^dZdZdZddlZddlZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl Z ddlZddlZddlZddlZddlmZddlmZddlZ ddlZn #e$rdZYnwxYwdZddZdd ZGd d ZGd deZGddZGddZGddZ GddZ!GddZ"GddZ#GddZ$GddZ%Gdd Z&Gd!d"e&Z'Gd#d$Z(Gd%d&Z)Gd'd(Z*Gd)d*Z+Gd+d,Z,e,Gd-d.Z- dd/Z.d0Z/d1Z0d2Z1d3Z2d4Z3d5Z4d6Z5d7Z6d8Z7d9Z8dd:Z9d;Z:d<Z;d=ZZ=d?Z>d@Z?dAZ@dBZAdCZBdDZCdEZDdFZEdGZFdHZGdIZHdJZIdKZJdLZKdMZLdNZMdOZNdPZOdQZPdRZQ ddTZRddUZSdVZTdWZUddXZVdYZWdZZXd[ZYd\ZZd]Z[d^Z\d_Z]ddaZ^e/ddl_Z_ddl`Z`ddcZadddZbddeZcddfZdddhZeddiZfdgfdjZgddkZhddlZinejgZgejhZhddmZjddnZkdoZldpZmdqZndrZoddsZpddtZqdduZrddvZsddxZtdyZudd{Zvd|ZwddZxddZyddZzdZ{dZ|dZ}dZ~dZddZddZdZdZddZddZdZddZdZddZddZdZdZdZdZdZddZddZ ddZdZdZdZddZddZeZedkrejedSdS)aIRead and write TIFF(r) files. Tifffile is a Python library to (1) store numpy arrays in TIFF (Tagged Image File Format) files, and (2) read image and metadata from TIFF-like files used in bioimaging. Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, SGI, NIHImage, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, ZIF, QPTIFF, NDPI, and GeoTIFF files. Numpy arrays can be written to TIFF, BigTIFF, and ImageJ hyperstack compatible files in multi-page, memory-mappable, tiled, predicted, or compressed form. A subset of the TIFF specification is supported, mainly uncompressed and losslessly compressed 8, 16, 32 and 64-bit integer, 16, 32 and 64-bit float, grayscale and multi-sample images. Specifically, reading slices of image data, CCITT and OJPEG compression, chroma subsampling without JPEG compression, color space transformations, samples with differing types, 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 larger than 4 GB. STK, LSM, FluoView, SGI, SEQ, GEL, QPTIFF, NDPI, and OME-TIFF, are custom extensions defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics, Molecular Dynamics, PerkinElmer, Hamamatsu, and the Open Microscopy Environment consortium respectively. For command line usage run ``python -m tifffile --help`` :Author: `Christoph Gohlke `_ :Organization: Laboratory for Fluorescence Dynamics, University of California, Irvine :License: BSD 3-Clause :Version: 2020.6.3 Requirements ------------ This release has been tested with the following requirements and dependencies (other versions may work): * `CPython 3.6.8, 3.7.7, 3.8.3 64-bit `_ * `Numpy 1.16.6, 1.18.4 `_ * `Imagecodecs 2020.5.30 `_ (required only for encoding or decoding LZW, JPEG, etc.) * `Matplotlib 3.1 `_ (required only for plotting) Revisions --------- 2020.6.3 Pass 2908 tests. Support os.PathLike file names (#9). 2020.5.30 Re-add pure Python PackBits decoder. 2020.5.25 Make imagecodecs an optional dependency again. Disable multi-threaded decoding of small LZW compressed segments. Fix caching of TiffPage.decode function. Fix xml.etree.cElementTree ImportError on Python 3.9. Fix tostring DeprecationWarning. 2020.5.11 Fix reading ImageJ grayscale mode RGB images (#6). Remove napari reader plugin. 2020.5.7 Add napari reader plugin (tentative). Fix writing single tiles larger than image data (#3). Always store ExtraSamples values in tuple (breaking). 2020.5.5 Allow to write tiled TIFF from iterator of tiles (WIP). Add function to iterate over decoded segments of TiffPage (WIP). Pass chunks of segments to ThreadPoolExecutor.map to reduce memory usage. Fix reading invalid files with too many strips. Fix writing over-aligned image data. Detect OME-XML without declaration (#2). Support LERC compression (WIP). Delay load imagecodecs functions. Remove maxsize parameter from asarray (breaking). Deprecate ijmetadata parameter from TiffWriter.save (use metadata). 2020.2.16 Add function to decode individual strips or tiles. Read strips and tiles in order of their offsets. Enable multi-threading when decompressing multiple strips. Replace TiffPage.tags dictionary with TiffTags (breaking). Replace TIFF.TAGS dictionary with TiffTagRegistry. Remove TIFF.TAG_NAMES (breaking). Improve handling of TiffSequence parameters in imread. Match last uncommon parts of file paths to FileSequence pattern (breaking). Allow letters in FileSequence pattern for indexing well plate rows. Allow to reorder axes in FileSequence. Allow to write > 4 GB arrays to plain TIFF when using compression. Allow to write zero size numpy arrays to nonconformant TIFF (tentative). Fix xml2dict. Require imagecodecs >= 2020.1.31. Remove support for imagecodecs-lite (breaking). Remove verify parameter to asarray function (breaking). Remove deprecated lzw_decode functions (breaking). Remove support for Python 2.7 and 3.5 (breaking). 2019.7.26 Fix infinite loop reading more than two tags of same code in IFD. Delay import of logging module. 2019.7.20 Fix OME-XML detection for files created by Imaris. Remove or replace assert statements. 2019.7.2 Do not write SampleFormat tag for unsigned data types. Write ByteCount tag values as SHORT or LONG if possible. Allow to specify axes in FileSequence pattern via group names. Add option to concurrently read FileSequence using threads. Derive TiffSequence from FileSequence. Use str(datetime.timedelta) to format Timer duration. Use perf_counter for Timer if possible. 2019.6.18 Fix reading planar RGB ImageJ files created by Bio-Formats. Fix reading single-file, multi-image OME-TIFF without UUID. Presume LSM stores uncompressed images contiguously per page. Reformat some complex expressions. 2019.5.30 Ignore invalid frames in OME-TIFF. Set default subsampling to (2, 2) for RGB JPEG compression. Fix reading and writing planar RGB JPEG compression. Replace buffered_read with FileHandle.read_segments. Include page or frame numbers in exceptions and warnings. Add Timer class. 2019.5.22 Add optional chroma subsampling for JPEG compression. Enable writing PNG, JPEG, JPEGXR, and JPEG2K compression (WIP). Fix writing tiled images with WebP compression. Improve handling GeoTIFF sparse files. 2019.3.18 Fix regression decoding JPEG with RGB photometrics. Fix reading OME-TIFF files with corrupted but unused pages. Allow to load TiffFrame without specifying keyframe. Calculate virtual TiffFrames for non-BigTIFF ScanImage files > 2GB. Rename property is_chroma_subsampled to is_subsampled (breaking). Make more attributes and methods private (WIP). 2019.3.8 Fix MemoryError when RowsPerStrip > ImageLength. Fix SyntaxWarning on Python 3.8. Fail to decode JPEG to planar RGB (tentative). Separate public from private test files (WIP). Allow testing without data files or imagecodecs. 2019.2.22 Use imagecodecs-lite as a fallback for imagecodecs. Simplify reading numpy arrays from file. Use TiffFrames when reading arrays from page sequences. Support slices and iterators in TiffPageSeries sequence interface. Auto-detect uniform series. Use page hash to determine generic series. Turn off TiffPages cache (tentative). Pass through more parameters in imread. Discontinue movie parameter in imread and TiffFile (breaking). Discontinue bigsize parameter in imwrite (breaking). Raise TiffFileError in case of issues with TIFF structure. Return TiffFile.ome_metadata as XML (breaking). Ignore OME series when last dimensions are not stored in TIFF pages. 2019.2.10 Assemble IFDs in memory to speed-up writing on some slow media. Handle discontinued arguments fastij, multifile_close, and pages. 2019.1.30 Use black background in imshow. Do not write datetime tag by default (breaking). Fix OME-TIFF with SamplesPerPixel > 1. Allow 64-bit IFD offsets for NDPI (files > 4GB still not supported). 2019.1.4 Fix decoding deflate without imagecodecs. 2019.1.1 Update copyright year. Require imagecodecs >= 2018.12.16. Do not use JPEG tables from keyframe. Enable decoding large JPEG in NDPI. Decode some old-style JPEG. Reorder OME channel axis to match PlanarConfiguration storage. Return tiled images as contiguous arrays. Add decode_lzw proxy function for compatibility with old czifile module. Use dedicated logger. 2018.11.28 Make SubIFDs accessible as TiffPage.pages. Make parsing of TiffSequence axes pattern optional (breaking). Limit parsing of TiffSequence axes pattern to file names, not path names. Do not interpolate in imshow if image dimensions <= 512, else use bilinear. Use logging.warning instead of warnings.warn in many cases. Fix numpy FutureWarning for out == 'memmap'. Adjust ZSTD and WebP compression to libtiff-4.0.10 (WIP). Decode old-style LZW with imagecodecs >= 2018.11.8. Remove TiffFile.qptiff_metadata (QPI metadata are per page). Do not use keyword arguments before variable positional arguments. Make either all or none return statements in a function return expression. Use pytest parametrize to generate tests. Replace test classes with functions. 2018.11.6 Rename imsave function to imwrite. Readd Python implementations of packints, delta, and bitorder codecs. Fix TiffFrame.compression AttributeError. 2018.10.18 ... Refer to the CHANGES file for older revisions. Notes ----- The API is not stable yet and might change between revisions. Tested on little-endian platforms only. Python 32-bit versions are deprecated. Tifffile relies on the `imagecodecs `_ package for encoding and decoding LZW, JPEG, and other compressed images. Several TIFF-like formats do not strictly adhere to the TIFF6 specification, some of which allow file or data sizes to exceed the 4 GB limit: * *BigTIFF* is identified by version number 43 and uses different file header, IFD, and tag structures with 64-bit offsets. It adds more data types. Tifffile can read and write BigTIFF files. * *ImageJ* hyperstacks store all image data, which may exceed 4 GB, contiguously after the first IFD. Files > 4 GB contain one IFD only. The size (shape and dtype) of the up to 6-dimensional image data can be determined from the ImageDescription tag of the first IFD, which is Latin-1 encoded. Tifffile can read and write ImageJ hyperstacks. * *OME-TIFF* stores up to 8-dimensional data in one or multiple TIFF of BigTIFF files. The 8-bit UTF-8 encoded OME-XML metadata found in the ImageDescription tag of the first IFD defines the position of TIFF IFDs in the high dimensional data. Tifffile can read OME-TIFF files, except when the OME-XML metadata are stored in a separate file. * *LSM* stores all IFDs below 4 GB but wraps around 32-bit StripOffsets. The StripOffsets of each series and position require separate unwrapping. The StripByteCounts tag contains the number of bytes for the uncompressed data. Tifffile can read large LSM files. * *NDPI* uses some 64-bit offsets in the file header, IFD, and tag structures. Tag values/offsets can be corrected using high bits stored after IFD structures. JPEG compressed tiles with dimensions > 65536 are not readable with libjpeg. Tifffile can read NDPI files < 4 GB and decompress large JPEG tiles using the imagecodecs library on Windows. * *ScanImage* optionally allows corrupt non-BigTIFF files > 2 GB. The values of StripOffsets and StripByteCounts can be recovered using the constant differences of the offsets of IFD and tag values throughout the file. Tifffile can read such files on Python 3 if the image data are stored contiguously in each page. * *GeoTIFF* sparse files allow strip or tile offsets and byte counts to be 0. Such segments are implicitly set to 0 or the NODATA value on reading. Tifffile can read GeoTIFF sparse files. Other libraries for reading scientific TIFF files from Python: * `Python-bioformats `_ * `Imread `_ * `GDAL `_ * `OpenSlide-python `_ * `PyLibTiff `_ * `SimpleITK `_ * `PyLSM `_ * `PyMca.TiffIO.py `_ (same as fabio.TiffIO) * `BioImageXD.Readers `_ * `CellCognition `_ * `pymimage `_ * `pytiff `_ * `ScanImageTiffReaderPython `_ * `bigtiff `_ Some libraries are using tifffile to write OME-TIFF files: * `Zeiss Apeer OME-TIFF library `_ * `Allen Institute for Cell Science imageio `_ * `xtiff `_ References ---------- 1. TIFF 6.0 Specification and Supplements. Adobe Systems Incorporated. https://www.adobe.io/open/standards/TIFF.html 2. TIFF File Format FAQ. https://www.awaresystems.be/imaging/tiff/faq.html 3. MetaMorph Stack (STK) Image File Format. http://mdc.custhelp.com/app/answers/detail/a_id/18862 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. https://docs.openmicroscopy.org/ome-model/5.6.4/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. https://micro-manager.org/wiki/Micro-Manager_File_Formats 8. Tags for TIFF and Related Specifications. Digital Preservation. https://www.loc.gov/preservation/digital/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 11. ZIF, the Zoomable Image File format. http://zif.photo/ 12. GeoTIFF File Format https://gdal.org/drivers/raster/gtiff.html Examples -------- Save a 3D numpy array to a multi-page, 16-bit grayscale TIFF file: >>> data = numpy.random.randint(0, 2**12, (4, 301, 219), 'uint16') >>> imwrite('temp.tif', data, photometric='minisblack') Read the whole image stack from the TIFF file as numpy array: >>> image_stack = imread('temp.tif') >>> image_stack.shape (4, 301, 219) >>> image_stack.dtype dtype('uint16') Read the image from the first page in the TIFF file as numpy array: >>> image = imread('temp.tif', key=0) >>> image.shape (301, 219) Read images from a sequence of TIFF files as numpy array: >>> image_sequence = imread(['temp.tif', 'temp.tif']) >>> image_sequence.shape (2, 4, 301, 219) Save a numpy array to a single-page RGB TIFF file: >>> data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8') >>> imwrite('temp.tif', data, photometric='rgb') Save a floating-point array and metadata, using zlib compression: >>> data = numpy.random.rand(2, 5, 3, 301, 219).astype('float32') >>> imwrite('temp.tif', data, compress=6, metadata={'axes': 'TZCYX'}) Save a volume with xyz voxel size 2.6755x2.6755x3.9474 micron^3 to an ImageJ formatted TIFF file: >>> volume = numpy.random.randn(57*256*256).astype('float32') >>> volume.shape = 1, 57, 1, 256, 256, 1 # dimensions in TZCYXS order >>> imwrite('temp.tif', volume, imagej=True, resolution=(1./2.6755, 1./2.6755), ... metadata={'spacing': 3.947368, 'unit': 'um'}) Get the shape and dtype of the volume stored in the TIFF file: >>> tif = TiffFile('temp.tif') >>> len(tif.pages) # number of pages in the file 57 >>> page = tif.pages[0] # get shape and dtype of the image in the first page >>> page.shape (256, 256) >>> page.dtype dtype('float32') >>> page.axes 'YX' >>> series = tif.series[0] # get shape and dtype of the first image series >>> series.shape (57, 256, 256) >>> series.dtype dtype('float32') >>> series.axes 'ZYX' >>> tif.close() Read hyperstack and metadata from the ImageJ file: >>> with TiffFile('temp.tif') as tif: ... imagej_hyperstack = tif.asarray() ... imagej_metadata = tif.imagej_metadata >>> imagej_hyperstack.shape (57, 256, 256) >>> imagej_metadata['slices'] 57 Read the "XResolution" tag from the first page in the TIFF file: >>> with TiffFile('temp.tif') as tif: ... tag = tif.pages[0].tags['XResolution'] >>> tag.value (2000, 5351) >>> tag.name 'XResolution' >>> tag.code 282 >>> tag.count 1 >>> tag.dtype '2I' Read images from a selected range of pages: >>> image = imread('temp.tif', key=range(4, 40, 2)) >>> image.shape (18, 256, 256) Create an empty TIFF file and write to the memory-mapped numpy array: >>> memmap_image = memmap('temp.tif', shape=(256, 256), dtype='float32') >>> memmap_image[255, 255] = 1.0 >>> memmap_image.flush() >>> del memmap_image Memory-map image data of the first page in the TIFF file: >>> memmap_image = memmap('temp.tif', page=0) >>> memmap_image[255, 255] 1.0 >>> del memmap_image Successively append images to a BigTIFF file, which can exceed 4 GB: >>> data = numpy.random.randint(0, 255, (5, 2, 3, 301, 219), 'uint8') >>> with TiffWriter('temp.tif', bigtiff=True) as tif: ... for i in range(data.shape[0]): ... tif.save(data[i], compress=6, photometric='minisblack') Append an image to the existing TIFF file: >>> data = numpy.random.randint(0, 255, (301, 219, 3), 'uint8') >>> imwrite('temp.tif', data, append=True) Iterate over pages and tags in the TIFF file and successively read images: >>> with TiffFile('temp.tif') as tif: ... for page in tif.pages: ... for tag in page.tags: ... tag_name, tag_value = tag.name, tag.value ... image = page.asarray() Save two image series to a TIFF file: >>> data0 = numpy.random.randint(0, 255, (301, 219, 3), 'uint8') >>> data1 = numpy.random.randint(0, 255, (5, 301, 219), 'uint16') >>> with TiffWriter('temp.tif') as tif: ... tif.save(data0, compress=6, photometric='rgb') ... tif.save(data1, compress=6, photometric='minisblack', contiguous=False) Read the second image series from the TIFF file: >>> series1 = imread('temp.tif', series=1) >>> series1.shape (5, 301, 219) Read an image stack from a series of TIFF files with a file name pattern: >>> imwrite('temp_C001T001.tif', numpy.random.rand(64, 64)) >>> imwrite('temp_C001T002.tif', numpy.random.rand(64, 64)) >>> image_sequence = TiffSequence('temp_C001*.tif', pattern='axes') >>> image_sequence.shape (1, 2) >>> image_sequence.axes 'CT' >>> data = image_sequence.asarray() >>> data.shape (1, 2, 64, 64) Create a TIFF file from an iterator of tiles: >>> def tiles(): ... data = numpy.arange(3*4*16*16, dtype='uint16').reshape((3*4, 16, 16)) ... for i in range(data.shape[0]): yield data[i] >>> imwrite('temp.tif', tiles(), dtype='uint16', shape=(48, 64), tile=(16, 16)) z2020.6.3)#imwriteimreadimshowmemmaplsm2binTiffFile TiffFileError TiffSequence TiffWriterTiffPageTiffPageSeries TiffFrameTiffTagTIFF FileHandle FileSequenceTimerlazyattrnatural_sorted stripnulltranspose_axes squeeze_axes create_output repeat_nd format_sizeastypeproductxml2dictpformatnullfunc update_kwargs parse_kwargsaskopenfilename _app_showimsaveN)Iterable)ThreadPoolExecutorc t|ddddddddd }t|d d d d d}|ddW|ddtdtjdt |d|d<|sttr/tfddDrtj stdtdszimread..ks')C)C!u*)C)C)C)C)C)C?*no files foundseekr%r:)r!get TypeErrorwarningswarnDeprecationWarningpop isinstancestranyglob ValueErrorhasattrosPathLikelenrasarrayr )r=kwargs kwargs_file kwargs_seqtifimseqs` r>rr;s*  Kfih)++Jzz'4  , ::eT " " .I   8:L    7++u - eS ! ! %c)C)C)C)Cd)C)C)C&C&C %Ie$$E /-.. .v&& 53 "455  JJ!OO!HE ec2;/ 0 0 -GE64J4J -%//;// -3"s{,,V,, - - - - - - - - - - - - - - - - e * *z * *'eu}&&v&&''''''''''''''''''s$= FFF/ G  G G c 2t|dddd}|3tj|}t||jz}|j}n) |j}|jj}n#t$rd}d}YnwxYw|dd}d|vrM||krG| dd s1| d d s| d d sd |d<d|vr||d<t|fi|5} | j |||fi|cdddS#1swxYwYdS) aRWrite numpy array to TIFF file. Refer to the TiffWriter class and its asarray function for documentation. A BigTIFF file is created if the data size in bytes is larger than 4 GB minus 32 MB (for metadata), and 'bigtiff' is not specified, and 'imagej' or 'truncate' are not enabled. Parameters ---------- file : str, path-like, or binary stream File name or writable binary stream, such as an open file or BytesIO. data : array_like Input image. The last dimensions are assumed to be image depth, 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, datatype of an empty array to save to the file. kwargs : dict Parameters 'append', 'byteorder', 'bigtiff', and 'imagej', are passed to TiffWriter(). Other parameters are passed to TiffWriter.save(). Returns ------- offset, bytecount : tuple or None If the image data are written contiguously, return offset and bytecount of image data in the file. appendbigtiff byteorderimagejNr%bigsizel|FtruncatecompressT) r!numpydtyperitemsizer]nbytes ExceptionrJrEr save) filedatashapercrUtifargsr.r]r_rXs r>rr~sF68Y XNNG | E""u~~.O  ;D ,II   DIII jjM22G  7NN He,,  J..  :u--  " '!!(  D $ $G $ $6sxeU55f55666666666666666666s$ AA/.A//D  DDr+c &|M|K|d||dtjt|fi|}|t d|d}nt |fi|5} |<| j|}|jst d|j\}} |j }|j }n8| j |}|j t d|j }|j }|j }| j |jz}dddn #1swxYwYtj|||||dS)aReturn 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 or path-like Name of the TIFF file which stores the array. shape : tuple Shape of the empty array. dtype : numpy.dtype Datatype of the empty array. page : int Index of the page which image data to memory-map. series : int Index of the page series which image data to memory-map. mode : {'r+', 'r', 'c'} The file open mode. Default is to open existing file for reading and writing ('r+'). kwargs : dict Additional parameters passed to imwrite() or TiffFile(). NT)rirjrc returnoffsetalignz"image data are not memory-mappabler%C)updaterALLOCATIONGRANULARITYrrOrr6is_memmappable is_contiguousrjrcseriesr-r]charrbr) filenamerjrcpagerumoderUresultr-rX_s r>rrsB U. ,    ,,V,, >ABB Bh ) )& ) ) /Sy*K$%IJJJ .   F+=($%IJJJ  MEJ.E / / / / / / / / / / / / / / / <%vuc B BBsBC//C36C3c,eZdZdZdZdZfdZxZS)rz2Attribute whose value is computed on first access.funcc||_dSr9r})selfr~s r>__init__zlazyattr.__init__s  r@c||S ||}n!#t$r}t|d}~wwxYw|tur(t t |||jjSt||jj||Sr9)r~AttributeError RuntimeErrorNotImplementedgetattrsuper__name__setattr)rinstanceownervalueexc __class__s r>__get__zlazyattr.__get__ s  K $IIh''EE $ $ $s## # $ N " "511493EFF F$),e444 s ;6;)r __module__ __qualname____doc__ __slots__rr __classcell__rs@r>rrsT<<I         r@rceZdZdZdS)rz-Exception to indicate invalid TIFF structure.N)rrrrr:r@r>rrs7777r@rczeZdZdZ ddZdddddddddddddddddddddidd fd Zd Zd Zd ZdZ dZ dZ dS)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 instances are not thread-safe. TiffWriter's main purpose is saving nD numpy array's as TIFF, not to create any possible TIFF format. Specifically, SubIFDs, ExifIFD, and GPSIFD tags are not supported. FNch|r t|dd5}|} t|5}|dkr|jst d|j}|j}|jj|_ dddn #1swxYwY| |n#| |wxYw dddn #1swxYwYn#ttf$rd}YnwxYw|dvrtjd krd nd }n|d vrtd ||r|rtjdt"||_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|_'|r4t|dd|_(|j( dddSt|dd|_(|j()ddd ||r3|j()tUj+|dzdddn0|j()tUj+|dzd |j(|_ |j()tUj+||j&zddS)!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, path-like, 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, 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 hyperstacks do not support BigTIFF or compression. The ImageJ file format is undocumented. When using compression, use ImageJ's Bio-Formats import function. rbr%)ryr.forcez)cannot append to file containing metadataNF)N=|little<>rrzinvalid byteorder z$writing nonconformant BigTIFF ImageJTQ8s HI4szr+bwbIIMMHHH+*),rtellr is_appendablerr] is_bigtiffr6next_page_offset _ifdoffsetrCOSErrorFileNotFoundErrorsysrOrGrH UserWarning _byteorderbool_imagej _truncate _metadata _colormap_descriptionoffset_descriptionlen_descriptionlenoffset_tags_shape _datashape _datadtype _dataoffset_databytecounts _tagoffsets_bigtiff _offsetsize_tagsize _tagnoformat _offsetformat _valueformat_fhwritestructpack) rrhr\r]r[r^fhposrXs r>rzTiffWriter.__init__-sF   4a888 %B''))C %%b\\IS%009J0&35K'L'L!L(+ I&)nG.1i.HDO IIIIIIIIIIIIIII   % % % % % % % % % % % % % % %./     ( ( ("}88cII j ( (=)==>> >  Og O M@+ N N N#F|| "# %&"  #  % DM D DM #D !$D  $D  !DM D DM #D !$D  $D   K!$U;;;DH HMM!Q     !$T:::DH HNNU33I> ? ? ? Av{9u+ts|d?kr|ddd4z|ddz}|d d kr?t|d d}6|6d krd nt|!|6z}6|6f|d dz}|} |>|}n#t~$rYnwxYw||)kr/|4d ks|s|d d ks |d d krtd@||'kr|4dkrtdA|r|-dBvrtdC|rtdD|d9vrtdE|te|}|d d zr|d d zd z|d <n|d d z|d <t_|}| t|krt{dF||Idc}|ddz }ts||_J|9dQdRd |dS|r|9dedRd |dS|rtc|tr/ts|dfks |d*dgkrtdhnI |jLdi}n7#t~$r*|MLdi}YnwxYw|9djdRd |dS|9dkd&d |-|-dlkr|9dmdnddor|9dpd&d |.|9dqdnd |d |9drdnd |d/|rR|9dsdnd |d |9dtdnd |d |0r(|9dudnd |d.|9dvdnd |d |r|9dwdnd ||s/|j6dxks$d dddydz|j6}<|9d{d&|4||dvrtdd}d }=|9dd&d |jO|-dkr|9dd&dd||9ddd |:|d |9ddd |:|d ts|dkr'|d}>|>d nt]tHjR|>}>n |jrd }>nd}>|9dd&d |>n1|js*|9ddd d|9ddd d|9dd&d d | cfd}?| } |rts|dkra|d|d zd z |d z|d|d zd z |d zf}@| o#|d|d ko|d|d k} n|d|d zd z |d z|d|d zd z |d z|d|dzd z |dzf}@| o5|d|d ko#|d|d ko|d|dk} t|@|d z}At||d z|j zg|Az}B|?|B}C|9|7|C|A|B|9|8b|Ad g|Az|C|Az}C| s|nt|||@}n| r|s| |r"t|ddg|d z}Bn)t|dd|j zg|d z}B|?|B}C|9|7|C|d |B|9|8b|d d g|d z|9ddnd |d/|C|d z}Cnt|d d|j z}D| | rd|Dzn|d/} | d kr|=} n6| |d/kr |d/} n!|r| |=zrtjU| |=z |=z} |9ddnd | |d/| zd z | z}E|E|d z}F| |Dz}G|Gg|Fz}B|G|D|E| z|d/z zz}Gt|Ed z |F|ED]}H|G|B|H<|?|B}C|9|7|C|F|B|9|8b|Fd g|Fz|C|Fz}C|| std|D]};|9|;| r-tHjW|-}Ir |I|/ffd } n|r|I|/|fd} n|I|/fd} tede|}J|jYs!|js| s|J| zdkrtdt| rd n|d D]}K|J}L|Ldzr|Zd|Ld z }L|[|j\|Zdb|L|[|L|Kdkrtj^}M|MZd|#tse|M}N|MZd_deD|M}O|MZdbd teD] \}P}Q|N|P|$zzczdz}"|Qd }R|Qd}S|Sr|M}T|Tdzr|MZd|Td z }T|M[|"|MZdb|L|Tz|M[|T|MZ|S|R|8kr|"|Tf}U|R|7kr|"|Tf}V|RdQkr2|Sadr|L|Tz|_|L|Nz|P|$zzdz|_ |R|8kr|"df}U|R|7kr|"df}V"|M}W|Wdzr|MZd|Wd z }W|[|Wd |}X| |X| zz | z}Y|[|Yd |X|Yz }X| r0||| n||n|r| ||A|Bd znt||d z}Zt|d t|@zD]}[t|}\|\$| rd |B|[<n||Bd 7|\jN|Zkrtd|\j d|| r3| |\};|Z|;ts|;|B|[<||\n| r|j dd krt{d|d/| zd z | z}Fd }]||KD]`}^t|FD]N}H|^d |H| z|Hd z| zf}_| |_}_|Z|_ts|_|B|]<|]d z }]Oan|||K|U\}"}T|M[|"|Trc|MZdb|L|Tz|M[|T|X}"|BD]&}`|MZdb|"|"|`z }"'n|MZdb|X| ro|V\}"}T|M[|"|Tr7|MZdb|L|Tz|M[|T|MZd|Cg|BR|}J|[|L|Z|Mc|d|[|J|L|Oz|_\|Kd kr deDe||_ed4|!z|_ ||_|X|_f|B|_g| re|_|r|Xt|BfSdS)aJ"Write 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 instead of 'data', an empty array is saved. This option cannot be used with compression or multiple tiles. If 'shape', 'dtype', and 'tile' are specified, 'data' must be a sequence or iterator over all individual tiles in image. Image data are written uncompressed in one strip per plane by default. Dimensions larger than 2 to 4 (depending on photometric mode, planar configuration, and SGI mode) are flattened and saved as separate pages. If the data size is zero, a single page with shape (0, 0) is saved. The SampleFormat and BitsPerSample tags are derived from the data type. Parameters ---------- data : numpy.ndarray, sequence of numpy.ndarray, or None Input image or tiles. shape : tuple or None Shape of the empty or tiled array to save. Used only if 'data' is None or a sequence of tiles. dtype : numpy.dtype or None Datatype of the empty or tiled array to save. Used only if 'data' is None or a sequence of tiles. 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 according to TIFF.PHOTOMETRIC. 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 interleaved or in separate planes. By default, this setting is inferred from the data shape. If this parameter is set, extra samples are used to store grayscale images. 'CONTIG': last dimension contains samples. 'SEPARATE': third last dimension contains samples. extrasamples : tuple of {'UNSPECIFIED', 'ASSOCALPHA', 'UNASSALPHA'} Defines the interpretation of extra components in pixels. 'UNSPECIFIED': no transparency information (default). 'ASSOCALPHA': single, true transparency with pre-multiplied color. 'UNASSALPHA': independent transparency masks. tile : tuple of int The shape ([depth,] length, width) of image tiles to write. If None (default), image data are written in strips. The tile length and width must be a multiple of 16. If a tile depth is provided, the SGI ImageDepth and TileDepth tags are used to save volume data. Tiles cannot be used to write contiguous series, except if tile matches the data shape. Few software can read the SGI format, e.g. MeVisLab. contiguous : bool If True (default) and the data and parameters are compatible with previous saved ones, the image data are stored contiguously after the previous one. In that case, 'photometric', 'planarconfig', and 'rowsperstrip' are ignored. Metadata such as 'description', 'metadata', 'datetime', and 'extratags' are written to the first page of a contiguous series only. If False, start a new contiguous series. 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 of a contiguous series if possible (uncompressed, contiguous, not tiled). Other TIFF readers will only be able to read part of the data. compress : int, str, or (str, int) If 0 or None (default), data are written uncompressed. If 0-9, the level of ADOBE_DEFLATE compression. If a str, one of TIFF.COMPESSORS, e.g. 'LZMA' or 'ZSTD'. If a tuple, the first item is one of TIFF.COMPESSORS and the second item is the compression level. Compression cannot be used to write contiguous series. Compressors may require certain data shapes, types or value ranges. For example, JPEG requires grayscale or RGB(A), uint8 or 12-bit uint16. JPEG compression is experimental. JPEG markers and TIFF tags may not match. rowsperstrip : int The number of rows per strip. By default, strips will be ~64 KB if compression is enabled, else rowsperstrip is set to the image length. Bilevel images are always stored in one strip per plane. predictor : bool If True, apply horizontal differencing or floating-point predictor before compression. Predictors are disabled for 64-bit integers. subsampling : {(1, 1), (2, 1), (2, 2), (4, 1)} The horizontal and vertical subsampling factors used for the chrominance components of images. The default is (2, 2). Currently applies to JPEG compression of RGB images only. Images will be stored in YCbCr color space. Segment widths must be a multiple of the horizontal factor. Segment lengths and rowsperstrip must be a multiple of the vertical factor. 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 of a contiguous series only. datetime : datetime, str, or bool Date and time of image creation in '%Y:%m:%d %H:%M:%S' format or datetime object. Else if True, the current date and time is used. Saved with the first page of a contiguous series only. resolution : (float, float[, str]) or ((int, int), (int, int)[, str]) X and Y resolutions in pixels per resolution unit as float or rational numbers. A third, optional parameter specifies the resolution unit, which must be None (default for ImageJ), 'INCH' (default), or 'CENTIMETER'. subfiletype : int Bitfield to indicate the kind of data. Set bit 0 if the image is a reduced-resolution version of another image. Set bit 1 if the image is part of a multi-page image. Set bit 2 if the image is transparency mask for another image (photometric must be MASK, SamplesPerPixel and BitsPerSample must be 1). software : str Name of the software used to create the file. Must be 7-bit ASCII. Saved with the first page of a contiguous series only. metadata : dict Additional metadata to be saved along with shape information in JSON or ImageJ formats in ImageDescription or IJMetadata tags. If None, do not write a ImageDescription tag with shape in JSON format. If ImageJ format, values for keys 'Info', 'Labels', 'Ranges', 'LUTs', 'Plot', 'ROI', and 'Overlays' are saved in IJMetadata and IJMetadataByteCounts tags. Refer to the imagej_metadata_tag function for valid values. Strings must be 7-bit ASCII. Saved with the first page of a contiguous series 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 bytes values. value : sequence 'Count' values compatible with 'dtype'. Bytes must contain count values of dtype packed as binary data. writeonce : bool If True, the tag is written to the first page of a contiguous series only. )r%NNONEnoneFNz!cannot save compressed empty file__iter__zdata is not iterablerp?rDrr%Tz+ImageJ does not support non-contiguous data)r%r%z,saving zero size array to nonconformant TIFFc3JK|]}ttj|VdSr9)enumargr EXTRASAMPLE)r;ess r>r?z"TiffWriter.save..s@""24("--""""""r@ ADOBE_DEFLATE zinvalid compression level iurrfzcannot apply predictor to z¬ writing description to ImageJ fileBHhfz"ImageJ does not support data type Brrz for RGBz%ImageJ does not support planar imagesBHz#invalid data dtype for palette moderrczinvalid color map shapec34K|]}t|VdSr9intr;r<s r>r?z"TiffWriter.save..s(22AQ222222r@rc3"K|] }|dkV dSrDNr:rs r>r?z"TiffWriter.save..s&++q1u++++++r@zinvalid tile shaper:)r%rDrrznot a RGB(A) image)rrDrrDzinvalid CFA imagec3&K|] }|dV dSr%Nr:)r;ets r>r?z"TiffWriter.save..Is&77rRU777777r@z#must specify DNG tags for CFA image)r%rDrzinvalid SubfileType MASKuint16r)zlen(datashape) not in (5, 6)rz#invalid data shape for palette modez#not a RGB image (samplesperpixel=2))rDzcannot compress bilevel imagezcannot save tiled bilevel imagezcannot save bilevel image as zdatasize != product(datashape)axiszdatashape[-2] != data.shape[-2]EDc.tj|zg|RSr9)rr)fmtvalr]s r>rzTiffWriter.save..packs;y35555 5r@c t|tstj|} tj|}n%#t $r}t d||d}~wwxYw|}|dkrKt|ddz}t|x}}| d}|dkr|}n|dz }|f}n\t|trGtj |}t||zrt dt||z}t|dkr"|t|dd z}|d } d || |g} d} tj ||z krt|tr!|  |nx|dkrZt|ttt jfr|d}|   ||n|   t%||zg|Rn|  dt|tr|} nt|t jrN|j|krt)d |jj|krt)d |} nBt|ttfr t%||zg|R} n  ||}  |d | | |fdS)Nzunknown dtype sasciisr%rDzinvalid packed binary datarHHzvalue.size != countzvalue.dtype.char != dtyper@)rKrrTAGS DATA_DTYPESKeyErrorrObytestrrSfindbytesrcalcsizer[tuplelistrbndarrayrLr.rrcrvtobytesjoin)coderccountr writeoncetifftyperrawcountdtsizeifdentryifdvalue offsetformat offsetsizertags valueformats r>addtagzTiffWriter.save..addtagsdC(( 'y D+E2 D D D !9%!9!9::C DH||w//%7#&u::- ::g..a<<$HHMHE5)) -//u::&C$%ABBBE f,5zzA~~U3B3Z(b T422\8446HHu%%-;;eU++LOODDe$<$<====aZZ!%%u})EFF) %aOODDdd5%6H6H$I$IJJJJOODD)-c%jj5.@)I5)I)I)I%K%KLLLL\1 5 5666eU++ 2$HHu}55 2zU***+@AAA{'500*+FGGG$}}HHt}552#tCJJ$6????HH#tE511H KKsxx118YG H H H H Hs= AAA@Bcddlm} ||}n(#t$r||d|d}YnwxYw||}|j|jfS)Nr%FractionrD) fractionsr) from_floatrFlimit_denominator numerator denominator)argmax_denominatorr)rs r>rationalz!TiffWriter.save..rationals * * * * * * -'',, - - -HSVSV,, -##O44A; - -s"AAr )rInfoLabelsRangesLUTsPlotROIOverlaysinfolabelsrangeslutsplotroioverlays) truncatedr s@1:zinvalid datetime stringz%Y:%m:%d %H:%M:%S2Gr)rr%=BCur)rQr<rcS@z&wrong number of extrasamples specifiedRr%rr)rDrD)rrDrZrrDzinvalid subsampling factorsztile shape not a multiple of z'JPEG subsampling requires RGB(A) images)Nr[z$TiffWriter: cannot apply subsamplingr[2I(ct|dkr ddd|S|d}|r|dz}|dkrdS|d krdS|d krdSdS) NrDrrrrr% rrrS) bytecountsrar. bytecounts r>bytecount_formatz)TiffWriter.save..bytecount_formatss:!##3''--"1 I +%N 5  s5  sqyys3r@rfz&cannot write non-contiguous empty filec6|d}|||S)Nrrr:)ri compressorlevel predictors r>raz!TiffWriter.save..compresss)$9T333D%:dE222r@c"||||ddS)Nrr) subsampling colorspace outcolorspacer:)rirnrorrs r>raz!TiffWriter.save..compresss*%:dE{12!EEEEr@c|||Sr9r:)rirnros r>raz!TiffWriter.save..compresss%:dE222r@c|dSNr%r:xs r>z!TiffWriter.save..s !A$r@r7z%data too large for standard TIFF filer r@c3&K|] }|dV dSrr:r;ts r>r?z"TiffWriter.save..s&"6"6A1Q4"6"6"6"6"6"6r@sz invalid tile z != zdata.shape[2] != 1c"g|] }|d | Srr:)r;tags r> z#TiffWriter.save..s!;;;3r7;;;;r@F)r&)irrrOrbrc newbyteorderrvrPrTrjisnativerrdrrr array_equalr_write_remaining_pages_write_image_descriptionrrrr write_empty write_arrayrrrGrHrrrrrrr PHOTOMETRIC MINISBLACK MINISWHITERGBCFAPALETTE PLANARCONFIGCONTIGSEPARATErrsequencerKrrupper COMPRESSIONkind PREDICTORS imagej_shaperSrM reshape_ndMASKrreshaperpackbitsrcopyrr!imagej_metadata_tagimagej_descriptionrqjson_descriptionencoderrLstrftime_nowr.rmax log_warningRESUNIT iter_tilesmathceilrange COMPESSORSsortedrrrCrioBytesIOr enumerateendswithnext getbufferflushrrrsum)grrirjrcrn photometric planarconfig extrasamplestile contiguousror`ra rowsperstriprprrcolormap descriptiondatetime resolution subfiletypesoftwaremetadata ijmetadata extratagsrtileiter datashape datadtype datadtypecharbilevelindexdatasize input_shaper- tagnoformattagsizerrrrrrr extrasamples_ compresstag predictortag compresslevelvolumeijrgbijshapendimsamplesperpixel bitspersamples0 tagbytecounts tagoffsetsr%r1r sampleformat maxsamplingunitrktilesnumtilesdatabytecountsbytecountformatrowsize numstrips1 numstrips stripsizer<rnfhpos pageindexifdposifd tagoffset ifdoffsettagindexrrrrdataoffsetsoffsetdatabytecountsoffsetifdsize dataoffsetskiptilesize tileindexchunk stripindexplanestripr.r]r!r"rr#r$sg ` @@@@@@r>rgzTiffWriter.saves^$BXO 0 0 0H < F !DEEEHI E**77 BBI%NMM  5#49I4,, 9 !7888HI E**77 BBI%NMM=y4:?'BCHHDH I I JOM#: (: 3&  ?#B-!++BBEy%011H!# 2Ie,1A55Ie,11y))I,>>H q==DH#  ? 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F3a*Q-!8!8 9 9 9 F3a*Q-!8!8 9 9 9:""!!} LqqgdlD.I.I  F3Q % % % % # F3a ( ( ( F3a ( ( ( F3Q " " "2:    "\ J :4yyA~~1XQ'!+Q71XQ'!+Q7 (!HQ'(!HQ' 1XQ'!+Q71XQ'!+Q71XQ'!+Q7 (!HQ'(!HQ'(!HQ'  u~~a0H b )I,>>@BJKN..~>>O F=/8^ L L L F:|XsX~ F F F-8O 9X1%dD%88 & :W& : (< L"))ABB-"8"8!9E!H!DIabbM**Y-??"ACH8"L..~>>O F=/58^ L L L F:|U1XsU1X~ F F F F3Qb * * *-a8OOeBCCj))I,>>G#3;Ju//r a* b ))$Ry  - !; - $ ,*D E E +!, F3Q - - -)l2Q6<GJ"U1X-I$w.I'[94N J$=b $IJ JI:>9jAA . .$-q!!..~>>O F=/9n M M M F:|Yi H H H- 9O < <EFF F  A FAJJJ  35J 3.8 3333333 3/9 )4EEEEE /9 3333 d///  F"&, F2: F 9,,DEE EJ>???HHSMMM $$@@@@AAAGGIIE GGFOOO HHS]]__ % % % HHJJJ GGENNN$y0DOA~~;;t;;; ,#%-  7DJ 7!3~#6#666ts$?i i"!i"/u1u43u4cD |jr|jrdS|jd|jdzdz }|dkrd|_d|_d|_d|_dS|j}|}|dzr| d|dz }tj }|j |j z}|j}|j |jz}|j}|j} t#|j} t%j} | ||t)|j| } | dd|jD| } | ||dt-|jD]%\}}| ||zz|zdz}|d}|d}|r| }|dzr| d|dz }| | | ||||znI#t0$r<|jr%t5jd t8d |_YdSt;d wxYw| || |||jkr||f}||jkr|df}'| }|dzr| d|dz }|jsE|||zzd kr9|jr#t5jd t8d |_dSt;d t%jtA||z}|}tC|D] }| | z } |\}}| ||rh| ||||z| || }|jD]&}| |||||z }'n| ||| ||z }| | | |||| | " | ||dz zz } || | ||d| |"|}||j#| ||||$|||| z|_#d|_d|_d|_d|_dS) z(Write outstanding IFDs and tags to file.Nr%rDrr r@c3&K|] }|dV dSrr:r~s r>r?z4TiffWriter._write_remaining_pages..s&44A1Q4444444r@rztruncating ImageJ fileTz#data too large for non-BigTIFF filel)%rrrrrrrrrrrrrrrrrrrrrSrrrCrfrrGrHrrOrrrrrrr)rpagenorrrr!r"rrr pagedatasizerrrrrr-rrrrrifdsrr{r.s r>rz!TiffWriter._write_remaining_pagessz T^  FQ$/!"44q8 A::DJ"DO#D #'D F X  19  HHUOOO QJE{);; % o(99 -% 4/00 jll $${C OO44555HHJJ  #((4444444555HHJJ  $$|Q''(((&tz22 1 1MHcG!33j@1DFq6DFE 1hhjj7IIe$$$1HC   LIIdd<==>>>> LLL| &> LLL)-$%JKKK L   %   4+++(. %)))$*DL!((** Q;  IIe    qLG} D6)9!9J!F!F|  6 DDD!%BCC Cz%& 01122v ( (A , &J+KFC HHV    : $$|Vc\::;;; # 0##DIIdd<88999dNFF# $$|Z88999 g F HHY    IIdd<00 1 1 1 JJs}} ' ' ' ' W ++  ) 44 a(())) !!"""ggii     lE**+++    )+ #s%"I2J>Jc|jr|jddks |jdkrdS|jdu}|jr)|jddv}t |j||fi|j}nt|jfi|j}|}|d|j }|j }|j |j|j ||j |j|j tj|j|jzt'||j |d|_d|_d|_ dS)z'Write metadata to ImageDescription tag.r%rDNrr)rrrrrrrrrrrrrCrrrrrrrS)r colormappedisrgbrrs r>rz#TiffWriter._write_image_descriptions q!Q&&&!++ FnD0 < NKOv-E, GG7;~GGKK+4?MMdnMMK"((** !"74#7"78 hmmoo  d-... {###  d0111 v{4?T5G#G#&{#3#355 6 6 6  c"#%&" r@c>tjS)zReturn current date and time.)rnowrs r>rzTiffWriter._now;s $$&&&r@c|js|||jdS)z,Write remaining pages and close file handle.N)rrrrclosers r>rzTiffWriter.close?sH~ *  ' ' ) ) ) %%''' r@c|Sr9r:rs r> __enter__zTiffWriter.__enter__F r@c.|dSr9rrexc_type exc_value tracebacks r>__exit__zTiffWriter.__exit__I r@)FNFF) rrrrrrgrrrrrrr:r@r>r r s  DIhKhKhKhKTD5Dt$B%Tt]R JJJJX u$u$u$p!!!