remaining_pages..Js4A1Q44rrztruncating ImageJ fileTz#data too large for non-BigTIFF filel) rrrrrrrrrrrrsrrrioBytesIOr.rror%r?rrrr,rrrnrgetvaluer)r^rfhposrrrr dataoffset pagedatasizepagenorifd tagoffset ifdoffsetrr offset2valuerstripoffset2offsetstripoffset2valuerY stripoffsetrGr8s @r rMz!TiffWriter._write_remaining_pages/szzT^^  XX  19 HHUO QJEOO )) %% '' --%% 4//0 Q$//!"44q8 6 jjl ${C O45HHJ  #((4445HHJ  $|Q'(&tzz2 1MHc$x''99JFJL1vhhj7IIe$1HC&LIId<u=>  #a&!q6T---)5&(+%Q4+++%)"$0!3 16 88:> IIe ggi}}sxxzF':!:[!H|| 67!%BC Cv %A'')C GGDOO $ HHT,, - GGCL!IoDO , &J!)*+ $|Z89+, $|S3D-DEF*+(  00(DIId<=>4'K( HHS\\^ $+ %. #q!L|| &>?)-$%JKK Ls)P111Q1% Q1c|jr!|jddk(s|jdkry|jdu}|jr4|jddv}t |j||fi|j }n t|jfi|j }|jd}|d|jdz }|jj}|jj|j|jj||jj|j|jjtj |j"|j$zt'|dz|jj|d|_d|_d|_ y)z(Write meta data to ImageDescription tag.rr&Nrrutf-8)rrrrrrerrfencoderrrr%rrrrrrr.)r^ colormappedisrgbr{rs r rNz#TiffWriter._write_image_descriptionseq!Q&&&!+ nnD0 <<KKOv-E, 7;~~K+4??MdnnMK"((1 !"NQR>R S   c"#%&" r`c>tjjS)zReturn current date and time.)r|nowr^s r rhzTiffWriter._nows  $$&&r`c|js|j|j|jj y)z,Write remaining pages and close file handle.N)rrMrNrclosers r rzTiffWriter.closes/~~  ' ' ) %%' r`c|Srrrs r __enter__zTiffWriter.__enter__ r`c$|jyrrr^exc_type exc_value tracebacks r __exit__zTiffWriter.__exit__  r`)FNFF) rgrorprqr_rArMrNrhrrrrr`r r r sx&qKj -e 9Na$H !D'r`r c,eZdZdZ d/dZedZedZedZ dZ d0dZ ed Z d Z d Zd Zd ZdZdZdZdZdZdZdZdZdZdZd1dZedZedZedZedZedZ edZ!edZ"ed Z#ed!Z$ed"Z%ed#Z&ed$Z'ed%Z(ed&Z)ed'Z*ed(Z+ed)Z,ed*Z-ed+Z.ed,Z/ed-Z0ed.Z1y)2r aRead 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. 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. byteorder : '>', '<' The endianness of data in the file. '>': big-endian (Motorola). '>': little-endian (Intel). is_flag : bool If True, file is of a certain format. Flags are: bigtiff, movie, shaped, ome, imagej, stk, lsm, fluoview, nih, vista, 'micromanager, metaseries, mdgel, mediacy, tvips, fei, sem, scn, svs, scanimage, andor, epics, pilatus, qptiff. All attributes are read-only. Examples -------- >>> # read image array from TIFF file >>> imsave('temp.tif', numpy.random.rand(5, 301, 219)) >>> with TiffFile('temp.tif') as tif: ... data = tif.asarray() >>> data.shape (5, 301, 219) Nc d|vr|d=td|jD]L\}} |dddk(r2|ddtjvr| &| r)t ||t | @t d|zt|d|||} | |_t ||_ | j|i|_ | jd  d d d | jd } d d dt j"} | | k(|_t'j(| dz| jd d } | dk(rd|_t'j(| dz| jd\}}|s|dk7r td| |_d|_| dz|_d|_| dz|_d|_| dz|_| dz|_n\| dk(rLd|_| |_d|_| dz|_d |_| dz|_d|_| dz|_| dz|_n tdt;||_|j>r|j@jBd k\s8|j<d jDd!k7s|j<d!jDd!k7r1|jG|jI|jKy|rd|j<_&yy#t$r tdwxYw#tN$r| jQwxYw)"aInitialize instance from file. Parameters ---------- arg : str or open file Name of file or open file object. The file objects are closed in TiffFile.close(). name : str Optional name of file in case 'arg' is a file handle. 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. multifile : bool If True (default), series may include pages from multiple files. Currently applies to OME-TIFF only. movie : bool If True, assume that later pages differ from first page only by data offsets and byte counts. Significantly increases speed and reduces memory usage when reading movies with thousands of pages. Enabling this for non-movie files will result in data corruption or crashes. Python 3 only. kwargs : bool 'is_ome': If False, disable processing of OME-XML metadata. fastijz!the fastij option will be removedNrrzzunexpected keyword argument: %srv)rWnamerSrGrrrrrrznot a TIFF filebigrrrTrrrzinvalid BigTIFF filerrQ8srFrrI4szinvalid TIFF filer&))DeprecationWarningitemsrM FILE_FLAGSrhrrr r _multifiler_filesr%readrr,rr8rKrunpackrrr tagnosizerr tagformat1 tagformat2 TiffPagesrOis_lsm filehandlerG compression_lsm_load_pages_lsm_fix_strip_offsets_lsm_fix_strip_bytecounts useframesr?r)r^rrrSrGrmovier0rCrkrr8 sys_byteorderrcrzeros r r_zTiffFile.__init__sL v x $%HI I ,,. IJC2Aw%CGt$>$UD#tE{3 AC GHH  I$T&t Ly/wwo 5  GGAJ 4$'4RWWQZ@ %(37 FM%6DMmmIORWWQZ@CG"}"&#)==T1A2771:#N D:?$%;<GK)K>KKK1c|jS)zReturn file handle.rrs r rzTiffFile.filehandleWs xxr`c.|jjS)zReturn name of file handle.)rrrs r rUzTiffFile.filename\sxx}}r`c| tj|jjS#t$rYywxYw)z3Return status of file handle as stat_result object.N)osfstatrfilenor?rs r rzTiffFile.fstatas3 88DHHOO-. .  s ,/ ;;c|jjD]}|jji|_y)zClose open file handle(s).N)rvaluesrr)r^r3s r rzTiffFile.closeis5;;%%' #C NN " # r`c|jstjgS||d}| |j|}|j }n |j}|net|tr||g}nNt|tr||}n8t|tjr|Dcgc]}|| }}n t d|s td|jrt|||d}n'||r|jr|j |j"j$z} |dk(rA|dj&r2|j(j+| |j,|j}n|!t/||j,|j"}|j(j1|j|j(j3| t5|j,|d }n3t7|d k(r|dj9|| }nt||| }|y| |j,|_|St7|d k(r|dj,|_|Sd|dj,z|_|S#tt f$rY:wxYwcc}w#t$ro t;j<d |j,d|j,d|j,z|_n&#t$rd|dj,z|_YnwxYwY|SwxYw)aBReturn image data from multiple TIFF pages as numpy array. By default, the data from the first series is returned. Parameters ---------- key : int, slice, or sequence of page indices Defines which pages to return as array. series : int or TiffPageSeries Defines which series of pages to return as array. out : numpy.ndarray, str, or file-like object; optional Buffer where image data will be saved. If None (default), a new array will be 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. validate : bool If True (default), validate various tags. Passed to TiffPage.asarray(). maxworkers : int Maximum number of threads to concurrently get data from pages. Default is 1. If None, up to half the CPU cores are used. 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. If the bottleneck is I/O or pure Python code, using multiple threads might be detrimental. Nrz&key must be an int, slice, or sequencezno pages selectedF)out maxworkerssqueezerT)rnativer&)rvalidate)rrzfailed to reshape  to r)rOr;arrayrRrr_pagesr(inttypesslice collectionsIterabler,is_nih stack_pagesrSr8r<rTrPr memmap_arrayrDrr% read_arrayrr.r/rr) r^rCrRrrrrOkrXtypecodes r r/zTiffFile.asarrayosBzz;;r? " ;6>F   V,MMEJJE ;  X &3ZLE U ##JE [11 2'*+!U1X+E+DE E01 1 ;; CJPUVF [V ~~ (9(99Hh58#:#:55fllFMM?'V\\6<<HC$$V]]333gfll3T4Z1_1X%%#%AF CJGF >  ; :%||  Z1_ 8>>FL !58>>1FL yi(  ,B ::MM8> fllS$)6<<#7FL!:#(58>>#9FL:  :sNI"! I8I="I54I5= K5AK  K5 K.+K5-K..K54K5c|jsgS|jj}|jj}g}djD](}t |d|zdst |d|z}n||j_||j_|s|j }|Dcgc]}t |jdkDs|}}t|D] \}}||_ |Scc}w)zReturn related pages as TiffPageSeries. Side effect: after calling this function, TiffFile.pages might contain TiffPage and TiffFrame instances. z(ome imagej lsm fluoview nih mdgel shapedrzFz _%s_seriesr) rOrkeyframesplitre_generic_seriesrsrDror)r^rrrRrrrs r rRzTiffFile.seriesszzIJJ(( ::&&>DDF DtUT\51;|d':;=  ) & ))+F$8s177|a'7!88f% DAqAG  9s 0C0C0c |jjr|jd}|j}|j}t |jdkDrt |jf|z}d|z}t |jdd||j |dgS|jjd|jjg}g}i}tj}|jD]f}|js|j|j|j|vfz}||vr||j|P|j||g||<h|D]o}||} | d}|j}|j}t | dkDrt | f|z}d|z}|jt | ||j |dq|S) zReturn image series in file.rr&rNrstypeFGeneric) rOrrDaxesr.TiffPageSeriesr<clearloadrM DECOMPESSORSrr6) r^rVrDrrXkeysrR compressionsrCrOs r rzTiffFile._generic_seriess ::  ::a=DJJE99D4::"TZZ*U2Tztzz!}eTZZWU   (( JJ %D::** 4+;+;|+KLLCf}s ""4( C #fs  % C3KE8DJJE99D5zA~U -Tz MMueTZZYO   r`c |j}d|_t|}d}dx}x}x}x}}g} d} | |k\r | S| |_|| }|jst j dyd}d}t|j} | jdd}| d}| jd d} d | vr6| d }t|t|k(r|}nd}t j d |g} t|}t|t|j\}}|rt j d yd |cxkr|| z krnn||jjz}| rd }ng|jr%|j|z|| d zjkrd} n6d} t!| d z| |zD]}||}||_| j#|!|| | ||||| | |z } )z%Return image series in "shaped" file.Tc |d}|s:|j}|j}t|dkDrt|f|z}d|z}t|}t|} |jr| |kDr| |zdk(r|d}d|z}| |zf|z} t |||}|}|jt|||j||d|y#t $r(} tjt| Yd} ~ Xd} ~ wwxYw)Nrr&rTShaped)rrr$) rDrr.rrQ reshape_axesr,rrrr6rr<) rRrOrrDrarr$rVrGresizerls r append_seriesz.TiffFile._shaped_series..append_series$s8D yyu:> ZME1E:D5>DW%F!!ftm 8J$ $ITz4)E1 &#D%9 MMJJ"'  & c!f%% &sB?? C0C++C0Nrz(invalid shape metadata or corrupted filerrDr$raxes do not match shapez&series shape does not match page shaper&F)rOrr.r is_shapedrrjson_description_metadatar@rdivmodrD_dtyper=is_finalrSrnr6)r^rOlenpagesr&rrrDrarrRrrr$spagesrGnpagesmodjrVs r _shaped_serieszTiffFile._shaped_seriess u: @487747%7'D ^ [#ENU|H%% HIDE01C1CDH<<+Dw'G [$7I!'t9G ,#EDMM";<ZF7#D wx~~'>?KFC FG6-X--000F%% $.uqy1A1H1HH %I!&I"519efn=,$Qx(0  d+, &&$wi P VOE_r`c dj_dj_jj d fd} |}|rg njjg}g}dvr%|jd|jddvr%|jd|jd d vrFjd k(rjd d r%|jd |jdjdt |r t|ndz}|dkDr"|j||jdjddk(r=|jjdd|jjddnjdd dk(r`jddt!|zjd dz}t#jd|zt#jd dz}n6|jj|jj|xrEtjdk(xr+j$dt|j&zdzk7}t) |j*|d|gS#t$rt j dYywxYw)z#Return image series in ImageJ file.Trc^jsyjdd}|dkryj\}}|tjj zdzk7s|||zzj jkDr ttdkDr|||zzdjkDryy)NFimagesrr&rT) r-r@rQrrD bitspersamplerrGr,r.rS)r6rSr ijrVrOr^s r is_hyperstackz.TiffFile._imagej_series..is_hyperstacks==VVHa(F{ ..MFE,t/A/AAQFFEFN*T__-A-AA l"5zA~&56>"9E!HOO"Kr`z)invalid ImageJ metadata or corrupted fileNframesTslicesZchannelsr hyperstackFrKr6r&rSIrImageJ)rr$)rOrrimagej_metadatar,rrrr6rtr@r.rrextendrDrrrQr7rr<) r^r9r?rDrremainr$r8rVrOs ` @@@r _imagej_serieszTiffFile._imagej_serieszs $    ! ! Qx & &J FE JJOO  r> LLH & KK  r> LLH & KK       !"&&u*E LLJ ( KK #e*-E'%.qQ A: LL KK  99Q<3  LLAB ( KK !" & YYr]d "JJqOeEl2TZZ^CE ! %,tDIIabM/BBD LL $ KK "  RDJJ1$ R""1%$:L:L)LPQ)QQ  udjj$h)   Y  MME F  s KK#"K#cd|j_d|j_|jj|j}t t |d}djd|D}td|D}t|j||jdj||dd gS) z%Return image series in FluoView file.Tr Dimensionsr'c3K|]>}|ddkDs tjj|djd@yw)r&rrN)rM MM_DIMENSIONSr@rZrs r r!z,TiffFile._fluoview_series..s< :;qtaxD   " "1Q4::< 5 s A6Ac3JK|]}|ddkDs t|dywrrrs r r!z,TiffFile._fluoview_series..s":A1c!A$i:s ## ImageNameFluoViewrr) rOrrrfluoview_metadatarreversedrrrr<)r^mmmmhdrrDs r _fluoview_serieszTiffFile._fluoview_seriess#     # #HR -./ww ?C  :::   1 ## _    r`cd|j_d|j_|jj|j}|ddvr9t j d}|dddz |ddk(rfd }nfd }nd }|jd}t|g|j|j|d gS)z#Return image series in MD Gel file.FrFileTag)rfloat32 ScalePixelr&rc2|jddzzS)NrVrastyper{scales r transformz)TiffFile._mdgel_series..transforms88I.!3e;;r`c,|jdzS)NrVrYr[s r r]z)TiffFile._mdgel_series..transforms88I.66r`NMDGel)r]r) rOrrrmdgel_metadatar;r<rrDr)r^mdr<r]rVr\s @r _mdgel_serieszTiffFile._mdgel_seriess %      i=H $KK *E|$E!HuQx'E)}!< 7Izz!}  E499 QX   r`cd|j_d|j_|jj|jd}t |jdk(r|j }|j }n2t |jf|j z}d|j z}t|j||j|dgS)z Return image series in NIH file.Trr&rNIHr) rOrrrr.rDrrr<)r^page0rDrs r _nih_serieszTiffFile._nih_series s#    1  tzz?a KKE::D_&4E#Dtzz5%++t5QRRr`c (ddlm}|jdj} |j |}d|j_ d|j_ |jj|jjdd}||i|_|j"j$}i}g}|D]} | j&j)d rt jd n| j&j)d rf| D]`} | jjd d j)ds0| D]+} | D]"} | D]} | j&ddj)ds#| j&d}| jjdd}t*j,|}d| jvrpt/| jjdd}t/| jd}t/| jd|z}t1j2|||}n4| Dcgc])}|j&j)dr |j4+}}||f||<%.c| j&j)ds| j((jdd}| D]$}|j&j)ds |j((jdd}d j7t9(d}t;(fd|D}t=|dd}d}d}|D]}|j&j)dr]|j(|%t?(jd |}dg||zz}n)t?(jd d|k7r tAd!|| dg||zz}|j&j)d"s|j(t?