@'''r@r c eZdZdZ d6dZedZedZedZedZ e d Z d Z d7d Z e d Zd ZdZdZdZdZdZdZdZdZdZdZdZdZdZdZd8dZe dZe d Z e d!Z!ed"Z"e d#Z#ed$Z$ed%Z%e d&Z&e d'Z'e d(Z(e d)Z)e d*Z*ed+Z+e d,Z,e d-Z-ed.Z.ed/Z/ed0Z0e d1Z1e d2Z2e d3Z3e d4Z4ed5Z5dS)9raoRead image and metadata from TIFF file. TiffFile instances must be closed using the 'close' method, which is automatically called when using the 'with' context manager. TiffFile instances are not thread-safe. Attributes ---------- pages : TiffPages Sequence of TIFF pages in file. series : list of TiffPageSeries Sequences of closely related TIFF pages. These are computed from OME, LSM, ImageJ, etc. metadata or based on similarity of page properties such as shape, dtype, and compression. is_flag : bool If True, file is of a certain format. Flags are: bigtiff, uniform, shaped, ome, imagej, stk, lsm, fluoview, nih, vista, micromanager, metaseries, mdgel, mediacy, tvips, fei, sem, scn, svs, scanimage, andor, epics, ndpi, pilatus, qpi. All attributes are read-only. NTc f|rdD]} | |vr|| =td| dd|vrtd|D][\} } | dddkr7| ddtjvr!| t || t | Jtd | t|d ||| } | |_t ||_ | j |i|_ i|_ ||n||_ | d | d } dddd| dd} n#t $rt#dwxYwt%j| dz| dd d }|dkrst%j| dz| d \}}|d ks|dkrt#d| dkrtj|_nytj|_ng|dkrR| dkrtj|_nI|ddrtj|_n!tj|_nt#dt7||_|jrR|jjdks,|jd j dks|jdj dkr|!dS|j"r2|j#s+|jjdkr|j$dS|rd|j_%dSdS#tL$r| 'wxYw) aEInitialize instance from file. Parameters ---------- arg : str or open file Name of file or open file object. The file objects are closed in TiffFile.close(). name : str Optional name of file in case 'arg' is a file handle. offset : int Optional start position of embedded file. By default, this is the current file position. size : int Optional size of embedded file. By default, this is the number of bytes from the 'offset' to the end of the file. multifile : bool If True (default), series may include pages from multiple files. Currently applies to OME-TIFF only. kwargs : bool 'is_ome': If False, disable processing of OME-XML metadata. )r1r0r/zTiffFile: the z argument is ignoredr6zthe TiffFile 'pages' argument is no longer supported. Use TiffFile.asarray(key=[...]) to read image data from specific pages. Nris_zunexpected keyword argument: r)ryr,r-r.r%rrr)rrsEPrznot a TIFF filerrr rzinvalid BigTIFF fileris_ndpiFzinvalid TIFF filergrDT)(rrFitemsr FILE_FLAGSrrrr _multifiler,_files _decoders_masterrCreadrrrunpackBIG_BEtiffBIG_LE CLASSIC_BErENDPI_LE CLASSIC_LE TiffPagesr6is_lsm filehandler. compression_lsm_load_pages is_scanimager_load_virtual_frames useframesrfr)rr/r,r-r.r*r+rrUr7rrheaderr]versionr"zeros r>rzTiffFile.__init__gs0  K= N N&==s  L L L LMMM&  -... %llnn K K Urr7e##ABB4?(B(B(c4;;777#$IC$I$IJJJ $T&t L L Ly//wo &ttG 1  GGAJJJWWQZZF 7$'C@@L  7 7 7#$5666 7mIOVAaC[AA!DG"}}#)=T1A2771::#N#N D199 a'(>???## $ DII $ DIIB## $DIIZZ 5110!% DII $DII#$7888#4DJ{ ,$--:a=,11:a=,11$$&&&&&" ,O ,(,(<(E(E //11111 ,'+ $$$ , ,    HHJJJ  s15*L D54L5EE4L7L>L L0c|jjSr9)rr]rs r>r]zTiffFile.byteorders y""r@c"|jjdkS)Nr)rr-rs r>rzTiffFile.is_bigtiffsy B&&r@c|jS)zReturn file handle.rrs r>r&zTiffFile.filehandles xr@c|jjS)zReturn name of file handle.)rr,rs r>rwzTiffFile.filenamesx}r@c| tj|jS#t$rYdSwxYw)z3Return status of file handle as stat_result object.N)rQfstatrfilenorfrs r>r5zTiffFile.fstatsE 8DHOO--.. .   44 s *- ;;c~|jD]}|ji|_dS)zClose open file handle(s).N)rvaluesr&r)rrXs r>rzTiffFile.closesA;%%'' # #C N " " " " r@c|jstjgS||d}||jn- |j|}n#tt f$rYnwxYw|j|n||j|n|t|ttj fr |gnQt|tr |n3t|trfd|Dnt dstd||r|j r|j|jjz}djrBt|t$r-|dkr'|j||j|j }n|t-||j|j}|j|j |j|t3|j|}nCt5dkrd|| }nt9|| }|dS|s |j|_n#t$rX t;d |jd |jd |jz|_n%#t$rd djz|_YnwxYwYn?wxYwt5dkrdj|_nd djz|_|S) aReturn image data from selected TIFF page(s) as numpy array. By default, the data from the first series is returned. Parameters ---------- key : int, slice, or sequence of indices Defines which pages to return as array. If None (default), data from a series (default 0) is returned. If not None, data from the specified pages in the whole file (if 'series' is None) or a specified series are returned as a stacked array. Requesting an array from multiple pages that are not compatible wrt. shape, dtype, compression etc is undefined, i.e. may crash or return incorrect values. series : int or TiffPageSeries Defines which series of pages to return as array. out : numpy.ndarray, str, or file-like object Buffer where image data will be saved. If None (default), a new array will be created. If numpy.ndarray, a writable array of compatible dtype and shape. If 'memmap', directly memory-map the image data in the TIFF file if possible; else create a memory-mapped array in a temporary file. If str or open file, the file name or file object used to create a memory-map to an array stored in a binary file on disk. maxworkers : int or None Maximum number of threads to concurrently get data from multiple pages or compressed segments. If None (default), up to half the CPU cores are used. If 1, multi-threading is disabled. Reading data from file is limited to a single thread. Using multiple threads can significantly speed up this function if the bottleneck is decoding compressed data, e.g. in case of large LZW compressed LSM files or JPEG compressed tiled slides. If the bottleneck is I/O or pure Python code, using multiple threads might be detrimental. Returns ------- numpy.ndarray Image data from the specified pages. See TiffPage.asarray for operations that are applied (or not) to the raw data stored in the file. Nr%c g|] }| Sr:r:)r;kr6s r>rz$TiffFile.asarray../ s+++!U1X+++r@z&key must be an int, slice, or sequencezno pages selectedroutrD)r= maxworkersz$TiffFile.asarray: failed to reshape  to r)r6rbarrayrurrF_getlistrKrintegerslicer&rOr-r]rcrvrsrLr& memmap_arrayrjrrC read_arrayrrSrT stack_pagesr)rr7rur=r>typecoderzr6s @r>rTzTiffFile.asarraysA\z #;r?? " ;6>F >JEE V,i(    LE ;  ^J'',,EE c5=1 2 2 F3ZLEE U # # F#JEE X & & F++++s+++EEDEE E 2011 1 ;6;fm;~ (99Ha' >sC(( >8OO55flFM;;?'V\6<HHC$$V]33333gfl334>> ZZ1__1X%%#*%EEFF CJGGGF >4 ; :%|  : : : :N-3\NN?E|NN $)6<#7FLL!:::#(58>#9FLLL: :ZZ1__ 8>FLL 58>1FL sE <AA+ H88 J.I21J2JJJJJcV|jsgS|jj}|jjj}g}dD]3}t |d|zdrt |d|z}n4||j_||j_|s|}t |D] \}}||_ |S)zReturn related pages as TiffPageSeries. Side effect: after calling this function, TiffFile.pages might contain TiffPage and TiffFrame instances. )lsmomer^shapedfluoviewsismdgeluniformrF_series_)r6r+keyframerr_series_genericr)rr+rQrur,r<r s r>ruzTiffFile.seriesc sz IJ( :&,   DtUT\511 9zD'899;;  ) &  ,))++F f%%  DAqAGG r@c P|j}|dd|_|jr|g}g}i}|D]L}|js |j}||vr|||1|||g||<M|D]w}||}|d}|j}|j}t|dkrt|f|z}d|z}|t|||j |dxt|dk|_ |S)zgReturn image series in file. A series is a sequence of TiffPages with the same hash. Fr%rDrGenericr) r6_clearr+cache_loadrjhashr[axesrSr rc is_uniform) rr6rzkeysrurxr7rjrZs r>rRzTiffFile._series_generic sU   U ;  KKMMM % %D: )Cf}}s ""4(((( C   #fs   C3KE8DJE9D5zzA~~U -Tz MMueTZINNN    f++* r@c0|jd}|j}|j}|j}|jp|j }|j|}t|}|dkr |f|z}d|z}|jrd}n |jrd}nd}t|||||gS) z+Return all images in file as single series.r%validaterDr ScanImageNIHImageUniformrU) r6rjrZrcr)is_nihrArSr ) rrxrjrZrcr_r6lenpagesrs r>_series_uniformzTiffFile._series_uniform sz!} y )8T[9 ##X#66u:: a<<K%'E:D   DD [ DDDueUDtDDDEEr@c |j}d|_t|}d}dx}x}x}x}}g} d} | |krn| |_|j}|jst ddSd}d}t |j} | dd}| d}| d d} d | vr<| d }t|t|kr|}nd}t d |g} t|}|dkr&t|t|j \}}nd }d}|rt d dSd |cxkr || z kr|nny||j j z}| rd }ne|j r|j|z|| d zjkrd} n?d} t| d z| |zD]&}||}||_| |'|| | ||||| | |z } t| d k|_| S)z%Return image series in "shaped" file.Tc  |d}|s9|j}|j}t|dkrt|f|z}d|z}t|}t|} |jr!| |kr| |zdkr|d}d|z}| |zf|z} t |||}|}n6#t $r)} td| jj d| Yd} ~ nd} ~ wwxYw| t|||j ||d|dS) Nr%rDrTzShaped series: : Shaped)r,rrA) rjrZrSrrt reshape_axesrOrrrr[r rc) rur6rZrjrr,rArxr.resizers r>r[z'TiffFile._series_shaped..append sp8D & yu::>> ZZME1E:D5>>DW%%F! 2ftmm 8J8J$ $ITz4)E1 #D%99   Ecm&<EEEE  MMueTZ$(x9NNN     s B C)C  CNr%z1Shaped series: invalid metadata or corrupted filer,rjrArZz&Shaped series: axes do not match shaperDz5Shaped series: series shape does not match page shapeF)r6r+rSrQ is_shapedrjson_description_metadatarErdivmodrj_dtyperdis_finalr-rr[r[)rr6rdr[rQrZrjrr,rurrrAspagesr.npagesmodjrxs r>_series_shapedzTiffFile._series_shaped s u::   8487747%7'D5   "EN~H% GIIItDE01CDDH<<++Dw'G [$77I!!'t99G ,,#EED HIIIZF7##Daxx$T78>+B+BCC  KMMMt6----X------00 ,FF% , $.uqy1A1HHH %II!&I"519efn==,,$Qx(0  d++++ F664y I I I VOEk5 nf++* r@c j d _d _ d j fd} |}n #t$rt dYdSwxYw|r g n dd dt } dd} d d} d d}g}g}|dkr*|||d |dkr*|||d |dkrA|rt|nd|kr*|||d ||rt|ndz} | dkr*|| |d j ddkrJd |vrF| j dd| j ddn j ddkrE| j dd| j ddn j dddkrj j ddt|z j ddz}t j d|zt j ddz}n4| j | j |o@tjdko( jdt| jzdzk} d_t% | j|d| gS)z#Return image series in ImageJ file.Tr%cPjsdSdd}|dkrdSj\}}|tjjzdzks|||zzjjkrttdkr|||zzdj krdSdS)NFimagesr%rDrT) rqrErtrrjrr&r.rOrSr-)ryr-rmetarxr6rs r> is_virtualz+TiffFile._series_imagej..is_virtual0 s= uXXh**F{{u .MFE,,t/AAQFFFEFN*T_-AAA ll"5zzA~~&56>"9E!HO"K"Ku4r@z1ImageJ series: invalid metadata or corrupted fileNryframesrDsliceschannelsTZrprSrSIrImageJ)rrA)r6r+rQimagej_metadatarOrrErSr[rrZextendrjrrrtrr[r rc)rr{ isvirtualryr|r}r~rjrZremainrArzrxr6s` @@@r>_series_imagejzTiffFile._series_imagej& s Qx#        ( " II    K L L L44   FEE!!!HE(CJJ//(A&&(A&&88J** A:: LL KK    A:: LL KK    a<r?z,TiffFile._series_fluoview.. sV22!q)--adjjllC@@(022r@c3XK|]%}|ddkt|dV&dSrrrs r>r?z,TiffFile._series_fluoview.. s4::A1c!A$ii::r@Tr% ImageNameFluoViewr,r) r6rAfluoview_metadatarreversedrrr[r rc)rr6mmmmhdrZrjs r>_series_fluoviewzTiffFile._series_fluoview s ##U#33  #HR -..//ww22 $22222::::::: 5%q ";j B B B  r@cNd|j_d|j_|j}|ddvrEt jd}|dddz |ddkrfd }nfd }nd }|jd}d|_t|g|j||j |d gS)z#Return image series in MD Gel file.Fr%FileTag)rfloat32 ScalePixelrDrc:|ddzzS)Nrrrascales r> transformz)TiffFile._series_mdgel..transform s88I..1E99r@c4|dzS)Nrrrs r>rz)TiffFile._series_mdgel..transform s88I..66r@NMDGel)rr) r6r+rQmdgel_metadatarbrcr[r rjrZ)rmdrcrrxrs @r> _series_mdgelzTiffFile._series_mdgel s %     i=H $ $K **E|$E!HuQx'E)}!!::::::777777Iz!} D64:udi%.W > > >  r@c\|jd}|d}t|}|j}d|vr%d|vr!|d|jz}|d|jz}n*|dkr|j}|j}n|f|jz}d|jz}d|_t|||j|d gS) z(Return image series in Olympus SIS file.Fr^r%rjrZrDrTSISrU) r6rArS sis_metadatarjrZr[r rc)rr6rxrdrrjrZs r> _series_siszTiffFile._series_sis s ##U#33Qxu::   b==Vr\\wK$*,Ef: )DD ]]JE9DDK$*,E?D 5%T F F F  r@c f%&'ddlm}|jdj} ||}n#|j$r}}t d|jjd| | d }||}n#t$rYYd}~dSwxYwYd}~nd}~wwxYwd|j_ d|j_ d|j_|jd |jd d}||i|_|jj}i}g}|D]} | jd rt d n| jd r4| D]0} | jddds2| D]} | D]} | D]} | jddds%| jd}| jdd}t.j|}d| jvrvt3| jdd}t3| jd}t3| jd|z}t5j|||}n d| D}||f||<2| jds| j%%dd}| D]}|jds|j%dt;%d}%fd|Dx&}t=&dd}d}d'|D]}|jd r|j%|Ot?%d!''dg|'zz}'dkr&'fd"tA|D}n6t?%d!d'krtCd#| dg|'zz}|jd$s|j%t?%d%d}t?%d&d%%vrdnd}t?%d'|}%fd(|ddD} t5j"||dd}n #tB$rt d)YwxYw|D]}|jd s|$|j#|j#}|jd|j|<n|j#|jvr|j$s gccccS|jd*} tKtLj'|||+} d| j_ d| j_ d| j_| jd n1#tPtRtBf$rt d,|YnwxYw| |j|j#<| *|j|j#j}! tW|r|ntY|!D]}"|!||"z|||"z<n#tZ$rt d-YnwxYwny|j}! tW|r|n)t]tY|!tY|D]}"|!||"z|||"z<#tZ$rt d-YwxYwt_d.|DrQd}#|D]}"|"r|"|"jkr|"}#n|#KtA|D];\}"}#|#r4|#j0|#j1j_|#j1j|#j0}#|#||"<n<'dkrx|#j2dkrm|dd/kra|0d/}"|d|"||"dzdz||"|"dzz}&d|"&|"dzdz&|"|"dzz&|#j3ti&tY|#j3 dkrAt d0|#j3ti&tY|#j3 d~|D]6}"|"2 |#|"_ #tj$r}t d|Yd}~.d}~wwxYw7|6to|&|#j8|||d12~|D]}$ts|$j3&|:D]\}\}}|$j;0|}"tY|}&|"|kr"|$j;<||d|$_;_&|"xx|zcc<&=|"dz||$j;<|||zd|$_;ti&|$_3|D])}$t}|$j3|$j;\|$_3|$_;*tY|dk|_?|S)3z(Return image series in OME-TIFF file(s).r% ElementTreez OME series: rhignoreerrorsNTrQUUID BinaryOnlyz'OME series: not an ome-tiff master fileStructuredAnnotations NamespacerlmodulorAlongTypeotherStartSteprDEndcPg|]#}|jd|j$S)Label)rrtext)r;labels r>rz(TiffFile._series_ome.. s@.&.&.&,1+09+=+=g+F+F.&(- .&.&.&r@ImageNamePixelsDimensionOrderc@g|]}td|zS)Sizerr;axattrs r>rz(TiffFile._series_ome.. s*#J#J#JrCVb[(9$:$:#J#J#Jr@rChannelSamplesPerPixelcHg|]\}}|dkr |zn|S)rpr:)r;r<rrjspps r>rz(TiffFile._series_ome.. sK,B,B,B(-28:SyyE!HOOeAh,B,B,Br@z3OME series: cannot handle differing SamplesPerPixelTiffDataIFD NumPlanes PlaneCountc\g|](}td|zd)S)Firstr%)rrErs r>rz(TiffFile._series_ome.. s3NNNb3txx" a8899NNNr@z"OME series: invalid TiffData indexFileName)rzOME series: failed to read zOME series: index out of rangec3K|]}|duV dSr9r:rs r>r?z'TiffFile._series_ome..U s&//QqDy//////r@rpz3OME series: incompatible page shape %s; expected %sOME)parentr,r)@ xml.etreerr6r fromstring ParseErrorrrrdecoderrfrWr+rQrXattribrErrdirnamerrr AXES_LABELSfloatrbarangerrrrrrOravel_multi_indexrrrrQpathrrrrrS IndexErrorminallrrrrjrrr[r rcrrrZreplaceinsertrr[)(retreeomexmlrootr root_uuidrrruelementannotrmodulalongrnewaxisstepstartstopr;r,pixelsrZidxshaper.rrirnumidxuuidfnamerXr6r<rQserierrjrs( @@@r> _series_omezTiffFile._series_ome s 222222A* ##F++DD    Fs}'=FFFF G G G h77>>@@''//   tttttt     #   $'''KOOFD11  $' ("p p G{##L11 EFFF{##$;<< A$AAE <++K,.00080B0B! !&AA%*AAE).AA',y"~'>'>w'G'G!-$,',y}*/,*:*:67*K*K*.*:7*C#*el#:#:+01A1A&!1L1L+M+MD,1%,w2G,H,HE+0e1D+E+E+LD-2\%t-L-LFF.&.&5:.&.&.&F 18/@t #AAA*;''00 >D88FD))D!K K z**844}wwx-=(>??@@#J#J#J#JT#J#J#JJuSbSz**"JJJJDx((33 !#{<"%dhh/@#&F&F"G"GC$(6TS[#9D"Qww,B,B,B,B,B1:4,B,B,B!*;Q!?!?@@CGG",.I#J#JJ | $v58,,Z88! ;Ddhhua0011Cdhh{$AAANNOOCdhh|S99::CNNNND"INNNC!#5c8CRC=II%!!!#$HIII !!%,J,J#x0088%$$,1F(, I59[5FDK 22!Ydk99#'?*(* $(K $;E &&.$&GLL%$@$@,0'"'"'"37 6: 356 2 #  > > > >$+-> #K&&& +$K%$K$K!M!M!M %&69DK 2IIKKK $ DI 6 <J%*#+E333u::%F%F??05cAgS1W ?)JJJ'(HIIIIIJ $ J%*'* JCJJD 0J0J&&??16cAgS1W ? *JJJ'(HIIIIIJ//$///// AQ!*__#$#'0"" 8#"=E^HO1:'/'U5#hn2E2E1E1F1F+G%H%HHHM eS%8%8$8$9$9:;; >>A}>)1AJJ+>>>'(%  "4*.TGGGDWK Z ' 'E%%E+1<<>> M M''wJ$$T**6{{8t##!&!3!3D'1!E!EEJJ!HHH%HHHLLQ---!&!3!3D$.!!L!LEJJ,,EKK L LE&25; &K&K #EKf++* s3 B:B5=BB5 B-%B5,B--B55B:S""S? >S? 5A.W$$)X X 4ZZ! Z! .A[??\ \ b"" c ,c c c ^ |j tj d}|jdjdkr*|dddd} ddd kr|d z } d dd kr|d z }|d d d}t fd|D} dd}|jtdd dd}|dj }t|||||dg}|jd j r|jtd d dd}|dj }d }d}|t|krO|t|dz kr9|||z}|d z }|t|kr|t|dz k9|d ||djz}|d |dz}|t|||||dd|_|S)z-Return main and thumbnail series in LSM file.ScanTyper%rrprlXYXYC DimensionPrDP DimensionMMNrc3bK|])}ttj|V*dSr9)rrCZ_LSMINFO_DIMENSIONS)r;r<lsmis r>r?z'TiffFile._series_lsm.. s8MM1c$t9!<=>>MMMMMMr@rFr^LSMrCYX LSMreduced) lsm_metadatarCZ_LSMINFO_SCANTYPEr6rrrErrArCrcr is_reducedrSrjr[r[) rrZrjr,r6rcrucpr<rs @r> _series_lsmzTiffFile._series_lsm sG 'Z(89 :a= $ ) )<<R((00u==D 88L! $ $q ( ( CKD 88L! $ $q ( ( CKDDDbDzMMMMMMMMMxx## ##E!T1$5$5#FFa 5%4e L L L  :a= # J''aq(9(9E'JJE!HNEBAs5zz//a#e**q.&8&8eAhQs5zz//a#e**q.&8&8"1"Ia.E8e#D MMueUDt$0222      r@c<|j}d|_d|_d|_d|_|d|||d}|dddD] }||_ |d}|dddD] }||_ dS)z%Load and fix all pages from LSM file.TrDr%Nrr)r6rWr+rQrX_lsm_fix_strip_offsets_lsm_fix_strip_bytecounts)rr6rQrxs r>r(zTiffFile._lsm_load_pages s   T """ ##%%% &&(((8##A#J % %D$DMM8!$Q$K % %D$DMM % %r@c|jjdkrdS|j}t|}|jd}|j}d}dD]!}|j|dvr||j|z}"|dkrd}dD]}||dkr|j|}n|r~t|d |z|z\}} | dkrtd |||d f} tj t|  | } tj | dd} n(tj | d d } |djdd|djddkr | d ddd f} d} d} | jD]o}|t!|}g}|jdD]'}|| kr| dz } ||| z|} (t%||jdf|_pdS) zUnwrap strip offsets for LSM files greater than 4 GB. Each series and position require separate unwrapping (undocumented). rgNr%rD)r%rDPMrDrrrzmod != 0r.)r&r.r6rSrurZrjrorrbrrrmoveaxis_offsetscountsflatrr[r)rr6rsrurZ positionsr<ntimesdivrtrjindiceswrappreviousoffsetrx dataoffsets currentoffsets r>rzTiffFile._lsm_fix_strip_offsets sD ? % ' ' F UQ{  - -A{1~%%V\!_,  q==F  7c>>#\!_FE" 8!&!i-&*@AAS!88&z222"FC3,wu~~66>>uEE.!Q77l6**222q99G 8 "1 %a (58+B1+Ea+H H Hc44R4i(G M MAQ=DK!%!4Q!7 / /  >11EMD""=4#7888!."' "4"4d6I!6L"LD   M Mr@cL|j}|djdkrdSt|d}t|dz }t |D]\}}|jdzr|j\}}||kr||dzjdd}n,t|dd|dzz|jj }t|}tt|dz D]}||dz||z ||<||dz |d<|t|f|_dS)zSet databytecounts to size of compressed data. The StripByteCounts tag in LSM files contains the number of bytes for the uncompressed data. r%rDNc(|jddSrw)r)ps r>rzz4TiffFile._lsm_fix_strip_bytecounts.. sA,rz"TiffFile._lsm_fix_strip_bytecounts sP  8 1 $ $ Fu"B"BCCCUa '' = =GAtzA~ "&"5 GZ6zz"1q5\8;A> !q:b>/A!A!%00 j))J3z??Q.// < < 'A ; 1 ''"+5JrN")5+<+<" __getattr__zTiffFile.__getattr__. s 8t & &: uA5566E D$ & & &L~& K K4 K KMM Mr@c|Sr9r:rs r>rzTiffFile.__enter__9 rr@c.|dSr9r r s r>rzTiffFile.__exit__< rr@r%Oc &dt|jjt|jrdnddd|jg}|jr|d|dd|jDt|j d kr*|t|j d t|j d kr*|t|j d t|j d kr*|t|j d d |}| dd  dd }|t|jjt#ddzt|z }dkr|S|g}|dd|j Ddkr(|fd|j Dn~|j r(|fd|j DnO|j rH|j dr;|t&|j ddkrt+|jD]x}t-||dzrct/||dz}|rN|d|t3|dzyd| ddS)aReturn string containing information about TiffFile. 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 '{}'rlz little-endianz big-endianrBigTiff c3>K|]}|VdSr9lowerr;rs r>r?z#TiffFile.__str__..T s*;;1QWWYY;;;;;;r@rD Pagesz Seriesz Files z  rrr% c34K|]}t|VdSr9rLr;r s r>r?z#TiffFile.__str__..b s(::c!ff::::::r@rc3VK|]#}|t|V$dS)Ndetailwidth)r __str__)r;r!r:r;s r>r?z#TiffFile.__str__..d sF}$$QvU$CC$}}}r@c3K|]9}|jdt|jdV:dS)r%Nr9)r6r r<)r;r r:r;s r>r?z#TiffFile.__str__..j sVwqz-$$QWQZe$LL----r@r9rz{}_METADATA {}r;height z )rrr.byteorder_isnativer]rr[rflagsrSr6rurrformatsnipstrr,rrr r<rrPrrr)rr:r;r:r,ms `` r>r<zTiffFile.__str__? s   & &!$.11 5BB&#%%%)^5   ? # KK " " " CHH;; ;;;;;<<< tz??Q   KK3tz??222 3 3 3 t{  a   KK3t{++444 5 5 5 t{  a   KK3t{++333 4 4 4yy||FD))11%>>{{ DHM3r519s4yy+@#A#A B BDD Q;;Kv DII::dk:::::;;; Q;; KK!Z     [  KK![     Z DJqM  KK  AvU KK    Q;;tz**  4 !344d[&899A -44 $ 'v{ K K K {{4  ((6:::r@cNfdttjDS)zReturn set of file flags.c^h|])}td|z|*Srrr/r;r,rs r> z!TiffFile.flags.. E   tUT\** JJLL   r@rrrrs`r>rBzTiffFile.flags 8    t//    r@c |jdjp |jddj}|rd|_|S#t$rYdSwxYw)zFile has MD Gel format.r%rDT)rWF)r6is_mdgelrEr[r)rismdgels r>rPzTiffFile.is_mdgel sm  1 &7 q--6  ("'N   55 s=A A Ac0|j}|d}|js|jrdS |j}d|_|j}dD]/}||j|kr ||_dS0n#t $r Y||_dSwxYw ||_n #||_wxYwdS)z2Return if file contains a uniform series of pages.r%TF)rDrr)r6r)rcr+rYaspager)rr6rxr+hr<s r>r[zTiffFile.is_uniform s Qx     4 (I#EO A ! !8??$$)Q.. (EOOO / !   'EOOO  ! (EOOiEO ' ' ' 'ts/=A)'A)(B ) A>3B =A>>B BcJ|jp|jp|jp |jp|j S)z;Return if pages can be appended to file without corrupting.)r%is_stk is_imagej is_fluoviewis_micromanagerrs r>rzTiffFile.is_appendable sA K ${ $~ $ $#   r@cP|jsdStd|jDS)z9Return tifffile metadata from JSON descriptions as dicts.Nc3K|]@}|jdkt|jdjVAdS)rKr%N)rr/rnr6rmr7s r>r?z+TiffFile.shaped_metadata.. sT  v||~~)) &agaj&: ; ;))))  r@)rmrrurs r>shaped_metadatazTiffFile.shaped_metadata sC~ 4  [      r@c8|jsdS|jdjS)zReturn OME XML.Nr%)r)r6rrs r> ome_metadatazTiffFile.ome_metadata s"{ 4z!}((r@cN|jsdS|jdjdjS)z0Return LSM metadata from CZ_LSMINFO tag as dict.Nr%l)r%r6r#rrs r>r zTiffFile.lsm_metadata *{ 4z!}!%(..r@c|jsdS|jd}i}|jdj|d<|jr|jd|d<|jd}|||j|jd}|||j|jd }|||j|jdj}|d |d <|d |d <|d |d < tj d t|d|d Dd|d<tj dt|d|d Dd|d<n6#t$r)}td|jjd|Yd}~nd}~wwxYw|S)z*Return STK metadata from UIC tags as dict.Nr%] NumberPlanesPlaneDescriptions\^_ ZDistance TimeCreated TimeModifiedc g|] }t| Sr:julian_datetimer;dts r>rz)TiffFile.stk_metadata.. s/FFF""%FFFr@ DateCreatedzdatetime64[ns]rDatetimeCreatedc g|] }t| Sr:rnrps r>rz)TiffFile.stk_metadata.. s/HHH""%HHHr@ DateModifiedDatetimeModifiedzSTK metadata: rh)rVr6r#rrsplitrErqrrbr@ziprOrrr)rrxrzruic2tagrs r> stk_metadatazTiffFile.stk_metadata s1{ 4z!}!%5!1!7~   G*.*:*@*@*F*FF& 'immE"" ? MM#) $ $ $immE"" ? MM#) $ $ $immE"" ? MM#) $ $ $)E"(%k2{ ' 6}!(!8~ J(- FFW]+W]-CDDFFF&)()()(F$ %*/HHW^,gn.EFFHHH&*(*(*(F% & & J J J H)?HH3HH I I I I I I I I J s(A:F## G-GGc|jsdS|jd}t|j}|jd}|, ||jn#t$rYnwxYw|S)z,Return consolidated ImageJ metadata as dict.Nr%)rWr6imagej_description_metadatar#rErqrrf)rrxrzrs r>rzTiffFile.imagej_metadata s~ 4z!},T^<<immE"" ?  ci((((     sA## A0/A0c|jsdSi}|jd}||jdj|jdj|d<|S)z.Return consolidated FluoView metadata as dict.Nr%9:Stamp)rXr6rqr#r)rrzrxs r>rzTiffFile.fluoview_metadata sZ 4z!