(jd#d}t?(jd$d#(vrdnd}t?(jd%|}|ddD cgc] } t?(jd&| zd"}!} t1jB|!|dd}!|D]<}|j&j)ds |j4|j vr|jDs gccccS|jd(}" tGtHjJj7||"}#d|#j_ d|#j_ |#jj|#|j |j4<|#jQ|j |j4j}$ tS|r|n tU|$D]}%|$||%z||!|%z< |j}$ tS|r|n tU|$D]}%|$||%z||!|%z<tYd+|Drbd}&|D]}%|%s|%|%jk(s|%}&n|&sdt[|D]V\}%}&|&s |&j\|&j^j_ |&j^j|&j\}&|&||%<n|D] }%|%|&|%_ |&j`}|jcte||||||d,-' |D]}'t;|'jf}|jiD]\}\}}|'jjj]|}%tU|}||%|k(r#|'jjjm||d|'_5Z||%xx|zcc<|jo|%dz||'jjjm|||zd|'_5tq||'_3|D]/}'ts|'jf|'jj\|'_3|'_51|S#|j $rj}t jd|z |jddjd}|j |}n#t$rYYd}~ywxYwYd}~'d}~wwxYwcc}wcc} w#t@$rt jd'YdwxYw#tLtNt@f$rt jd)|"zYwxYw#tV$rt jd*Y1wxYw#tV$rt jd*YwxYw).z(Return image series in OME-TIFF file(s).r cElementTreez ome-xml: %srignoreNTUUID BinaryOnlyz$ome-xml: not an ome-tiff master fileStructuredAnnotations Namespacer'modulorAlongTypeotherStartStepr&EndLabelImageNamePixels PixelTypeDimensionOrderc3@K|]}td|zyw)SizeNr)raxattrs r r!z'TiffFile._ome_series..R sCSfrk!23CsrChannelr5z'cannot handle differing SamplesPerPixelTiffDataIFD NumPlanes PlaneCountFirstzome-xml: invalid TiffData indexFileNamezome-xml: failed to read '%s'zome-xml: index out of rangec3$K|]}|du ywrrrs r r!z'TiffFile._ome_series.. s/QqDy/OME)parentrr): xml.etreerirOr{ fromstring ParseErrorrrdecoderr?rrrattribr@rrdirnamerrprM AXES_LABELSfloatr;arangetextrrOrrrr,ravel_multi_indexrr rpathrrrrnr. IndexErrorallrorrr<r6rrDrrreplacerr squeeze_axes))r^etreeomexmlrootrluuidrrorRelementannotrkmodulalongrnewaxisstepstartstoplabelslabelrpixelsr<rrDrGifdsspprCrnumr~idxfnamer3rOrrseriers) @r _ome_serieszTiffFile._ome_series si3A** ##F+D $   {{vt,Tl ((""H G{{##L1 DE{{##$;<$AE <<++K<EEhO !&A%*AE).A',yy"~'>'>w'G$,',yy}*/,,*:*:67*K*.*:*:7*C#*ell#:+01A1A&!1L+MD,1%,,w2G,HE+0e1D+E+LD-2\\%t-LF6;.&,1+099+=+=g+F). .&F.& 18/@t #AAAA0;;''0>>D88FD)D!d zz**84}}d3wwx-=(>?@CdCCuSbz*#9IDxx((3#{{<"%dhh/@#&F"GC$(6TS[#9D *;Q!?@CG",-V"WW | $v588,,Z8 ;;Ddhhua01Cdhh{$AANOCdhh|S9:CDH"INb3txx" a89NCN!#55c5":F !%!I#xx008$99DKK7#'??(* $(KK $;E&&.rww||GU/K&L6: 356 2 #  069DKK 2IIK $ DII 6 < <I%*#33u:%F?05cAgS1W ? 5!I8!% I%*#33u:%F?05cAgS1W ?m9Iv/$// AQ!**_#$   '0" 8#=E^^HOO11:'/'<' M''wJJ$$T*6{8t#!&!3!3D'1!EEJ!H%HLLQ-!&!3!3D$.!!LEJ M ,EK ' LE&25;; &K #EK L W  MM-!+ , w9@@I''/    T.&VO&! &GH !$%,-> #K& ( .Lu.T U %& *I$MM*GHI *I$MM*GHIs_&&.a"6%a' a,A%b +c+c*&a5a2aa a aaaa,b b ,c c c' &c' *d d c  |j tj d}|jdjdk(r"|j ddj dd} j ddd kDr|d z } j d dd kDr|d z }|d d d}t fd|D} j dd}d|j_|jd d d}|dj}t|||||dg}|jd jrd |j_|jd d d}|dj}d\}}|t|kr>|t|dz kr-|||z}|d z }|t|kr|t|dz kr-|d ||djz}|d |dz}|jt|||||d|S)z6Return main image series in LSM file. Skip thumbnails.ScanTyperrrKr'XYXYC DimensionPr&P DimensionMMNrc3\K|]#}ttj|%ywr)rrMCZ_LSMINFO_DIMENSIONS)rrlsmis r r!z'TiffFile._lsm_series.. s&M1c$t99!<=>M),rxLSMrM)r&rCYX LSMreduced) lsm_metadatarMCZ_LSMINFO_SCANTYPErOrtrr@rrr<r is_reducedr.rDr6) r^rrDrrOr<rRcprrs @r _lsm_serieszTiffFile._lsm_series s  ''Z(89 ::a= $ $ )<<R(00u=D 88L! $q ( CKD 88L! $q ( CKDDbDzMMMxx#  3Q3a udUST ::a= # #"#DJJ JJqt!t$E!HNNEEBs5z/a#e*q.&8eAhQs5z/a#e*q.&8"1Ia.E8e#D MMueUDt<X  r`c@d|j_d|j_d|j_|jd}|jdddD] }||_ d|j_|jd}|jdddD] }||_ y)zLoad all pages from LSM file.Tr&Nrr)rOcacherr)r^rrVs r rzTiffFile._lsm_load_pages s #  ::a=JJqt!t$ %D$DM %  ::a=JJssO %D$DM %r`cx|jjdkry|j}t|}|jd}|j }d}dD]&}|j |dvs||j |z}(|dkDrd}dD]}||dk(s |j |}n|rt|d |z|z\}} | dk(sJ|||d f} tjt| j| } tj| dd} n%tj|jd d } |djd|djdkDr  d ddd f} d} d}  jD]J}||}g}|jD]"}|| kr| dz } |j|| z|} $t!||_ Ly) zUnwrap strip offsets for LSM files greater than 4 GB. Each series and position require separate unwrapping (undocumented). rNrr&rPMr&rr;rr.)rrGrOr.rRrrDr+r;rrramoveaxis dataoffsetsflatr6r)r^rOr0rRr positionsrntimesdivr1rDindiceswrappreviousoffsetrVr currentoffsets r rzTiffFile._lsm_fix_strip_offsets s ??  % '  UQ{{  -A{{1~%V\\!_,  - q=F 7c>#\\!_F !&!i-&*@ASaxx"FC3,,wu~6>>uE..!Q7ll6*222q9G 8   "U1X%9%9!%< <c4R4i(G 2A8DK!%!1!1 /  >1EMD""=4#78!.  / %[1D  2r`c |j}|djdk(ryt|d}t|dz }t |D]\}}|j dzr|j |j}||kr||dzj d}n,tdd|dzz|jj}|fztfdtt|D|_y) zSet databytecounts to size of compressed data. The StripByteCounts tag in LSM files contains the number of bytes for the uncompressed data. rr&Nc |jdSrA)r)ps r rz4TiffFile._lsm_fix_strip_bytecounts..3 sAMM!,<r`rBrrc3:K|]}|dz|z ywrr)rr2offsetss r r!z5TiffFile._lsm_fix_strip_bytecounts..@ s'(01A+(s) rOrrmr.rorrdatabytecountsrqrrGrrn)r^rOr0rrV bytecounts lastoffsetrs @r rz"TiffFile._lsm_fix_strip_bytecounts( s  8  1 $ u"<=Ua ' GAtzzA~&&G,,J6z"1q5\55a8 !q:b>/A!A488==Q  -G"'(5:3z?5K(#D  r`c|ddtjvr>|jsytt |jd|}t ||||St d|jjd|d)z,Return 'is_flag' attributes from first page.rNFr'' object has no attribute ') rMrrOrrerhrbrmrg)r^rrks r __getattr__zTiffFile.__getattr__D sg 8t &::A56E D$ &L37>>3J3JD Q  r`c|Srrrs r rzTiffFile.__enter__P rr`c$|jyrrrs r rzTiffFile.__exit__S rr`c dt|jjddd|jg}|jr|j d|j dj d|jDt|jdkDr'|j d t|jzt|jdkDr'|j d t|jzt|jdkDr'|j d t|jzd j |}|jd d jdd }|t|jjtddzt|z z}dkr|S|g}|j dj d|jDdk\r&|j!fd|jDn%|j!fd|jDdk\rot#|jD]W}t%||dzst'||dz}|s%|j |j)dt+|dzYdj |jddS)aReturn string containing information about file. The detail parameter specifies the level of detail returned: 0: file only. 1: all series, first page of series and its tags. 2: large tag values and file metadata. 3: all pages. z TiffFile '%s' LittleEndian BigEndianrBigTiffrc3<K|]}|jywrrZrr!s r r!z#TiffFile.__str__..h s;1QWWY;r&%i Pagesz %i Seriesz%i Files z z rrr c32K|]}t|ywrrrrs r r!z#TiffFile.__str__..u s:c!f:rrc3RK|]}|tj| yw)Ndetailwidth)TiffPage__str__)rrrrs r r!z#TiffFile.__str__..x s0}$$QvU$Cs$'c3K|]8}|jd'tj|jd:yw)rNr)rOrr)rrrrs r r!z#TiffFile.__str__.. sAwwqz-$$QWWQZe$Ls>Arz _METADATA rheight z )rrrGr8rr6rflagsr.rOrRrrsnipstrrmaxrCrmr-rerZpformat)r^rrinforms `` r rzTiffFile.__str__V s=   & { 3DNN C  ?? KK " CHH; ;;< tzz?Q  KK S_4 5 t{{ a  KK c$++&66 7 t{{ a  KK c$++&67 8yy||FD)11%>gdhhmmSUQYT5J-KLL Q;Kv DII:dkk::; Q; KK!ZZ  KK![[  Q;tzz* 4 !34d[&89A !% 'v{ K {{4 ((6::r`cZtfdttjDS)zReturn set of file flags.c3\K|]#}td|zr|j%ywryrelowerrrr^s r r!z!TiffFile.flags.. s- tUT\* JJL rsetrmrMrrs`r rzTiffFile.flags s( t/   r`c |jdjxs|jdjS#t$rYywxYw)zFile has MD Gel format.rr&F)rOis_mdgelrrs r rzTiffFile.is_mdgel s@ ::a=))CTZZ]-C-C C  s36 AAc.|jjS)zReturn if file is a movie.)rOrrs r is_moviezTiffFile.is_movie szz###r`cT|jsytd|jDS)z9Return Tifffile metadata from JSON descriptions as dicts.Nc3K|]C}|jjdk(r$t|jdjEyw)shapedrN)rrr*rOr)rs r r!z+TiffFile.shaped_metadata.. s= ww}}(* &aggaj&:&: ; sA A )r)rrRrs r shaped_metadatazTiffFile.shaped_metadata s,~~  [[   r`cf|jsyt|jdjdS)zReturn OME XML as dict.Nrr)rrrOr{rs r ome_metadatazTiffFile.ome_metadata s,{{  1 112599r`c|jsyd}|jdjjd|zdz|}t ||S)z;RS$R(' *F% &   2 MM,q0 1 1  2s65#E=E3'/E=E8% E=3 E== F)F$$F)c|jsy|jd}t|j}d|jvr+ |j |jdj |S|S#t $rY|SwxYw)z,Return consolidated ImageJ metadata as dict.Nr IJMetadata) is_imagejrOimagej_description_metadatarrLrkr?)r^rVrXs r rBzTiffFile.imagej_metadata sy~~ zz!},T^^< 499 $  dii 5;;< v    s(A-- A:9A:c|jsyi}|jd}|j|jdj|jdj|d<|S)z.Return consolidated FluoView metadata as dict.Nr MM_HeaderMM_StampStamp) is_fluoviewrOrLrrk)r^rXrVs r rNzTiffFile.fluoview_metadata s\ zz!} dii ,223))J/55w r`ch|jsy|jdjdjS)z:Return NIH Image metadata from NIHImageHeader tag as dict.NrNIHImageHeader)r rOrrkrs r nih_metadatazTiffFile.nih_metadata s.{{ zz!}!!"23999r`c|jsy|jdj}d|vr|djSd|vr|djSy)z5Return FEI metadata from SFEG or HELIOS tags as dict.NrFEI_SFEG FEI_HELIOS)is_feirOrrk)r^rs r fei_metadatazTiffFile.fei_metadata sX{{ zz!}!!   #)) ) 4  %++ + r`ch|jsy|jdjdjS)z,Return SEM metadata from CZ_SEM tag as dict.NrCZ_SEM)is_semrOrrkrs r sem_metadatazTiffFile.sem_metadata+ s-{{ zz!}!!(+111r`c|jddD]}d|jvs|j}nyi}tddD]/}tj|}||vr||j ||dd<1|S)z6Return consolidated metadata from MD GEL tags as dict.Nr MDFileTag饂i)rOrrnrMTAGSrk)r^rVrrXrrs r r`zTiffFile.mdgel_metadata2 sJJrN Ddii'yy  %' 0D99T?D4#Dz//F48   0  r`c4|jdjS)zReturn Andor tags as dict.r)rO andor_tagsrs r andor_metadatazTiffFile.andor_metadataC zz!}'''r`c4|jdjS)z'Return EPICS areaDetector tags as dict.r)rO epics_tagsrs r epics_metadatazTiffFile.epics_metadataH rIr`ch|jsy|jdjdjS)zReturn TVIPS tag as dict.NrTVIPS)is_tvipsrOrrkrs r tvips_metadatazTiffFile.tvips_metadataM s-}} zz!}!!'*000r`c`|jsyt|jdjS)z:Return MetaSeries metadata from image description as dict.Nr) is_metaseriesmetaseries_description_metadatarOr{rs r metaseries_metadatazTiffFile.metaseries_metadataT s)!! .tzz!}/H/HIIr`c`|jsyt|jdjS)z7Return Pilatus metadata from image description as dict.Nr) is_pilatuspilatus_description_metadatarOr{rs r pilatus_metadatazTiffFile.pilatus_metadata[ s' +DJJqM,E,EFFr`c|jsyt|j}|j|jdj dj |S)z2Return consolidated MicroManager metadata as dict.NrMicroManagerMetadata)is_micromanagerread_micromanager_metadatarrLrOrrk)r^rXs r micromanager_metadatazTiffFile.micromanager_metadatab sI## +DHH5 djjm(()?@FFG r`cJ|jsyi} t|j\}}||d<|j| t |j dj|d<|S#t$rY3wxYw#t$r#}tjd|zYd}~|Sd}~wwxYw)z DM  a( $r`c|jS)z2Return if pages/frames are currently being cached.)rtrs r rzTiffPages.cache s{{r`cdt|}|jr|s|j||_y)z@Enable or disable caching of pages/frames. Clear cache if False.N)rrtrr^rks r rzTiffPages.cache s&U  ;;u JJL r`cD|jtk(xr ttuS)z?Return if currently using TiffFrame (True) or TiffPage (False).)rr TiffFramerrs r rzTiffPages.useframes s~~*Hy/HHr`c6|r t|_yt|_y)z0Set to use TiffFrame (True) or TiffPage (False).N)rzrrrrxs r rzTiffPages.useframes s',r`c.|jjS)z!Return index of current keyframe.)rsrrs r rzTiffPages.keyframe s~~###r`c|jj|k(ry|js!d|cxkrt|jkrSnnP|j|}t |t r||_yt |tr|j|j|<|j}t |_ |||_||_ y)z;Set current keyframe. Load TiffPage from file if necessary.Nr) rsrrqr.rOr(rrzrSrrr)r^rrVrs r rzTiffPages.keyframe s >>  5 (  ==A8TZZ8::e$D$)!%D),$(KK 5!NN !e"r`cT|js|jd|jS)z7Return offset where offset to a new page can be stored.r)rq_seekrurs r rzTiffPages.next_page_offset s"}} JJrN###r`cJ|jj}|j}|j}|js|j dt |D]J\}}t|ts|j||j|j||}|||<Ly)z#Read all remaining pages from file.rrrN) rrrsrOrqrror(rr%rr)r^rrrOrrVs r rzTiffPages.load s [[ # #>> }} JJrN ' GAt$) ~~dkkX~Na  r`c^|j}|jrt|dkry|d|_|r:t |ddD](\}}t |t r|j||dz<*yttur4t |D]%\}}t |ts|j||<'yy)zADelete all but first page from cache. Set keyframe to first page.r&Nr) rOrtr.rsror(rrSrzr)r^fullyrOrrVs r rzTiffPages.clear s {{c%j1n q $U12Y/ /4!$1#';;E!a%L /h &$U+ +4dI.#{{E!H +'r`c||j}|sy|jj}|jr t d|j sd|cxkrt |kr8nn5||}t|tr|n |j}|j|y|jj}|jj}|jj} |jj} |jj} t j"} |d}t|tr|n |j}t ||kr|j| | | |j%| d} | dkDr t'd || z| | zz|_|j|j.| ||j%|d}|dk(rd|_ng||j0k\r t+j,d |zd|_n8|j3|d|cxkrt |krnnnt ||kr|t |k\r t5d ||}|jt|tr|y|jy#t($r%t+j,d|z|d=d|_Y~wxYw) z&Seek file to offset of specified page.NzFileHandle is closedrrsuspicious number of tagscorrupted tag list at offset %iTrplist index out of range)rOrrclosedrcrqr.r(rrSr%rrrrrrrrr,r?rrrurGr6r)r^rmaxpagesrOrrVrSrrrrrrtagnos r rzTiffPages._seek sV   [[ # # 9956 6 ==A3U3?B4<$%@AA $*I#5#GD GGD(( )L"''**=>qAF{ $   86AB $  LL E&CJ&9%j8#< CJ 67 7U|  42D D5  ?&HI"I $   s+J +J;:J;c2t|jdkDS)z'Return True if file contains any pages.r)r.rOrs r __bool__zTiffPages.__bool__@ s4::""r`cf|js|jdt|jS)zReturn number of pages in file.r)rqrr.rOrs r __len__zTiffPages.__len__D s"}} JJrN4::r`c|j}|s td|dk(r||St|tr{|j d\}}}|j s)t ||t|kDr|jdt|j t|Dcgc]}|| c}S|j r|t|k\r td ||}t|ts|S|j||j|j||j}|jr|||<|Scc}w#t$rd}YpwxYw)z,Return specified page(s) from cache or file.rrrDrr)rOrr(r rrqrr.rrnrrrrrsrt)r^rCrOrrrYrrVs r __getitem__zTiffPages.__getitem__J s) 67 7 !8:  c5 ! [[3NE4==Su%5E %B 2%*CKKE ,C%DEDGE E ==SCJ.67 7 :D$)K 3~~dkkt~~~N ;;E#J !F D s D8D== E  E c#JKd} |||dz }#t$rYywxYww)zReturn iterator over all pages.rr&N)r)r^rs r __iter__zTiffPages.__iter__h s=  1g Q  s# # # #NT)i@)rgrorprqr_rmrsetterrrrrrrrrrrrr`r rr s2B \\II::$$__##$$$  +"<E|# <r`rc eZdZdZdZdZdZdZdZdZ dZ dZ dZ dZ dZdZdZdZdZdZdZdZdZdZd3dZ d4dZ d5d Zd Zed Zej<d Zed Z edZ!edZ"edZ#d6dZ$edZ%edZ&edZ'edZ(edZ)edZ*edZ+edZ,edZ-edZ.edZ/edZ0edZ1edZ2ed Z3ed!Z4ed"Z5ed#Z6ed$Z7ed%Z8ed&Z9ed'Z:ed(Z;ed)Zed,Z?ed-Z@ed.ZAed/ZBed0ZCed1ZDed2ZEy)7raTIFF image file directory (IFD). Attributes ---------- index : int Index of page in file. dtype : numpy.dtype or None Data type (native byte order) of the image in IFD. shape : tuple Dimensions of the image in IFD. axes : str Axes label codes: 'X' width, 'Y' height, 'S' sample, 'I' image series|page|plane, 'Z' depth, 'C' color|em-wavelength|channel, 'E' ex-wavelength|lambda, 'T' time, 'R' region|tile, 'A' angle, 'P' phase, 'H' lifetime, 'L' exposure, 'V' event, 'Q' unknown, '_' missing tags : dict Dictionary of tags in IFD. {tag.name: TiffTag} colormap : numpy.ndarray Color look up table, if exists. All attributes are read-only. Notes ----- The internal, normalized '_shape' attribute is 6 dimensional: 0 : number planes/images (stk, ij). 1 : planar samplesperpixel. 2 : imagedepth Z (sgi). 3 : imagelength Y. 4 : imagewidth X. 5 : contig samplesperpixel. rr&Nr'c ||_||_d|_d|_d|_d|_d|_i|_d|_d|_ |j}|j|_ tj|j|j!|j"d}|dkDr t%d |j(}|j!||z}|j}| }t+|D]} ||z } t-|j||||z} | j6} | |vr| } | || <nd} d | |fz} | |vr| || <nt8j:j=| d} | su| dd d vrt?| j@t4stC|| | j@|sy|jDr |jFn|jHr |jJ|jLs"|jr4|jjLr|jd jO||jPs"|jr|jjPrd|_)|jTrd |vr||d j@sm|d }|jW|jXt[||jj\|j|j^d|dj^|d _ d|vrD ta|dj@|dj@|jj\|d_ d |vre|d } | j^dk(r| j@|_1n?| j@d|jdtgfdDr|_1n d|_1d|vre|d} | j^dk(r| j@|_4n?| j@d|jdtgfdDr|_4n d|_4d|vr'd|vs|dj^dkDr|jj|_6|jh|jbf}t8jnj=|d}|tqj|}|x|_|_|jj}|jr}|jR}|jd}|jTrO|jRdk(sJ|dj@}|dj^}|jtdk(r7|dd|||f|_|dk(r|||f|_d|_nI||||f|_d|_n6||d||df|_|dk(r|||f|_d|_n||||f|_d|_|dk(r|jdd|_nNtqjv|ddk7rd|j z|_ntqjvtqjx|ddk7rd|j z|_nd|j z|_n|jzdk(s|dkDr}|jtdk(r7dd||||f|_|dk(r|||f|_d|_n~||||f|_d|_nkd||||df|_|dk(r|||f|_d|_nG||||f|_d |_n4dd|||df|_|dk(r||f|_d|_n|||f|_d!|_d"|vr|d"j@|_n d#|vr|d#j@|_nd$|_d%|vr|d%j@|_ nhd&|vr|d&j@|_ nOt}|j|jbd'zzf|_ |j~dk7rt1j2d(t|jt|j k(sJy#t&$rt%d|jzwxYw#t,j.$r)} t1j2t5| Yd} ~ (d} ~ wwxYw#t&$r)} t1j2t5| Yd} ~ $d} ~ wwxYw))zlInitialize instance from file. The file handle position must be at offset to a valid IFD. rNr'rrrrr&z%s%irzsof desr7rrr.IJMetadataByteCountsc3.K|] }|dz ywrrrvrks r r!z$TiffPage.__init__.. 4E!H 4r2c3.K|] }|dz ywrrrs r r!z$TiffPage.__init__..$ rrr*r?YXYXSSYXr r=r!r;rrZYXSSZYXZYX TileOffsets StripOffsetsr9TileByteCountsStripByteCountsrz"required ByteCounts tag is missing)ArrrDrr<r,rrrrrrrSrrrrrr,r?rrnTiffTagErrorrrrrrMTAG_ATTRIBUTESr@r(rkrhis_andorrGis_epicsrKr_fix_lsm_bitspersampleis_vista imagedepthr'r% valueoffset read_uic1tagr8r rBr7rr*r imagelengthrx SAMPLE_DTYPESr; imagewidthrurrrtrrr.)r^rrrrrrrCrrYrrltagnamerruic1tagr<rrrruictagplanesrks @r r_zTiffPage.__init__ s            ggi  NMM&"4"4bggf>N>N6OPQRSEt| !<== ..www'yyu 3A W E dkk4+HIhhGd" T !WaL0D4'%(T   &&**44D8y(CIIs1KD$ 23 36  == OO ]] OO ;;4::$++*<*< IIo & = =d C ==TZZDKK,@,@DO ;;9,T)_5J5J9oG GGG'' ($0 %%  Y%% %DO ! 4  &+:&,,/066KK)),\"( d "'CyyA~%(YY" "8D$8$894e45).D&).qD& T !~&CyyA~$'II! "8D$8$894e45(-D%(-aD% D T)T.-A-G-G!-K$($4$4! !!4#5#55""&&ud3  KK&E#(( T[&& __ __ .. ;;??a' '')_**F)_**F  A%%q![*oV "a'"(+z!BDJ $DI"(+z?!SDJ %DI%; TUV "a'"(+z!BDJ $DI"(/; !SDJ %DI{!ZZ^ 6+.!34$))O 5::f]&;<AB$))O $))O    "o&9  A%#  ?"-z?!KDJ %DI",k:!WDJ &DI#  ?"1; !KDJ %DI"1:{J!WDJ &DIa[*aHDKQ):6   (+zB !  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Raise ValueError if format is unsupported. Parameters ---------- out : numpy.ndarray, str, or file-like object; optional Buffer where image data will be saved. If None (default), a new array will be 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, all length-1 dimensions (except X and Y) are squeezed out from the array. If False, the shape of the returned array might be different from the page.shape. lock : {RLock, NullContext} A reentrant lock used to synchronize reads from file. If None (default), the lock of the parent's filehandle is used. reopen : bool If True (default) and the parent file handle is closed, the file is temporarily re-opened and closed if no exception occurs. maxsize: int or None Maximum size of data before a ValueError is raised. Can be used to catch DOS. Default: 16 TB. validate : bool If True (default), validate various parameters. If None, only validate parameters and return None. rNzdata are too large %szdata type not supported: %s%izcannot decompress %sr2r&c3BK|]}|jdz ywrrk)rrrs r r!z#TiffPage.asarray.. s*O1syy|+;*Ozsample formats do not match %srz chroma subsampling not supportedzfile handle is closedrrrSrT)rrzunsupported JPEG precision %i JPEGTablesr`c6|||||jdSNr)ra)rr\tabler7 colorspaces r decompressz$TiffPage.asarray..decompress&s  5-DLLRPPr`)rr @rUrzdata and sample size mismatchcjdk(r j} tj||S#t$r3t |dzzdzz}tj|d||cYSwxYw)Nrr)ryrTr; frombufferr,r.)rrxlenr7r<r^s r rz TiffPage.asarray..unpack3s}~~*$)::D$//8<<%D!$A=A+= >=TUCUV$//%4(CC Ds49A0/A0ct|||Sr) unpack_rgb)rrr7s r rz TiffPage.asarray..unpackCs%a=AAr`ct||||Sr) unpack_ints)rrr7runlens r rz TiffPage.asarray..unpackHs'q(M6JJr`)rrrrzinvalid tile data WRITEABLErrr<r)rr<rr.zfailed to reshape from r)Frrrrr,rr<rr7rrMrrr r*rkis_chroma_subsampledruNotImplementedErrorrrlockropenrr,rrrr8rT fillorderoffsets_bytecountsis_tiled tilewidth tilelength tiledepthrrPrrQrr%rrKbyteswapviewrJreverse_bitorder identityfuncrQrtr(r buffered_readrDrrr;zerosrarqrGryrcumsumrxr decode_floatsr)-r^rrrreopenmaxsizerself_rrrrDrrrrlsb2msbrristiledrrrtwtltd tileshaperrXrrrrwritableplrvrGr strip_sizerrrGr7r<rs-` @@@r r/zTiffPage.asarray sHT}}{{gdkk2a7 yy x'74;;/'9 !83t{{;K!KLLzz! 3(($*<*<=>t'8'88 !7$:J:J:O:O!OPP%>*99>c*OSYY*O&P$%E %QRR((  A%):):a)?)*LMM \\ $ $,rwwD  ;YYFGGI!"9::  ;  __ && __ ** ;;((5::5..A%#66-- IJIy(1,:B *Q.:=By(1,:BaaYZYb E#J 59EIFF    ! d** *F (?t22 M5L M M   #C6 J #xSI J{6<<#8#8%V\\%>%>%@A ("3u5F**4+;+;.>?DD $"/) Q"66!F*a/$%DEE'/ D DM51'/}B !) fK !+BB)"dGZH&3D/5%d+D!$H#!LLBeN#(<<2U#KD1,133R)^+R*_,R)^+ )OBU1X~!"BOBq>%&YB!U1X~)*BFBM&3N [j[,;,  Q NO!..@ $$)$"6"66J+*2tWjI"E 0 7&u-E"5MEv{{EJJ FKKRWDWXD38$>Q 8J8J{{!!d&6&6!&;1$ V"EvF1$&v.  #zz   HHJ A ; ;V M M  J JR&4 &9:!KK 59AA"E 1662 $Ra"1 yy3 4|  6<<(#djj/; sJ -]  ] 2]&8]3(_6 ]]#&]03A<_32_36A aac0|j|i|}|j}|j} tj} | | j k(r|j }|jdd|jzks|jjdvr td|r)|jdkDr|dz}|jd}d|jvr|jdk(r|d n|d }t!||}|S| | j"k(rd |j$vr|tj&}|j(} |j$d j*dk(r| f} t-| D]:\} } | |vs |jdk(r|d d ddd| zgf}n|d d d ddd| zgf}|S|S|jdk(r |d d df}|S|d d d df}|S| | j.k(r t1| | j2k(r t1| | j4k(r t1t1)zAReturn image data as RGB(A). Work in progress. r&rrzcannot apply colormapruint8S.rrr8N.r)r/rrtrMrQrUrzrDr7r<rTr,rrZrruapply_colormaprSr EXTRASAMPLErr rorRrr` SEPARATED)r^ralpharzdmindmaxargsr0rCrtrQrrexss r asrgbzTiffPage.asrgbsEt||T,V,}}&& && +-- -}}H~~a 1d&8&8#88DJJOOSWC'NH#??73dii'+'8'8A'=tF|47!$1D> ;KOO +*= ,,E#00 99^,22a7$0?L' 5FAse|,,1#'aAq1u-=(=#>D#'Aq!QU+;(;#.sL  Z]*ga!en<V 1q5@QUV@VV s+.)rr7rrrrrrrrrr.r'rrnrs)r^rrs @@r rQzTiffPage.is_contiguouss%   q D$6$6o$M  $)) #4>>1##doo5>>B&??R' )499,$$77""(( w<1 1:z!}, , ;;# 3w$rYwxYw)z0Return string containing information about page.r') memmappablefinalrwrzrc3$K|]}|r| ywrrrs r r!z#TiffPage.__str__..<s &)  rrc32K|]}t|ywrrrs r r!z#TiffPage.__str__..?4AQ4rrc3$K|]}|r| ywrrrs r r!z#TiffPage.__str__..Bs  rTILEDr&c3<K|]}|jywrrrs r r!z#TiffPage.__str__..Os8!'')8rzTiffPage %i @%i %src|jSr)rrs r rz"TiffPage.__str__..Zs qvvr`rB)rNrCOUNTSOFFSETSrrrrrrzDATA %sr) rrzrrerZrrDrM SAMPLEFORMATrrr7rQrtrrruryrrrrSrrmrr6rr.rrkr/r?) r^rrrrrrtlinesvlinesrrks r rzTiffPage.__str__2s ==D $$T62 2: D4.Dzz|   yy 444$$T%6%67<P>PR (()9)9:??#'==b151A1AQ1F((--B262C2Cq2H))..b/3~~/B++/3~~/B++   8TZZ89#  .% DKK'FF Q;Kvyy$++--=> .ts- 4.  rrrs`r rzTiffPage.flagsps( "4??3   r`c,t|jSz"Return number of array dimensions.r.rDrs r rz TiffPage.ndim{4::r`c,t|jSz#Return number of elements in array.)rrDrs r rGz TiffPage.sizestzz""r`c|jsy|j}d|dji}t|jj D]m}|j }d|cxkrdksn|j}t |jdkDr|jddn |j}|||<||j=o|S)zjReturn consolidated metadata from Andor tags as dict. Remove Andor tags from self.tags. NIdAndorIdir)rrrkrrrr.r)r^rrXrrrkrs r rGzTiffPage.andor_tagss}} yyY--. ((*+ C88D$%%IIE#&sxx=1#4388AB<#((D F4LSXX  r`c|jsyi}|j}t|jjD]}|j}d|cxkrdksn|j }|dk(r,t j jt||d<n_|dk(rt||d<nK|dk(rt||d<n7|d k(rt||d <n#|jd d \}}t|||<||j=|S) z~Return consolidated metadata from EPICS areaDetector tags as dict. Remove areaDetector tags from self.tags. Ni timeStampuniqueID epicsTSSeci epicsTSNsec:r&) rrrrrrkr| fromtimestamprrrrZr)r^rXrrrrkrCs r rKzTiffPage.epics_tagss}} yy ((*+ C88DD(5(IIEu}&.&7&7&E&EeEl&S{#%(Zz"'*5z|$(+E }%"[[a0 U$Ums SXX! " r`c|jsy|j}|dj}|ddk7rtjdiS|d|d|dd}t j }t j}t|dD]}|d |d zz|d zd z\}}} } |j||}|dk(r| } nKt j|} || j| | | z} |d k(r| dkDr | d d k(r| dd } | dkDr| n| d} ||vr ||| } | ||<d|vrV|dj} tj| } t| dk(r| jdj!} | |d<d|vr5tj|djj!} | |d<d|vrT|dj} tj| jdj#j!} | |d<d|vrG|dj} tj| jdj!} | |d<n d|vrt|dj}id|dd|dd|dd|dd|d d |d!d"|dd#|d$d%|d d&|d'd(|d)d*|d+d,|d-d.d/|d.d0d1|d0d2d3|d2d|d4<|S#t$rYwxYw)5z7Return consolidated metadata from GeoTIFF tags as dict.NGeoKeyDirectoryTagrr&zinvalid GeoKeyDirectoryTagr)KeyDirectoryVersion KeyRevisionKeyRevisionMinorrrr鱇rrIntergraphMatrixTagr)rrIntergraphMatrixModelPixelScaleTagModelPixelScaleModelTiepointTag)rr ModelTiepointModelTransformationTagModelTransformationrRPCCoefficientTagERR_BIASERR_RANDLINE_OFFSAMP_OFFLAT_OFFLONG_OFFr HEIGHT_OFF LINE_SCALEr SAMP_SCALE LAT_SCALEr LONG_SCALE HEIGHT_SCALE LINE_NUM_COEFFr!zLINE_DEN_COEFF 5SAMP_NUM_COEFFISAMP_DEN_COEFFRPCCoefficient)rhrrkrrrMGEO_KEYS GEO_CODESrnr@rEr?r;rr.ratolistrr6)r^rgkdrXgeokeysgeocodesrkeyidtagidr rSrkrsxsysz tiepoints transformstprr2rryzrpccs r rizTiffPage.geotiff_tagss yy'(.. q6Q; MM6 7I$'q6q6 #A -->>3q6] "E*-a%!)meai!m*L 'E5%KKu-Ez))E*W ++FVe^DE>eaiE"I4D!