} di&,---)E*0w r@cN|jsdS|jdjdjS)z:Return NIH Image metadata from NIHImageHeader tag as dict.Nr%2)rcr6r#rrs r> nih_metadatazTiffFile.nih_metadata rar@c|jsdS|jdj}|d}||jS|d}||jSdS)z5Return FEI metadata from SFEG or HELIOS tags as dict.Nr%xz)is_feir6r#rEr)rr#rs r> fei_metadatazTiffFile.fei_metadata# s^{ 4z!}!hhuoo ?9 hhuoo ?9 tr@cN|jsdS|jdjdjS)z,Return SEM metadata from CZ_SEM tag as dict.Nr%F)is_semr6r#rrs r> sem_metadatazTiffFile.sem_metadata1 rar@c|jsdS|jdj}i} ||djn#t $rYnwxYw ||djn#t $rYnwxYw|S)z:Return Olympus SIS metadata from SIS and INI tags as dict.Nr%鿂)is_sisr6r#rqrrf)rr#rzs r>rzTiffFile.sis_metadata8 s{ 4z!}!  MM$u++ , , , ,    D   MM$u++ , , , ,    D  s# A A  A  A22 A?>A?c|jddD]}d|jvr |j}ndSi}tddD]1}||vrtj|}||j||dd<2|S)z6Return consolidated metadata from MD GEL tags as dict.Nr饂i)r6r#rrr r)rrxr#rzrr,s r>rzTiffFile.mdgel_metadataI sJrrN  D !!y"4%'' 0 0D49T?D#Dz/F48   r@c&|jdjS)zReturn Andor tags as dict.r%)r6 andor_tagsrs r>andor_metadatazTiffFile.andor_metadataZ z!}''r@c&|jdjS)z'Return EPICS areaDetector tags as dict.r%)r6 epics_tagsrs r>epics_metadatazTiffFile.epics_metadata_ rr@cN|jsdS|jdjdjS)zReturn TVIPS tag as dict.Nr%J)is_tvipsr6r#rrs r>tvips_metadatazTiffFile.tvips_metadatad s*} 4z!}!%(..r@cR|jsdSt|jdjS)z:Return MetaSeries metadata from image description as dict.Nr%) is_metaseriesmetaseries_description_metadatar6rrs r>metaseries_metadatazTiffFile.metaseries_metadatak s+! 4.tz!}/HIIIr@cR|jsdSt|jdjS)z7Return Pilatus metadata from image description as dict.Nr%) is_pilatuspilatus_description_metadatar6rrs r>pilatus_metadatazTiffFile.pilatus_metadatar s* 4+DJqM,EFFFr@c|jsdSt|j}||jdjdj|S)z2Return consolidated MicroManager metadata as dict.Nr%)rYread_micromanager_metadatarrqr6r#r)rrzs r>micromanager_metadatazTiffFile.micromanager_metadatay sK# 4+DH55 djm(/5666 r@cV|jsdSi} t|j\}}||d<||n#t$rYnwxYw t |jdj|d<n6#t$r)}td|j j d|Yd}~nd}~wwxYw|S)zscanimage_metadatazTiffFile.scanimage_metadata s  4 !8!B!B Iw"+F;  MM' " " " "    D  P$B 1 )%+%+F= ! ! P P P Ns}/ENNNN O O O O O O O O P s'1? A  A "A33 B&=B!!B&c8|jsdS|jdjS)z0Return GeoTIFF metadata from first page as dict.Nr%) is_geotiffr6 geotiff_tagsrs r>geotiff_metadatazTiffFile.geotiff_metadata s" 4z!}))r@)NNNTNNNNNNr%r))6rrrrrpropertyr]rr&rwrr5rrTrurRrervrrrrrr r(rrr&rrr<rBrPr[rr\r^r rzrrrrrrrrrrrrrrrr:r@r>rrMs2JN*.bbbbH##X#''X'XXX vvvvp$$X$L&&&PFFF(^^^@[ [ [ z       4   (]]]~###J%%%.4M4M4Ml===: M M M?;?;?;?;B  X   X X(   X    X ))X)//X/ ##X#J  X X&//X/   X //X/ X X ((X(((X(//X/ JJXJ GGXG XX&**X***r@rceZdZdZdZedZejdZedZejdZedZ e jdZ ed Z dd Z ddZ dZ ddZddZddZddZdZdZdZdZd S)r$zSequence of TIFF image file directories (IFD chain). Instances of TiffPages have a state (cache, keyframe, etc.) and are not thread-safe. cd|_g|_d|_d|_t|_d|_d|_d|_t|trj||_|j }| |_tj|jj||jjd}nEd|jvr3|j|_|jj }|jdj}|d}n d|_dS|dkrt+dd|_dS||jkrt+d|d|_dS||t |jd}|j|||_|j2|j|d dd|_d|_dSdS) zInitialize instance and read first TiffPage from file. If parent is a TiffFile, the file position must be at an offset to an offset to a TiffPage. If parent is a TiffPage, page offsets are read from the SubIFDs tag. NFr%JTz!TiffPages: file contains no pagesTiffPages: invalid page offset rrD)rr6_indexed_cachedr _tiffpage _keyframe_cache_nextpageoffsetrKrr&rrrrifdoffsetformatr ifdoffsetsizer#rrr.rCr[r)rrrr-r"rxs r>rzTiffPages.__init__ s    ! # fh ' '  DK"B#%7799D ]6;#>#%776;+D#E#EGGGHJFF FK   -DK'Bk#&,GQZFF DM F Q;; ; < < < DM F RW   D&DD E E E DM F  1--- $   ' J  gabbk * * * DMDLLL ( 'r@c|jS)z2Return if pages/frames are currently being cached.)rrs r>rWzTiffPages.cache s {r@clt|}|jr|s|||_dS)z@Enable or disable caching of pages/frames. Clear cache if False.N)rrrVrrs r>rWzTiffPages.cache s8U  ; u  KKMMM r@c>|jtko ttuS)z?Return if currently using TiffFrame (True) or TiffPage (False).)rr r rs r>r+zTiffPages.useframes s~*Hy/HHr@c0|rtnt|_dS)z0Set to use TiffFrame (True) or TiffPage (False).N)r r rrs r>r+zTiffPages.useframes s',9r@c|jS)zReturn current keyframe.rrs r>rQzTiffPages.keyframe ~r@c*t|}|dkr|t|z}|jj|krdS|dkr|jd|_dS|js|t|jkrO|j|}t |tr ||_dSt |tr|j |j|<|j }t|_ | ||_||_ n #||_ wxYw|j|j|<dS)z;Set current keyframe. Load TiffPage from file if necessary.r%N) rrSrrr6rrKr r r-r_getitem)rrrxtiffpages r>rQzTiffPages.keyframe sE  199 SYY E > 5 ( ( F A::!Z]DN F = 0EC OO33:e$D$)) !%$ ** 0$(K 5!>! &!]]511DN%DNNXDN % % % % N 5s C88 DcH|js|d|jS)z7Return offset where offset to a new page can be stored.r)r_seekrrs r>rzTiffPages.next_page_offsets&}  JJrNNN##r@NFTc` |||||S#t$r|YnwxYw|S))Return specified page from cache or file.)r_rWrS)rr)rr7defaultr_rWrSs r>rEz TiffPages.gets^ ==heF!     s  ++c|jrdS|j}|sdS|js|d|jsdS|jj}||j}t|D]]\}}t|ttj fr7| |||j||}|||<^d|_dS)z#Read all remaining pages from file.NrrrQT)rr6rrrrr&rrrKrrbrBrCr)rrQr6rr<rxs r>rXzTiffPages._load)s <  F   F}  JJrNNN{  F [ #  ~H ''  GAt$em 455  ~~dkX~NNa r@c |j} t|dkrtd|d}|jd}t|dkrtd|d|d|dz }|d|dz |ks|d|dz |krtd|d|j }|jdd|jz }|dks||krtd||g}|jj j |z }tt|j|z||D]E\}} | |zg} | d kr| nd } | t|j|dzd | || F||_d |_d |_d |_d S#t$$r} t'd| Yd } ~ d Sd } ~ wwxYw)zCalculate virtual TiffFrames.rDzpages already loadedr%zdata not contiguousrrrzpage offsets not equidistantr^rN)rrr-r"rirQTz*TiffPages: failed to load virtual frames: )r6rSrOrrrrYr-rr&r.rrr[r rrrrfr) rr6rxrideltapage1 offsetoffsetfilesizerr-r"rs r>r*zTiffPages._load_virtual_frames>s= $ L5zzA~~ !78888D,Q/J:!## !6777 JJqMMM!HuQx'EQx%("e++uQx%(/Be/K/K !?@@@MM!diM88E /215 DLa<%#7#7 !?@@@5ME{-2U:H!*51E195,B,B"C"C   v!L01#)E>>t #{#ai# '#-!%     DJDKDL DMMM L L L JSJJ K K K K K K K K K LsF*F55 G?GGch|j}|sdS|d|_|rGt|ddD].\}}t|ts|j |j||dz</nIt tur;t|D]+\}}t|t r|j |j||<,d|_dS)zADelete all but first page from cache. Set keyframe to first page.Nr%rDF) r6rrrKrr-r r r)rfullyr6r<rxs r>rVzTiffPages._cleargs   Fq  +$U122Y// / /4!$,,/1H#';E!a%L /h & &$U++ + +4dI..+4;3J#{E!H r@c|j}t|}|dkrtd|jj}|jrt d|jsd|cxkr|kr@nn=||}t|tr|n|j }| |dS|jj }|j } |j} |j} |j} |j} t$j}|d}t|tr|n|j }|d}||kr| | || || d}|dkrt+d|n4#t,$r't/d |d ||d=|d z}d |_YnwxYw|| z|| zz|_| |j|| || d}|dkrd |_n||jkrt/d |d |_nv|||d z }d|cxkr|krnnnK|dkr>|ddD]3}|t|tr|n|j krt+d4||k||krtd||}| t|tr|n|j dS)z/Seek file to offset of page specified by index.r%zindex out of rangezseek of closed fileNri@zsuspicious number of tags z&TiffPages: corrupted tag list of page  @ rDTrdzinvalid circular IFD reference)r6rSrrr&closedrOrrKrr-rCrrrr tagnosizerrrrrrfrrr.r[)rrmaxpagesr6rdrrxr-rr!r"rrrrtagnor!s r>rzTiffPages._seekysr u:: q==122 2 [ # 9 4233 3 = A111111111,>??B4<<'(NU(N(NOOO    ---$*--"IA  $  $*I#5#GD GGD( ) ) )VL"''**=*=>>qAF{{ $   HfHHIII $  LL MHE$$$$H$$$$$3ssNNAz!S'9'9"G!!qxHH+,LMMMIM!!R H  122 2U|  4-->4;?????s$=E"".FFc  |j |j}|+ttt |}n=t |t rt|}nt |tr|d\}}}|j s;t||t |j kr| dtt|t |j }nkt |ttjfr;d|_|dkr|j |gS  |g||_S#||_wxYwt!d|j}t%||_r |jj|rd|_ fd|D} | d|j||_|r||_n#||_|r||_wxYw| S) zReturn specified pages as list of TiffPages or TiffFrames. The first item is a TiffPage, and is used as a keyframe for following TiffFrames. NrFr%*key must be an integer, slice, or iterableTc(g|]}|Sr:r:)r;r<getitemr_s r>rz&TiffPages._getlist..s%777aWWQ))777r@)rr+iterrrSrKr&rCrrrr6rrrbrBrFrrrQrYr) rr7r+r_r+rrr{rQr6rs ` @r>rAzTiffPages._getlists-^ ;uSYY''((CC X & & Js))CC U # # J [[33NE4= Su%5%5DJ%G%G 2uckk#dj//::;<S   +~*H  "!DN ,777773777E LLDN + + +&DN ,!+&DN ,!+++++ s E E).*G))G;ct|}|j}|dkr|t|z}n=|jr6|t|kr#t d|dt|d|rt n|j}|t|kr||}|jrB|s@t|ttj fs|r||j krtd|Sn5t|t |fr|r||j krtd|S| |||j||j}|r||j krtd|js|r|||<|S)rr%zindex z out of range()zpage hash mismatchr)rr6rSrrr rrrKrbrBrYrrrr)rr7r_rWrSr6rrxs r>rzTiffPages._getitems#hh  77 3t99 CC ] Hsc%jj00FcFFUFFFGG G%9884> U  :D{ 6 !$em(<== AH $9$9*+?@@@K D8X"677 =DI 5 5&';<<<  3x 3HHH  5DI--344 4 ; % E#J r@c8|j}|jt|ttjfr|dkr||S|St|t r|d\}}}|js6t||t|kr| dfdt|t|DSt|trfd|DStd)Return specified page(s).r%rrc&g|] }|Sr:r:r;r<rs r>rz)TiffPages.__getitem__..%s!HHH1GGAJJHHHr@c&g|] }|Sr:r:r;r;rs r>rz)TiffPages.__getitem__..(!,,,1GGAJJ,,,r@r)r6rrKrrbrBrCrrrrSrrr&rF)rr7r6rrr{rs @r> __getitem__zTiffPages.__getitem__s - cC/ 0 0 axxSz!73<<  c5 ! ! I [[33NE4= Su%5%5E %B%B 2HHHHs{{3u::/F/F(GHHH H c8 $ $ -,,,,,,, ,DEEEr@c#Kd} ||V|dz }n#t$rYnwxYw/|jr d|_dSdS)zReturn iterator over all pages.r%TrDN)rrrr)rr<s r>rzTiffPages.__iter__,s~   mmA&&&&&Q       ; DLLL  s $ 11c2t|jdkS)z'Return True if file contains any pages.r%)rSr6rs r>__bool__zTiffPages.__bool__8s4:""r@cb|js|dt|jS)zReturn number of pages in file.r)rrrSr6rs r>__len__zTiffPages.__len__<s)}  JJrNNN4:r@)NFNTTr9)NTT)FNN)rrrrrrrWsetterr+rQrrErXr*rVrrArrrrrr:r@r>r$r$ s4 4 4 lX \\IIXI:::X_++_+8$$X$    *'L'L'LR$K@K@K@K@Z////b@FFF*    ###r@r$ceZdZdZdZdZdZdZdZdZ dZ dZ dZ dZ dZdZdZdZdZdZdZdZdZdZdZdZdCdZed ZdDd Z dEd Z dFdZdGdZ dZ!e"dZ#e#j$dZ#edZ%edZ&edZ'edZ(edZ)edZ*edZ+dHdZ,edZ-e"dZ.e"dZ/edZ0ed Z1ed!Z2ed"Z3e"d#Z4e"d$Z5e"d%Z6e"d&Z7e"d'Z8e"d(Z9ed)Z:ed*Z;e"d+Ze"d.Z?e"d/Z@e"d0ZAe"d1ZBe"d2ZCe"d3ZDe"d4ZEe"d5ZFe"d6ZGe"d7ZHe"d8ZIe"d9ZJe"d:ZKe"d;ZLe"d<ZMe"d=ZNe"d>ZOe"d?ZPe"d@ZQe"dAZRedBZSdS)Ir aTIFF image file directory (IFD). Attributes ---------- index : int Index of the page in file. dtype : numpy.dtype or None Data type (native byte order) of the image in IFD. shape : tuple of int Dimensions of the image in IFD, as returned by asarray. axes : str Axes label codes for each dimension in shape: '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 : TiffTags Multidict like interface to tags in IFD. colormap : numpy.ndarray Color look up table, if exists. shaped : tuple of int Normalized 6 dimensional shape of the image in IFD: 0 : number planes (stk), images (ij), or 1. 1 : separate samplesperpixel or 1. 2 : imagedepth Z (sgi) or 1. 3 : imagelength Y. 4 : imagewidth X. 5 : contig samplesperpixel or 1. All attributes are read-only. r%rDr|r:Nrlc N||_||_d|_d|_d|_d|_d|_tx|_}d|_ d|_ |j }|j }| |_ tj|j||jd}|dkrt)d|jdn-#t*$r t)d|jd|jwxYw|j|jz}|j} | } || |z} t/|D]{} | | z } t1|| | | | z|| z} n>#t($r1}t3d|jd |jjd |Yd}~^d}~wwxYw|| ||sdSt:jD]Q\}}| |} | 5|d vrtC| j"tFs;tI||| j"R| d d } | r | j"|_%| d} | r0|j&dkr%| j"dkrd |_&n| j"dkrd|_&|j's|jrE|jj'r9|d(||j)d kr|j*d krd |_*n|j+s|jr|jj+rd |_,nr|j-rk| d} | T| j"sM|.| j/ta||j1| j| j2d|dj2| _"d|vrw tg|dj"|dj"|j1|d_"n>#t*$r1}t3d|jd |jjd |Yd}~nd}~wwxYw| d} | \| j2d kr | j"|_4nD| j"d|j5tmfdDr|_4n d|_4| d} | \| j2d kr | j"|_7nD| j"d|j5tmfdDr|_7n d|_7d|vrd|_8nDd|vr@d|vs|dj2d kr |j9|_8tu|j8|j9|_8|j7|j4f}t:j; |d}|tyj|}|x|_|_|j9}|j=}|j,}|j5}|j-r@|d krt}d|d} | j"}| j2}|j?d kr8|d d |||f|_|d kr|||f|_d|_nJ||||f|_d|_n7||d ||d f|_|d kr|||f|_d|_n||||f|_d|_|d kr|jd d|_n@tyj@|d dkrd!|jz|_ntyj@tyjA|d"dkrd#|jz|_nd$|jz|_n|jBdks|d kr{|j?d kr8d d ||||f|_|d kr|||f|_d|_n||||f|_d%|_nmd ||||d f|_|d kr|||f|_d|_nH||||f|_d&|_n5d d |||d f|_|d kr||f|_d|_n|||f|_d'|_d(|vr|d(j"|_ nd)|vr|d)j"|_ d*|vr|d*j"|_ n_d+|vr|d+j"|_ nHt|j|j4d,zzf|_ |j)d krt3d|jd-|r|j8r|j'sttjF||j8zd z |j8z }|j?dkr ||j5z}|t|j kr,t3d|jd.|j d||_ |t|j kr,t3d|jd/|j d||_ | d0} | ] t|HdI}|| j"|_JdS#t*$rYdSwxYwdS)1zlInitialize instance from file. The file handle position must be at offset to a valid IFD. r:Nrlr%r TiffPage : suspicious number of tagsz: corrupted tag list at offset rh)r2rBr2rDrrrrWrgrcr|c3.K|]}|dz VdSrr:r;vrs r>r?z$TiffPage.__init__.. +33q58|333333r@rSc3.K|]}|dz VdSrr:rs r>r?z$TiffPage.__init__..rr@rLrKrlzSTK imagedepth must be 1YXYXSSYXrjrrkrrZYXSSZYXZYXrrrrrz: ByteCounts tag is missingz!: incorrect StripByteCounts countz: incorrect StripOffsets count遤)KrrrjrKrcrprZTiffTagsr#rrrr&rr-rrrrrrrfrrrrrraddrTAG_ATTRIBUTESrrErKrrLr description1rr%_fix_lsm_bitspersampler'rpis_vista imagedepthrVrC valueoffset read_uic1tagr]rrrrrMrr imagelengthr SAMPLE_DTYPESrb imagewidthrOrrdiffrrrrfloorrStypeitemnodata)rrrrQr#rrrrrrrir{rrrr,rcrrrruictagplanes maxstripspytypers @r>rzTiffPage.__init__s{        #::% D { ggii  M "''$."9"9;;;<>Et||#G GGG   >DJ>>04 >>   K$.0 ,8www''u  A  H fd8X5G+G&H'(244    M MMcm.DMMMM   HHSMMMM  F-3355 / /JD$((4..C:%%jC.H.H%dCI...hhs!h$$  * # D hhsmm  (4#q((yA~~#&  a#'  ; 4: $+*<  I , ,T 2 2 21$$1)<)?#BD 1$$G GGG  @4, @T[ @DJd//!3557;7HIJJI A%%T11 C 34444M MMM'+&9*9*&E#C 01111J JJJ$(#3JYJ#? hhuoo ? ejjmm002233$fSY//      ?sP>AC*C? E** F%4'F  F% 7O O= 'O88O= A f f"!f"c jjjjvrjjjjSfd}jfd}||S jdkrdnt jjn?#t$r2}t|dddfd }||cYd}~Sd}~wwxYw j dkrdnt j j n?#t$r2}t|dddfd }||cYd}~Sd}~wwxYwj d Ij d jdkr1tfd jDrfd }||Sjr$jd vs jd krfd}||Sjrjjjdgnjjjdgjdkr jd<t7\jd d\ jr5 zdz z zdz z zdz z fd  fdn zdz z fd djd vrjdvrfd}||Sjd krt?dj drt?dj ddd dj vrnMj!dkrd n?j!d krjdkrd x n$t "j!j jdkr tFj$n tFj%d# fd }||StMjjj'j(j)zjdvrXjzzdzrtUdj dj dkrtMjj(j)fdn)tWjt6rfd nfd! fd"}||S)$a/Return decoded segment, its shape, and indices in image. The decode function is implemeted as a closure. Parameters ---------- data : bytes Encoded bytes of a segment (aka strile, strip or tile) or None for empty segments. index : int The index of the segment in the Offsets and Bytecount tag values. tables : bytes or None For JPEG compressed segments only, the value of the JPEGTables tag if any. Returns ------- segment : numpy.ndarray Decoded segment or None for empty segments. indices : tuple of int The position of the segment in the image array of normalized shape: (0, separate sample, depth, length, width, contig sample). shape : tuple of int The shape of the segment: (depth, height, width, contig samples). The shape of strips depends on their linear index. Raises ValueError or NotImplementedError if decoding is not supported. c:|jjjj<|Sr9)rrrrY)rrs r>rWzTiffPage.decode..caches7=DK  )$) 4Mr@NcPtdjdjj)Nrz: data type not supported: )rOrrrargsrUrs r>rzTiffPage.decode..decodesC ? ??(?*.*<??r@rDr)rc8tdjd|NrrhrOrrr*rUrs r>rzTiffPage.decode..decode$ !@TZ!@!@3!@!@AAAr@c8tdjd|r,r-r.s r>rzTiffPage.decode..decoder/r@rSc38K|]}|jdz VdSrr)r;r<rs r>r?z"TiffPage.decode.. s.%J%J1a#)A,&6%J%J%J%J%J%Jr@cBtdjdj)Nrz: sample formats do not match )rOrr)r*rUrrs r>rzTiffPage.decode..decode s<$CDJCC7:yCCr@rrrc4tdjd)Nr": chroma subsampling not supported)NotImplementedErrorrr)s r>rzTiffPage.decode..decodes%)N NNNr@c`d|zzz|zzzz|zzz|zzdffSrwr:)rdepthlengthstdepthstlengthstshapestwidthr;s r>rz TiffPage.decode..indices.se%&.5"8956>2e;gE%'61H<%/ r@cv||S|d|dz|dz|dz}|j|krd|_|d|}|j|kr||_n t|dz |dt|dz |dt|dz |df|_n}#t$rpt d|jd|t j||j}t|j|}|d||d|<||}YnwxYw|S) Nr%rDrrrrzreshape: incomplete tile r,) r.rjrrOrrbzerosrcr) rirrjr.rimdepthimlengthimwidthsampless r>rz TiffPage.decode..reshape9sd<KQx%(*U1X5a@9t##!#DJ;D9$$!&DJJ0'!* 4eAh??71: 5uQx@@'!* 4eAh??# & &000#L LLULL"Kdj99"49d33#';%4% yy//0 sA"B<s r>rz TiffPage.decode..indices^sa&('(2 (WQZ"788  ~%r@c||S|d|dz|dz|dz}|j|krd|_|d|}|j|kr||_n|dd|d|df|_|S)Nr%rDrrr)r.rj)rirrjr.s r>rz TiffPage.decode..reshapeps<KQx%(*U1X5a@9t##!#DJ;D9$$!&DJJ"'q2uQxq!ADJ r@)rrcDtdjdjd)Nrz: cannot decode JPEG with z bits per sample)rOrrr)s r>rzTiffPage.decode..decodesC$EDJEE $ 2EEEr@rz: disabling LSB2MSB for JPEGz: disabling predictor for JPEGrXrrc |\}}||||fS|||dd} |||}|||fS)NrDr)tablesrsrtrjr:) ri segmentindexrIrrjrs decompressrrtrs r>rzTiffPage.decode..decodesw&w|44 u<--!z!)"/!* wtUE22UE))r@)rr @rz: data and sample size mismatchrc tj|S#t$r?jdz}t ||z|z}tj|d|cYSwxYw)Nr)rb frombufferrOrrS)ribpsr.rcrs r>rzTiffPage.decode..unpacks~@ +D%888!@@@,1CII,3D +D$K????? @sAA! A!c0t|jSr9) unpack_rgbr)rircrs r>rzTiffPage.decode..unpacks!$t/ABBBr@c8t|jzSr9)packints_decoder)rircrDrr>s r>rzTiffPage.decode..unpacks&&%!3Ww5Fr@c4|\}}||||fS jdkrt||}8|d|dz|dz|dz}||jz} |}|||}  |d|}|||fS)Nrr<r%rDrrrr=) fillorderbitorder_decoderd) rirJrrjr.rKrcrrrr unpredicts r>rzTiffPage.decode..decodes"7<00LE5|UE))~""&t666%Qx%(*U1X5a@!z$D5>,ABBB6$<rrrYr;s` @@@@@@@@@@@@@@@@@@@@r>rzTiffPage.decodes> 9 +5 5 5;&0; ;      :       5==  !1$$! !.t/?@  ! ! !"%c((1R4. B B B B B B B5==  !  !~""  -dn=  ! ! !"%c((1R4. B B B B B B B5==  ! 9==   ))C.CyA~~#%J%J%J%J %J%J%J"J"J~ uV}}$   !  V + +t/@A/E/E     5==  = O~tJGG(94?ANG   ! !.GBK...5+7G.2k!""o+7G =Y w&*w6E)A-(:Fw&*w6E                    F)A-(:F & & & & & & & & & &$   &  v % %!00 uV}}$~""H HHH J JJJJ Mdi!Q&& ! !Q&&$))122J $ 0 01A B B H !Q&&(5 )6  * * * * * * * * * *5==  DK1DK4DDEE  !5 5 5"W,w6!;  K KKK~"" DK$455 @ @ @ @ @ @ @*E 2 2  C C C C C C C           & & & & & & & & & & &"uV}}s<'%B C 'C>C C  %C33 D/='D*$D/*D/Fc#K|j}|js |j\}}nQ||ur|j}|j}n>|j}|jd}|g}|ddD]} || z }|||jj} || j}i} |j dvr5d|j vr,| dh|ddj | d<| ||fd } ||dkr|j }|d kr&| j|j||d d D]} | | VdSt|5}| j|j||d d D]}|| |Ed{V ddddS#1swxYwYdS)zpReturn iterator over decoded segments in TiffPage. See the decode function for return values. r%Nrr4[)lockrDrIc:|j|i|}| ||S|Sr9r)r* decodeargsrQr~rzs r>rz!TiffPage.segments..decodes1$X_d9j99FtF||#Mr@rT)rfr3rF)rQrtrrrr[rr&rfr'r#_gettagsrr> read_segmentsr'map)rrfr>r~r3rQr"rir-rjrrirsegmentexecutorsegmentss r>rozTiffPage.segmentssh =% '"&"5 GZZ   &G,JJ!0J'*FhG'_ ' ' )#v&&&& [ # <7D  6 ) )hm##'+}}E(5(&(&&'())*(,,18$%/      a!,J >>+2+$4d & &fWoo%%%% & &$J// >8 0 0(t$U!!!>>H (||FH==========> > > > > > > > > > > > > > > > > > >s4EEETc |j}|jrt|jdkrdS|jj}||j}|5|j}|r/|r|ntd|j ddddn #1swxYwYt|trn|dkrh|j ra|5| |jj|jjz|j|jdd} dddn #1swxYwYn|jr+|jrt)d|j d|t+||j|j}|5||jdd||jj|jjzt|j|} dddn #1swxYwY|jd krt3| | |jd krFt6j|j} |jd kr| | d | nb| | d | }|| dd<nLt+||j|j} | d}|j||fd } || ||dD]} |j| _|rE |j| _n7#t@$r*tCd|j d| jd|jYnwxYw|r|"| S)avRead image data from file and return as numpy array. Raise ValueError if format is unsupported. Parameters ---------- out : numpy.ndarray, str, or file-like object 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 (default), 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 seeks and 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. maxworkers : int or None Maximum number of threads to concurrently decode strips ot tiles. If None (default), up to half the CPU cores are used. See remarks in TiffFile.asarray. Returns ------- numpy.ndarray Numpy array of decompressed, depredicted, and unpacked image data read from Strip/Tile Offsets/ByteCounts, formatted according to shape and dtype metadata found in tags and parameters. Photometric conversion, pre-multiplied alpha, orientation, and colorimetry corrections are not applied. Specifically, CMYK images are not converted to RGB, MinIsWhite images are not inverted, and color palettes are not applied. An exception are YCbCr JPEG compressed images, which are converted to RGB. r%Nrz: file handle is closedrr-r6r<rrDrrVc |\}\}}}}}}} ||j}n)|d|j|z d|j|z d|j|z f}|||||| dz||| dz||| dzf<dS)Nr%rDr)r!rrr) decoderesultrQr=rmr{r dlwrjs r>r~zTiffPage.asarray..funcs5A2+!Q1aU?&oGG%&>x':Q'>&>&?x';a'?&?&>x':Q'>&>'?@G (/Aq58|Oq58|Oq58|O$%%%r@T)r~rfr>r3z: failed to reshape r?)#rQrKrrr&rfropenrrrKrLrsrDr]rprvrrtr\r7rrCrErWrXrprr[rrorjrOrr) rr=squeezerfreopenr>rQrrrzrYr~r{s r>rTzTiffPage.asarray-s{Z= '(/":":a"?"?4 [ # <7D  I IYF IIGGIIII!GDJGGGIII  I I I I I I I I I I I I I I I sC A  8OO  #   O-0DDO.q1!4)                #4 % )N NNN#C(/JJ  +A.q1222O-0DDHO,,'               !Q&&F3333!Q&& -h.@A %**If26:::::$)F@@@C #F111I#3IIF)C OO,4# / / / / ]]$#     '~    L LL)/LL;C>LL    HHJJJ sJ9BB  B 4ADD  D A(G  GG! J..1K"!K"c |jdi|}|j}|jtjjkr|j}|jdd|jzks|j j dvrtd|j d|r2| dkr|dz}|d}d |jvr|jdkr|d n|d }t#||}n-|jtjjkr|jr_| tj}t+|jD];\} } | |vr2|jdkr|d d ddd| zgf}n|d d d ddd| zgf}nasrgbzTiffPage.asrgbsTt|%%f%%=  4#3#; ; ;(Hq!Ax'=$===#4// C CCC 4<<>>C''NH#??733hm##'/'<'A'AtF||tAw!$11DD  !T%5%9 9 9$ '= ,E'(=>>FAse||#0A55#'aAq1u-=(=#>DD#'Aq!QU+;(;#rz%TiffPage._gettags..s9777C=CH$5$53$5$5$5r@r#)rrrfs ` r>rjzTiffPage._gettagss/777749777 7r@c|S)z Return self.r:rs r>rSzTiffPage.aspages r@c|S)zReturn keyframe, self.r:rs r>rQzTiffPage.keyframes  r@cdS)zSet keyframe, NOP.Nr:)rrs r>rQzTiffPage.keyframes  r@c6d|jvrdSt|S)z'Return sequence of sub-pages (SubIFDs).rr:)r#r$rs r>r6zTiffPage.pagess" di  2r@ct|j|jj|j|j|j|j|j|j |j |j |j |j |j|jf zS)zReturn checksum to identify pages in same series. Pages with the same hash can use the same decode function. )rYrKrr]r`r_r^rrrrWrprrrr'rs r>rYz TiffPage.hashsp K %!"!! !   r@cT|jrdSt|jddkrdS|jdks|jdks |jdkr]|jdkr|jdddkrdSt 2ttj t|jdSdS)z>Return maximum number of threads for decoding strips or tiles.rDr%rr Nr) rtrSrr'rWrprarr MAXWORKERSrs r>r>zTiffPage.maxworkers&s   1 t"1% & & * *1  q DNa$7$74>Q;N;N1$$)rzTiffPage._offsetscounts5s<   - $ 2 FII |, ,!444r@cd|jdks |jdvrdSd|jvrh|j|jks#|j|jzs|jdzs |jdzrdSd|jvr*d|jvr!|j|jks|j|jzrdS|j |j tdkrddfS|j s|j rdtfStfd t!tdz DrdtfSdS) zlReturn offset and size of contiguous data, else None. Excludes prediction and fill_order. rDrrrLrMNrLrrNrOr%c3lK|].}|dko||z|dzkV/dSr%rDNr:r;r<rir"s r>r?z)TiffPage.is_contiguous..]s_   qMQ  O71: 1 #=Q#O      r@)r'rr#rr`rr_rr^rrrSrVr%rrr)rrir"s @@r>rtzTiffPage.is_contiguous=s  q D$6o$M$M4 $)  4>11#do52>B&2?R'2 t""""$77Odn48t"( w<<1  1:z!}, , ; /$+ /1:s:. .      3w<rqzTiffPage.is_finalds=   '!# '!# '&&  r@cn|jjjo$|jo|jd|jjzdkS)9Return if page's image data in file can be memory-mapped.r%)rr&is_filerqrtrcrdrs r>rszTiffPage.is_memmappablersA K " * A  A"1% (;;q@  r@r)c:jkrt||Sd}dD]-}td|z}|r|}n.d"fd }dddd jDd t j j j d d t jj jrd ndjrdndjrdnd|d|d|d|dft%djDz|fzDfD}djdjd|}|dkr|S|j|dz|g}|dkrVdD]S}|dz}t|d}|r9||dt1|T|dkr_ |dt1||dz n#t4$rYnwxYwd!|S)#z4Return string containing information about TiffPage.rl) memmappablefinalrrrDc~t|} t|d}n#t$rYdSwxYw||kr|SdS)Nr,rl)rr)r,robjrrs r>tostrzTiffPage.__str__..tostrs]$%%C V,,!   rr d{{ 2s $ 22r2c3BK|]}||VdSr9r.r7s r>r?z#TiffPage.__str__..sF  .3 GGII      r@ryc34K|]}t|VdSr9r6rs r>r?z#TiffPage.__str__..(44AQ444444r@{}{}r,c3K|]}||V dSr9r:rs r>r?z#TiffPage.__str__..s>r@REDUCEDrTILEDr'rrprWc3>K|]}|VdSr9rr0s r>r?z#TiffPage.__str__..s*::!AGGII::::::r@r @r%r;)ndpirFr4rzDATA {}rr>r@r)rQr r<rrrrjrCr SAMPLEFORMATrr,rrrr is_maskr]rrBrr-r#r[rrTrf)rr:r;rr,rr:s` r>r<zTiffPage.__str__}s3 =D $$T6599 9:  D4..D zz||       yy  4444444 %%d&788=&(()9::?%)_< ""&,6B#'=8bm,,n--k**k** ::tz::::: ;g       6?4:>>>>>> Q;;Kdi''q'>>? A::! D Dg~tT511DKK4::<< B B74== B BCCC A::  J--DLLNN% KKK    {{4   s*A I88 JJcNfdttjDS)zReturn set of flags.c^h|])}td|z|*SrHrIrJs r>rKz!TiffPage.flags..rLr@rMrs`r>rBzTiffPage.flagsrNr@c*t|jSz"Return number of array dimensions.rSrjrs r>rz TiffPage.ndim4:r@c*t|jSz#Return number of elements in array.)rrjrs r>r.z TiffPage.sizestz"""r@c|jsdSd|jdji}|jD]I}|j}d|cxkrdksn|j}t |dkr |ddn|}|j||<J|S)z5Return consolidated metadata from Andor tags as dict.NIdir)is_andorr#rrr,rS)rrzrrr,s r>rzTiffPage.andor_tagss} 4 $-.9 % %C8D$%%%%%%%%8D"4yy1}}488$D9F4LL r@c|jsdSi}|jD]}|j}d|cxkrdksn|j}|dkr0tjt ||d<V|dkrt||d<o|dkrt||d<|d krt||d <|d d \}}t|||<|S) zLReturn consolidated metadata from EPICS areaDetector tags as dict. Ni timeStampuniqueID epicsTSSeci epicsTSNsecrDrD) is_epicsr#rrr fromtimestamprrrwr)rrzrrrr7s r>rzTiffPage.epics_tagss  } 49 , ,C8DD((((5((((IEu}}&.&7&E&E%LL'"'"{##%(ZZz""'*5zz|$$(+E }%%"[[a00 U$Umms  r@c|jsdS|j}i}dD]}||j||<tjD]\}}||vr||j||<|S)z9Return consolidated metadata from Hamamatsu NDPI as dict.N)MakeModelSoftware)rr#rr NDPI_TAGSr)rr#rzr,rs r> ndpi_tagszTiffPage.ndpi_tagss| 4y1 , ,D:+F4LL...00 0 0JD$t||#Dz/t  r@cx|jsdS|j}|dj}|ddkrtdiS|d|d|dd}tj}tj}t|dD]} |d |d zz|d zd z\}}} } n)#t$r} td | Yd} ~ Ad} ~ wwxYw| ||}|dkr| } no ||j| | | z} n##t$rtd |d YwxYw|d kr| dkr| ddkr | dd} | dkr| n| d} ||vr# ||| } n#t$rYnwxYw| ||<| d} | Xtj | j} t| dkr'| d} | |d<| d} | .tj | j|d<| d} | Utj | jd} | |d<| d} | Ctj | jd} | |d<| d} | | j}id|dd|dd|dd|dd |d d!|d"d#|d$d%|d&d'|d d(|d)d*|d+d,|d-d.|d/d0d1|d0d2d3|d2d4d5|d4d|d6<|S)7z7Return consolidated metadata from GeoTIFF tags as dict.N鯇r%rDz(GeoTIFF tags: invalid GeoKeyDirectoryTagr)KeyDirectoryVersion KeyRevisionKeyRevisionMinorrrrzGeoTIFF tags: z not found鱇rr逄rrrIntergraphMatrixModelPixelScale還)rr ModelTiepoint؅ModelTransformationERR_BIASERR_RANDLINE_OFFSAMP_OFFLAT_OFFLONG_OFFr HEIGHT_OFFr LINE_SCALEr SAMP_SCALE LAT_SCALEr LONG_SCALEre HEIGHT_SCALE LINE_NUM_COEFFr!zLINE_DEN_COEFF 5SAMP_NUM_COEFFISAMP_DEN_COEFFRPCCoefficient)rr#rrrGEO_KEYS GEO_CODESrrfrErrbr@rSrtolistrx)rr#gkdrzgeokeysgeocodesrkeyidtagidrr-rrrrpccs r>rzTiffPage.geotiff_tagss 4y5k q6Q;; B C C CI$'q6q6 #A  ->3q6]] " "E .1!eai-Q2N.O+ueVV   2S22333 KKu--Ezz K-ffun.DEEE B B B BCCCHE>>eaiiE"I4D4D!#2#JE!&a  +HUOE22EE D!F5MMhhuoo ?K **E5zzR f--4466).F% &hhuoo ?(- CI(>(>(E(E(G(GF$ %hhuoo ?K **227;;CCEELLNNE&+F? #hhuoo ?K **226::AACCE,1F( )"hhuoo ?9D(DG(DG(DG(DG ( 47 ( DG (d1g(d1g(d1g(T!W(d2h(R(!$r"u+("42;(!$r"u+( !$rss)!(F# $$ s<B  C*CC)DD"!D"E.. E;:E;c|jdzS)z'Page is reduced image of another image.rDrrs r>r zTiffPage.is_reducedws#%%r@c|jdzS)z!Page is part of multi-page image.rrrs r> is_multipagezTiffPage.is_multipage|s$&&r@c|jdzS)z,Page is transparency mask for another image.rrrs r>rzTiffPage.is_masks%''r@c|jdzS)z%Page is part of Mixed Raster Content.rrrs r>is_mrczTiffPage.is_mrcs&((r@cd|jvS)zPage contains tiled image.rLrrs r>r]zTiffPage.is_tiledsdir@c|jd}| |jdkS|jdko|jdko|jdvS)z&Page contains chroma subsampled image.r]Nr[rrD)rr)r#rErr'rrrrs r>r\zTiffPage.is_subsampledsYimmC   ?9& &   ! +!Q& + F* r@cV|j|jfD]}|sdS|dddkr|cSdS)z/Return ImageJ description if exists, else None.NrImageJ=rrrrs r>rWzTiffPage.is_imagejsV!,d.?@ # #K tt2A2)++"""",tr@c|j|jfD]/}|sdS|dddkrd|vr|cS|dddkr|cS0dS)z?Return description containing array shape if exists, else None.NrD{z"shape":rshape=rrs r>rmzTiffPage.is_shapeds!,d.?@ # #K tt2A2#%%* *C*C""""2A2(**""""+tr@cd|jvS)zPage contains MDFileTag tag.rrrs r>rPzTiffPage.is_mdgel !!r@cd|jd}|duo|jdddkS)z'Page contains Media Cybernetics Id tag.pNrsMC TIFF)r#rErrs r> is_mediacyzTiffPage.is_mediacys5immE""$>39RaR=J#>>r@cd|jvS)zPage contains UIC2Tag tag.rcrrs r>rVzTiffPage.is_stkr r@cd|jvS)zPage contains CZ_LSMINFO tag.r`rrs r>r%zTiffPage.is_lsmr r@cd|jvS)z$Page contains FluoView MM_STAMP tag.rrrs r>rXzTiffPage.is_fluoviewr r@cd|jvS)z!Page contains NIHImageHeader tag.rrrs r>rczTiffPage.is_nihr r@c&d|jvod|jvS)z0Page contains SGI ImageDepth and TileDepth tags.rOrNrrs r>is_sgizTiffPage.is_sgis !8ety&88r@c|jdkS)zSoftware tag is 'ISS Vista'.z ISS Vistarrs r>rzTiffPage.is_vistas} ++r@c|jdks |jdkrdS|j}|do|dS)z>Page contains MDS MetaSeries metadata in ImageDescription tag.rD MetaSeriesF z )rrr startswithrrrts r>rzTiffPage.is_metaseriessK :>>T]l::5  ||L))Gajj.G.GGr@cP|jdks|jsdS|jdddkS)z.Page contains OME-XML in ImageDescription tag.rDFrNzOME>rrrs r>r)zTiffPage.is_omes2 :>>!1>5$..r@cp|jdks|jsdS|j}|dddko |dddkS)z4Page contains Leica SCN XML in ImageDescription tag.rDFNzrrs r>is_scnzTiffPage.is_scnsI :>>!1>5  "v))@af.@@r@cd|jvS)z'Page contains MicroManagerMetadata tag.rrrs r>rYzTiffPage.is_micromanagerr r@cd|jvS)z.Page contains Andor Technology tags 4864-5030.rrrs r>rzTiffPage.is_andorsty  r@cN|jdddko|jdddkS)zPage contains Pilatus tags.NrzTVX TIFFr# )rrrs r>rzTiffPage.is_pilatuss0}RaR J.O43CBQB3G43OOr@c.|jdkp |jdkS)z&Page contains EPICS areaDetector tags.zEPICS areaDetectorrrrs r>rzTiffPage.is_epicss%   4 4 5} 44 r@cd|jvS)zPage contains TVIPS metadata.rrrs r>rzTiffPage.is_tvips r r@c&d|jvpd|jvS)z*Page contains FEI_SFEG or FEI_HELIOS tags.rrrrs r>rzTiffPage.is_fei !7Udi%77r@cd|jvS)zPage contains CZ_SEM tag.rrrs r>rzTiffPage.is_semr r@c(|jdddkS)zPage contains Aperio metadata.NrzAperio Image Libraryrrs r>is_svszTiffPage.is_svss$(>>>r@cp|jdddkp#|jdddkpd|jddvS)z!Page contains ScanImage metadata.Nrz state.configzSI.LINE_FORMAT_VERSIONz scanimage.SIir$rs r>r)zTiffPage.is_scanimagesO  SbS !^ 3 9}SbS!%== 9!1$%%!88 r@c(|jdddkS)z1Page contains PerkinElmer tissue images metadata.NzPerkinElmer-QPIrrs r>is_qpizTiffPage.is_qpi&s }SbS!%666r@cd|jvS)zPage contains GeoTIFF metadata.rrrs r>rzTiffPage.is_geotiff-r r@c&d|jvpd|jvS)z#Page contains Olympus SIS metadata.rrrrs r>rzTiffPage.is_sis2r'r@c&d|jvod|jvS)zPage contains NDPI metadata.rrs r>rzTiffPage.is_ndpi7s !6cTY&66r@r9)NNNF)NTNTN)FNNNNNNr)Trrrrrrrrr`r_r^rrrrr'rrWrrprrrrrr!rrrrorTrrjrSrrQrr6rYr>rrtrqrsr<rBrr.rrrrr rrrr]r\rWrmrPr rVr%rXrcrrrr)rrYrrrrrrr+r)r0rrrr:r@r>r r Csx++ZKJKJIJIMOLLKLIKILHHKL F||||| mmXm^ 5>5>5>5>nAENNNN`7;"5555n7777 X__X X.  X 55X5$$X$L   X    X A!A!A!A!F  X X##X#  X X6  X ffXfP&&X&''X'((X())X)  X    X  X  X ""X"??X? ""X"""X"""X"""X"99X9,,X,HHXH//X/ AAXA""X"!!X!PPXP  X ""X"88X8""X"??X?  X 77X7 ""X"88X877X777r@r ceZdZdZdZdZdZ ddZddZdZ dZ d Z d Z e d Zejd Ze d Ze dZe dZdZddZdS)r aLightweight 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 image data from file, not for introspection of metadata. )rrr-rrFNcPd|_||_||_||_|||f|_||_dS||j|_n|j||hd}n|jrhd}nhd}gx}} | |D][\} } | dks| dkr| j }| dks| dkr| j } -| d kr(|j | j krtd |jd \|std |jd || f|_| ||_dSdS) z{Initialize TiffFrame from file or values. The file handle position must be at the offset to a valid IFD. N>rrrr>rJrr>rJrrrrrrrrrJ TiffFrame z incompatible keyframez: missing required tags)rrrr-rr&rrCrtrjrrrrrQ) rrrr-rQr"rir#rrrrs r>rzTiffFrame.__init__Os    "):"5D %DN F > +0022DKK   " "6 * * *  '''DD  # -"??DD,,,D')) nt,,  ID#s{{dckk!i  !$!4 !A!A"CCCC J HTZHHH I I I)>9  $DMMM r@c |jj}|jj}tj}|t n|}g}|5||j ||j| |j d}|dkrtd|j dn-#t$r td|j d|jwxYw|j|j z}|j} | } |jdd} | | |z} t!|D]} | | z } || | | | dzd}|r||vr+ t#|j| | | | z|| z}n>#t$r1}t%d|j d|jjd|Yd}~d}~wwxYw|||f dddn #1swxYwY|S) z)Return list of (code, TiffTag) from file.Nr%rr9rz : corrupted page list at offset rrh)rr&rrr NullContextrCr-rrrrrrfr tagformat1rrrrrr[)rrrfrrrr#rrrr codeformattagbytesr{rrrs r>rjzTiffFrame._gettagss [ #{ $ {}}}$ # )# ) GGDK  t/1H1HII!L4<<'LTZLLL    #CCC59[CC   dn4IlGxH!,Jwww//H5\\ ) )G#vj(8X\3I*JKKANT.. !$+"*8X5G+G"H"+h"688CC%;TZ;;=1;;58;;HHHH   T3K(((( ))# )# )# )# )# )# )# )# )# )# )# )# )# )# )# )J sUGA B%$G%*CA=G $E21G2 F-<'F(#G(F--GGGc|jtd|jd|jj|jt |j|jS)zReturn TiffPage from file.Nr9z%: cannot return virtual frame as pager)r-rOrrr&rCr rs r>rSzTiffFrame.aspages` ; NTZNNN  ##DK000 4:6666r@cj|jtd|jdtj|g|Ri|S)z4Read image data from file and return as numpy array.Nr9: keyframe not set)rrrr rTrr*rUs r>rTzTiffFrame.asarraysG > !JDJJJJKK K6t666v666r@cj|jtd|jdtj|g|Ri|S)z>Read image data from file and return RGB image as numpy array.Nr9rA)rrrr rrBs r>rzTiffFrame.asrgbsF > !JDJJJJKK K~d4T444V444r@cj|jtd|jdtj|g|Ri|S)z3Return iterator over decoded segments in TiffFrame.Nr9rA)rrrr rorBs r>rozTiffFrame.segmentssG > !JDJJJJKK K 7777777r@c|jS)zReturn keyframe.rrs r>rQzTiffFrame.keyframerr@ch|j|krdS|jtd|jdt|jdt|jkrtd|jd|jr |jr'|jddf|jdff|_||_dS)z Set keyframe.Nr9z: cannot reset keyframer%z: incompatible keyframerD)rrrrSrrr]rt)rrQs r>rQzTiffFrame.keyframes >X % % F > %@TZ@@@  t"1% & &#h.B*C*C C C@TZ@@@       ! $Q'*-'*-#D "r@c|jtd|jd|jjr%|jdd|jjdfSdS)z5Return offset and size of contiguous data, else None.Nr9rAr%rD)rrrrtrrs r>rtzTiffFrame.is_contiguouss] > !JDJJJJKK K > ' N&q)!,dn.J1.MM Mtr@cX|jtd|jd|jjS)rNr9rA)rrrrsrs r>rszTiffFrame.is_memmappables3 > !JDJJJJKK K~,,r@cX|jtd|jd|jjS)z1Return checksum to identify pages in same series.Nr9rA)rrrrYrs r>rYzTiffFrame.hashs3 > !JDJJJJKK K~""r@c|tjvrt|j|St |jjd|)zReturn attribute from keyframe.r%)r FRAME_ATTRSrrrrrrr,s r>r&zTiffFrame.__getattr__sL 4# # #4>400 0~& K K4 K K   r@r%r)c|jd}d}nydddd|jDt|jfD}t |j|dz }|d krE|j\}}t||d z |d z }t||d z |d z }d |d|d|}d|j d|j d|S)z5Return string containing information about TiffFrame.Nrlr2c3K|]}|VdSr9r:r7s r>r?z$TiffFrame.__str__.. s2;;1Q;;;;;;r@ryc34K|]}t|VdSr9r6rs r>r?z$TiffFrame.__str__.. s(1M1MQ#a&&1M1M1M1M1M1Mr@rrrrr> z Keyframe z Offsets z Bytecounts r9r) rrrjrLrcr r<rrrr-)rr:r;r:kfofbcs r>r<zTiffFrame.__str__s > !DBB99;;1M1M$*1M1M1M)M)M),TZ):;;;;;D!!$. !CCB A::(FB519VaZ@@@B52:fqjAAABG"GGGG2GGD?DJ??$+?????r@rr6r)rrrrrrPr6rrjrSrTrrorrQrrtrsrYr&r<r:r@r>r r =sQ  MIH E=A*.0%0%0%0%d----^777777 555 888 X_""_"*X--X- ##X#    @@@@@@r@r c@eZdZdZdZdZedZdZd dZ d S) raTIFF tag structure. Attributes ---------- name : string Name of tag, TIFF.TAGS[code]. code : int Decimal code of tag. dtype : str Datatype of tag data. One of TIFF DATA_FORMATS. count : int Number of values. value : various types Tag data as Python object. offset : int Location of tag structure in file. valueoffset : int Location of value in file. All attributes are read-only. )rrrcrr-rc|j}|j}|j}|j}tj}||_||zdz|_||j|dd\} } ||j |dd\} } tj | } n #t$rtd| wxYwd|| t| dz| d}t j|}||ks| tjvr||j| dx|_}|dks||j|z krtd||| tjvr"tj| }|||| | |} n}| d ks| dkr | d d krt+||| | |} nQ||||} n1| d d ks| d kr | d|} n||| d|} | tjvo| tjvo| d k}|r| d d krxt1| dt2r]| d} t5t7| } n#t:$rt=d | dd} YnwxYw| tjvr[tj|  tAfd| D} n,#tB$r}t=d | d|Yd}~nd}~wwxYw|rtE| dkr| d} | |_#| |_$| |_%| |_&dS)z$Initialize instance from tag header.rNunknown tag data type {}{}{}r%rDrzinvalid tag value offsetrrrr TiffTag z!: coercing invalid ASCII to bytes1Bc3.K|]}|VdSr9r:)r;rrs r>r?z#TiffTag.__init__..ps+!6!61!!A$$!6!6!6!6!6!6r@rh)'r&rr]r"rrr-rr< tagformat2r DATA_FORMATSrrrCrr TAG_READERSr!r.rC read_bytesr TAG_TUPLErKr bytes2str stripasciirUnicodeDecodeErrorrTAG_ENUMrrOrSrrcrr)rr tagheaderrrrr]r"rrtype_rrrcrr.r-readfuncprocessrrs @r>rzTiffTag.__init__2s  {N _  $z1A5fT_im<< evdoy}== u D%e,EE D D D B B BCC C DooiU1X)>aIIs## *  (8 8 8(.t/@%(H(H(K KD vzzVbgn44#$>??? GGFOOOt'''+D1 YujII! eBi3.>.>"2y% KKsBGGDMM222Y#  !%4%LEEF3ete --E ( ( DN*     %uRyC''JuQx,G,G'!HE !*U"3"3"9"9";";<<%   FtFFF   t}$$M$':!!6!6!6!6!6!6!666EE!::: 84 8 83 8 899999999: %u::??!!HE    s67B B'.J J-,J-K-- L7LLcptj|jt |jS)z+Return name of tag from TIFF.TAGS registry.)rr rErrLrs r>r,z TiffTag.name|s$y}}TYDI777r@cv|jdks |jdkrdStd|jdtjdg|jR}tjd|d|_|j |jtjd|j d |_dS) zCorrect LSM bitspersample tag. Old LSM writers may use a separate region for two 16-bit values, although they fit into the tag value element of the tag. rWrNrXz": correcting LSM bitspersample tagrzTiffTag._fix_lsm_bitspersamples 9  tzQ FLtyLLLMMM E/DJ///!=u55a8t/000]5&*;*@*@*C*CDD r@r%r)c|dkrdnd|z}d|jt|jdz|jd}dt j|jd}|r|jd|d|j }n|jd|j }d |d|d|j d }|d |} |jdkrt|j }n+ttd |j D}n'#t$rt|j || }YnwxYw|dkr||z }|d |}n|d|zz }|S)z3Return string containing information about TiffTag.r%rDrrrr:r,rrXr2Nc34K|]}t|VdSr9)enumstrr;rs r>r?z"TiffTag.__str__..s(%E%EQgajj%E%E%E%E%E%Er@r>r4)rCrrrcrrr getallrr-rrnrrrrf)rr:r;r?tcoder,liners r>r<zTiffTag.__str__skkq6z dj3tz!}+=+==tz!}MMxx ((B7788  1i77$77$+77DDi004;00D>$>>>>$*:>>>FUF| DzQ ++%E%E$*%E%E%E E EFF D D DDJeFCCCEEE D Q;; EMD
rrsz.MIHHHT88X8EEE r@rcpeZdZdZdZdZdZdZdZdZ dd Z dd Z d Z d Z d ZdZdZdZddZdS)raGMultidict like interface to TiffTag instances in TiffPage. Differences to a regular dict: * values are instances of TiffTag. * keys are TiffTag.code (int). * multiple values can be stored per key. * can be indexed with TiffTag.name (str), although slower than by key. * iter() returns values instead of keys. * values() and items() contain all values sorted by offset stored in file. * len() returns the number of all values. * get() takes an optional index argument. * some functions are not implemented, e.g. update, setdefault, pop. _dict_listc.i|_|jg|_dS)zInitialize empty instance.Nrtrs r>rzTiffTags.__init__s j\ r@cx|j}|jD]}||vr|||<dS|j||idSz Add a tag.N)rrvr[)rrrrts r>rz TiffTags.addsZx + +A1}}$ J  tSk * * * * *r@c4|jS)zReturn new view of all codes.)rur\rs r>r\z TiffTags.keyssz   r@cHd|jD}t|dS)z1Return all tags in order they are stored in file.c3HK|]}|D]}|VdSr9)r8)r;rtrs r>r?z"TiffTags.values..s7::aqxxzz::!:::::::r@c|jSr9rq)rs r>rzz!TiffTags.values..s!(r@r{rvr)rr#s r>r8zTiffTags.valuess.::4::::d 2 23333r@cHd|jD}t|dS)z>Return all (code, tag) pairs in order tags are stored in file.c3HK|]}|D]}|VdSr9rr;rtr<s r>r?z!TiffTags.items..s7::q ::1:::::::r@c|djSNrDrqr<s r>rzz TiffTags.items..s 1Q4;r@r{r~rrs r>rzTiffTags.itemss.::DJ:::e!6!67777r@Nc<|/||jvr |j|St|ts|Sd} |j|}n#t$r|cYSwxYw||vr||St|ts|S|D]}|j|kr|cS|S)z3Return tag of code or name if exists, else default.Nr%)rurKrLrvrr8r,)rr7rrr#rs r>rEz TiffTags.gets =dj  z#&c3'' E :e$DD   NNN  $;;9 #s## N;;==  Cx3 s A AAc*g}|jD]"}||vr|||"|r|St|ts|S|jD]?}|D]$}|j|kr||n%|sn@|r|n|S)z@Return list of all tags of code or name if exists, else default.)rvr[rKrLr8r,)rr7rrzr#rs r>rpzTiffTags.getallsJ  Dd{{ d3i((((  M#s## NJ  D{{}}  8s??MM#&&&E#  ,vvW,r@c||jvr |j|St|tst||jD]}|j|kr|cSt|)z>Return first tag of code or name. Raise KeyError if not found.)rurKrLrr8r,)rr7rs r>rzTiffTags.__getitem__s{ $*  :c? "#s## 3-- :$$&&  Cx3 smmr@c0||dSry)r)rrrs r> __setitem__zTiffTags.__setitem__s  r@cd}|jD] }||vrd}||= |rdSt|tst||jD]2}|D]}|j|kr ||j=d}nn3|st|dSz Delete all tags of code or name.FTN)rvrKrLrr8r,r)rr7foundr#rs r> __delitem__zTiffTags.__delitem__sJ  Dd{{II  4#s## 3-- J  D{{}}  8s??SX EE#  3-- tr@c||jvrdSt|tsdS|jD]}|j|krdSdS)zReturn if tag is in map.TF)rurKrLr8r,)rr rs r> __contains__zTiffTags.__contains__-sf 4:  4$$$ 5:$$&&  Cx4tt ur@cDt|S)zReturn iterator over all tags.)rr8rs r>rzTiffTags.__iter__8sDKKMM"""r@cBd}|jD]}|t|z }|S)zReturn number of tags.r%rvrSrr.rts r>rzTiffTags.__len__<s.  A CFFNDD r@r%r)cg}g}g}|D]}||dz}||d||dkrvt||krc|dkr$|jdvrt |j||dz}nt |j||d z}||jd ||d ||dkr?|r=|d |d |d |S) .Return string with information about TiffTags.rDrNr%r)rrrrrr>rr4r@) r<r[rrSrrrr,r)rr:r;r:tlinesvlinesrrs r>r<zTiffTags.__str__CsP 6 6CKKeAgK..E MM%---// 0 0 0zzc%jj500A::#(.B"B"B#CIU6A:NNNEE#CIU6B;OOOE 44U44555 DIIf%%&&& A::&: KK    KK F++ , , ,yyr@r6r9r)rrrrrrrr\r8rrErprrrrrrr<r:r@r>rrs #I""" +++!!!444 888 *----*   2   ###r@rceZdZdZ ddZdZedZedZ edZ ed Z d Z d Z d Zd ZdZdS)r aSeries of TIFF pages with compatible shape and data type. Attributes ---------- pages : list of TiffPage Sequence of TiffPages in series. dtype : numpy.dtype Data type (native byte order) of the image array in series. shape : tuple Dimensions of the image array in series. axes : str Labels of axes in shape. See TiffPage.axes. offset : int or None Position of image data in file if memory-mappable, else None. NFc Jd|_||_t||_d||_t j||_|r|nd|_|r|nd|_ ||_ |r||_ n|r|dj |_ nd|_ | stt|dkrat|dj} | dkr+tt|j| z|_dSt||_dSt||_dS)zInitialize instance.r%rlNrD)r_pagesrrjrrZrbrcrr,rrrSrr_len) rr6rjrcrZrr,rrrAr s r>rzTiffPageSeries.__init__js   5\\ GGDMM [''  (DDb  (DDb "   DKK  (/DKKDK #SZZ1__a''A1uu 3 3q 899 JJ E DIIIr@c x|jr2|jjdd|i|}|j||}|SdS)z;Return image data from series of TIFF pages as numpy array.ruNr:)rrTr)rrUrzs r>rTzTiffPageSeries.asarraysN ; (T[(?????F~)//Mtr@c|jsdSd}|jD]S}|dS|jsdS|s|jd|jdz}/||jdkrdS||jdz }T|jd}|jd}|js|jrt |jdkr|S||t |j|jj zzkr|SdS)z-Return offset to series data in file, if any.Nr%rD) rrqrtrWrmrSrrjrcrd)rrrxr-s r>r-zTiffPageSeries.offsets { 4K ) )D|tt= tt (+d.@.CCd(+++tt 4%a( (CC{1~#A& N dn #dk2B2Ba2G2GM &74:..1DDD D DMtr@c*t|jSrrrs r>rzTiffPageSeries.ndimrr@cDtt|jSr)rrrjrs r>r.zTiffPageSeries.sizes74:&&'''r@c|S)z'Return sequence of all pages in series.r:rs r>r6zTiffPageSeries.pagess  r@ct|}|dkr ||jz}t|jdkrId|cxkr |jkr7nn4|jdj}|jj||zS|j|S)z3Return specified page of series from cache or file.r%rD)rrrSrrrr6r)rr7rs r>rzTiffPageSeries._getitems#hh 77 49 C t{  q Q%8%8%8%8ty%8%8%8%8%8KN(E;$--eck:: :{3r@cR|jt|ttjfr |St|t r-fdt ||jDSt|trfd|DStd)rc&g|] }|Sr:r:rs r>rz.TiffPageSeries.__getitem__..s!GGG1GGAJJGGGr@c&g|] }|Sr:r:rs r>rz.TiffPageSeries.