#2JE!&a +HUOE2E"F5M# "& !D (./55EKK&E5zR f-446).F% & 4 'KK%9 : @ @AHHJE(-F$ %  %+,22EKK&..w7??AHHJE&+F? # #t +1288EKK&..v6==?E,1F( ) & $ &+,22D(DG(DG(DG(DG ( 47 ( DG (d1g(d1g(d1g(T!W(d2h(R(!$r"+("42;(!$r"+( !$rs)!(F# $& {!s K  KKcd|jvS)zPage contains tiled image.r+rrs r rzTiffPage.is_tileddii''r`cZd|jvxr|jdjdzS)z'Page is reduced image of another image.r/r&rrkrs r rzTiffPage.is_reduced s. 499,V;K1L1R1RUV1VVr`cZd|jvxr|jdjdk7S)z&Page contains chroma subsampled image.YCbCrSubSamplingr>rmrs r rzTiffPage.is_chroma_subsampled%s4"TYY.499 4 %64 r`c^|j|jfD]}|sy|dddk(s|cSy)z/Return ImageJ description if exists, else None.NrzImageJ=r{ description1r^r{s r r/zTiffPage.is_imagej,s>!,,d.?.?@ #K2A)+""  #r`c~|j|jfD]"}|sy|dddk(rd|vr|cS|dddk(s |cSy)z?Return description containing array shape if exists, else None.Nr&{z"shape":rshape=rqrss r r)zTiffPage.is_shaped5sY!,,d.?.?@ #K2A#%* *C""2A(*""  #r`cd|jvS)zPage contains MDFileTag tag.rCrjrs r rzTiffPage.is_mdgel@rkr`c`d|jvxr|jdjdddk(S)z'Page contains Media Cybernetics Id tag.MC_IdNrsMC TIFFrmrs r is_mediacyzTiffPage.is_mediacyEs3$))#R '(:(@(@!(D (RRr`cd|jvS)zPage contains UIC2Tag tag.rrjrs r r'zTiffPage.is_stkJDII%%r`cd|jvS)zPage contains CZ_LSMINFO tag.rrjrs r rzTiffPage.is_lsmOstyy((r`cd|jvS)z$Page contains FluoView MM_STAMP tag.r3rjrs r r5zTiffPage.is_fluoviewTsTYY&&r`cd|jvS)zPage contains NIH image header.r7rjrs r r zTiffPage.is_nihYs 499,,r`c>d|jvxrd|jvS)z,Page contains SGI image and tile depth tags.r-r.rjrs r is_sgizTiffPage.is_sgi^s!tyy(E[DII-EEr`c |jdk(S)zSoftware tag is 'ISS Vista'.z ISS Vistar~rs r rzTiffPage.is_vistacs}} ++r`c|jdkDs|jdk7ry|j}|jdxr|j dS)z>Page contains MDS MetaSeries metadata in ImageDescription tag.r& MetaSeriesF z )rr~r{ startswithrpr^ds r rRzTiffPage.is_metaserieshsE ::>T]]l:   ||L)Gajj.GGr`cv|jdkDs |jsy|j}|dddk(xr|dddk(S)z.Page contains OME-XML in ImageDescription tag.r&FNrr{rs r rzTiffPage.is_omepG ::>!1!1   "v))@af.@@r`cv|jdkDs |jsy|j}|dddk(xr|dddk(S)z4Page contains Leica SCN XML in ImageDescription tag.r&FNrrrzrrs r is_scnzTiffPage.is_scnxrr`cd|jvS)z%Page contains Micro-Manager metadata.rZrjrs r r[zTiffPage.is_micromanagers&22r`cd|jvS)z$Page contains Andor Technology tags.r(rjrs r rzTiffPage.is_andorr|r`cN|jdddk(xr|jdddk(S)zPage contains Pilatus tags.NrzTVX TIFFr# )r~r{rs r rVzTiffPage.is_pilatuss1}}Ra J.O43C3CBQ3G43OOr`cB|jdk(xs|jdk(S)z&Page contains EPICS areaDetector tags.zEPICS areaDetectorr{r~rs r rzTiffPage.is_epicss*    4 4 5}} 44 r`cd|jvS)zPage contains TVIPS metadata.rNrjrs r rOzTiffPage.is_tvipss$))##r`c>d|jvxsd|jvS)z&Page contains SFEG or HELIOS metadata.r:r;rjrs r r<zTiffPage.is_feis!TYY&C,$))*CCr`cd|jvS)z!Page contains Zeiss SEM metadata.r?rjrs r r@zTiffPage.is_sems499$$r`c&|jdddk(S)zPage contains Aperio metadata.NrzAperio Image Libraryr{rs r is_svszTiffPage.is_svss$(>>>r`ct|jdddk(xs%|jdddk(xsd|jddvS)z!Page contains ScanImage metadata.Nrz state.configzSI.LINE_FORMAT_VERSIONz scanimage.SI.irrs r razTiffPage.is_scanimagesQ   Sb !^ 3 :}}Sb!%== :$"2"245"99 r`c&|jdddk(S)z1Page contains PerkinElmer tissue images metadata.NzPerkinElmer-QPIrrs r rzTiffPage.is_qptiffs }}Sb!%666r`cd|jvS)zPage contains GeoTIFF metadata.r5rjrs r rhzTiffPage.is_geotiffs$tyy00r`r)NTNTl@T)FNNNNrk)Frgrorprqrrrrrrr7rrrxrrurrtryrrzr~r{rrr_r/rrrmrrr rrQr-rPrrrrGrGrKrirrrr/r)rrzr'rr5r rrrRrrr[rrVrrOr<r@rrarrhrr`r rrs s"JJKJIJIMOLLKLIKILHHKLe1R  IZ   =~__KK$/$/L      <!|  ##(:``D((WW ####((SS&&))''--FF,,HHAAAA33&&PP  $$DD%%??  77 11r`rcreZdZdZdZdZiZdZdZdZ dZ e dZ e d Z e d Zd Zdd Zy )rzaLightweight TIFF image file directory (IFD). Only a limited number of tag values are read from file, e.g. StripOffsets, and StripByteCounts. 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 data from file, not for introspection of metadata. Not compatible with Python 2. )rrrrSrrFcf||_||_||_d|_d|_t j }|j}|j|_ ||j|j|jd}|dkDr td hd}|j}|j dd} |j||z} | }t#|D]u} ||z }|| | ||dzd} | |vr t%|| |||z} | dk(s| d k(rt/|d | j0T| d k(s| d k(s_t/|d | j0wy#t$rtd|jzwxYw#t$j&$r(}t)j*t-|Yd}~d}~wwxYw)zpRead specified tags from file. The file handle position must be at the offset to a valid IFD. Nrrrz corrupted page list at offset %i>DErrrrrrr)rrrrrrrrrrSrrrr,r?rrrnrrrrrrhrk)r^rrrrrrtagcodesr codeformatrCrYrrrls r r_zTiffFrame.__init__s !   "   ggi  O6--rwwv7G7G/HI!LEt| !<== (..&&r* www'u ;A W E*d5519&=>qAD8# fd557?&CDs{dckmSYY7 . : ; O?$++MN N O"==  c!f% s$?E7E5"E25F0F++F0c|jjj|jt |j|j dS)zReturn TiffPage from file.Nr)rrr%rSrrrs r rzTiffFrame.aspages5 ##DKK0 4::EEr`c>d|d<tj|g|i|S)z4Read image data from file and return as numpy array.Fr)rr/r^rr0s r r/zTiffFrame.asarrays) #z6t6v66r`c>d|d<tj|g|i|S)z>Read image data from file and return RGB image as numpy array.Fr)rrrs r rzTiffFrame.asrgbs%"z~~d4T4V44r`c|jjr(|jdd|jjddfSt|j|jS)rNr&)rrQrrrrs r rzTiffFrame.offsets_bytecounts!sS == & &##BQ')D)DQR)HH H#D$4$4d6I6IJJr`c|jjr(|jd|jjdfSy)z5Return offset and size of contiguous data, else None.rr&N)rrQrrs r rQzTiffFrame.is_contiguous(s; == & &##A& (C(CA(FF F 'r`c.|jjS)r )rrPrs r rPzTiffFrame.is_memmappable.s}}+++r`c|tjvrt|j|St d|j j d|d)zReturn attribute from keyframe.rr)rM FRAME_ATTRSrerrbrmrgr^rs r rzTiffFrame.__getattr__3sB 4## #4==$/ /37>>3J3JD Q  r`cdjddjd|jDt|jfD}d|j|j |fzS)z1Return string containing information about frame.rc3 K|]}|ywrrrs r r!z$TiffFrame.__str__..?s A s rc32K|]}t|ywrrrs r r!z$TiffFrame.__str__..@s .s!61!A$!6r)*rr8rrrrrrrrM DATA_FORMATSrrrrr TAG_READERSrrGr% read_bytesrEr read_numpy TAG_TUPLEr(r bytes2str stripasciirUnicodeDecodeErrorrrTAG_ENUMrr,rr.rr<r rk)r^r tagheaderr0rr8rrrtype_r rkr<rrGrSreadfuncprocessrlrGs @r r_zTiffTag.__init__`s?   $$ && 779z1A5V.. "1 > ef//12? u D%%e,E)USq]%:E!HEEs# * (8(8 8(.v/B/BE(J1(M MD vzVbggn4mm$>?? GGFOt'''++D1 YujI! eBi3.>"2y% K"eBi3&6sBGGDM2"2y% K 2Y# !%4LE3et -E (( ( VT-G VEUVJ  uRyC'JuQx,G!HE !*U"3"9"9";< t}}$MM$'*!!6!66Eu:?!!HE    i D-- :U BC C DF&  G$NO "*MM#a&))*s6K ="K1L "K.1#LL M #MM c|tjj|jt |jSr)rMrEr@rrrs r rz TiffTag.names#yy}}TYYDII77r`c|jdk(r|jdk(rtjd|j|j }t j||jd|_ |jj|jt jd|jjd|_ yyy)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. rz correcting LSM bitspersample tagrzqAD     " "4#3#3 4uf.?.?.D.DQ.GHDJ !0 r`cR|dkrdnd|z}d|jt|jdz|jdfz}d|j|j||j fd|z}|jt jvrl|jdk(r7t j|j|jj}n>ttd|jD}nt|j||}|dkr ||z }|d|}|S|d |zz }|S) z/Return string containing information about tag.rr&rz%i%szTiffTag %i %s %s @%i Nc34K|]}|jywr)r)rrs r r!z"TiffTag.__str__..s%Aaff%Asrr) r rr<rrrrMrrkrr)r^rrrtcodelinerks r rzTiffTag.__str__skq6z$**s4::a='994::a=II %yy$))UD,<,<=fuE F 99 %zzQ dii0<AA%Adjj%A ABDJJeFCE Q; EMD>3JJKDIE DIr`c|jr<|jj||}|j|j|}|Sy)z;Return image data from series of TIFF pages as numpy array.)rRrN)rr/r])r^rrXs r r/zTiffPageSeries.asarraysD ;;[[((#(>F~~)/M r`c|jsyd}|jD]\}|y|jsy|s |jd|jdz}7||jdk7ry||jdz }^|jd}|jd}|js |jrt |jdk(r|S||t |j|jjzzk(r|Sy)z-Return offset to series data in file, if any.Nrr&) rr-rQr/r)r.rrDr<r=)r^rrVrSs r rSzTiffPageSeries.offsets{{ KK )D|==((+d.@.@.CCd((++ 4%%a( (C ){{1~##A& NNdnn#dkk2Ba2GM &74::.1D1DDD DM Er`c,t|jSr!r"rs r rzTiffPageSeries.ndim+r#r`c>tt|jSr%)rrrDrs r rGzTiffPageSeries.size0s74::&''r`c|S)z'Return sequence of all pages in series.rrs r rOzTiffPageSeries.pages5s  r`c|jS)z%Return number of TiffPages in series.)rrs r rzTiffPageSeries.__len__; yyr`ct|jdk(rMd|cxkr|jkr8nn5|jdj}|jj ||zS|j|S)zReturn specified TiffPage.r&r)r.rrrrrO)r^rCrs r rzTiffPageSeries.__getitem__?s^ t{{ q Q%8tyy%8KKN((E;;$$US[1 1{{3r`c#"Kt|j|jk(r|jD]}|y|jj}|jdj }t |jD] }|||zyw)z)Return iterator over TiffPages in series.rN)r.rrrrOrrn)r^rVrOrrs r rzTiffPageSeries.__iter__Fs~ t{{ tyy (    KK%%EKKN((E499% 'EAI&& 'sB Bc djd|jrtd|jzdnddjd|jDt |j |j |jdt|jz|jrd |jzndfD}d |j|fzS) z,Return string with information about series.rc3$K|]}|r| ywrrrs r r!z)TiffPageSeries.__str__..Ss     rz'%s'rr'rc32K|]}t|ywrrrs r r!z)TiffPageSeries.__str__..Wrrrz Offset=%izTiffPageSeries %i %s) rrrrDrr<rrr.rOrSr)r^rs r rzTiffPageSeries.__str__Qs II  4899*B/"444DJJ  S_,/3{{t{{*  '$**a88r`)NNNNFr)rgrorprqr_r/r rSrmrrGrOrrrrrr`r rrs. #@4((   '9r`rcfeZdZdZddiZGddeZedfdZdZ dZ d Z d Z d Z dd ZdZy )r aSequence of TIFF files. The image data in all files must match shape, dtype, etc. Attributes ---------- files : list List of file names. shape : tuple Shape of image sequence. Excludes shape of image array. axes : str Labels of axes in shape. Examples -------- >>> # read image stack from sequence of TIFF files >>> imsave('temp_C001T001.tif', numpy.random.rand(64, 64)) >>> imsave('temp_C001T002.tif', numpy.random.rand(64, 64)) >>> tifs = TiffSequence('temp_C001*.tif') >>> tifs.shape (1, 2) >>> tifs.axes 'CT' >>> data = tifs.asarray() >>> data.shape (1, 2, 64, 64) ra # matches Olympus OIF and Leica TIFF series _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4})) _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))? _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))? _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))? _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))? _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))? _?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))? c eZdZy)TiffSequence.ParseErrorNrrr`r rrrr`rc <t|tjr t|}t|trt t j |}t|}|s tdt|dtjr,|Dcgc] }ttj|"}}nt|dts td||_ t|dr|fd}||_ |jj|||_ |j|j sd|_y y cc}w#|j"$rKd|_t%|f|_d|_t+dt-t%|D|_Yy wxYw) a\Initialize instance from multiple files. Parameters ---------- files : str, pathlib.Path, or sequence thereof Glob pattern or sequence of file names. Binary streams are not supported. imread : function or class Image read function or class with asarray function returning numpy array from single file. pattern : str Regular expression pattern that matches axes names and sequence indices in file names. By default, the pattern matches Olympus OIF and Leica TIFF series. r$rznot a file namer/cd|5}|j|i|cdddS#1swYyxYwr)r/)rrr0im_imreads r rz%TiffSequence.__init__..imreads4U^7r%2::t6v6777s&/rr9c3"K|]}|f ywrrrs r r!z(TiffSequence.__init__..s!B11$!Bs N)r(pathlibPathrr)rr+rr,rr-r _patternsr@r_parserrr.rD _startindexrrn_indices)r^rrrrr0r!rs @r r_zTiffSequence.__init__sN" eW\\ *JE eZ ("499U#34EU -. . eAh -389aSa)9E9E!Hj1./ / 69 %G 7 ~~))'7;  C KKM99 %:( CDIe*DJ#D !!Bc%j0A!BBDM  Cs%D<#EAFFc dj|jddt|jzd|jzdt |j zgS)z4Return string with information about image sequence.rrz size: %iz axes: %sz shape: %s)rrr.rrrDrs r rzTiffSequence.