__getitem__..rr@r) rrKrrbrBrCrrrr&rF)rr7rs @r>rzTiffPageSeries.__getitem__s- cC/ 0 0 73<<  c5 ! ! HGGGGs{{49/E/E(FGGG G c8 $ $ -,,,,,,, ,DEEEr@c#Kt|j|jkr|jEd{VdS|jj}|jdj}t |jD]}|||zVdS)z%Return iterator over pages in series.Nr%)rSrrrr6rr)rr6rr<s r>rzTiffPageSeries.__iter__s t{  ty ( ({ " " " " " " " " "K%EKN(E49%% ' 'EAI&&&&& ' 'r@c|jS)z!Return number of pages in series.)rrs r>rzTiffPageSeries.__len__ yr@c jdd|jrt|jdnddd|jDt |j|j|jt|j d|j r d|j ndfD}d |j d|S) z4Return string with information about TiffPageSeries.r2c3K|]}||V dSr9r:r7s r>r?z)TiffPageSeries.__str__..s>            r@rrlryc34K|]}t|VdSr9r6rs r>r?z)TiffPageSeries.__str__..rr@r1@zTiffPageSeries ) rr,rDrjrLrcrZrrSr6r-r)rr s r>r<zTiffPageSeries.__str__s II   26B49("---4444444DJ  tz??***'+{:"T["""<    322q222r@)NNNNF)rrrrrrTrr-rrr.r6rrrrr<r:r@r>r r Xs"EI6;####4X6X((X(X     F F F'''33333r@r cLeZdZdZddiZ d dZdZdZdZd Z d Z dd Z dS)raSeries of files containing array data of compatible shape and data type. Attributes ---------- files : list List of file names. shape : tuple Shape of file series. Excludes shape of individual arrays. axes : str Labels of axes in shape. rZa # 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}))? Nc|d}|t}|_|rddl}t|tt jfrddl}||_n$tjdstdt|tr:| j |}|r ||}nft|t jrt j |g}n6t|tr!tj|}|r ||}d|D}|stdt|dr+t|jstd |fd }nt|std |r|fd }d } t#|f} t%d t't#|D} d} j||}|rB t-|||\} } } } n*#t$r} t/d| dYd} ~ nd} ~ wwxYwt1| t#|krt/d|_|_|_| _| _| _| _ dS)aInitialize instance from multiple files. Parameters ---------- fromfile : function or class Array read function or class with asarray function returning numpy array from single file. files : str, path-like, or sequence thereof Glob filename pattern or sequence of file names. Default: \*. Binary streams are not supported. container : str or container instance Name or open instance of ZIP file in which files are stored. sort : function Sort function used to sort file names when 'files' is a pattern. The default (None) is natural_sorted. Use sort=False to disable sorting. pattern : str Regular expression pattern that matches axes and sequence indices in file names. By default (None), no pattern matching is performed. Axes can be specified by matching groups preceding the index groups in the file name, be provided as group names for the index groups, or be omitted. The predefined 'axes' pattern matches Olympus OIF and Leica TIFF series. axesorder : sequence of int Indices of axes in pattern. N*r%rwzinvalid containerc6g|]}tj|Sr:)rQfspathr0s r>rz)FileSequence.__init__..<s ---!1---r@rBrTzinvalid fromfile functionch|5}|jdi|cdddS#1swxYwYdS)Nr:)rT)rrUhandle _fromfile0s r>fromfilez'FileSequence.__init__..fromfileFsZ&&4&)6>33F33444444444444444444s '++cj|5}tj|5}|fi|cdddcdddS#1swxYwY ddddS#1swxYwYdSr9) _containerrwrrr)rrUhandle1handle2 _fromfile1rs r>rz'FileSequence.__init__..fromfileQs&_))%00=GGLLNN33=w)z'< A% A>%A) )A>,A) -A>>BBrc3K|]}|fVdSr9r:rs r>r?z(FileSequence.__init__..Xs$88888888r@rYz*FileSequence: failed to parse file names (rz8FileSequence: files are missing. Missing data are zeroed)!rrfnmatchrKrLrQrRzipfileZipFilerPrOfilternamelistrrNcallablerTrSrr _patternsrEparse_filenamesrrrr=r2rrZrj_indices _startindex)rrr=r4r3r2r5rrrZrjr startindexrrrs` @@r>rzFileSequence.__init__sb: =E <!D#  $ NNN)c2;%788 6")//)"<"<T_f55 6 !4555%%% (t'?'?'A'A5II( DKKE r{ + + $Yu%%&EE s # # $Ie$$E $U --u--- /-.. . 8Y ' ' :H,-- > !<===!J 4 4 4 4 4 4(## :899 9  =!J = = = = = = U 88eCJJ&7&788888 .$$Wg66  I I3B7I4/4/0eWjj I I IGGGGIIIIIIII I 5>>SZZ ' ' J L L L!   JJLL   %sH44 I>IIc |jrt|jn |jd}tj|d}d|jj|dt|jd dd|j Dd|j fS) z7Return string with information about file FileSequence.r%r zfiles: z shape: {}, c34K|]}t|VdSr9r6rs r>r?z'FileSequence.__str__..xs((D(DAQ(D(D(D(D(D(Dr@zaxes: ) rrLr=rQrrwrrrrSrCrjrZ)rrhs r>r<zFileSequence.__str__ps'+Is4?###DJqMw}}T""2&zz N #  'c$*oo ' '   tyy(D(D(D(D(DDD E E TY     r@c*t|jSr9)rSr=rs r>rzFileSequence.__len__|s4:r@c|Sr9r:rs r>rzFileSequence.__enter__rr@c.|dSr9r r s r>rzFileSequence.__exit__rr@cT|jr|jd|_dSr9)rrrs r>rzFileSequence.closes+ ? $ O ! ! # # #r@rDc  |rz6FileSequence.asarray..func..s DDDtq!QUDDDr@N)rxrrbrrjr)rrimrUrzrs r>r~z"FileSequence.asarray..funcs]DDs5$2B'C'CDDDE+E4:>>Eu////BF5MMMr@rrDr)rKrrr=rjrrcrrSmultiprocessingr cpu_countrxrr'rl)rrh ioworkersr=rUrrjr~rrrrnr{rzs` ` @r>rTzFileSequence.asarrays4  $$$ A$t}TZ%5@@@@@ 4=0000 0 T]4:a= 3 3F 3 3 RX%sE:::.RX...        tz??Q  II  )a-- " " " "O5577!;Q??I q== #DM4: > > # # uUE"""" #$I.. (!dDM4:FFA                 s)%EE"Er)NrDN) rrrrrrr<rrrrrTr:r@r>rrs     I>B)-f&f&f&f&P     ::::::r@rc.eZdZdZddddeffd ZxZS)r zSeries of TIFF files.Nc\t||dn||||dS)z-Initialize instance from multiple TIFF files.Nz*.tif)r4r3r2)rr)rr=r4r3r2rrs r>rzTiffSequence.__init__sD  u}GG%dG  = = = = =r@)rrrrrrrrs@r>r r sO!Td==========r@r c8eZdZdZdZd$dZdZd%dZd Zd Z d Z d&dZ d'dZ d(dZ d)dZdZdZdZd*dZdZdZdZdZedZedZedZed Zed!Zed"Zejd#ZdS)+raBinary file handle. A limited, special purpose file handle 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_closerrNc||_d|_||_||_d|_||_||_d|_d|_t|_ | dS)aInitialize file handle from file name or another file handle. Parameters ---------- file : str, path-like, binary stream, or FileHandle File name or seekable binary stream, such as an open file or BytesIO. mode : str File open mode in case 'file' is a file name. Must be 'rb' 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. NrlTF) rrrrrrrrrr;rrw)rrhryr,r-r.s r>rzFileHandle.__init__s_(         ]]  r@c|jrdSt|jtjrtj|j|_t|jt rtj|j|_tj |j\|_ |_ t|j|j |_d|_|jd|_nt|jt r|jj|_|jd|_|xj|jjz c_d|_|j sX|jr@tj|jj \}}|d|j||_ n|jj |_ |j r$|j |jj krt%d|jj |_ |jj |_ n t'|jdr |jn#t*$rt%dwxYw|j|_|j|j|_d|_|j sO tj |jj\|_ |_ n#t.$r d |_ YnwxYw |jj|_ n#t.$rYnwxYwt%d |jr|j|j|jq|j}|j|jd |j|_|j| |jd|_dS#t*$r d|_YdSwxYw) zOpen or re-open file.NTr%FrzFileHandle has wrong moderCzbinary stream is not seekablezUnnamed binary streamzNthe first parameter must be a file name, seekable binary stream, or FileHandler)rrKrrQrRrrLrrealpathrwrrrwrrrrsplitextrOrPrrfr,rryrCrr6r)rr,extrs r>rwzFileHandle.opens 8  F dj"+ . . /4:..DJ dj# & &. F))$*55DJ$&GMM$*$=$= !DItzDJ 33DHDK|#   J / /& Fz~DH|#  LLDJ. .LLDK: 2<2 " 0 01A B BID#$(!>!>4!>!>DJJ!%!1DJz >djDJ,<<< !<===)DJ DII TZ ( ( F B !!!! B B B !@AAA BzDH|##z00 DK: 99,.GMM$(-,H,H)DItzz%999!8DJJJ9 !X] !    EFF F < ( HMM$, ' ' ' : (--//C HMM$, * * *DJ HMM#    ! HOO   DLLL ! ! ! DLLLL !sBH))I6J==KKK'' K43K4% OOOrc^|dkr|jr|j}|j|S)z5Read 'size' bytes from file, or until EOF is reached.r%)rrrrrr.s r>rzFileHandle.read[s, !88 8:Dx}}T"""r@c6|j|S)z@Read up to len(b) bytes into b, and return number of bytes read.)rreadinto)rbs r>rzFileHandle.readintoasx  ###r@c6|j|S)zWrite bytes to file.)rr)r bytestrings r>rzFileHandle.writeesx~~j)))r@c4|jS)z"Flush write buffers if applicable.)rrrs r>rzFileHandle.flushisx~~r@r%rrpc||jstdtj|j|||j|z||S)z+Return numpy.memmap of data stored in file.z%cannot memory-map file without fileno)rcryr-rjorder)rrOrbrrr)rrcrjr-ryrs r>rDzFileHandle.memmap_arraymsL| FDEE E|DHE#'<"'u666 6r@cn|j}tj|}|dkr||jn|j}||jz}n ||jz}|tj||n|}|j|krtd||}||krtd|d|jj s1|j s| d| }n*|jj |j kr| d|$t|dr| |S)z2Return numpy array from file in native byte order.r%Nz size mismatchzfailed to read z bytesTr)rrbrcrrerdemptyrOrrbyteswaprrPr)rrcrr=rr.rzns r>rEzFileHandle.read_arrayus> X E"" 199!$4::#*DEN*EE5>)D.1kUE***s =D _-- - KK   99;t;;;<< <|$ "> &%%%((**FF \ "en 4 4 OOD ! ! ! ?sG$$   r@Tc#Kt}|dkrdS|dkrdnd} | dkrk| dkr_||j}|5|| |j| } dddn #1swxYwYnd} |r| | fn| | fgVdS||j}|d}fdt |D} nfdt |D} |rt | d} |j} |jj} d}||krg}d}|5||krw||krq| |\} }}|dkr7|dkr1| ||| || f||z }n|d| f|dz }||kr||kqdddn #1swxYwY|r |Ed{Vn|V||kdSdS) aFReturn iterator over segments read from file and their indices. The purpose of this function is to * reduce small or random reads * reduce acquiring reentrant locks * synchronize seeks and reads * limit the size of segments read into memory at once (ThreadPoolExecutor.map is not collecting iterables lazily). Parameters ---------- offsets, bytecounts : sequence of int offsets and bytecounts of the segments to read from file. indices : sequence of int Indices of the segments in the image. Default: range(len(offsets)). sort : bool If True (default), segments are read from file in the order of their offsets. lock: A reentrant lock used to synchronize seeks and reads. buffersize : int Approximate number of bytes to read from file in one pass. Default: 64 MB. flat : bool If True (default), return an iterator over individual (segment, index) tuples. Else return an iterator over a list of (segment, index) tuples that were acquired in one pass. Returns ------- items : (bytes, int) or [(bytes, int)] Iterator over individual or lists of (segment, index) tuples. rDNr%ic2g|]}|||fSr:r:rs r>rz,FileHandle.read_segments..s(NNN1GAJ 1 6NNNr@c>g|]}|||fSr:r:)r;r<rirr"s r>rz,FileHandle.read_segments..s<000!WQZA?000r@c|dSrr:rxs r>rzz*FileHandle.read_segments..s adr@r{)rSrrCrrrrr[)rr"rirr3rf buffersizerr:rrirorCrr<rzr.r-rjs ``` r>rkzFileHandle.read_segmentssJW A:: F Q;; AAgajE% 1$$!););<:D<<IIgen---8==E):;;D<<<<<<<<<<<<<<<#'<4--tUm_ < < < F <:D  J ?NNNNNf NNNHH000000!&v000H  <hNN;;;Hyx} &jjFD  Z''AJJ/7{,E69zzi!mmV  ttI&>??? ) tUm444FAZ''AJJ                !!!!!!!!! )&jjjjjjs%F??GGrDctj} ||j|||}n#t$rtj|}||j|jz}tt||jz}|j |}| ||||}YnwxYw|dkr|dn|S)zReturn numpy record from file.r]NrDr%) rbrecrrrfrcrrdrrrr)rrcrjr]rrecordr.ris r> read_recordzFileHandle.read_recordsi M\\$(E5I\NNFF M M MK&&E} en48E??++enrzFileHandle.write_emptysD !88 F  dQh""" wr@c ||jdS#t$r0|j|YdSwxYw)z!Write numpy array to binary file.N)tofilerrfrr)rris r>rzFileHandle.write_arraysa + KK ! ! ! ! ! + + + HNN4<<>> * * * * * * +s6AAcD|j|jz S)zReturn file's current position.)rrrrs r>rzFileHandle.tellsx}}--r@c|jri|dkr%|j|j|z|dS|dkr8|jdkr-|j|j|jz|zddS|j||dS)zSet file's current position.r%Nr)rrrCr)rr-whences r>rCzFileHandle.seeks < {{ dlV3V<<<{{tzA~~ dlTZ7&@!DDD  ff%%%%%r@cj|jr)|jr$|jd|_dSdSdS)z Close file.N)rrrrs r>rzFileHandle.closesF ; 48  HNN   DHHH    r@c|Sr9r:rs r>rzFileHandle.__enter__#rr@c.|dSr9r r s r>rzFileHandle.__exit__&rr@cv|jrtjd|dtt |j|S)z-Return attribute from underlying file object.z FileHandle: z# not implemented for embedded files)rrGrHrrrrLs r>r&zFileHandle.__getattr__)sE <  MJtJJJ   tx&&&r@c|jSr9)rrs r>r,zFileHandle.name2 zr@c|jSr9)rrs r>rzFileHandle.dirname6rr@cVtj|j|jSr9)rQrrrrrs r>rzFileHandle.path:sw||DItz222r@c|jSr9)rrs r>r.zFileHandle.size>r r@c|jduSr9r2rs r>rzFileHandle.closedBsx4r@c|jSr9)rrs r>rfzFileHandle.lockFr r@cV|rtjn t|_dSr9) threadingRLockr;rrs r>rfzFileHandle.lockJs#*/BY_&&&[]] r@)rNNNr)r%rrprN)NTNNTrrY)rrrrrrrwrrrrrDrErkrrrrrCrrrr&rr,rrr.rrfrr:r@r>rrs/:I @D!D!D!L#### $$$***   6666BEI7;YYYYv 3 3 3 3   +++... & & & & '''XX33X3X  X X [CC[CCCr@rc"eZdZdZdZdZdZdS)r;zINull context manager. >>> with NullContext(): ... pass r:c|Sr9r:rs r>rzNullContext.__enter__Yrr@cdSr9r:r s r>rzNullContext.__exit__\s r@N)rrrr_NullContext__slotsrrr:r@r>r;r;OsCG     r@r;c0eZdZdZdZddZdZdZdZdS) OpenFileCachezKeep files open.)r=pastrfr.Ncxg|_i|_|tn||_t ||_dS)zInitialize open file cache.N)rr=r;rfrr.)rr.rfs r>rzOpenFileCache.__init__es4  %)\KMMMt II r@c|j5||jvr|j|xxdz cc<n?|jr8|d|j|<|j|ddddS#1swxYwYdS)zRe-open file if necessary.rDN)rfr=rrwrr[)rr&s r>rwzOpenFileCache.openls Y - -TZ'' :&&&!+&&&&" -!!!)* :&   ,,,  - - - - - - - - - - - - - - - - - -sAA44A8;A8c|j5||jvr|j|xxdzcc<d}t|j}||jkrd||kr^|j|}|j|dkr*||j|=|j|=|dz}n|dz }||jkr||k^ddddS#1swxYwYdS)z%Close openend file if no longer used.rDr%N)rfr=rSrr.r)rr&rr.s r>rzOpenFileCache.closevs/ Y # #TZ'' :&&&!+&&&49~~TY&&54<clearzOpenFileCache.clears Y ? ?(,TZ-=-=-?-?(@(@ ? ?$ Hq==$$&&& :. $)//*"="=>  ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?sA/BB  B r9) rrrrrrrwrr"r:r@r>rr`s`1I---###$?????r@rcVeZdZdZdZejZd dZd dZ d dZ d dZ d Z d Z d ZdS)rz%Stopwatch for timing execution speed.)startedstoppeddurationNr,c|t||dd|_tx|_|_dS)z#Initialize timer and print message.NTendrr%printr&rclockr$r%rmessager)s r>rzTimer.__init__s>   's$ / / / / &+kkmm3 t|||r@c|t||dd|_tx|_|_|jS)z$Start timer and return current time.NTr(r%r*r-s r>rz Timer.startsB   's$ / / / / &+kkmm3 t||r@ct|_|t||d|j|jz |_|jS)z$Return duration of timer till start.NTr()rr,r%r+r$r&r-s r>rz Timer.stopsD{{}}   's$ / / / / t|3 }r@cnt|}|t|dt||ddS)z6Print duration from timer start till last stop or now.Nr,r)Tr()rLr+)rr.r)msgs r>r+z Timer.printsA$ii   's # # # # cs$''''''r@c|jdkr"t|jz }n|j}t t j|}d}|t|kr6|||dzdvr'|dz }|t|kr|||dzdv'|||dzdkr|dz }||ddS) zAReturn duration from timer start till last stop or now as string.r%)secondsrz0:0010203040506070809rDrDNz s)r&rr,r$rLr timedeltarS)rr&r r<s r>r<z Timer.__str__s =A  {{}}t|3HH}H "8444 5 5 #a&&jjQqQwZ+BBB FA#a&&jjQqQwZ+BBB Qq1uW:   FAABB%|||r@c|Sr9r:rs r>rzTimer.__enter__rr@c.|dSr9)r+r s r>rzTimer.__exit__rr@)Nr,r6)rrrrrtime perf_counterr,rrrr+r<rrr:r@r>rrs//2I  E4444((((   r@rceZdZdZdZdZdS) LazyConstzEClass whose attributes are computed on first access from its methods.c>||_t|d|_dS)Nr)_clsrr)rclss r>rzLazyConst.__init__s sI.. r@ct|j|}t|s|S|}t||||Sr9)rr>rr)rr,r~rs r>r&zLazyConst.__getattr__sHty$''~~ KdE""" r@N)rrrrrr&r:r@r>r<r<s8OO///r@r<ceZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd ZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZdZ dZ!d Z"d!Z#d"Z$d#Z%d$Z&d%Z'd&Z(d'Z)d(Z*d)Z+d*Z,d+Z-d,Z.d-Z/d.Z0d/Z1d0Z2d1Z3d2Z4d3Z5d4Z6d5Z7d6Z8d7Z9d8Z:d9Z;d:Zd=Z?d>Z@d?ZAd@ZBdAZCdBZDdCZEdDS)ErzNamespace for module constants.c Gdd}|S)Nc>eZdZdZdZdZdZdZdZdZ dZ dZ dZ d Z d Zd S) &TIFF.CLASSIC_LE..ClassicTiffLer:rrrrkr ClassicTiffLerDJIGIJLM"OIKGJJJJr@rHr:)rHs r>r#zTIFF.CLASSIC_LE2 r@c Gdd}|S)Nc>eZdZdZdZdZdZdZdZdZ dZ dZ dZ d Z d Zd S) &TIFF.CLASSIC_BE..ClassicTiffBer:rrrz>Irz>Hr>HHz>I4sNrGr:r@r> ClassicTiffBerMrIr@rOr:)rOs r>r!zTIFF.CLASSIC_BErJr@c Gdd}|S)Nc>eZdZdZdZdZdZdZdZdZ dZ dZ dZ dZ dZd S) TIFF.BIG_LE..BigTiffLer:rrr BigTiffLerRrIr@rTr:)rTs r>r z TIFF.BIG_LE2 r@c Gdd}|S)Nc>eZdZdZdZdZdZdZdZdZ dZ dZ dZ dZ dZd S) TIFF.BIG_BE..BigTiffBer:rrrz>QrrNz>Q8sNrGr:r@r> BigTiffBerXrIr@rYr:)rYs r>rz TIFF.BIG_BErUr@c Gdd}|S)Nc>eZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd S) TIFF.NDPI_LE..NdpiTiffLer:rrrrkrrSrrErrjrFNrGr:r@r> NdpiTiffLer\&rIr@r]r:)r]s r>r"z TIFF.NDPI_LE%s2 r@c2Gdd}|dS)Nc^eZdZdZdZdZdZdZddZddZ d Z d Z d Z d Z d ZdZdS)"TIFF.TAGS..TiffTagRegistryaRegistry of TIFF tag codes and names. The registry allows to look up tag codes and names by indexing with names and codes respectively. One tag code may be registered with several names, e.g. 34853 is used for GPSTag or OlympusSIS2. Different tag codes may be registered with the same name, e.g. 37387 and 41483 are both named FlashEnergy. cXi|_|jg|_||dSr9)rurvrq)rr/s r>rz+TIFF.TAGS..TiffTagRegistry.__init__Ds, "j\  C     r@ct|tr|}|D]\}}|||dS)z6Add codes and names from sequence or dict to registry.N)rKdictrr)rr/rr,s r>rqz)TIFF.TAGS..TiffTagRegistry.updateIsUc4((&))++C"%))JD$HHT4(((())r@c|jD]*}||vr|||krdS||vr||vr |||<|||<dS+|j||||idS)zAdd code and name to registry.N)rvr[)rrr,rts r>rz&TIFF.TAGS..TiffTagRegistry.addPs@@AqyyQtW__1}}Q"&$"&$J%%tT4&>?????r@cHd|jD}t|dS)z*Return all registry items as (code, name).c3~K|]8}|D]!}t|dt|V"9dSr)rrKrrs r>r?z;TIFF.TAGS..TiffTagRegistry.items..^sc33q 331&qtS1133333333r@c|dSrwr:rs r>rzz:TIFF.TAGS..TiffTagRegistry.items..`s 1Q4r@r{r~rs r>rz(TIFF.TAGS..TiffTagRegistry.items\s633DJ333e8888r@Nc6|jD]}||vr ||cS|S)z/Return first code/name if exists, else default.rv)rr7rrts r>rEz&TIFF.TAGS..TiffTagRegistry.getbs3&&Aaxx v  r@c6fd|jD}|r|n|S)z7Return list of all codes/names if exists, else default.c(g|]}|v|Sr:r:)r;rtr7s r>rz=TIFF.TAGS..TiffTagRegistry.getall..ks"AAAQq!C&r@ri)rr7rrzs ` r>rpz)TIFF.TAGS..TiffTagRegistry.getallis-AAAA$*AAA!'4vvW4r@cP|jD]}||vr ||cSt|)z4Return first code/name. Raise KeyError if not found.rvr)rr7rts r>rz.TIFF.TAGS..TiffTagRegistry.__getitem__ns:&&Aaxx v  smm#r@chd}|jD]}||vrd}||}||=||=|st|dSrrm)rr7rrtrs r>rz.TIFF.TAGS..TiffTagRegistry.__delitem__us\%%Aaxx $ !#cFeH("3--'((r@c(|jD] }||vrdS dS)z&Return if code or name is in registry.TFri)rr rts r>rz/TIFF.TAGS..TiffTagRegistry.__contains__s-$$Aqyy#tt!ur@cDt|S)z+Return iterator over all items in registry.)rrrs r>rz+TIFF.TAGS..TiffTagRegistry.__iter__sDJJLL)))r@cHd}|jD]}|t|z }|dzS)z!Return number of registered tags.r%rrrs r>rz*TIFF.TAGS..TiffTagRegistry.__len__s3##ACFFNDDqy r@cddd|DS)rzTiffTagRegistry((( {} ))z, c3.K|]\}}d|d|dVdS)(rrNr:)r;rr,s r>r?z=TIFF.TAGS..TiffTagRegistry.__str__..sU!A!A%/T4"7T!6!6T!6!6!6!A!A!A!A!A!Ar@)rCrrrs r>r<z*TIFF.TAGS..TiffTagRegistry.__str__sY5<<LL!A!A37::<<!A!A!AAABBBr@r9)rrrrrrqrrrErprrrrrr<r:r@r>TiffTagRegistryr`8s   ! ! !  ) ) ) @ @ @ 9 9 9      5 5 5 5  $ $ $ ( ( (    * * * ! ! ! 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 ! ! $ $ ! # < , $         L ) % &/  r@c ddddddddddd S) Nr6 r7 rrrpr= rC rA ) r6 r7 rrCH WAVELENGTHTIMErEVENTEXPOSUREr:r:r@r>rzTIFF.MM_DIMENSIONS#s1   r@cddlm}gdtfdtfdtfdtfd|fd|fd tfd tfd tfd tfd dtfdtfdtfdtfdtfdtfdtfdtfddd|fd|fd|fd|fdtfdtfdtfdd d!d"d#d$d%d&d't fd(d)|fd*|fd+d,d-d.d/d0d1d2tfd3d4tfd5d6tfd7|fd8|fd9tfd:tfd;tfd<|fd=|fd>tfd?tfd@tfdA|fdB|fdCtfdDtfS)ENr%r( AutoScaleMinScaleMaxScaleSpatialCalibration XCalibration YCalibrationCalibrationUnitsr ThreshStateThreshStateRed)tagid_10NThreshStateGreenThreshStateBlue ThreshStateLo ThreshStateHiZoom CreateTime LastSavedTime currentBuffer)grayFitN)grayPointCountNgrayXgrayYgrayMingrayMax grayUnitName StandardLUT wavelength) StagePosition (%i,2,2)u4)CameraChipOffsetr ) OverlayMaskN)OverlayCompressN)OverlayN)SpecialOverlayMaskN)SpecialOverlayCompressN)SpecialOverlayN ImageProperty) StageLabel%ipAutoScaleLoInfoAutoScaleHiInfo) AbsoluteZz(%i,2)u4)AbsoluteZValidz(%i,)u4)rIr)GammaRedr) GammaGreenr) GammaBluer) CameraBinr`NewLUT)ImagePropertyExN PlaneProperty) UserLutTablez (256,3)u1RedAutoScaleInfoRedAutoScaleLoInfoRedAutoScaleHiInfoRedMinScaleInfoRedMaxScaleInfoGreenAutoScaleInfoGreenAutoScaleLoInfoGreenAutoScaleHiInfoGreenMinScaleInfoGreenMaxScaleInfoBlueAutoScaleInfoBlueAutoScaleLoInfoBlueAutoScaleHiInfoBlueMinScaleInfoBlueMaxScaleInfo)r*r)rrLroread_uic_image_propertyr(s r>UIC_TAGSz TIFF.UIC_TAGS#s '&&&&&D # D  D  D "3 ' D X & D X & D   %D SMD C D s #D  D   %D  $D c "D c "D SM!D "? +#D $o .%D &c "'D ( )D * %+D ,h -D .h /D 0 !1D 2 !3D 4S !5D 6C 7D 83 9D : ,;D < /=D > "?D @ &AD B CD D )ED F -GD H %ID J5 6KD L "MD N )OD P )QD R &SD T *UD V WD X YD Z [D \ ]D ^ _D `sOaD b &cD dc "eD f *gD h  %iD j"8 ,kD l"8 ,mD n $oD p $qD r"3 'sD t$X .uD v$X .wD x!# &yD z!# &{D |!# &}D ~#H -D @#H -AD B  %CD D  %ED D r@cidtddgtfdddgtfddgtfddgtfddgtfd dgtfd dgtfd dgtfd dd gtfddgtfddgtfddgtfddgtfddgtfddgtfddd gtfddgtfiddgtfddd gtfddgtfddgtfddgtfddgtfddgtfddgtfddgtfddgtfd dgtfd!dgtfd"dgtfd#dgtfd$tddgtfd%dgtfd&dgtfdgtfdgtfdgtfdgtfd'S)(NDetectorrD Pixel_sizerSiliconr Exposure_timeExposure_periodTau Count_cutoffThreshold_setting Gain_settingrN_excluded_pixelsExcluded_pixels Flat_field Trim_file Image_pathr Energy_rangeDetector_distanceDetector_VoffsetBeam_xyFluxFilter_transmission Start_angleAngle_incrementDetector_2theta PolarizationAlphaKappaPhi Phi_incrementChi Chi_incrementOscillation_axisN_oscillationsStart_position)Position_increment Shutter_timeOmegaOmega_increment)rCrLrrr:r@r>PILATUS_HEADERzTIFF.PILATUS_HEADER$s( %4..)3/( Aq65/(  U|(  qc5\ ( U| ( QC< (  aS#J(  1#u(  aVSM(  1#s(  Sz(  A3*(  1#s(  A3*( A3,!( " aVUO#( $ 1#u%( ( & !e '( ( A)( * aS#J+( , "QC<-( . QC QCrrzTIFF.ALLOCATIONGRANULARITYL$s ))r@cTddl}t|dzdS)Nr%rrD)rrr)rs r>rzTIFF.MAXWORKERSQ$s/?,,..!3Q777r@N)Frrrrr#r!r rr"r r]r_rrcrrrrrr r rr r rr r rrr r\rrrr[rrZrKrr0 r4 rrrc r r rrrr r rr$ r& r0 r9 r r r" r* r8 rD rn r r rr r8 rrrr:r@r>rrs))"""""d  d  d  L# # # JJJJ   2   .999v&         !!!      0   :   $W W W r::333j===~       "      .(*" " " H   2 2 2 h? ? ? B   <                    F F F P1 1 1 f             - - - ^9 9 9 v! ! ! F    H H H T+ + + Z*** 88888r@rc |dkr|dz}d}|dz}d} |dz} |dz} n.|dkr|d z}d}|d z}d } |dz} |d z} ntd |i}|d}g} tj} |}t | |kr | |||d}|dkrt dn##t$rtd|YnwxYwi}|| |z}|}d}t|D]}| | |||dz\}}| | ||dz|| z\}}|| z }| |t|} tj |}n #t$rt d|wxYwd||t!|dz|d}tj|}||ks||vr| ||d}|dks||j|z krt d|||||vr||d}||||||}n|dks|dkr |ddkrt)|||||}nu||vs |ddkr | |||}nEt+|||||}n1|ddks|dkr |d |}n| ||d |}||vr)|tjvrt |dkr|d}|dkrt|ddkrht/|t0rS t3t5|}n##t8$rtd|dYnwxYw|||<| |||| |||d}|dkrnH||jkrtd|dn)||t | |k| r|dkr| d} | S)z|Read tags from chain of IFDs and return as list of dicts. The file handle position must be at a valid IFD header. rrrrrr I4srrrQ8szinvalid offset sizeNrgr%rzsuspicious number of tagsz(read_tags: corrupted tag list at offset rVrWrDzinvalid tag value offset rrrr z0read_tags: coercing invalid ASCII to bytes (tag rz read_tags: invalid page offset ()rOrrrrSrrrfrrrErLrr\rrCrrr.rCr^rr_rKrr`rarrbr[)rr]r"tagnames customtagsmaxifdsr!rrrr<r[rzrr-rr#rirrr{rrerrr,rcrr.rfs r> read_tagsrB W$sjQ 3  #o % & q 3  #o % & .///  F ]F WWYYF f++   F; (:(:;;A>Et||#$?@@@    K6KK L L L E www''ggiiu, , A &T% /-BCCKD%!6*d519ego3M.NOOLE5 W E<<c$ii00D F)%0 F F F#$DU$D$DEEE F//)USq]]-BE!HMMC?3''Dj  DJ$6$6 e44Q7A::"'D.!8!8'(LF(L(LMMM:%%)$/2H$HRE5*MMEEaZZEAII%)s2B2B&r9eUJOOEEX%%rc)9)9"F3 66EE&r9eUJOOEErc!!UaZZete sE%4%L11:%%$dn*D*Du::??!!HEzzeBi3..:eU3K3K.%j&7&7&=&=&?&?@@EE)( $((( DJJ d   bggj&9&9::1= Q;;  RW   D6DDD E E E  K f++  N'Q,, Ms0 :CC('C( F  F=6.N%%OOct|||tjd}dD]+} t||||<#t$rY(wxYwd|vru|ddd} |dkr!t|ddd|d<n,|dkr&|dddd |d<n#t$rYnwxYw|S) z,Read EXIF tags from file and return as dict.rDrA )rr)rNrsASCIIsUNICODEutf-16)rB rrc r`rfr)rr]rcrr"exifr,idcodes r>rr$s RJ J J JD2 "4:..DJJ    D m$RaR( ---&/]0CABB0G&H&H]##>))&*=&9!""&=&D&DX&N&N]#    D  Ks"= A  A "AB66 CCc>t|||tjdS)z+Read GPS tags from file and return as dict.rDrD )rB rr rr]rcrr"s r>rr$s RJ q I I IIr@c2ddi}t||||dS)z8Read Interoperability tags from file and return as dict.rDr3rD )rB )rr]rcrr" tag_namess r>rr$s&+,I RJ 1 E E EEr@c|ddkrdn ||dz}|tj|jz}||}t ||kr#t dt |d|d|S)z,Read tag data from file and return as bytes.rr rz&read_bytes: failed to read all bytes (z < r)rbrcrdrrSrrr]rcrr"ris r>r^r^$s9##CCU2Y)>E U[   ((E 775>>D 4yyE KSYY K K5 K K K    Kr@cP||S)z5Read tag data from file and return as unicode string.)rrrI s r> read_utf8rO $s 775>> " ""r@c`|ddkrdn ||dz}|||S)z2Read tag data from file and return as numpy array.rr rrErI s r>rr$s69##CCU2Y)>E == & &&r@cR|||dz|}d|_|S)z7Read ColorMap data from file and return as numpy array.r)rr)rErj)rr]rcrr"cmaps r>rr$s* ==U2Y. 6 6DDJ Kr@c||} tjt|S#t $rt dYdSwxYw)z2Read JSON tag data from file and return as object.zread_json: invalid JSONN)rjsonloadsrrrOrrM s r>rr%sk 775>>D/z)D//0022333 ///-....../s2A A'&A'cl|tj|}t|}d|dD|d<|d}t |d|d|d|dt |d f|d<|S) z9Read FluoView mm_header tag from file and return as dict.rc g|]e}t|d|d|d|dt|dffS)r%rDrrr)r`r)r;rts r>rz"read_mm_header.. %sk$$$  1Q4   !A$!adIadOO4I4I4K4KL$$$r@rr r%rDrrr)rrr recarray2dictr`r)rr]rcrr"mmhrts r>rr %s ..9. = =C   C$$\"$$$C  MA!A$1qtQqT9QqT??3H3H3J3JLC  Jr@c4||dzdS)zARead FluoView mm_stamp tag from file and return as numpy.ndarray.r rrQ rI s r>rr%s ==T)1 - --r@c|dvs|dkrtdi}|dkrI|dd|z|d}d|ddd f|ddd fz i}nw|rut|D]e}t jd |d d } | d vr|d Jt|| |d\} } | || <f|S)zuRead MetaMorph STK UIC1Tag from file and return as dict. Return empty dictionary if planecount is unknown. )r`r rzinvalid UIC1Tagr`rr%s   L  I$4$4*+++ F }}ua%i0088BBvaaad|fQQQTl:; !u ! !AM$ 33A6E,,, &r5*TJJJKD% F4LL Mr@c |dks|dkrtd|dd|z|d}|dddf|dddfz |ddd f|ddd f|ddd f|ddd fd S)z8Read MetaMorph STK UIC2Tag from file and return as dict.r`rzinvalid UIC2Tagr] rNr%rDrrrr)rjrrrkrurlrOrErrr]rcrb r"r8s r>rr4%s }} S((*+++ ]]5!j. 1 1 9 9*a H HFAAAqD\F111a4L0aaad|aaad|qqq!t qqq!t   r@c|dks|dkrtd|dd|z|d}d|dddf|ddd fz iS) z8Read MetaMorph STK UIC3Tag from file and return as dict.r`rzinvalid UIC3Tagr] r WavelengthsNr%rDrd re s r>rrB%ss }} S((*+++ ]]5!j. 1 1 9 9*a H HF 6!!!Q$<&A,6 77r@c|dks|dkrtdi} tjd|dd}|dkrnt |||d \}}|||<Q|S) z8Read MetaMorph STK UIC4Tag from file and return as dict.r rzinvalid UIC4TagTrErr%Frq)rOrrrra ) rr]rcrb r"rzrr,rs r>rrJ%s }} S((*+++ F dBGGAJJ//2 A:: "2ujGGG et  Mr@cdfd } tj|\}}n#t$rd||fcYSwxYwtjdd}|rj}|tdfvrK|} | dkr&|t ur|dfSt d|d | || fS| |d |z}|} n~|tur |} ni||ur|d } | d | dz } nG|turt|d } n*|turt} n|t ur|} d | cxkrd krZnnWtj | d | d dd} tt| } n|rd} t d|n~td| |dkrg} t!|D]} |} d | cxkrd krnnnktj | d | d dd} tt| } | | |rt d|td| nd|z}d|vr||z}d|vr?|dd } | jdd kr| d| dz } nUtj | tj|} t+| dkr| d } |r|dz|| fS)zgRead a single UIC tag value from file and return tag name and value. UIC1Tags use an offset. rDctjd|dd|z}|dkr|dn|S)NrrrrDr%)rrr)rrrs r>read_intzread_uic_tag..read_int_%sB l%lllBGGAI,>,>?? A::uQxx50r@_TagIdrNrrlz%read_uic_tag: invalid offset for tag rr{rr%r r rz$read_uic_tag: corrupt string in tag z"read_uic_tag: invalid string size r z#read_uic_tag: invalid string size: rz%irtr|).rDr)rr rrrrLrrCror rrrr`rrOrr[rErjrrS)rrrb r-rk r,rcr)roffrr.r{strings` r>ra ra X%s111111,mE* ee ,,,++++,}Q"H ggii d # #(**CQwwC<<8OKDKKcKKSy GGCLLL }Tz  #  (   a58# / ! !!- ) ) )'++ #xzz     u     MT***bggdmm<r r %s =bggajj ) )! ,D =DRWWT]] 3 3A 6ss ;D-rwwqzz22KE4 qyy dBGGAJJ//a58#}S"''!**--a0 jjj"''$--88; Te 4 4 44r@c$|dkrtdtjd|d\}}|dvrtd|dd|t jtjj krRg}d}tjD]@\} }|t j|j z }||krn| | |fAn tj}| || }t|}tj D]\\} } | |d | zd} | dkr(||  | ||| <M#t$rYYwxYw|S) z1Read CZ_LSMINFO tag from file and return as dict.rzinvalid CZ_LSMINFO structurerr%sC7888#)= #C#C L.///7888GGBNNN DO44===? * *KD% EK&&/ /Dn$$ NND%= ) ) ) )/nnW n::GG$$G/5577   f > X_a00 A::   "F2JJGDMM    D  Ns1F F  F ctjd|dd}|d|S)z>Read LSM sequence of float pairs from file and return as list.r r %8 =rwwqzz * *1 -D ==t= , ,,r@ctjd|dd}|d|S)z0Read LSM positions from file and return as list.rkrr%rz r{ r| r} s r>read_lsm_positionsr %r~ r@ctjd|d\}}|dd|zzkrtdgS|d|S)z2Read LSM time stamps from file and return as list.zr r %s^-rwwqzz22KD% AI GHHH ==e= , ,,r@cttjd|dd}g}|dkrtjd|d\}}}tt ||dz }||||f|dz}|dk|S)zCRead LSM events from file and return as list of (time, type, text).rs rrDr%zr r &s M% , ,Q /E F !))$mFBGGBKK@@ue)BGGEBJ$7$78899 ueU+,,,   !)) Mr@cdggd}|}tjd|d\}}}}}}||krt d|St ||d<|||z|d|dz |df} | |d <|||z|||z } g} t| dkrptjd | d dd }| t| dd|z| d|zd } t| dkp| |d<|S)z>Read LSM ChannelColors structure from file and return as dict.F)Monor ColorNameszr r &sr < >| L LF}}F8GGC'M WWTG^ $ $F E f++//}T6"1":..q1 YvaDj122333D " f++//!F< Mr@ci}|g}tj}tjd|dddkrtd|S|d |d|d \}}}|d kr0t t ||}nZ|dkr&|d |dd}n.|d kr&|d |dd}nd}|t jvr1||t j|}g} | ||<| }n|t j vr/||i} || | }nJ|t j vrt j |}|||<n$|dkr| }n ||d|d<|sn~|S)z9Read LSM ScanInfo structure from file and return as dict.rkrr%iz1read_lsm_scaninfo: invalid LSM ScanInfo structurerTzr r +&s EWF ]F }T2771::&&q)Z77GHHH GGAJJJ"#VFBGGBKK88ud A::i 6677EE aZZF4,,Q/EE aZZF4,,Q/EEE D3 3 3 MM% 259DF E$KEE d6 6 6 MM% F LL EE d9 9 96u=DE$KK j JJLLEE*/E%E%%% &  E"F Lr@cTi}tjd|d\}}}} } } } } |dkrtdt t | |d< t jd| z| dz| |||d<n#t$rYnwxYw|d | z}td | d zd D]}tjd |||d z\}}}|||dkrtjd |d \}}}}}}tj d|}||z|d<||z|d<||d<t t ||d<t t ||d<|dkr|S)zrRead OlympusSIS structure and return as dict. No specification is avaliable. Only few fields are known. z<4s6xhhhhh6x32sh<sSIS0zinvalid OlympusSIS structurer,ilrDrrr%zrr[&s F>DmBGGBKK?)?);UFD#udD( 7888y//F6N %.td{EAIs/3V==z       771x< D 1hlA & &!'vtAq1uH~!F!F  a<<:@-$bggcll;4;4 7VT4gwV$$A#'!8F< #'!8F< &)F? ##,Yw-?-?#@#@F< $-i.@.@$A$AF= ! ! ]]  Ms)!B BBc||}tt|} t|S#t$r+}t d|jjd|icYd}~Sd}~wwxYw)z.Read OlympusSIS INI string and return as dict.zolympusini_metadata: rhN)rr`rolympusini_metadatarfrrr)rr]rcrr"inistrrs r>rr&s WWU^^F y(( ) )F"6*** KCM,BKKcKKLLL sA A7 A2,A72A7ci}|tj|}tjD]"\}}||||<#|ddkr|tj|}|dt dkrt diStjD]{\}}|drD|| dd } t| d ||<^||||<|d D](} |d| zxxdzcc<|d| zxxdzcc<)n|j dkrt diS|S)z.Read TVIPS EM-MENU headers and return as dict.rr rr l*UUz0read_tvips_header: invalid TVIPS v2 magic numberrC rE rrre)nullrr] geA PixelSizerDz/read_tvips_header: unknown TVIPS header version) rrrn rr rrrrrrr-) rr]rcrr"rzr,r,typestrr rs r>rr&s F ^^D0I^ F FF--- gd|**,,t  iA 4 JJ '?c*oo - - J K K KI!1 5 5MD'!!#&& 54L((**11(81LL(666t %d|2244t  . .D &- . . .# 5 . . . ;% & & &# - & & & & . 1  EFFF Mr@ci}i}tt||}|D]w}|}|dri}|||dd<; |d\} } n#t$rYawxYwt| || <x|S)z0Read FEI SFEG/HELIOS headers and return as dict.[rDrr) r`rr splitlinesrrrwrOr) rr]rcrr"rzsectionrirrr7rs r>rr&s FG Yrwwu~~.. / /D!! % %zz|| ??3   G!(F4":   CJC    H e}} MsB B*)B*c ddi}d}tt||}|D]v}|r|},|r |d\} } n<#t$r/ |dd\} } n#t$rYY{wxYwYnwxYw| } d} | \} } t| ttf}|| kr|} | } nA#t$r4t| ttf}|| kr|} | dvrd} n| d vrd } YnwxYw| | f||<| r||xx| fz cc<d}K|dxxt|ttffz cc<x|S) zRead Zeiss SEM tag and return as dict. See https://sourceforge.net/p/gwyddion/mailman/message/29275000/ for unnamed values. rlr:NrrDrD)NoOffF)YesOnT) r`rrr isupperr/rwrOrfrrrr)rr]rcrr"rzr7rirrr,rrrrQnumbers r>rr&s "XF C Yrwwu~~.. / /D!! 8 8 <<>> 8**,,CC  8 "jjoo ee   "&**S!"4"4KD%% HH %  KKMMED !{{}}1C<00Q;;"ED ! ! !U|44U??"EM))!EEm++ E ! ::<</F3K 's w& CC 2JJJ6$e 557 7JJJJ MsH:B C B87C 8 CC CC  C &=D$$;E"!E"c|tj|}||}t |}|dd|d|d<|dd|d|d<|S)z7Read NIH_IMAGE_HEADER tag from file and return as dict.rr Nr r r )rrr rrY )rr]rcrr"rs r>rr&sq t, BBA y!!AaA7OQ{^O,AgJglq{l#AdG Hr@c<|d tjd|d\}}|dks|dkrt|dtjd|d\}}}}|dks|d krtn#t$rt d wxYwt t||d d }|d krt|dd |d ni}||fS)a;Read ScanImage BigTIFF v3 static and ROI metadata from open file. Return non-varying frame data as dict and ROI group data as JSON. The settings can be used to read image data and metadata without parsing the TIFF file. Raise ValueError if file does not contain valid ScanImage v3 metadata. r%z<2sHrrrrzrr&s!GGAJJJ <#]62771::>> 7   BO  '-}Wbggbkk'J'J$wu I  AO". <<<:;;;<iss(;<<==J8= yS$t444rH x s BB++CcN|d ddd|d}n#t$rtdwxYwi}|dt j|dz|d \}}}}}}} } | d krtd t ||d | d |d <|dkrtd||t j|dz|d\} } | dkrtdt j|d| zz|d| z} | d d d| dd d| dd d| dd d| dd dd|d<|dkrtd||t j|dz|d\} } | dkrtdt ||d | d |d<|dkrtd||t j|dz|d\} } | d krtdt ||d | d |d!<|S)"zRead MicroManager non-TIFF settings from open file and return as dict. The settings can be used to read image data without parsing the TIFF file. Raise ValueError if the file does not contain valid MicroManager metadata. r%rr)rrrznot a MicroManager TIFF filerIIIIIIIIrLi$#z#invalid MicroManager summary headerNSummaryiCz!invalid MicroManager index headerrp i4IIIIIrrrDrr)rSliceFramePositionr IndexMapiz#invalid MicroManager display headeridDisplaySettingsi}z$invalid MicroManager comments headerie rU )rCrrrOrrr)rr]rz index_header index_offsetdisplay_headerdisplay_offsetcomments_headercomments_offsetsummary_headersummary_lengthr,rris r>rr'sGGAJJJ9,,RWWQZZ8 99978889FGGAJJJ  i*,bggbkk::   >???!"i~tLLF9x<===GGLM)d"2BGGAJJ??MFE <=== =Wu_4bggb5j6I6I J JD!9addaddAJqt!t* F:"">???GGNM)d"2BGGAJJ??MFE >??? )"iud K KF (""?@@@GGOM)d"2BGGAJJ??MFE ?@@@"2y$tDDF: Ms 6Act)zRead MetaSeries non-TIFF hint catalog from file. Raise ValueError if the file does not contain a valid hint catalog. )r7)rs r>read_metaseries_catalogr ['s   r@c |sdSddd|g}dg}g}d}d}d}d }d d |fd d |fdd|fdd|fdd|fdd|fdd|ff} | D]\} } } | |vr| } n| |vr6|dkr | ddd} || } t| trt| }n| g} d}|| t j|dz|z| D]E}| ||}|||t|F|sdSd|}d|}||z}t||d<t j|dt|zzg|R}ddt||d fd!dt|d"z|d ffS)#aReturn IJMetadata and IJMetadataByteCounts tags from metadata dict. The tags can be passed to TiffWriter.save() as extratags. The metadata dict may contain the following keys and values: Info : str Human-readable information as string. Labels : sequence of str Human-readable labels for each channel. Ranges : sequence of doubles Lower and upper values for each channel. LUTs : sequence of (3, 256) uint8 ndarrays Color palettes for each channel. Plot : bytes Undocumented ImageJ internal format. ROI: bytes Undocumented ImageJ internal region of interest format. Overlays : bytes Undocumented ImageJ internal format. r:IJIJJIJIrrr%cD|dddd|zSNrE beler )rrir]s r>_stringz$imagej_metadata_tag.._string'&{{8Dt&<&_doublesz%imagej_metadata_tag.._doubles's){9c$ii8@4@@@@r@c*|Sr9)rr s r>_ndarrayz%imagej_metadata_tag.._ndarray's||~~r@c|Sr9r:r s r>_bytesz#imagej_metadata_tag.._bytes'rr@r3infor4lablr5rangr6lutsr7plotr8roi r9overrNrrDrr@r|rTrr)r/rKrrSr[rrr)rr]r,ribodyr r r r metadata_typesr7mtyper~r8rrris r>rre'sy. r'**95 6FJ DIIIAAA '" 7G$ 7H% (# &!  Wf%N+))UD 99;;( " "))++CC     $$B$KE# fd # # KKEEXFE efk)c/5AAABBB ) )E4y))D KK      c$ii ( ( ( ( ) r 88D>>D XXf  F D=DKKJqMY#J*?@N:NNNJ SYYd+ S__):t< r@c Vd}d}d}d}d|fd|fd|fd|fd |fd |fd |fd }|d |D|std|dddvrtd|d}|dks|dkrtd|dz dz} tj|d| zz|dd| dzz} d| dzz} d} i} t | ddd| dddD]\}}g}||t|tf\}}t|D];}| dz } | || z}| ||| |||} <|dkr|dn|| | <| S)a]Return IJMetadata tag value as dict. The 'Info' string can have multiple formats, e.g. OIF or ScanImage, that might be parsed into dicts using the matlabstr2py or oiffile.SettingsFile functions. 'ROI' and 'Overlays' are returned as bytes, which can be parsed with the ImagejRoi.frombytes() function of the roifile package. cD|dddd|zSr rhr s r>r z imagej_metadata.._string'r r@cXtj|dt|dzzz|S)Nrtr)rrrSr s r>r z!imagej_metadata.._doubles's(}Y#Ta*@A4HHHr@cTtj|dddS)Nr{rrJ)rbrOrr s r>_lutzimagej_metadata.._lut's%g..66r3???r@c|Sr9r:r s r>r zimagej_metadata.._bytes'rr@r3r4r5r6r7r8r9)r r r r r r r c,i|]\}}|ddd|S)Nrr:rG s r>rH z#imagej_metadata..'s(III$!Q1TTrT7AIIIr@zno ImageJ metadataNr)r r zinvalid ImageJ metadatar%ri$z#invalid ImageJ metadata header sizer4sIrrD) rqrrOrrrxrEr`r^rr[r)ririr]r r r r r header_sizentypesr,rcounterrzr rr8r,r~r{pos1s r>rr'sVIIIIII@@@ '"G$H%$&!f%NII.2F2F2H2HIIIJJJ /-... 8) ) )2333Q-KR;,,>???Ao! #F ]9uv~5tAq6A:~>> description = 'ImageJ=1.11a\nimages=510\nhyperstack=true\n' >>> imagej_description_metadata(description) # doctest: +SKIP {'ImageJ': '1.11a', 'images': 510, 'hyperstack': True} c<ddd|S)NTF)truefalser.)rs r>_boolz*imagej_description_metadata.._bool(su--ciikk::r@rrznot a ImageJ image description)r rwrfrrrrO)rrrzrrr7rrcs r>r}r}'s;;;F&&((   zz#HC    H iikkiikk5%(  E eCjj    s v9::: Ms!6 AA B  BBFc |rtd||dd}t||}|ddv}g}d|g} | d t |dd |d }|d n%|d t ||ddkr| d|d||sd}|r|r|d||ddkr| d|d|ddkr5| d|d||d|7|dt ||D]5\} } | dvr,|| d| 6d| |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 supportedNrz1.11a)rgbrrrzimages=rTzhyperstack=truez hyperstack=rrDz channels= grayscalezmode=zslices=r%zframes=z loop=falsezloop=)ryr~r}r|rr4rl) r7rJrr[rrr/rr) rjr  colormapedr- hyperstackrylooprUr[rzr7rs r>rr(sH"G!"EFFF**Xw// C ( ( (E )v C F!!! "F MM1GE#2#J//11222  '(((( 6D$4$466777 Qx!|| ,%(,,--- |C|&d& ndnn%%% Qx!|| *a**+++ Qx!|| *a**+++ < MM, ' ' '  *d4jj**0022333llnn44 U @ @ @ MMSYY[[22522 3 3 3 99Vf_t+ , ,,r@c~td|D}t|}d|cxkrdkrnntd||ddvo|dk}|r|ddvrtd |s!|dkr|ddkrtd |s |ddkr 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) c34K|]}t|VdSr9rrs r>r?zimagej_shape..Y(s(((Q#a&&((((((r@rDrz1invalid ImageJ hyperstack: not 2 to 6 dimensionalNrrrz*invalid ImageJ hyperstack: not a RGB imagez.invalid ImageJ hyperstack: not a non-RGB imagerr)rrSrO)rjr rs r>rrP(s ((%((( ( (E u::D4||||!|||||LMMM {Bi6!.dQh GuRy&&EFFF K4199raIJJJ *eBi1nnD!E)) AH  % ,,r@c V||tj|S)zReturn JSON image description from data shape and other metadata. Return UTF-8 encoded JSON. >>> json_description((256, 256, 3), axes='YXS') # doctest: +SKIP b'{"shape": [256, 256, 3], "axes": "YXS"}' rj)rqrU dumps)rjrs r>rrh(s( OO%O   :h  r@c&|dddkrDtd|dddD}t|S|dd d kr"|ddd krtj|St d |) aReturn metatata from JSON formated image description as dict. Raise ValuError if description is of unknown format. >>> description = '{"shape": [256, 256, 3], "axes": "YXS"}' >>> json_description_metadata(description) # doctest: +SKIP {'shape': [256, 256, 3], 'axes': 'YXS'} >>> json_description_metadata('shape=(256, 256, 3)') {'shape': (256, 256, 3)} Nrrc34K|]}t|VdSr9rrs r>r?z,json_description_metadata..(s(CCc!ffCCCCCCr@rr,rrDr}zinvalid JSON image description)rrwrcrU rV rO)rrjs r>rnrnu(s2A2(""CCk!B$&7&=&=c&B&BCCCCC%    2A2#+bcc"2c"9"9z+&&& 5{ C CCr@c|dstd|ddh}i}|g}d}|D]}|s|}|s|ddkr|ddd krl|d =|d }|d d}|rd ||||<|dd dkr(t j||d}d|_|||<d}|d d }|dd dkrg}n ||vrg}d}ni}|||||<|r||| dd }t|d krd||d<E|\} } | dd dkr3| d| Dt| || <|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 DescriptionFr%z End]rrDr4rzLUT r{r)rrTrzRGB c34K|]}t|VdSr9r)r;r s r>r?z0fluoview_description_metadata..(s(==3s88======r@) rrOr rrrbr@rjr[rwrSrr) rignoresectionsrzsectionscommentrrr r,rr7rs r>fluoview_description_metadatar(sR  ! !# & &?=>>>02HI FxHG&&((+9+9 ::<>BCCyG##RL"2,AbDz=$(IIgdm$<$>'+GDGMMOO $  U rr7f   NN==u{{}}=== = = = =#)%++--#8#8GCIIKK Mr@ci}|ds|SdD]}||d}|dD]rdddkrd}dtjvri t jdd |d <n0#t$r#dd d||<YnwxYwtjd\}t|dtr|d}nfd |D}tur|dd krdg}tfd|D}tkrd|}nt|d kr|d}|||<t|S)aReturn metatata from Pilatus image description as dict. Return metadata from Pilatus pixel array detectors by Dectris, created by camserver or TVX software. >>> pilatus_description_metadata('# Pixel_size 172e-6 m x 172e-6 m') {'Pixel_size': (0.000172, 0.000172)} r"z#:=,()r,r4Nrr2r%z%Y-%m-%dT%H %M %S.%frrDc g|] }| Sr:r:)r;r<rrs r>rz0pilatus_description_metadata..(s///!d1g///r@notNaNc3.K|]}|VdSr9r:)r;rrcs r>r?z/pilatus_description_metadata..(s+00AuuQxx000000r@)rrrwrr8 rstrptimerrfrKrCrrrLrS)rrzrRr,rr8rcrrs @@r>rr(sF  ! !$ ' ' 22!))!S11 !!$'' 8t   zz||Aw 7$- - - 2%-%6%?%?HHTNN$:&<&<z"" 2 2 2"xxQRR11t  2 ,T!W5 gaj% ( ( 0'!*%FF////w///F E>>fQi500WF000000000 C<<XXf%%FF [[A  AYFt Ms6C*C32C3c|dstdi}|d}|ddd\}}|||<t |dkr|S|dd}|d|d<|ddD]P}|d \}}t |||<Q|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 descriptionr4r%NrDrrlz = )rrOrwrrsplitrSr)rrzlinesr7rrr s r>svs_description_metadatar'(s  ! !"9 : :=;<<< F   d # #Eq!!((q11JC++--F399;; 5zzQ !HNN3  Eq!!F2Jabb 44ZZ&& U$U[[]]33syy{{ Mr@c|}|sgS t|}n8#t$r+}td|jjd|gcYd}~Sd}~wwxYwg}|dD]}i}|dD]}|dd}t|dkr<|\}}t|||<g|d}|r&d |vr|d  ||g|d <| ||S) zReturn metadata from MetaMorph image description as list of dict. The MetaMorph image description format is unspecified. Expect failures. zstk_description_metadata: rhNre rDrDr%rl) rr`rbrrrrwrSrr[)rrrzrrtrrr,rs r>stk_description_metadatar*)s ##%%K   ,,  H)? H H3 H H     F""6** KK'' ( (D::c1%%D4yy1}}" e"("7"7$**,,Q (Qww" U++++!&" a Ms* A AAAc|dstdddlm}||}t t ddfd|i}d|vr|dd d |d<|S) z:Return metatata from MetaSeries image description as dict.rz$invalid MetaSeries image descriptionr%rc$t|ddS)Nonrm )asboolrxs r>rzz1metaseries_description_metadata..@)s&D%00r@)rrrc|D]Z}|j}|s|i||j< d|vr6|d}|d}|d}|vr||||<U|||<[|S)Nidrr)rr) rrzchildrr<rrparsetypess r>r2z.metaseries_description_metadata..parseC)s " "E\F $)E%$4$4uy!v~~4L6N7O:: (a F1II !F1I r@rz r4)rrOrrrrrr)rrradictr2r3s @@r>rr5)s  ! !, / /A?@@@......   K ( (D00  E " E$OOE$]3;;L$OOm Lr@c t|S)z9Return metatata from ScanImage image description as dict.)r r*s r>rrZ)s  $ $$r@c tj|S#t$r*}td|jjd|Yd}~dSd}~wwxYw)z2Return metatata from ScanImage artist tag as dict.zscanimage_artist_metadata: rhN)rU rV rOrrr)artistrs r>scanimage_artist_metadatar8_)s~ z&!!!     I#-*@ I IC I I          s A AA c d}i}g}d}d}|D]}|}|dks |ddkr*|ddkr|ddkr|d d}ix||<}|d krgx|d <} gx|d <} h|d krg||<t|dkrd |vr gx||d<}|dkrd |vr gx||d<}|dkr.