__str__sOyy 1 c$**o-dii's4::.    r`c,t|jSr)r.rrs r rzTiffSequence.__len__s4::r`c|Srrrs r rzTiffSequence.__enter__rr`c$|jyrrrs r rzTiffSequence.__exit__rr`cyrrrs r rzTiffSequence.close r`Nc|j|jdg|i|}|j|jz}t|||j}|j dg|j}t |j|jD]k\}}t ||jD cgc] \} } | | z  }} } tj||j}|j|g|i|}|||<m||_|Scc} } w)zRead image data from all files and return as numpy array. The args and kwargs parameters are passed to the imread function. Raise IndexError or ValueError if image shapes do not match. rrr) rrrDrr<rar(rrr;r) r^rrr0rrDrXrrrr2s r r/zTiffSequence.asarraysT[[A 8 8 8 RXX%sE:.RXX. tzz: LE5'*5$2B2B'CDtq!QUDED++E4::>EU4T4V4BF5M     Es1D c R|js|jdtj|jtjtj z}|j |jd}|s|jd|d}t|dzr|jddjd|d d dD}|s|jdg}|jD]s}|j |d}|djd |d d dDk7r td |j|d d dDcgc]}|st|c}uttj|d }ttj |d }tdt#||D}t%|t|jk7rt'j(d|j+|_||_||_||_y cc}w)z#Get axes and shape from file names.zinvalid patternrz!pattern does not match file namesrrz*pattern does not match axis name and indexr'c3&K|] }|s| ywrrrrs r r!z&TiffSequence._parse..s4Q!q4Nc3&K|] }|s| ywrrrs r r!z&TiffSequence._parse..s.sCDAqa!eaiCrz*files are missing. Missing data are zeroed)rrrecompile IGNORECASEVERBOSEfindallrr.rr,r6rrr;rrqr(rrrrZrrDrr) r^rmatchesrrrrrD startindexs r rzTiffSequence._parses||//"34 4**T\\2==2::+EF//$**Q-0//"EF F"+ wS_ , MMF GJJL   %@s H$  H$ r)rgrorprqrr?rr r_rrrrrr/rrr`r r r csU:  I Y &.v1Cf   (&r`r ceZdZdZdZddZdZddZdZdZ dd Z dd Z dd Z d Z d ZdZd dZdZdZdZdZedZedZedZedZedZedZej8dZy)!r aBinary file handle. A limited, special purpose file handler that can: * handle embedded files (for CZI within CZI 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' 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 filno and can be memory-mapped. All attributes are read-only. ) r_file_mode_name_dir_lock_offset_size_closerNc||_d|_||_||_d|_||_||_d|_d|_t|_ |jy)aInitialize file handle from file name or another file handle. Parameters ---------- file : str, pathlib.Path, 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' or 'wb'. 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. Nr'TF) r rrrrrrrr NullContextrr)r^rBrWrrSrGs r r_zFileHandle.__init__9sU(         ]  r`c |jryt|jtjrt |j|_t|jt rtjj|j|_tjj|j\|_ |_ t|j|j|_d|_|j ]d|_nTt|jt"rP|jj|_|j d|_|xj |jj z c_d|_|jsu|j rNtjj%|jj\}}d||j |fz|_ n|jj|_ |jr.|j|jjk7r t'd|jj|_|jj|_ nt)|jdr |jj+|j|_|j |jj+|_d|_|jsA tjj|jj.\|_ |_ |jj2|_n t'd |j r%|jj5|j |j6z|jj+}|jj5|j d |jj+|_|jj5| |jj9d|_y#t,$r t'dwxYw#t0$r d |_ Y-wxYw#t0$rYwxYw#t,$r d|_YywxYw) zOpen or re-open file.NTrFz%s@%i%szFileHandle has wrong moder%zbinary stream is not seekablezUnnamed binary streamzNThe first parameter must be a file name, seekable binary stream, or FileHandler)rr(r rrrr)rrrealpathrrrrrrrr splitextr,r-rr?rrbrWr%rrr)r^rextrs r rzFileHandle.openYs  88  djj',, /TZZDJ djj* -))$**5DJ$&GGMM$**$= !DItzDJJ 3DHDK||#   J /zz~~DH||#  LLDJJ.. .LDK::<< " 0 01A1A BID#!*dDLL#-F!FDJ!%!1!1DJzzdjjDJJ,<,<< !<==))DJ DI TZZ ( B !zzDH||##zz0 DK::9,.GGMM$((--,H)DItz !XX]] 8  << HHMM$,, ' :: ((--/C HHMM$,, *DJ HHMM#  ! HHOO DLA B !@AA B&9!8DJ9"  ( ! DL !sCP:8AQ9Q)!Q9:QQ&%Q&) Q65Q69R  R cr|dkr|jr |j}|jj|S)z5Read 'size' bytes from file, or until EOF is reached.r)rrrrr^rGs r rzFileHandle.reads+ !8 ::Dxx}}T""r`c8|jj|S)zWrite bytestring to file.)rr)r^ bytestrings r rzFileHandle.writesxx~~j))r`c6|jjS)z"Flush write buffers if applicable.)rrrrs r rrzFileHandle.flushsxx~~r`c|js tdtj|j|||j |z||S)z+Return numpy.memmap of data stored in file.z%Cannot memory-map file without fileno)r<rWrSrDorder)rr,r;rrr)r^r<rDrSrWr!s r rzFileHandle.memmap_arraysE||DE E|| HH<<&(   r`c|j}tj|}|dkr |jn||jz}|m tj ||||} |rP| jjs:| jd| j| jj} | S|j} t|j |}|j#d}d} |dkDrn|jt||} t%| } | dk(rnB|| z}tj| |} | || | | j&z| | j&z } |dkDrnt)|dr|j+|j#| S#t $r:|j|} tj| ||j} YkwxYw)zReturn numpy array from file. Work around numpy issue #2230, "numpy.fromfile does not accept StringIO object" https://github.com/numpy/numpy/issues/2230. rTrrr)rr;r<rr=fromfilerrrrdrKrrrJrDrqr>rar.rGr-rr)r^r<r sep chunksizerrrrGrXrCrDrrs r rzFileHandle.read_arraysXX E""QYtzzEENN,B ; EE5#> fll33%V\\%>%>%@AM 3::t$kk"oQh773y$/0D4yH1} H D##D%0D-1C ) * TYY EQh 3 IIK{{5!!7 Ewwt}))$u=BBD EsF?G G ctj} |j|j|||}|dk(r|dS|S#t$rtj |}||j |jz}tt||jz}|jj|}|j||||}YwxYw)zReturn numpy record from file.r8r&r) r;recr#rr?r<rr=rsequencerr)r^r<rDr8r(recordrGrCs r read_recordzFileHandle.read_recordsii M\\$((E5I\NF"QJvay2F2 MKK&E} enn48E?+enn>> with NullContext(): ... pass c|Srrrs r rzNullContext.__enter__Lrr`cyrrrs r rzNullContext.__exit__Orr`N)rgrorprqrrrr`r rrDs r`rc.eZdZdZdZddZdZdZdZy) OpenFileCachezKeep files open.)rpastrrGNcfg|_i|_| tn||_t ||_y)zInitialize open file cache.N)rFrrrrrG)r^rGrs r r_zOpenFileCache.__init__Xs*  %)\KMt I r`c|j5||jvr|j|xxdz cc<nF|jr:|jd|j|<|jj |dddy#1swYyxYw)zRe-open file if necessary.r&N)rrrrrFr6)r^rs r 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QC QC~A!aQ1q I)iY9yE%eU5u M-m]=}C#cS3s K+k[;{G'gW7wO/o_?rrr`r REVERSE_BITORDER_BYTESzTIFF.REVERSE_BITORDER_BYTESs  ! r`cLtjtjdS)Nrr)r;rrMr rr`r REVERSE_BITORDER_ARRAYzTIFF.REVERSE_BITORDER_ARRAYs ; ;7KKr`c"ddl}|jSrA)mmaprN)r s r rNzTIFF.ALLOCATIONGRANULARITYs)))r`N)BrgrorprqrErrrrrrrr[rQrrrrVrr%rjrrrrrYrrrr]rrrrrrrrrrrXrYrr rrr r r r rJ r r r r r r r r r8 rIr r r r rNrr`r rMrMsS)m  ^4! F@ 2 ,3j&   ! 0 : $. `-^@DB   .&*" H 2 h? B <        F P1 f     E- ^9 v! F  I V+ Z $L*r`rMc|dk(r|dz}d}|dz}d} |dz} |dz} n)|dk(r|d z}d}|d z}d } |dz} |d z} n td |i}|d}g} tj} |j}t | |kr | ||j |d}|dkDr td i}|j | |z}|j}d}t|D]}| | |||dz\}}| | ||dz|| z\}}|| z }|j|t|} tj|}d||t#|dz|dfz}tj$|}||kDs||vr| ||d}|dks||j&|z kDrtj!d|z|j)|||vr||d}||||||}nv|dk(s |dkDr|ddk(rt+|||||}nT||vs|ddk(r| ||j |}n/t-|||||}n|ddk(s|dk(r|d |}n | ||d |}||vr%|tj.vrt |dk(r|d}|dk7r;|ddk(r3t1|t2r# t5t7|j9}|||<| j=||j)|| ||j |d}|dk(rnI||j&k\rtjd|zn!|j)|t | |kr| r |dk(r| d} | S#t $rtjd|zY1wxYw#t$rtj!d|zwxYw#t:$rtjd|zYwxYw)z|Read tags from chain of IFDs and return as list of dicts. The file handle position must be at a valid IFD header. rrrrrrrrrrrzinvalid offset sizeNrrrrrrrr&zinvalid tag value offset %irrrrrzinvalid page offset %i)r,rrrr.rr?rrrnr@rrMrrrrrrrGr%rrrr(rrrrrr6)rr8rtagnames customtagsmaxifdsrrrrrrrXrrSrrrCrrrYrrr rkrr<rrGrs r read_tagsr sN Q 3  #o % & q 3  #o % & .//  F ]]F WWYF f+  ; (:;A>Et| !<== www'ggiu* A T%%!)-DEKD%!*d519uw.OPLE5 W E<<c$i0D H))%0iU1X)>aIIC??3'Dj DJ$6 e4Q7A:"''D.!8!--(E(NOO:%)$/2H$RE5*MEaZEAI%)s2B&r9eUJOEX%rc)9"3 6E&r9eUJOErc!UaZet sE%4L1:%$dnn*Du:?!!HEzeBi3.:eU3KT%j&7&=&=&?@EDJU* X  d   bggj&9:1= Q;  RWW  MM2V; <  G f+ J'Q, MC  MM;fD E   Hmm$>$FGG H@*TMM"Kd"RSTs0+M-N"N*!NN"N'*!OOcDt|||tjd}dD]} t||||<d|vrE|ddd} |dk(rt|ddd|d<|S|dk(r|dddj d |d<|S|S#t$rYmwxYw#t$rY|SwxYw) z,Read EXIF tags from file and return as dict.r&r )rrrNrsASCIIsUNICODEutf-16)r rMrrr?r)rr8r<r rexifridcodes r rr4s RJ JD2 "4:.DJ m$Ra( --&/]0CAB0G&H]# K >)&*=&9!"&=&D&DX&N]# K4K      K s)BB B BB BBc>t|||tjdS)z+Read GPS tags from file and return as dict.r&r )r rMrrr8r<r rs r rrHs RJ q IIr`c*ddi}t||||dS)z8Read Interoperability tags from file and return as dict.r&rr )r )rr8r<r r tag_namess r rrMs +,I RJ 1 EEr`c|ddk(rdn||dz}|tj|jz}|j|}t ||k7r#t j dt ||fz|S)z2Read tag data from file and return as byte string.rrrz failed to read all bytes: %i, %i)r;r<r=rr.rrrr8r<r rrCs r rrSso9#CU2Y)>E U[[  ( ((E 775>D 4yE 8CIu;MMN Kr`cB|j|jdS)z5Read tag data from file and return as unicode string.r)rrr s r read_utf8r ]s 775>  ))r`cJ|ddk(rdn||dz}|j||S)z2Read tag data from file and return as numpy array.rrrgrr s r rrbs.9#CU2Y)>E == &&r`cD|j||dz|}d|_|S)z7Read ColorMap data from file and return as numpy array.r)rr)rrD)rr8r<r rcmaps r rrhs' ==U2Y. 6DDJ Kr`c|j|} tjtt |dS#t $rt jd|zYywxYw)z2Read JSON tag data from file and return as object.rinvalid JSON '%s'N)rjsonloadsunicoderr,rrr s r rrosO 775>D2zz')D/7;<< 2 )D012s';!AAc |jtj|}t|}|dDcgc]F}t |dj |d|d|dt |dj fHc}|d<|d}t |dj |d|d|dt |dj f|d<|Scc}w) z9Read FluoView mm_header tag from file and return as dict.r'rGrr&rrrr3 )r+rMr8 recarray2dictrr)rr8r<r rmmhrs r rrxs ..9. =C  C\"  1Q4   !A$!adIadO4I4I4KLC  MA!A$ ! ! !!A$ C  JsA Cc,|j|dzdS)zARead FluoView mm_stamp tag from file and return as numpy.ndarray.r: rr r s r rrs ==T)1 --r`cp|dvr|dk(sJi}|dk(r<|jdd|zj|d}d|dddf|ddd fz i}|S|ret|D]W}tjd |j d d} | d vr|j d At || |d \} } | || <Y|S)zuRead MetaMorph STK UIC1Tag from file and return as dict. Return empty dictionary if planecount is unknown. )r;r]rr;.read_ints9 funbgga%i.@A A:uQx050r`z_TagId%irNrr'z#invalid offset for uic tag '%s': %irYrrr%isrzcorrupt string in uic tag '%s'zinvalid string size: %irf rz%i(r).r&r)rMr rrrrrrr%r)r rrrrrr,rnr6rrDrr.)rr_r rSr rr<rroffrkrGrYstrings` r r r s1.mmE* e }}Q"H ggi d #*CQwC<8O CtSkQRSy GGCL }Tz  #  (  a58# / !!- ) )'+ #z  u MM%$, >qA#2FEi./E E MM:TA B6=> > %z" CA:DD 5 ut|RWWT]CAFsK"9V#45 V$ >EF !:T!ABB Ce  5=J&E %<MM%+A.E{{2!#f f 5MM%1G)HIE5zQa  a ;] .E!8:--.sKK76K7c,tjd|jdd}tjd|z|j|ddd}tjd|jd\}}|dk(r1tjd |jd }|d|dz }nStjd|jdd}tjd|z|j|d}t||| S) z:Read UIC ImagePropertyEx tag from file and return as dict.rr&rr Nrz X_a0 A:   "2JGDM  N   s E++ E76E7cxtjd|jdd}|jd|S)z>Read LSM sequence of float pairs from file and return as list.Read LSM ChannelColors structure from file and return as dict.F)MonorT ColorNamesz >| LF}}F8GGC'M WWTG^ $F E f+/}}T6"1:.q1 Yva!d(345D # f+/!F< Mr`cxi}|g}tj}tjd|jdddk7rtjd|S|jd |d|jd\}}}|d k(r$t t |j|}nD|dk(r|d |jdd}n#|d k(r|d |jdd}nd}|tjvr.|j|tj|}g} | ||<| }n|tjvr'|j|i} |j| | }nI|tjvrtj|}|||<n|d k(r|j}n||d|z<|s |SR)z9Read LSM ScanInfo structure from file and return as dict.r rrizinvalid LSM ScanInfo structurerz**,C  "jjo eKKMED !{{}1C<0Q;"ED ::</F3Ks w& C 2J6$e 57 7J;8< M1   !U|4U?"EM)!Em+ E !s$C??2D? D  D 3EEc|jtj|}|j|jj |}t |}|dd|d|d<|dd|d|d<|S)z7Read NIH_IMAGE_HEADER tag from file and return as dict.r'r Nr~ rf re )r+rMr rr<rJr )rr8r<r rr{s r rrsw t,, BA qww##I./AaA7,a n-AgJgm( $AdG Hr`c|jd tjd|jd\}}|dk7s|dk7rt|jdtjd|jd\}}}}|dk7s|d k7rt t t|j|d d }|d kDrt|dd |d ni}||fS#t$r t d wxYw)a;Read ScanImage BigTIFF v3 static and ROI metadata from open file. Return non-varying frame data as dict and ROI group data as JSON. 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 v3 metadata. rz<2sHrrrrz 7  BO  '-}}Wbggbk'J$wu I AO". is(;<=J8= yS$t4rH x  <:;;??!"i~tLF9x<==GGLMM)d"2BGGAJ?MFE <== ==Wu_4bggb5j6I JD!9addaddAJqt!t* F:">??GGNMM)d"2BGGAJ?MFE >?? )"iud KF ("?@@GGOMM)d"2BGGAJ?MFE ?@@"2y$tDF: Mg 97889s H!!H6ct)zRead MetaSeries non-TIFF hint catalog from file. Raise ValueError if the file does not contain a valid hint catalog. )r)rs r read_metaseries_catalogr< s   r`c ddd|g}dg}g}d}d}d}d}d d d |fd d d|fddd |fddd|fddd |fddd |fddd|ff} | D]\} } } } | j|vr| j} n| |vr0|dk(r| ddd} || }| t|} n|g}|j| tj|dz| z|D]6}| ||}|j||jt|8|sydj |}dj |}||z}t||d<tj|dt|zzg|}ddt||d fd!dt|d"z|d ffS)#aReturn IJMetadata and IJMetadataByteCounts tags from metadata dict. The tags can be passed to the TiffWriter.save function 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. IJIJJIJIrrrc6|jdddd|zSNr beler@ rrCr8s r _stringz%imagej_metadata_tags.._string {{8Dt&._doubless#{{9c$i8@4@@r`c"|jSr)tobytesrF s r _ndarrayz&imagej_metadata_tags.._ndarrays||~r`c|SrrrF s r _bytesz$imagej_metadata_tags.._bytesrr`Infoinfor&LabelslablNRangesrangLUTslutsPlotplotROIroi Overlaysoverrrrrr`r[rTrZr)rr.r6rrr)rr8r rbodyrG rJ rM rO metadata_typesrCmtyper r\rrkrCs r rkrks.'*95 6FJ DIA !W% 7D'* 7Ax( $) !V$ F# WdF+N$2)UE4 99;( "))+C    $B$KE# =KEXF efkk)c/5AAB )Ey)D KK    c$i ( ))$  88D>D XXf F D=DKJqMY#J*?@N:NJ SYd+ S_):t< r`c d}d}d}d}d|fd|fd|fd|fd |fd |fd |fd }|jtd |jD|s td|dddvr td|d}|dks|dkDr td|dz dz} t j |d| zz|dd| dzz} d| dzz} d} i} t | ddd| dddD]\}}g}|j|t|tf\}}t|D],}| dz } | || z}|j||| |||} .|dk(r|dn|| |j<| S)zReturn 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. c6|jdddd|zSrB )rrF s r rG z imagej_metadata.._stringrH r`cRtj|dt|dzzz|S)Nrr)rrr.rF s r rJ z!imagej_metadata.._doubless%}}Y#Ta*@A4HHr`cNtj|djddS)NrrrY)r;rrarF s r _lutzimagej_metadata.._luts"g.66r3??r`c|SrrrF s r rO zimagej_metadata.._bytesrr`rP rR rT rV PlotsrZ r\ )rQ rS rU rW rY r[ r] c36K|]\}}|ddd|fywrrrs r r!z"imagej_metadata..s =daa"gq\ =szno ImageJ metadataNr)r> r? zinvalid ImageJ metadatarri$z#invalid ImageJ metadata header sizer4sIrr&) rLrrr,rrr(r@rrrnr6r)rCrr8rG rJ re rO r_ header_sizentypesr rcounterrXr` r rrr\rYpos1s r rBrBsII@'"G$H%$6"f%N =n&:&:&< == -.. BQx))233Q-KR;,>??Ao! #F ]]9uv~5tAFQJ7O PF fqj.CG FF3Q3K16C u#'' %0@*/MN du A qLGG,,D MM$tC~y9 :C   -2QJvayFtzz|C Mr`c@d}i}|jD]X} |jd\}}|j}|j}tt |fD] } ||}n|||<Zd|vr t d|S#t$rYwwxYw#t$rYAwxYw)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} c.ddd|jS)NTF)truefalse)r)rs r _boolz*imagej_description_metadata.._bool' su-ciik::r`rrAznot a ImageJ image description)r rr?rrrr,)r{rr rXrrCrr<s r r0r0 s;F&&(  zz#HCiikiik5%( E Cj  s  v9:: M     s#BB B B BBc |r tdt||}|ddv}d|zg}g} |jdt|ddz|d }| jd n| jd t |z|d d kDr|jd|d z||sd}|r|r| jd|z|d d kDr|jd|d z|dd kDr*|jd|dz|| jd|| jdt |z|j D])\} } | j| j d| +dj|| zdgzS)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 z!ImageJ colormapping not supported)rgbrrz ImageJ=%sz images=%iNrTzhyperstack=truez hyperstack=%srr&z channels=%i grayscalezmode=%sz slices=%irz frames=%iz loop=falsezloop=%srrr')rr\r6rrrrr) rDrt colormapedrcr?rWloopr0rXr6rCrks r rere? s2!"EFF C (E )v CG# $F F MM+cr 334  '( oZ(889 Qx!| meAh./ |Cd i$&' Qx!| kE!H,- Qx!| kE!H,- < MM, '  i$t*,-lln6 U e456 99Vf_t+ ,,r`c,td|D}t|}d|cxkDrdkDr td||ddvxr|dkD}|r|ddvr td|s|dk(r|ddk7r td |s|ddk(r d d|z z|zSd d |z z|zd zS) zReturn shape normalized to 6D ImageJ hyperstack TZCYXS. Raise ValueError if not a valid ImageJ hyperstack shape. >>> imagej_shape((2, 3, 4, 5, 3), False) (2, 3, 4, 5, 3, 1) c32K|]}t|ywrrrs r r!zimagej_shape.. s(Q#a&(rr&rz1invalid ImageJ hyperstack: not 2 to 6 dimensionalrrrz*invalid ImageJ hyperstack: not a RGB imagez.invalid ImageJ hyperstack: not a non-RGB imagerr)rr.r,)rDrt rs r r\r\y s (%( (E u:D4|!|LMM {Bi6!.dQh uRy&EFF 419raIJJ eBi1nq4x 5(( 1t8 u $t ++r`c P|j|tj|S)zReturn JSON image description from data shape and other meta data. Return UTF-8 encoded JSON. >>> json_description((256, 256, 3), axes='YXS') # doctest: +SKIP b'{"shape": [256, 256, 3], "axes": "YXS"}' rD)rLr dumps)rDrs r rfrf s! OO%O ::h r`c|dddk(r0td|ddjdD}t|S|dd d k(r|ddd k(rtj|St d |) aReturn metatata from JSON formatted 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)} Nrrvc32K|]}t|ywrrrs r r!z,json_description_metadata.. sCc!fCrrr,r{ r&ru}zinvalid JSON image description)rrrr r r,)r{rDs r r*r* sx2A("Ck!B&7&=&=c&BCC%  2A#+bc"2c"9zz+&& 5{ CCr`c6|jds td|ddh}i}|g}d}|jD][}|s|j}|s|ddk(r|ddd k(rU|d =|d }|d d}|rd j ||||<|dd dk(r&t j ||d}d|_|||<~d}|d d }|dd dk(rg}n ||vrg}d}ni}|j||||<|rj||jdd }t|d k(rd|dj<|\} } | dd dk(r(jd| jD2t| j| j<^|S)alReturn metatata from FluoView image description as dict. The FluoView image description format is unspecified. Expect failures. >>> 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'}} r z"invalid FluoView image descriptionNzRegion Info (Fields)zProtocol DescriptionFrz End]rr&rrzLUT rr)rrTrzRGB c32K|]}t|ywrr)rrt s r r!z0fluoview_description_metadata.. s=3s8=r) rr,r rrr;rrDr6rr.rCrZ) r{ignoresectionsrXsectionscommentrr rr{rCrks r fluoview_description_metadatar s  ! !# &=>>02HI FxHG&&(+9::BCyG#RL"2,Abz$(IIgdm$'+GDGMMO $  U r7f  NN=u{{}= =#)%++-#8GCIIK W+9X Mr`ci}|jds|SdD]}|j|d}|jdD] }|dddk7r |j}|d}|dtjvr4 t j j dj|d |d <ktj|d\}t|dtr ||d}n|Dcgc]}|| }}tur |dd k(rd g}tfd|D}tk(rdj|}nt|d k(r|d}|||<|S#t$rdj|d d||<YwxYwcc}w)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)} rz#:=,()rrNrrrz%Y-%m-%dT%H %M %S.%fr&r&notNaNc3.K|] }|ywrr)rrr<s r r!z/pilatus_description_metadata..!s0AuQx0r)rrrrMr r|strptimerr?r(r rrrr.) r{rXr1rrrrrr<s @r rWrW sF  ! !$ ' 2!))!S1 2!!$' 8t  zz|Aw 7$-- - 2%-%6%6%?%?HHTN$:&z" ,,T!W5 gaj% ('!*%F'./!d1g/F/ E>fQi50WF000 C<XXf%F [A AYFt 56 M# 2"xxQR1t  20s92E% E8 E54E5c|jds tdi}|jd}|djj dd\}}|j||j<t |dk(r|S|djd}|dj|d<|ddD]@}|jd \}}t |j||j<B|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') {'Aperio Image Library': 'v1.0'} zAperio Image Library z invalid Aperio image descriptionrrNr&rr'z = )rr,rrrsplitr.rZ)r{rXlinesrCrkrrs r svs_description_metadatar #!s  ! !"9 :;<< F   d #Eq!((q1JC++-F399; 5zQ !HNN3 Eq!F2Jab 4ZZ& U$U[[]3syy{4 Mr`c|j}|sgS t|}g}|j dD]}i}|j dD]}|j dd}t |dkDr0|\}}t|j||j<S|dj}|sid|vr|dj||g|d<|j||S#t$rtjdgcYSwxYw)zReturn metadata from MetaMorph image description as list of dict. The MetaMorph image description format is unspecified. Expect failures. z+failed to parse MetaMorph image descriptionr r2r&rr') rrrrrrr.rZr6)r{rXrrrrrks r stk_description_metadatar .e!s6!T5;Qr`)rrrc|D]S}|j}|s|i||j<(d|vs-|d}|d}|d}|vr||||<O|||<U|S)Nidtyperk)rr) rrXchildrrrGrparsetypess r r z.metaseries_description_metadata..parseg!s "E\\F$)%$4uyy!v~4L6N7O: (a F1I !F1I " r`r`z r)rr,rrirrrr)r{rradictr r s @@r rSrS]!sx  ! !, /?@@/   K (DC1Q RE" $OE$]3;;L$Om Lr`ct|S)z9Return metatata from ScanImage image description as dict.)r# rs r rcrc~!s  $$r`c| tj|S#t$rtjd|zYywxYw)z2Return metatata from ScanImage artist tag as dict.r N)r r r,rr)artists r scanimage_artist_metadatar !s74zz&!! 4 )F234s !;;rYcdS)z2Try replace decorated function by module.function.c|Srr)r!s r rz_replace_by..!sQr`) importlib import_modulerr)module_functionpackagerprefixrldecorate_warnr s ` ` @@r _replace_byr !s r`c|j}|j}t|dkr td|jdvr td|jj dk(xs.t j dk(xr|jj dk(}|jd}|d d d z|d d z|_tj|d d| |r|d d d z|d d z|_tj|dd }tj|d d }|dd d d f}tj|}|j|}||_|S)aDecode floating point horizontal differencing. The TIFF predictor type 3 reorders the bytes of the image values and applies horizontal byte differencing to improve compression of floating point images. The ordering of interleaved color channels is preserved. Parameters ---------- data : numpy.ndarray The image to be decoded. The dtype must be a floating point. The shape must include the number of contiguous samples per pixel even if 1. rzinvalid data shapedfeznot a floating point imagerrrrNrrrrr.) rDr<r.r,rTr8rrr;rswapaxesascontiguousarray)rCrDr< littleendians r rr!s? JJE JJE 5zA~-.. zz566::''3. !Adjj&:&:c&A 99W Dse#eBCj0DJ LLBg483BZ%'%*4 >>$B 'D >>$B 'D TrT ?D  " "4 (D 99U DDJ Kr`z_tifffile.decode_packbitsctjddk(rtnt}g}|j}d} |||dz}|dz }|dkr|||||z||z }n|dkDr||||dzd|z z|dz }K#t $rYnwxYwtjddk(rdj |St|S)zuDecompress PackBits encoded byte string. PackBits is a simple byte-oriented run-length compression scheme. rrr&rr`)rrcordrrCrrr)encodedr\rX result_extendrns r rr!s++a.C'3\D FMMM A  WQZ 1$A FA3wga!a%01QSga!a%0C!G<=Q    "{{1~4388F G%-GsA B B  B z_tifffile.decode_lzwc t}|dz}tjtjddk(r"t dDcgc] }t |}}n"t dDcgc]}t|g}}|jdfd}ddtd d fd d td d fddtdd fddtdd fd}|d\}d|dkr td|dk7r tdd}d} g} | j} |}|z |dk(s|k\rn|dk(r:|dd} | j} d}|d\}|}|z |dk(rnV| | |n:|kr |}| | |ddz}n | }||ddz }|}| | ||dz }|} ||vr ||\}|dk7rtjd|zdj| Scc}wcc}w)a+Decompress LZW (Lempel-Ziv-Welch) encoded TIFF strip (byte string). The strip must begin with a CLEAR code and end with an EOI code. This implementation of the LZW decoding algorithm is described in (1) and is not compatible with old style LZW compressed files like quad-lzw.tif. rrrrY)rrc dz}||dz} d|d}|dzz}|z}|z S#t$r!d|ddt|z zzd}Y;wxYw)z@Return integer of 'bitw' bits at 'bitcount' position in encoded.rrz>Irr)r?r.)rrrbitcountr maskshrrs r next_codezdecode_lzw..next_code "sA  EEAI & ?$?1%D A  s{  ?$Gq3q6z$: :;A>D ?s .'AArrm 11111111100000000000000000000000rrNr 11111111110000000000000000000000rPrl 11111111111000000000000000000000rr 11111111111100000000000000000000)riiirrz(strip must be at least 4 characters longz strip must begin with CLEAR coderZNrr&z&unexpected end of LZW stream (code %i)r`)r.rrrrcrnchrrrCrr,r6rrr)r len_encoded bitcount_maxrnewtabler switchbitchbitwroldcoderX result_appendr table_appendlentabledecodednewcoder r r rs` @@@@r rr!sQg,K?L ]]F {{1~$)#J/qCF//(-c 31E1#J33 OOF  S+Q/ 0"c-q1 22s.232s.23 K "#&OD#tHQCDD{c;<< DG FMMM {D 3;(l2  3;QKE <EF 88F K03s G&+G+z_tifffile.unpack_intsc :dk(rvtj|d}tj|}|dzr5|jd|d|dzz z}|ddd|fjd}|j |Stj |}dvrtj||Sdvrt dz|jd vr t d tfd d D}||jk7r t d |dk(rdt|zz}|zdz}|rd|z }|dzz }tdzd|zzd}d|jz}tj} |t|dz|z|zzz} tj| f|} d} t!| D]G} | dz}||||z} | ||d}|| dzz}||z}||z | | <| z } | dz|zdk(sC| |z } I| S#t"$r!| ||d|t|z zzd}YXwxYw)aDecompress byte string to array of integers of any bit size <= 32. This Python implementation is slow and only handles itemsizes 1, 2, 4, 8, 16, 32, and 64. Parameters ---------- data : byte str Data to decompress. dtype : numpy.dtype or str A numpy boolean or integer type. itemsize : int Number of bits per integer. runlen : int Number of consecutive integers, after which to start at next byte. Examples -------- >>> unpack_ints(b'a', 'B', 1) array([0, 1, 1, 0, 0, 0, 0, 1], dtype=uint8) >>> unpack_ints(b'ab', 'B', 2) array([1, 2, 0, 1, 1, 2, 0, 2], dtype=uint8) r&z|BrrNr )r&rrrrrzitemsize not supported: %ibiuz invalid dtypec34K|]}d|zk\s |ywrNr)rrr=s r r!zunpack_ints..w"sB1A0AQBs )r&rrrzdtype.itemsize too smallr10rrr)r;r unpackbitsrarZr<r,r^nextr=r.rrTrrrlrnr?)rCr<r=r itembytesskipbitsshrbitsbitmaskdtypestrrrGrXr rrrrs ` r rrM"sw41}d+% A:<<Fa&1*n$=>D7F7 #++B/D{{5!! KK E?"e,,++5@AA zz))B BBIENN"344 {c$i-H, 1$Hx<!mh&G(S.3=0!4GUZZH ]]F SY]v'88'CD ED [[$% (FH 4[ !A  * + K(A&q)D A GOq H EV q  H ! M K(A9s1v3E(F$FGJD Ks5 G00'HHc \ tjttj| dkrt fd|Dst dt |zt fddD}tj|j|z}tj|jt|fj}t|D]\}}|ttj||dzdz }|tdd |zzd z}|rqjd z|zdz|z} | |jjd zkDr|j!d }|d | zdz d |zdz zz}|d | jd zz zz}||dd|f<|j#d S)aReturn array from byte string containing packed samples. Use to unpack RGB565 or RGB555 to RGB888 format. 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 ------- result : 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, '."sN1qENNQ$66Nrzsample size not supported: %sc3nK|],}tj|jdzk\s)|.ywr )r;r<r=)rrbitss r r!zunpack_rgb.."s+ FA%++a."9"9A"="Ea Fs*55BHIr&N0br rrrr)r;r<rrsrr,rr rr8rlrGr.rTror=rZra) rCr<r7rescaler+rXrrrGor s ` @r rr"sB KK E uyy' (D BJ3N NN83};MMNN F F FB   D%//B"6 7D [[$))S%78%** EFM* 3 C -A"89: : Sc !1 %% ..1$,q0C7A4::&&**HHSM !Q$(3 + +A !U^^a/01 1Aq!t   >>" r`z_tifffile.reverse_bitorderc |jd}tjtj||y#t $r"|j tjcYSt$r tdwxYw)ajReverse bits in each byte of byte string or numpy array. Decode data where pixels with lower column values are stored in the lower-order bits of the bytes (FillOrder is LSB2MSB). Parameters ---------- data : byte string or ndarray The data to be bit reversed. If byte string, a new bit-reversed byte string is returned. Numpy arrays are bit-reversed in-place. Examples -------- >>> reverse_bitorder(b'\x01\x64') b'\x80&' >>> data = numpy.array([1, 666], dtype='uint16') >>> reverse_bitorder(data) >>> data array([ 128, 16473], dtype=uint16) rrzslices of arrays not supportedN) rr;takerMr rb translater r,r)rCrs r rr"sf.Dyy! 4..$? ;~~d99:: D!"BCCDs7:(A8$A8ctj||d}tj|d|j}|rtj|}|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) r&rr)r;r rollaxisrr )imagerzcontigs r rr"sD. JJxQ /E NN5!UZZ 0E ''. Lr`ctj}t||}||jk(r|S||jk(r |ddddddfS||j k(r|ddddddddfS||j k(r|dddddddddfS||jk(rtj|ddS||jk(r"tj|ddddddddfS||jk(r%tj|ddddddddddfS||jk(r&tj|dddddddddddfSy)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) rMrrYr r rrrr;r rrr)r orientationrs r reorientr #s_""K+{3Kk)))  ,, ,S$B$\""  ++ +S$B$1_%%  ,, ,S$B$"a'((  ++ +~~eR,,  ,, ,~~eR,S$B$\::  ,, ,~~eR,S$B$1_==  ++ +~~eR,S$B$"a-?@@ ,r`cxtj|}g}g}g}t|j|j|D]@\}}}|j ||f|j |df|j ||zBtjjj|||dj|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. Example ------- >>> 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]]) rF) writeable) r;r/r(stridesrDrCr6lib stride_tricks as_stridedra)r{repeatsrarDr rr2rs r rr+#s,  aAG EGqyy!''731a aV1vq1u 99 " " - - 5'U .  ggr`ct|t}|r|n |j}t||k\r|Sd|t|z z|z}|r|S|j |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) r)r(rrDr.ra) data_or_shaperis_shaperDs r r_r_N#sa"-/H%M=+>+>E 5zT D3u:% & .E5>-"7"7">>r`ct|t|k7r tdtfdt||D\}}t|dj |fS)zReturn 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') z)dimensions of axes and shape do not matchc3BK|]}|ddkDs|dvs|yw)rr&Nr)rrrs r r!zsqueeze_axes..r#s%Paqtax1Q44<Psr')r.r,r(rr)rDrrs `r rrg#sS 5zSYDEEP3ud#3PQKE4 < &&r`c|D]}||vstd|z|j}t|D]}||vs||z}d|z}|j|}|j |Dcgc]}|j |c}}|Scc}w)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) zunknown axis %sr)r,rDrOra transposer)r rasaxesr~rDs r transpose_axesr v#s5 V .34 45 KKEv! T>9D5LE! MM% E OOf=TZZ^= >E L>s%Bct|}t|}t|t|k7r tdt|}t|}||k7rtd|d||r|syt dt|t|z }|r|d|zz}t|dz }d}d} g} |ddd D]w} || z}|dkDr%||dk(r| dk7r|dz}|dkDr||dk(r| dk7r| ||k(r-|| ||zk(r"| ||z} | j |||dz}g| j |ydj t| |dS) zReturn axes matching new shape. 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' r(zcannot reshape rr'rrr&Nr)rr.r,rrr6rrO) rrDnewshapeunknownrGnewsizelendiffrprodnsprodsrXnss r r$r$#sn %LEXH 4yCJ233 5>DhG weXFGG x!SZ#h-/0GdWn, E QA F E Fttn #" !eaA "' FA!eaA "' q>fa(88 U1X E MM$q' " FA MM' " # 778F78,- ..r`cXt|}|dk(r td|dk(r|dj|d|i|Std|D}|jd|f|jj z}|jj }t|||}|tjdz}|dkD|jj_ ttd ||jjj } || ||fd } |dkrt|D]\} } | | | nDt j"j%|5} | j'| |t)|ddd| j+d|jj_ |S#1swY6xYw) zRead data from sequence of TiffPage and stack them vertically. Additional parameters are passed to the TiffPage.asarray function. rzno pagesr&rc3&K|] }|| ywrr)rrs r r!zstack_pages..#s3qQ]3rN)rrr)rGrc|n|j|jj|j||jddd|||<|j |jjyy)z!Read, decode, and copy page data.NF)rrr)rrrr/rr)rVrr filecacherr0s r r\zstack_pages..func#sd   NN4;;11 2%DHY^^EELRCJ OODKK22 3 r`)r.r,r/r rrDr<rmultiprocessing cpu_countrrrrErro concurrentfuturesThreadPoolExecutormaprnr)rOrrrr0r0rerDr<r r\rrVexecutors r r r #s ZF {$$ {uQx$9C9&99 3E3 3E MM4M I,, ,E NN E UE *C$..0A5 #->ELL  J ell&=&=&B&BI"YT&4A~ ' GAt qM    2 2: > 5( LLueFm 4 5OO#'ELL J  5 5s F  F)cXt|}t|}t|t|k(sJd}tt||D]Q\}\}}|dkDr|dkDr||kDr |||<|||<|dz }(|dkDr|dkr t dt j dS|dk(rd}|d||d|fS)zReturn cleaned offsets and byte counts. Remove zero offsets and counts. Use to sanitize _offsets and _bytecounts tag values for strips or tiles. rr&zinvalid offsetzempty byte countN)rr.ror(r,rr)rcountsr2rr rgs r rr#s7mG &\F w<3v; && & As7F34 . 6Aq q5QU1u q FA UqAv-. . MM, - . Av  2A;r ""r`c#:Kt|}d}||kryg}|5d}||krS||krN|j||||} |j|j| || z }|dz }||kr||krNddd|D]} | ||krxyy#1swYxYww)z+Return iterator over blocks read from file.rr&N)r.r%r6r) rrrr buffersizelengthrrCrG bytecountr s r rr$s \F A f*  D#F  #&qM  BGGI./ !Q #F   EK  f*  s#BAB4B BBBc|tj||St|trW|dddk(rOt |dkDr|ddnd}t j ||5}tj||||cdddSt|tjrht|t|jk7r tdtj||js td|j|St|tj r t|}tj||||S#1swYxYw) aReturn numpy array where image data of shape and dtype can be copied. The 'out' parameter may have the following values or types: None An empty array of shape and dtype is created and returned. numpy.ndarray An existing writable array of compatible dtype and shape. A view of the same array is returned after verification. 'memmap' or 'memmap:tempdir' A memory-map to an array stored in a temporary binary file on disk is created and returned. str or open file The file name or file object used to create a memory-map to an array stored in a binary file on disk. The created memory-mapped array is returned. Nrrr)rsuffix)rDr<rWzincompatible output shapezincompatible output dtype)r;rr(rr.tempfileNamedTemporaryFilerrrrDr,can_castr<rarr)rrDr<rWr tempdirrs r rr$s& {{{5%((#sBQ8 3 X\#ab't  ( (WV D I<<%u4H I I#u}}% 5>WSYY/ /89 9~~eSYY/89 9{{5!!#w||$#h <<5D AA I Is EE c@fddd dfd}d|vsd|vryi}|jD]b}|j}|r|ddk(r|jd d \}jtfd d DrX|||<d|S||S)aEReturn Python object from Matlab string representation. Return str, bool, int, float, list (Matlab arrays or cells), or dict (Matlab structures) types. Use to access ScanImage metadata. >>> matlabstr2py('1') 1 >>> matlabstr2py("['x y z' true false; 1 2.0 -3e4; NaN Inf @class]") [['x y z', True, False], [1, 2.0, -30000.0], [nan, inf, '@class']] >>> d = matlabstr2py("SI.hChannels.channelType = {'stripe' 'stripe'}\n" ... "SI.hChannels.channelsActive = 2") >>> d['SI.hChannels.channelType'] ['stripe', 'stripe'] cdg} |\}}|n\|dk(r|jdn?|dk(r|jdn(|dk(r|jdn|j|||d}j|jd|S)Nr ;)]r )r r r )r r )rCr6)rtokensrGr next_tokens r lexzmatlabstr2py..lexQ$sa=DAqyCx j)c j)c j) a !"A  c r`ct|}|dk(ryd}||kr||dk(r|dz }||kr ||dk(r||k(rd|fS||dvr |||dzfS||dk(r2|dz}||kr||dk7r|dz }||kr ||dk7r|||dz|dzfS||dk(r2|dz}||kr||dk7r|dz }||kr ||dk7r|||dz|dzfS|}||kr||d vr|dz }||kr||d vr||||fS) NrrArr&z{[;]}rrrz {[;]})r.)rr rr2s r r! z matlabstr2py..next_tokend$slQ Q; &jQqTS[ FA&jQqTS[ ;7N Q47?Q4Q;  Q43;AAf*1Qf*1QQ<Q& & Q43;AAf*1Qf*1QQ<Q& & &jQqT1 FA&jQqT11vqyr`cjsStdk(r tSddk(r |rddk7sdddvr t ddSddk(r|rddk7sdddvr t S|rt fddDr t dd k(rSd vry d vry dddk(rLt jddjdDcgc] }t|c}jSdddk(rLt jddjdDcgc] }t|c}jSdvsdvr tS tS#t$r|r t cYSwxYwcc}wcc}w#t$rY>wxYw#t$rYnwxYw tS#t$r|r t YSwxYw)Nr&rrrrrc3&K|]}|v ywrr)rrrs r r!z.matlabstr2py..value..$s21Q2r"z ';[]{}@)rp TrueT)rq FalseFrzzeros(r rzones(.rl) rr.rr?r,r*r;rrrZonesr)rfailrs` r rkzmatlabstr2py..value$s  GGIH q6Q; 1v Q43;" q2w l"Qr7N Q43;" q2w l"H C2 22,  Q43;H   " " Ra5H ;;!B c0BC1ACDKKM M Ra5G ::q2w}}S/AB!s1vBCJJL L !8sax Qx q6M= $,& * DB      #8O # l" #sS E9F2F" F . F/9FF F,+F,/ F;:F;? G G#"G#c|j} |dS#t$rYnwxYwgx}}|g}|D]}|dvrg}|j||dvrS|j}t |dk(rt |dt tfr|d}|d}|j|r|j|t |dk(rt |dt tfr|d}|S)NT)r+ z[{z]}r&rr)rr,r6r r.r(rr)rrXadd2levelsrGrr" rks r r zmatlabstr2py..parse$s GGI & &   Q &ADy d#dJJLq6Q;:adT3K#@!Abz A E!H% & v;!  6!9tSk BAYF s  )) rr%rr&c3&K|]}|v ywrr)rr1rs r r!zmatlabstr2py..$s/a16/r"z ';[]{}<>rI)r rrr*) r r rrrrr" r! rks @@@@r r# r# <$s*&6.`2 v~ %%' D::::c1%DAq A/;//8AaD  =r`c<|j|}|dkr|S|d|S)zReturn string truncated at first null character. Clean NULL terminated C strings. For unicode strings use null='\0'. >>> stripnull(b'string\x00') b'string' >>> stripnull('string\x00', null='\0') 'string' rN)r)r r rs r rr$s)  DA!e6,&!*,r`cvt|}|r#|dz}dt||cxkrdkrnnn|r#d}|d|dzS)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'' r&rrN)r.byte2int)r rs r rr$sN F A  Q xq " (S (   'AE?r`cf|jj}||vry||vryt)zdReturn string as bool if possible, else raise TypeError. >>> asbool(b' False ') False TF)rrr)rkrp rq s r r r $s4 KKM   !E } ~ +r`c|ttttf}|D] } ||cS|S#tt t tf$rY,wxYw)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' )rrr rr,rbrUnicodeEncodeError)rkr typs r rZrZ %sZ }UFI- u:  LNI7IJ   s,AAcL||krd|zSdD]}|dz}||ksd||fzcSy)zReturn file size as string from byte size. >>> format_size(1234) '1234 B' >>> format_size(12345678901) '11.50 GiB' z%i B)KiBMiBGiBTiBPiBg@z%.2f %sNr)rG thresholdrs r rr#%sE i}3,  ) d|+ +,r`c|S)zOSingle argument identity function. >>> identityfunc('arg') 'arg' r)rs r rr4%s  Jr`cy)z>> nullfunc('arg', kwarg='kwarg') Nr)rr0s r nullfuncrC >%s  r`cB t||S#t$r|fcYSwxYw)z{Return tuple containing value if value is not a sequence. >>> sequence(1) (1,) >>> sequence([1]) [1] )r.rrs r r)r)G%s) E  xs  c"d}|D]}||z} |S)zReturn product of sequence of numbers. Equivalent of functools.reduce(operator.mul, iterable, 1). Multiplying numpy integers might overflow. >>> product([2**8, 2**30]) 274877906944 >>> product([]) 1 r&r)iterableprodrs r rrW%s& D    Kr`cRfd}tjdt||S)zReturn human sorted list of strings. E.g. for sorting file names. >>> natural_sorted(['f1', 'f2', 'f10']) ['f1', 'f2', 'f10'] ctj|Dcgc]}|jr t|n|!c}Scc}wr)rrisdigitr)rr1numberss r sortkeyznatural_sorted..sortkeys%s38:!8LM1199;QA-MMMs$Az(\d+)rB)rrrm)rF rL rK s @r rri%s&Njj"G ( ((r`iZ c2|tj|zS)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) )r| timedelta) timestampepochs r excel_datetimerQ z%s 8%%i0 00r`c $|dkry|dz}|dkDr)tj|dz dz }|d|z|dzz z }||dkDrdnd z}tj|d z d z }tjd |z}tj||z d z }||z tjd |zz }||d krdndz } || dkDrdndz } t|d\} }t|d\} }t|d\} }tj| | || | | |S)zReturn datetime from days since 1/1/4713 BC and ms since midnight. Convert Julian dates according to MetaMorph. >>> julian_datetime(2451576, 54362783) datetime.datetime(2000, 2, 2, 15, 6, 2, 783) iODNr&i#g@}@g+@rEg@iliki6i`i)mathtruncr+r|) julianday milisecondr{rrgr1rrldaymonthyearhourminuteseconds r r)r)%s.GA A7{ A Nh67 QY! ## Q[Td+A AI'(A 6A:A AEW$%A a%$**Wq[) )C a$hB 'E   .Dj.9D* I6FJ D1FJ   T5#tVVZ PPr`c|dk(s|tjk(ryddd}|j|||tjk(S)zcReturn if byteorder matches the system's byteorder. >>> byteorder_isnative('=') True rTrrr)rr8r@)r8rs r byteorder_isnativer^ %sCC9 5# &D 88Iy )T#---@ @@r`ci}t|jj|D]N\}}|dd\}}|ddk(rtt |}n|j dkr|j }|||<P|S)zReturn numpy.recarray as dict.Nrr&r)r(r<descrrrrrZ)recarrayrXr` rkrr<s r r r %s|FHNN00(; uBQi e 8s?i./E ZZ!^LLNEt  Mr`ctddlm}dx|r|\dfd|j|S)zReturn XML as dict. >>> xml2dict('1') {'root': {'key': 1, 'attr': 'name'}} rrhr'cdtttfD] } ||cS|S#t$rYwxYwr)rrr r?)rkrGs r rZzxml2dict..astype%sAuf% A x     s # //c |j} r|jddd}||jrindi}t|}|rt j t}t |D]4}|jD]\}}||j |!6||jDcic]'\}}|t|dk(r  |dn |)c}}i}|jr6||j fd|jjD|jrH|jj}|s |jr|r ||| dz<|S |||<|Scc}}w)Nr r&rrc3>K|]\}}|z|fywrr)rrrrZats r r!z/xml2dict..etree2dict..%s"K$!Q266!9-Ksrk) rr rrr  defaultdictr rr6r.rLrr)rGrCrchildrendddcrrrrZrf etree2dictsanitizers r rk zxml2dict..etree2dict%s]ee **S!$R(C "d +7 ((.B*h/ ,HHJ,DAqqELL+, ,NPhhjFJaAs1v{vad|q AA 88 cFMMK!((..:JK K 6666<<>D188+1$t|}|dks |dks|dkry|dk(r,d}t||t|z dz|zz|}|dkryd} nZdtd|zz}t||t|dzz dz|zz|}|dkryd|zt|dzz}|dz |zdz} ||dk(r|}n8d t|cxkrdkr$nn!tt j ||z}|d kr||z }|dk(s| dk(rd |d |fg} d}d}d|z}nh|| |krd |fg} n[|d kr|| |z z} | || d fg} nE||k\s|dkr||z} d |d | fg} n-||z} |||z dz z}d |d | f|| z |z d f||z |||z d fg} t |}g}| D]\} }||j|tj|}tjd d |}td t||D]}}|d|zd|z|dzz|dkDr||| zzn|}|d jfdtd d|zdDz }|d |t|z zz }|||||zz }|j|dj|}tjd dk(r|j!d}|S)zReturn hexdump representation of byte string. >>> hexdump(binascii.unhexlify('49492a00080000000e00fe0004000100')) '49 49 2a 00 08 00 00 00 0e 00 fe 00 04 00 01 00 II*.............' r&rr'r`rs%%0%ix: s%xrNrs [^\x20-\x7f]. c3.K|] }||dzyw)rNr)rrrhs r r!zhexdump..7&sOA1QQ<Or r)r.rqabsrrS floorrgr6binasciihexlifyrsubrnrr version_infor)rrrsnipatroellipsisrGaddr bytesperlinenlinesr rendend1end2rXhexstrstrstrrr@rhs @r hexdumpr %sX w6%IJDQ ! S..6us4!8}'<&Bv%MNPTU ! L 3tax=0(|+a/ ~1 S[ 1 TZZ01 z& {fkgm|,-.L  6V+g, 10'%&/*+ 6 VaZV#gdsm$%f$v23   D[4  & D['$+-0 1  "H F w ? MM( # !!'*($8q#g, 5 Aq1uq1u|a'778A(. U#A Oq!l:JA1NOO OA Q( (A A ,- -A MM!    ZZ F aw' Mr`cZ|j}t|dkrytjddk(r |j S|jrydtfd|DS#t $rYnwxYw |j dj S#t $rYywxYw) zReturn if all characters in string are printable. >>> isprintable('abc') True >>> isprintable(b'') False r&Trrrzd0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ!"#$%&'()*+,-./:;<=>?@[\]^_`{|}~ c3&K|]}|v ywrr)rr1 printables r r!zisprintable..]&s2a1 >2r"N) rr.rrw isprintabler?risalnumr)r r s @r r r A&s\\^F 6{Q a %%' ' >>  F 26222    ==)557 7   s#A// A;:A;?B B*)B*cdD]\}}|j||}|rdD]\}}|j||}|jS)z)Return string with compressed whitespace.))r r)r/ r)rr) rrr))rr)z[ r r r r )rr)r compactr{rgs r clean_whitespacer `&s]&11%&U *DAq^^Aq)F * <<>r`c ddlm}t|ts|j d}|j t j|}|j|dd|jj}t|}|jdd jd d S#t$r0t|tr t|}|jdd}YZwxYw) zReturn pretty formatted XML.rNrT) pretty_printxml_declarationencodingz> >> snipstr('abcdefghijklmnop', 8) 'abc...op' Ns...u…r&rrrrq r) r(rr.r r6rr rrS rs r) r rrx ry r r rXrlinelenrsplitlenr~ r s r rr&s fe $HH ME""$JF D < MM( # d) e  MM& !  =EQJE U a  7U?34E 19 W Eqy A:*z feVWo. fVen- aZ MM(VEEMO%<< = g !2 MM&55=1H< =.H8q=(D(?D MM&$-(2VDE]B CA DD&% zz&!!yy  r`c ||S#t$r2 ||jcYS#t$rtd|zwxYwwxYw)zReturn enum member from its name or value. >>> enumarg(TIFF.PHOTOMETRIC, 2) >>> enumarg(TIFF.PHOTOMETRIC, 'RGB') zinvalid argument %s)r?rZr,)rrs r rYrY&sV:Cy : : $ $ :2S89 9 ::s A)AAAci}|D]}||vs||||<||=|jD]\}}||vr ||||<||=|||<|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)r0r keyvaluesrXrCrks r r'r'&szF &= +F3Ks  oo' U &= +F3Ks F3K  Mr`c H|jD]\}}||vs |||<y)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 Nr )r0r rCrks r update_kwargsr 's/ oo' U f F3K r`cddl}|j||ddg}d|vrd|jD]P}|j}|j ds%|ddj d}|D] }||vsyt |yy)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 `_ rNz-mzTIFF-hulsErrorMessage: rutf8) subprocess check_outputr rrrr,)rUjhoverjr rrerrorrs r validate_jhover ('s  ! !5(D*"E FCCNN$ D::jjdk(r%tj(j}| s|}|jjdk(r[tj*jj,}tj,}||k(rtj,|kD}jjdk(r\tj.jj,}tj,}||k(rtj,|kD}nd }t0j2d} |j5dddd |j7|d!d"d#d$% j8j:j<j?||rtA|jCnd}|jEd&dzzd'|d&zz d(d)d*d+,|jG| } |r tI|d-}|j?|d./|Hjj&d0k(rd1}n"jjd2vs|d k(rd3}nd4}|d5k(r|d6z }|jLtjNd7zj f||||d8| | s|jQfd9}d:}|| _)|_*|_+rtYd7zd t[j gt]Dcgc]V}|j_|jad;d&|dzzd|zd j|dz d d?d@j|zAX}}|D] }d|_1 |f fdB ffdC ffdD } j8jedE|tg|D]\}}|ji|ffdF  | fS#t $rjjdz}YwxYw#t $rYpwxYw#tJ$rY wxYwcc}w)GaPlot n-dimensional images using matplotlib.pyplot. Return figure, subplot and plot axis. Requires pyplot already imported C{from matplotlib import pyplot}. Parameters ---------- bitspersample : int or None Number of bits per channel in integer RGB images. photometric : {'MINISWHITE', 'MINISBLACK', 'RGB', or 'PALETTE'} The color space of the image data. title : str Window and subplot title. figure : matplotlib.figure.Figure (optional). Matplotlib to use for plotting. subplot : int A matplotlib.pyplot.subplot axis. maxdim : int maximum image width and length. kwargs : optional Arguments for matplotlib.pyplot.imshow. )rSrgFrrrrrR)r`rRNrz not an imagerrrr.NrUrruir&r!g?rr1rmatplotlib.pyplotfontz sans-serifnormal)familyweightrG)g$@g333333@Tz1.0w)dpifigsizeframeon facecolor edgecolorgQ?g\(\?g?gffffff?g?g)bottomtopleftrighthspacewspacez Windows-1252rP)rGrgraybufviridiscoolwarmr`_rr9)vminvmaxr interpolationct|dz}t|dz} rdd||f||fzSd||f||fzS#t$rYywxYw)N?z%s @ %s [%4i, %4i]r&z%s @ [%4i, %4i]r')rr)rrfcuraxdatcurrentrCdimss r format_coordzimshow..format_coord=(sr CL CL +x{1a4/@'1a.PPP$QT Aq'99 9  s? ? A  A cy)Nr'r)rs r r zimshow..noneH(sr`g?g333333?g?z Dimension %iz0.5z %%.0f [%i])r valfmtc|t|jd<jdt||D]$\}}d|_|j |d|_&j jy)Nr&FT)rrset_datar(eventsonset_valcanvasdraw)r slidersrCctrlrr figurer s r set_imagezimshow..set_imagea(stuW~.668HQK NN8A; '"7G4 % e %  U# $  % MM   r`ctt|}|d<|||k(ry||j|k\rd}n|dkr|j|dz }|||<|y)Nrr&)rroundrD)rrrCr r r s r on_changedzimshow..on_changedk(sje %EHQK % 4(( 4(1,!GDM g r`c|j}d}t|dvr ||y|dk(r||dz|y|dk(r||dz |y|dk(r*|t|jdz k(rdd<y|dzd<y|dk(r*|dk(rt|jdz d<y|dz d<y|dk(r|j|dz |y|d k(r d|yy) Nr 0123456789r r&r updownr} home)rCrr.rD)rrCr rCrr r s r on_keypressedzimshow..on_keypressedx(s))CA;D3x<'3%74=1,d374=1,d3#'3tzz?Q+>#>a D1H 59QYc$**o1 D1H 4::d+a/61d#r`key_press_eventc||Srr)rr{r s r rzimshow..(sjA.>r`)5r<r^rDrrr_r,r;r rrZr=rrS ceillogr?r(rrTabsoluteiinforqfinformodulesrcr r managerwindowtitler.r subplots_adjustsubplotr rr atleast_2dcolorbarr get_cursor_dataformat_cursor_datarrrnSliderrdrawon mpl_connectror )rCr r r r r7rtr r r r maxdimr0rdatamaxdtminpyplotrGr r rr sliderr r r r r r r r s` ` @@@@@@r rr's4L 8 #E zz#  2& TYY]tzz"~7O" <<>D88$"$" 99D ax((  TZZ^v->>$B/D>>$B/D JJrNTZZ^q0 0 2B1!44 2">>$B/D>>$B/D2$**R.F2 U! 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For use as skimage plugin.r N)rr showrs r _app_showr (s [[, -F KKMr`c ddlm}ddl}|}|j |j|jdi|}|j|S#t$r ddlm}m}Y^wxYw)z4Return file name(s) from Tkinter's file open dialog.r)TkN)r  filedialogr) Tkinterr  tkFileDialogrtkinterrwithdrawrLaskopenfilenamedestroy)r0r rr filenamess r rr(sc+) 4DMMOKKM* **4V4ILLN  +**+s AA+*A+c @ttjdddkr(tdtdtjzy|tj}ddl}|j ddd tz }|j}|d d d ddd|dddddd|ddddd|ddddd|d d!d"d#d$%|d&d'dd(d)|d*d+ddd,|d-d.ddd/|d0d1ddd2|d3d4ddd5|d6d7d8dd9:|d;d|j\}d?j|jr!ddl }|j|j@ys.tdAtj Bs|j#dCt%fdDdEDr(t'j&s tdFyd|j(s tdGd?Ht+j*} t-|j. I}|j(s&tdKt+j*|z dLzzj6rdM|_g} |j:dkDr||j(s tdNd?HdO} t+j*} |j<dk\r.|j?|j<P||j<dfg} n|j@dk\r_|j?|j@Q| |j@|j@jB|j@|j@fg} nng} tE|j@d|j:D]G\} } | jG|j?| Q| | jB|j@| fI|j(s&tdKt+j*|z dLzz|j(sGttt,jM|tO|jPTt|jS| r|j:dkDr ddl*} | jWdUddVl*m,}| D]`\}}}| |jZ|j\}}dW|j^vr< tajb||t|j^dWjdkD}|jfr= |jhdX}|jhdY}||kr|jZ|j\}} |r&tm|dJtm|dJtm|}ntm|dZtm|}d[}|jnd\vr)tjq|jnjr}tu|||||jv||jx|jz]c|j}yyy#t0$r9}|j2rtdJ|tj4dYd}~d}~wwxYw#tH$rN}| jGd| | jJdf|j2rtdR| |fzdSHYd}~d}~wwxYw#t0$r#}|j2rt|Yd}~d}~wwxYw#tH$rYwxYw#tj$rYwxYw#t~$r"}tjd^|zYd}~yd}~wwxYw)_z!Command line usage main function.rrg@z2This script requires Python version 2.7 or better.zThis is Python version %sNzusage: %prog [options] pathz!Display image data in TIFF files.z %%prog %s)usager{rcz-pz--pagerVrrzdisplay single page)destr defaulthelpz-sz--seriesrRz%display series of pages of same shapez --nomultifile nomultifile store_trueFz*do not read OME series from multiple files)ractionrrz --noplotsnoplotsrzmaximum number of plotsz --interpolinterpolINTERPOLbilinearzimage interpolation method)rmetavarrrz--dpir `zplot resolutionz--vminr zminimum value for colormappingz--vmaxr zmaximum value for colormappingz--debugdebugzraise exception on failuresz --doctestdoctestzruns the docstring examplesz-vz--detailrr)rr rz-qz--quietquiet)rrr) optionflagszSelect a TIFF file)r filetypeszNo file specifiedc3&K|]}|v ywrr)rrrs r r!zmain..)s #19 #r"r#zno files match the patternz Reading file structure...)r} )rrz%.3f msg@@TzReading image data... c&td|DS)Nc3&K|] }|| ywrrrs r r!z(main..notnone..$)s6a 6r)r rs r notnonezmain..notnone#)s6166 6r`rB)rRz Series %i failed: %s... r')rTkAggr rrA rB z rR)r)r r r r7rtr r zfailed to import matplotlib. %s)Brrrcprintargvoptparse OptionParser __version__ add_option parse_argsrr%testmodELLIPSISrrMrr r*r+r&rr rr?r$exitrnorgbrrVr/rRrror6r,rOrrrr matplotlibuserr r rr;rqrkr'r,rrrtrQrrr7rr r rrr)r/r0parseroptsettingsr%rr3rlr6r,rrr9rimgrVrRr r r rtrs @r mainr?(s S[[1 $ BC )CKK78 |xx  " "+7k)#F   ChV%BWX    4   9    &   ) e%:KL   -    -   *   * jxeQ?igl;&&(NHd 88D>DG$4$45 &$2F2F  LL, - #d ##yy . /Aw >> +5 IIKEt8+?+?'?@ >> iDIIK%/3678 zz F!~~ * 4 7  }}!;;8==;93x}};MtTUA% 8?? ; 8?? ; B BC 8??3%cjj1C83C3C&DE QDAq Q  [[[2GAHH4EszzRS}U Q>>iDIIK%$73#>?@ >>  hs3x+?@A IIK (""Q&-   NN7 # )&,$ !T6;%]]HMMd DII-$yyeDIIm,D,J,J&K KL  ::F"// ;"// ; 4<)1 $D,/Hc$iVME),S3t9=E* ##4/"&"2"243C3C"D"I"IK"&"4"4 +"*"3"3  7$ J KKM]'vw  >>  $N HHQKK N&Q tWQWW-=t&DE#>>!!">!Q"GRPP Q ~~a  <& $% B MMr r concurrent.futuresr r;r2 __docformat____all__rrrrr r r rrrzrr,rrr r rrErMrMr rrrrr rrrrrrrrrr r rr r r r r r rrrrrbr\r< rkrBr0rer\rfr*r rWr r rSrcr __package__r rrrrrrrr rr_rr r$r rrrr# rrr rZrrrC r)rr fromordinalrQ r)r^ r rr r r r rrrYr'r r r rr rr?rw rlongrr rrgr5 rrrrr)r r.rgr7rr`r r[sDGR 0   %  ,-+`C6LOCdv4CCL"@*v@*F&ffRK1vK1\"AHAHHGfGZ J J9VJ9Zh&6h&VsCsCl  &  /?F/?d( n *6n * n *bAfR(J F * ' 2&. 0 8 [| 5#L- - - 6-`8&#L  8>B M`:z J   7-t,0  D,?D*Z2BB% 4*54%P&R ()H*H2 #$S%Sl $%F&FR2j )*D+D><AB F?2 '0*/Z.b#4$!BHYx -, .,"   $)"%-$5$5$A$A&$I 1QB A 2-jGT3>  5&-`7!t:$6  6B8N     G"T TnA!DyH G IHeJG F."  z CHHTVr`