|d d} dt| D}|||<d} |d\} }|dkrd}n@d|vr-t d|dD}nt |}|d kr1||| <| | | ||d kr2| dkr ig|z|d <|| \} }||d || <|dkr| dddkr||| d}tjd|}|t|dd t|d dt|ddgK|| \} } ||| | <f| dddkr|||| dddkr|||||| <d |vrddi}g} g} t|d |d D]a\}}|d krV| | ||d | |bd | |d <t | |d < tj|ddd|d dd|dd<n#t $rYnwxYw tj|ddd|d dd |dd<n#t $rYnwxYw|D] }tj|dd!|d<!|S)"zUReturn OlympusSIS metadata from INI string. No documentation is available. cd}t|d}|t|kr$t||ddz }|d|}||fS)Nr% 0123456789rD)rSrstripr)r7rr<s r>keyindexz%olympusini_metadata..keyindexp)s^  <(( ) ) s3xx<<ABBLL1$Ebqb'CEzr@Nrlr%;r r]rD DimensionrZrjASDrrrx TimePosBandcg|]}dgiS)LUTr:)r;r{s r>rz'olympusini_metadata..)s<<<%<<r?z&olympusini_metadata..)s(BBAfQiiBBBBBBr@CountrrErkrrrrpfloat64int32r{)r rrrwrrr[rrordrxrErrrbr@rf)r r=rzbandszpostposrr section_namer rZrjnbandsibandr7rrlutsisaxesr<rybands r>r r i)s(F E D D!!##8%8%zz|| 2::aC  7c>>d2h#oo":L-/ /F< 7{**(**v*,,w%%&&')|$$$$&((:<>%'D5LF5MM!)#JC05F5M%(--''rr7e##,u-C"Ke44EJJU1Q3Z#eAaCj//3uQqSz??KMMMM"*#JC(-E%L%%RaRF""t'7 E""""RaRI%%$*: E""""$  3-w88  DAq1uu GKK1Q4::<<88999 Qv,,w #k 3K  9 !4S!9 9 :IGGs F       $)K 6N9 %&Bvk':6'B&B CW%N%Nvy!!      88k$u+w77U Ms$>O OO >P P,+P,Tc p |d}dtjttj| dkrt fd|Dst d|t fddD}tj|j|z}tj |j t|fj }t|D]\}}|ttj||d zdz }|td d |zzd z}|rbjd z|zd z|z} | |jjd zkr|d}|d | zd z d |zd z zz}|d | jd zz zz}||dd|f<|dS)aReturn array from bytes containing packed samples. Use to unpack RGB565 or RGB555 to RGB888 format. Parameters ---------- data : byte str The data to be decoded. Samples in each pixel are stored consecutively. Pixels are aligned to 8, 16, or 32 bit boundaries. dtype : numpy.dtype The sample data type. The byteorder applies also to the data stream. bitspersample : tuple Number of bits for each sample in a pixel. rescale : bool Upscale samples to the number of bits in dtype. Returns ------- numpy.ndarray Flattened array of unpacked samples of native dtype. Examples -------- >>> data = struct.pack('BBBB', 0x21, 0x08, 0xff, 0xff) >>> print(unpack_rgb(data, '>> print(unpack_rgb(data, '>> print(unpack_rgb(data, 'r?zunpack_rgb..)s/JJq1 22JJJJJJr@zsample size not supported: c3\K|]&}tj|jdzk"|V'dSrV)rbrcrd)r;r<bitss r>r?zunpack_rgb..)s= F FA%+a.."9A"="E"Ea"E"E"E"E F Fr@BHIrD0b1rrrr)rbrcrrrrOrrOr]rr.rSrvrrdrr) rircrrescalerqrzr<rProrXs ` @r>rRrR)sB!  } K  E uy'' ( (D  sJJJJMJJJJJ F}FFGGG F F F F F F F F FB  D%/B"6 7 7D [$)S%7%78%* E EFM**  3 C -A"78899 9 Sc !1 % %%  0.1$,q0C7A4:&***HHSMM !Q$(3 + +A !a5>A-./ /Aqqq!t >>"  r@rc,tj||S)zCompress Zlib DEFLATE.)zlibrariror=s r>r r *s}T5)))r@c*tj|S)zDecompress Zlib DEFLATE.)r_rKrir=s r>r r *t$$$r@c*tj|S)zCompress LZMA.)lzmarar`s r>r r *s}T"""r@c*tj|S)zDecompress LZMA.)rerKrbs r>r r *rcr@rcLt|ttfrZtj|d}tj|d}tj|d|dS|j}|j dkr| d|j }tj||}tdg|j z}d||<tj|d|t||}|j dkr| |S|S)z Encode Delta.r rr%rrrQN)rKr bytearrayrbrOrrrrcrviewrdrCrr)rirr=rrcr7s r>r r *s dUI. / / <#D555D:d+++D<aa1199;; ;  :  9911122Dz$T***T{{mdi'D |D!T%**%5DAAA :  99U## # r@c||jjsd}t|ttfr@t j|d}t j|dd|S|j j dkrX| d|j j }t j|||j }| |j St j|||j |S) z Decode Delta.Nr rr%)rrcr=rrQ)rrc) rB writeablerKrrhrbrOcumsumrrcrrird)rirr=ris r>r r 3*s ?39#6?C dUI. / / M#D555D<1DcBBBJJLL L :?c ! !996!46677D<4tzBBBD99TZ(( (|Dt4:3GGGGr@c~|sD|d|tj|dd |d}tj|d|||S#t $r||dcYSt$rtdwxYw)aReverse bits in each byte of bytes or numpy array. Decode data where pixels with lower column values are stored in the lower-order bits of the bytes (TIFF FillOrder is LSB2MSB). Parameters ---------- data : bytes or ndarray The data to be bit reversed. If bytes, a new bit-reversed bytes is returned. Numpy arrays are bit-reversed in-place. Examples -------- >>> bitorder_decode(b'\x01\x64') b'\x80&' >>> data = numpy.array([1, 666], dtype='uint16') >>> bitorder_decode(data) >>> data array([ 128, 16473], dtype=uint16) s@ `P0pH(hX8xD$dT4t L,l\<|B"bR2r J*jZ:zF&fV6vN.n^>~A!aQ1q I)iY9yE%eU5u M-m]=}C#cS3s K+k[;{G'gW7wO/o_?r%r{rrDr<zslices of arrays not supported) r[rbrOritaker translaterOr7)rir= _bitorderris r>rXrX@*s, L    % & & &   U-il'JJJ K K K H99W%%D Jy|Tt 4 4 4 4K 0 0 0>>)A,// / / / H H H%&FGG G Hs3A<<%B<#B<c|dkrtj|d}tj|}|dzr@|d|d|dzz z}|ddd|fd}||S|dvrtj||St d|dtj|d ) aDecompress bytes to array of integers. This implementation only handles itemsizes 1, 8, 16, 32, and 64 bits. Install the imagecodecs package for decoding other integer sizes. Parameters ---------- data : byte str Data to decompress. dtype : numpy.dtype or str A numpy boolean or integer type. numbits : int Number of bits per integer. runlen : int Number of consecutive integers, after which to start at next byte. Examples -------- >>> packints_decode(b'a', 'B', 1) array([0, 1, 1, 0, 0, 0, 0, 1], dtype=uint8) rDz|BrrNrz unpacking z-bit integers to r )rbrO unpackbitsrrr7rc)rircnumbitsrunlenr=s r>rTrTq*s. a<<#D$//D#D))Dz 4||B!fqj.(ABBAAAwwJ'//33;;u%% % o % %#D%00 0! 5 5 5+e$$ 5 5 5   r@c2g}|j}d} t|||dzdz}|dz }|dkr"||||dzd|z z|dz }n!|dkr|||||z||z }l#t$rYnwxYwt|S)awDecompress PackBits encoded byte string. >>> packbits_decode(b'\x80\x80') # NOP b'' >>> packbits_decode(b'\x02123') b'123' >>> packbits_decode( ... b'\xfe\xaa\x02\x80\x00\x2a\xfd\xaa\x03\x80\x00\x2a\x22\xf7\xaa' ... )[:-5] b'\xaa\xaa\xaa\x80\x00*\xaa\xaa\xaa\xaa\x80\x00*"\xaa\xaa\xaa\xaa\xaa' r%TrDrW)rrJrFr)encodedr= out_extendr<rs r>r r *sZ   !a%())A-Qs77JwqQw/37;<<<FAAWWJwqQw/000FA     D SzzsA-A:: BBctj||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) rDrr%)rbrnrollaxisrascontiguousarray)imagercontigs r>r}r}*sL. JxQ / / /E N5!UZ 0 0E /'.. Lr@c @ |stdtj|tjtjz}|fd}d|D}t |dkr&t j|d}nt j |}t |}d g}|D]}|||d\} i| dt t ks5tfdtt Drtdn |krtd t fd D | ˉ!d  fd D ttj|d }ttj|d } tdt%|| D} ||| fS)zReturn shape and axes from sequence of file names matching pattern. >>> parse_filenames(['c1001.ext', 'c2002.ext'], ... r'([^\d])(\d)(?P\d+)\.ext') ('ct', (2, 2), [(1, 1), (2, 2)], (1, 1)) zinvalid patterncg}g}d|jD}||}|stdd}t |D]\}}||dz|vrS||dz}|ds-t|}|dks|dkrtd|n|dr|}|d} t|}n #t$rtd|wxYw| || |d}d |t|fS) Nci|]\}}|| Sr:r:rG s r>rH z2parse_filenames..parse..*sBBBtq!aBBBr@z pattern does not match file namerDr%Azzinvalid index rrl) groupindexrsearchrOrgroupsisdigitrJisalpharrfr[rr) rr2rZrrmatchrr<rEs r>r2zparse_filenames..parse*sBBw'9'?'?'A'ABBB u%% A?@@ @ ellnn--  DAqy1u ""A&t||~~AAA2vvS()?!)?)?@@@1 z 9FF 9 9 9 !7!!7!7888 9 NN1    KKOOOBBwwt}}eGnn,,s 5DD"cLg|]!}tj|"Sr:)rQrnormpathr0s r>rz#parse_filenames..+s( 0 0 0QRW  a 0 0 0r@rDr%Nc3 K|]}|vV dSr9r:)r;r<r5s r>r?z"parse_filenames..+s(HH!1I-HHHHHHr@zinvalid axisorderz'axes do not match within image sequencec3(K|] }|V dSr9r:)r;r<rs r>r?z"parse_filenames..+s'221A222222r@rlc3(K|] }|V dSr9r:)r;r<rZs r>r?z"parse_filenames..!+s'221tAw222222r@rc3,K|]\}}||z dzVdSrr:rs r>r?z"parse_filenames..%+s.??1!a%!)??????r@)rOrecompile IGNORECASEVERBOSErSrQrr commonpathrMrrr[rrbrrrx) r=r2r5r2prefixrrrrjrrZrs ` @@r>rr*s= ,*+++j"-"*"<==G$----B 1 0% 0 0 0E 5zzQq**##E** [[F DG%fgg''C <D% NNc$ii//HHHHuSYY7G7GHHHHH0!!4555 RZZFGG G  2222 22222Csww2222 22222 %)G!,,, - -Euyq11122J ??E:(>(>??? ? ?E  ++r@c #K|j}tj||dfz|j}t |dkr|D]}|D]}t |dD]}t |dD]}t |d|d||dzz } t |d|d||dzz } d|| d| df<|d||dz||dz| z||dz||dz| zf|d| d| f<|VԌdSt |dkr@|D]>}|D]5}t |dD]} t |dD]}t |dD]}t |d|d| |dzz } t |d|d||dzz } t |d|d||dzz } d|| d| d| df<|| |dz| |dz| z||dz||dz| z||dz||dz| zf|d| d| d| f<|V7>dSdS) z=Return iterator over tiles in data array of normalized shape.rrrr%rDrrN)rjrbrrcrSrr) rirrrjrrxrtytxc1c2tzc0s r>rr++s JE Kb |+4: > > >E 4yyA~~ $ $D $ $a// $ $B#E!Hoo $ $ a%(R$q'\*ABB a%(R$q'\*ABB*+bcc233h*/aL"tAw,*;;aL"tAw,*;;=+crc3B3h $  $ $ $ $ $ Ta ( (D ( (a// ( (B#E!Hoo ( ("'a// ( (B!$T!WeAhd1g.E!F!FB!$T!WeAhd1g.E!F!FB!$T!WeAhd1g.E!F!FB34E"##rssBCC-038 "T!W b47lR.? ? "T!W b47lR.? ? "T!W b47lR.? ?!A4E#2#ssCRC-0 #(KKKK ( ( ( (  ( (r@crtj}t||}||jkr|S||jkr|ddddddfS||jkr|ddddddddfS||jkr|dddddddddfS||jkrtj |ddS||j kr$tj |ddddddddfS||j kr'tj |ddddddddddfS||j kr(tj |dddddddddddfS|S)a+Return reoriented view of image array. Parameters ---------- image : numpy.ndarray Non-squeezed output of asarray() functions. Axes -3 and -2 must be image length and width respectively. orientation : int or str One of TIFF.ORIENTATION names or values. .Nrrr) rr rrn ro rq rp rr rbswapaxesrs rt ru )r| orientationorients r>reorientrO+s F&+..Kfn$$ fo%%S$$B$\""fn$$S$$B$111_%%fo%%S$$B$"aaa'((fn$$~eR,,,fo%%~eR,,S$$B$\::fo%%~eR,,S$$B$111_==fn$$~eR,,S$$B$"aaa-?@@ Lr@c|tj|}g}g}g}t|j|j|D]L\}}}|||f||df|||zMtjj |||d |S)aReturn read-only view into input array with elements repeated. Zoom nD image by integer factors using nearest neighbor interpolation (box filter). Parameters ---------- a : array_like Input array. repeats : sequence of int The number of repetitions to apply along each dimension of input array. Examples -------- >>> repeat_nd([[1, 2], [3, 4]], (2, 2)) array([[1, 1, 2, 2], [1, 1, 2, 2], [3, 3, 4, 4], [3, 3, 4, 4]]) r%F)rk) rbrTrxstridesrjrr[lib stride_tricks as_stridedr)rrepeatsrrjrr<rur;s r>rrq+s,  aAG EGqy!'7331a aV1vq1u 9 " - - 5'U . , ,,3GG,<,<=r@ct|t}|r|n|j}t||kr|Sd|t|z z|z}|r|n||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)rKrrjrSr) data_or_shaperis_shaperjs r>rr+sr"-//H% >MM=+>E 5zzT D3u::% & .E >55-"7"7">">>r@ct|t|krtddtfdt||D\}}t|d|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 matchNrc3HK|]}|ddks |dv|VdSrr:)r;r<rs r>r?zsqueeze_axes..+sD55aQ4!88qtt||'3|||55r@rl)rSrOrxrr)rjrZrs `r>rr+s 5zzSYYDEEE |55553ud#3#35556KE4 << &&r@cD]}||vrtd||d}|j}t|D]}|vr |zd|z}||}|fd|D}|S)zReturn image with its axes permuted to match specified axes. A view is returned if possible. >>> transpose_axes(numpy.zeros((2, 3, 4, 5)), 'TYXC', asaxes='CTZYX').shape (5, 2, 1, 3, 4) z unknown axis NCTZYXrc:g|]}|Sr:r)r;rrZs r>rz"transpose_axes..+s#===TZZ^^===r@)rOrjrr transpose)r|rZasaxesrrjs ` r>rr+s33 V  1R1122 2 ~ KEv!! T>>9D5LE MM% E OO====f=== > >E Lr@ct|}t|}t|t|krtdt|}t|}||krtd|d||r|sdSt dt|t|z }|r|d|zz}t|dz }d}d} g} |ddd D]} || z}|dkr/||dkr#| dkr|dz}|dkr||dkr| dk| ||kr;|| ||zkr,| ||z} | |||dz}|r| |d }| |dt| |dS) zReturn axes matching new shape. By default, unknown dimensions are labelled 'Q'. >>> reshape_axes('YXS', (219, 301, 1), (219, 301)) 'YX' >>> reshape_axes('IYX', (12, 219, 301), (3, 4, 219, 1, 301, 1)) 'QQYQXQ' zaxes do not match shapezcannot reshape r?rlr%rrDNrr)rrSrOrrr[rr) rZrjnewshapeunknownr.newsizelendiffr<prodnsprodsrznss r>rjrj+s %LLEXH 4yyCJJ2333 5>>DhG w@5@@h@@AAA xr!SZZ#h--/00G-dWn, E QA F E Fuu"uo # #" !eeaA "'' FA!eeaA "'' q>>fa(888 U1X E MM$q' " " " FAA  # MM' " " " "G MM' " " " " 778F788,-- . ..r@c vt|}|dkrtd|dkr||d<|djdd|i|Std|Dj}|f|jz}|j}t|||}||dkr|j}t|tj }|dks|j rdx}}n|dkrd}nw|d kr$|j dkr|jdkr|jdkrd}nM|j d kr|jddd krdx}}n&d}n#|dkrdx}}n||ks |jd krd}n|}d}||d<|dkp|dk|jj_t)t+d ||jjj } || |fd} |d kr"t-|D]\} } | | | nV|jt1|5} | | |t5|D]} dddn #1swxYwY| d|jj_|S)zRead data from sequence of TiffPage and stack them vertically. Additional parameters are passsed to the TiffPage.asarray function. r%zno pagesrDr>r=c3K|]}||V dSr9r:)r;r!s r>r?zstack_pages..,s"33qQ]]]]]33r@Nrrrrr)r.rfc|\||jj|jd|jd||d|||jjdSdS)NF)rfryr=r:)rwrr&rTrfr)rxrr= filecacherUs r>r~zstack_pages..func>,sx   NN4;1 2 2 2 DL #inUE  # #! # # # OODK2 3 3 3 3 3  r@r:)rSrOrTrrQrjrcrr>rrrrtr'rWrprrr&rfrrrrr'rlrr")r6r=r>rUrspage0rjrcpage_maxworkersrr~r<rxrnr{s r>rFrF,s  ZZF {{$$$ {{)|uQx22C26222 33E333 3 3 #H_q5HEL 3q*#5#5#(<#:#?AAAI"Yv4444A~~ ''  GAt DqMMMM    + + x\\$uV}}==                  OO#'EL Js(H  H H w+c|tj||St|tr||dddkrnddl}t |dkr |ddnd}|d}|||5}tj||||cdddS#1swxYwYt|tjrrt|t|j krtd tj ||j std ||Stj||||S) 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%rz.memmap)r! suffix)rjrcryzincompatible output shapezincompatible output dtype)rbr@rKrLtempfilerSNamedTemporaryFilerrrrjrOcan_castrcr)r=rjrcryrrtempdirrs r>rrT,s& {{5%(((#sIBQB8 3 3 XX\\#abb''t >F  ( (WV ( D D I<%u4HHH I I I I I I I I I I I I I I I I#u}%%" 5>>WSY// / /899 9~eSY// :899 9{{5!!! <5D A A AAs9BB"%B"c~fddddfd}d|vsd|vri}|D]|}|}|r |dd kr%|d d \}tfd d Drn|||<}|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'] cDdg} |\}}|nt|dkr|dnM|dkr|dn1|dkr|dn||||d}|d|S)Nr Tr>)r?r )r r r?)r?r?)rr[)r tokensrr< next_tokens r>lexzmatlabstr2py..lex,s :a==DAqyCxx j))))c j))))c j)))) a   !""A   c r@c^t|}|dkrdSd}||kr#||dkr|dz }||kr ||dk||krd|fS||dvr |||dzfS||dkr@|dz}||kr#||dkr|dz }||kr ||dk|||dz|dzfS||dkr@|dz}||kr#||dkr|dz }||kr ||dk|||dz|dzfS|}||kr||d vr|dz }||kr ||d v||||fS) Nr%rwr,rDz{[;]}'rrz {[;]}rh)r r:r<rus r>rz matlabstr2py..next_token,sQ Q;;7 &jjQqTS[[ FA&jjQqTS[[ ;;7N Q47??Q4Q;  Q43;;AAf**1Qf**1QAX;A% % Q43;;AAf**1Qf**1QAX;A% % &jj1!1!1 FA&jj1!1!11vqyr@FcsStdkr2 tS#t$r|rt cYSwxYwddkr2|r ddks dddvrt ddSddkr*|r ddks dddvrt S|r)t fddDrt dd krSd vrd Sd vrd SdddkrKt jddddD SdddkrKt j ddddD Sdvsdvr tS#t$rYnwxYw tS#t$rYnwxYw tS#t$r|rt YnwxYwS)NrDr%rrrrc3 K|]}|vV dSr9r:)r;r<r s r>r?z.matlabstr2py..value..,s'221Q222222r@z ';[]{}r)rTrueT)rFalseFrzzeros(c,g|]}t|Sr:rrs r>rz/matlabstr2py..value..,sCCC1ACCCr@rrzones(c,g|]}t|Sr:rrs r>rz/matlabstr2py..value..,sBBB!s1vvBBBr@.r ) rrSrrfrOrMrbr@rwronesr)r fails` r>rzmatlabstr2py..value,s GGII H q66Q;; 1vv    '$,,&  Q43;; #" q2w ll"QrT7N Q43;; #" q2w ll"H  C2222 22222 ,,  Q43;;H  4 " " "5 RaR5H  ;CC!B$ c0B0BCCCDDKKMM M RaR5G  :BBq2w}}S/A/ABBBCCJJLL L !88saxx Qxx     q66M    D  #88O # # # # ll" # # #sE=AAG"" G/.G/3H HHH""H?>H?cj|} |dS#t$rYnwxYwgx}}|g}|D]}|dvrg}|||dvro|}t |dkr*t |dt tfr|d}|d}||||t |dkr*t |dt tfr|d}|S)NT)rz[{z]}rDr%r)rrOr[rJrSrKrrL)r rzadd2levelsrryrrs r>r2zmatlabstr2py..parse,sF GGII 5&&& &    D Q & &ADyy d####dJJLLq66Q;;:adT3K#@#@;!Abz A EE!HH%%%% v;;!   6!9tSk B B AYF s $ 11 r4r%%rrDc3 K|]}|vV dSr9r:)r;rRr;s r>r?zmatlabstr2py..-s'//a16//////r@z ';[]{}<>r)r rrwrM) rn r2rtrrrr;rrrs @@@@r>r r y,s**&6....`2 v~~ %%''  D::<>::c1%%DAq A////;///// 588AaDD 5==r@r cP||}|dkr|n |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' r%N)r)rn r r<s r>rr-s/  DA!ee66&!*,r@c~t|}|r|dz}d||cxkrdkrnnn|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'' rDrrNrh)rn r<s r>rara$-sl F A  Q vay    3         'AE'?r@struersfalserc|}||vrdS||vrdSt)zdReturn string as bool if possible, else raise TypeError. >>> asbool(b' False ') False TF)rr/rF)rrrs r>r.r.:-sC KKMM   ! !E }}t ~~u ++r@c|ttttf}|D]2} ||cS#tt t tf$rY/wxYw|S)zReturn argument as one of types if possible. >>> astype('42') 42 >>> astype('3.14') 3.14 >>> astype('True') True >>> astype(b'Neee-Wom') 'Neee-Wom' )rrr.r`rOrrFUnicodeEncodeError)rr3typs r>rrI-sn }UFI- 3u::   NI7IJ    D  Ls /AAcP||kr|dSdD]}|dz}||kr |dd|cSdS)zReturn file size as string from byte size. >>> format_size(1234) '1234 B' >>> format_size(12345678901) '11.50 GiB' z B)KiBMiBGiBTiBPiBg@z.2fr, ginormousr:)r. thresholdrs r>rr`-se i{{{3((  )  ''''' ' ' '  ;r@c|S)zOSingle argument identity function. >>> identityfunc('arg') 'arg' r:)r/r*rUs r>r r r-s  Jr@cdS)z>> nullfunc('arg', kwarg='kwarg') Nr:)r*rUs r>rr|-s  Fr@cDt|ttfr|n|fS)zReturn tuple containing value if value is not a tuple or list. >>> sequence(1) (1,) >>> sequence([1]) [1] >>> sequence('ab') ('ab',) )rKrrr2s r>rr-s#uudm44 B555(Br@cd}|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 rDr:)iterableprodr<s r>rr-s( D    Kr@cXfd}tjdt||S)zReturn human sorted list of strings. E.g. for sorting file names. >>> natural_sorted(['f1', 'f2', 'f10']) ['f1', 'f2', 'f10'] cBdtj|DS)NcXg|]'}|rt|n|(Sr:)rr)r;rRs r>rz3natural_sorted..sortkey..-s/MMM1199;;-QAMMMr@)rrw)rynumberss r>sortkeyznatural_sorted..sortkey-s#MM!8L8LMMMMr@z(\d+)r{)rrr)rrrs @r>rr-sENNNNNj""G ( ( ( ((r@cr|tjd}|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) NiZ )r fromordinalr6) timestampepochs r>excel_datetimer-s5 }!--f55 8%i00 00r@c <|dkrdS|dz}|dkr(tj|dz dz }|d|z|dzz z }||dkrdnd z}tj|d z d z }tjd |z}tj||z d z }||z tjd |zz }||d krdndz } || dkrdndz } 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) iODNrDi#g@}@g+@rPg@iliki6i`i)rtruncror) julianday milisecondrrrrRrtr r r r r r seconds r>roro-sVGtA A7{{ A Nh677 QY! ## Q[[TTd+A AI'((A 6A:A AEW$%%A a%$*Wq[)) )C a$hhB 'E   .Dj.99D* I66FJ D11FJ  T5#!66: ? ??r@c|dtjfvrdSddd}||||tjkS)zcReturn if byteorder matches the system's byteorder. >>> byteorder_isnative('=') True rTrr)bigr)rr]rE)r]r\s r>rArA-sHS#-(((t# & &D 88Iy ) )T#--@ @@r@ci}t|jj|D]_\}}|dd\}}|ddkrtt |}n|jdkr|}|||<`|S)zReturn numpy.recarray as dict.NrrDr)rxrcdescrr`rrr)recarrayrzrrr,rcs r>rY rY -sFHN0(;; uBQBi e 8s??i..//EE Z!^^LLNNEt Mr@cddlm}dx|r|\dfd||S)zReturn XML as dict. >>> xml2dict('1') {'root': {'key': 1, 'attr': 'name'}} >>> xml2dict('3.5322') {'level1': {'level2': 3.5322}} r%rrlct|ttfs|Sttt fD]} ||cS#t $rYwxYw|Sr9)rKrLrrrr.rf)rrs r>rzxml2dict..astype.sn%#u.. Luf%  A qxx     s A AAc|j} r|ddd}||jrindi}t|}|rt jt}t |D]@}|D])\}}|| |*A| fd|Di}|jr?|| fd|jD|j rJ|j }|s|jr|r ||| dz<n |||<|S)NrrDrcvi|]5\}}|t|dkr|dn |6S)rDr%rh)r;r;rrs r>rH z0xml2dict..etree2dict..'.sU///1a#a&&A++&&1,,,66!99///r@c3>K|]\}}|z|fVdSr9r:)r;r;rrats r>r?z/xml2dict..etree2dict..*.s8KK$!Q2666!99-KKKKKKr@r) rr%rr collections defaultdictrlrr[rqrr)rr7rtchildrendddcr;rrrr  etree2dictsanitizers r>rzxml2dict..etree2dict.se  )**S!$$R(C *""d +77  0(..B*h// , ,HHJJ,,DAqqELL++++,////#%88::///0A 8 L cFMMKKKKK!(..:J:JKKK K K K 6 &6<<>>D &18 &8+16$<rr.s/.....LB B   2 :e&&s++ , ,,r@Kr rrc (t|}|dks |dks|dkrdS|dkr6d}t||t|z dz|zz|}|dkrdSd} nldtd|zz}t||t|dzz dz|zz|}|dkrdSd|zt|dzz}|dz |zdz} ||dkr|}nAd t|cxkrdkr'nn$tt j||z}|d kr||z }|dks| dkrd |d |fg} d}d}d|z}n|| |krd |fg} nr|d kr|| |z z} | || d fg} nV||ks|dkr||z} d |d | fg} n7||z} |||z dz z}d |d | f|| z |z d f||z |||z d fg} |d n|d }g}| D]\} }|||tj |}tj d d|}td t||D]}|d|zd|z|dzz|dkr||| zzn|}|d fdtd d|zdDz }|d|t|z zz }|||||zz }||d |}|d}|S)zReturn hexdump representation of bytes. >>> hexdump(binascii.unhexlify('49492a00080000000e00fe0004000100')) '49 49 2a 00 08 00 00 00 0e 00 fe 00 04 00 01 00 II*.............' rDrrlr@rs%%0%ix: s%xrNr%...cp1252s [^\x20-\x7f]. c32K|]}||dzVdS)rNr:)r;r<rTs r>r?zhexdump..y.s/NN11QAX;NNNNNNr@ r )rSrabsrrrrr[binasciihexlifyrsubrrr)rr;r?snipatrellipsisr.addr bytesperlinenlinesr rr)end1end2rzhexstrstrstrr<rrTs @r>hexdumpr+7.s w<6%IJ!! !  2S...6us4!8}}'<&Bv%MN!! !  2L 3tax==0(|+a/ ~1 S[[    1     TZ0011 zz& {{fkkgm|m,-.L  6V++g, 10'%&&/*+ 6  VaZZV#gdsdm$%f$v23   D[4  & D['$+,,/ 0  ")vvxx/H/HH F  w ? MM( # # # !'**($88q#g,, 55  Aq1ua!elQ&6667A(. U##A NNNNa\9I10M0MNNNNN NA Q( (A 1|++, ,A MM!      ZZ  F ]]7 # #F Mr@c|}|sdS |S#t$rYnwxYw |S#t$rYdSwxYw)zReturn if all characters in string are printable. >>> isprintable('abc') True >>> isprintable(b'') False TN)r isprintablerfr)rn s r>r-r-.s\\^^F t !!###       }}**,,,      s. ;;%A%% A32A3cdD]\}}|||}|rdD]\}}|||}|S)z)Return string with compressed whitespace.))r)r4)rr4)r@r4) r,r2r,))r4r,)z[ r r0r0r0)rr)rn compactrrs r>clean_whitespacer2.sp&&11%%*  * *DAq^^Aq))FF <<>>r@c ddlm}t|ts|}|t j|}||dd|j j }t|}nJ#t$r=t|trt|}| dd}YnwxYw| dd d dS) zReturn pretty formatted XML.r%)rT) pretty_printxml_declarationencodingz> pformat_xmlr:.s (#u%% **,,Ckk"*S//**nnStT&)k&:<<nn ((( c5 ! ! !C..Ckk$''( ;;tS ! ! ) )$ 4 44sBB ACCr)cD||dkrd}||dkrd}tj}tjd|t|tt fr|dddvrHt|t rt|}|dkr|dd |z}nwt|}ngt|t rRt|rt|}t|}n$tjdi|t|||d S| }nKt|tj r|}nd dl}|||| }tjdi||dkrt|d }|d|St!|}t%||kr3d|d|dzdgz|| dzdz}|S)zcReturn pretty formatted representation of object as string. Whitespace might be altered. NrDr rJr)r linewidthr)zrr.s- ~! }   " $ $E SE::::#U|$$@ rr7==??1 1 1#u%% %nn{{+AI+&!#&& U # # J3 Jnn&s++&/////s%qIIIIjjll C & &@jjll nnSwn?? ##U### {{sD1116E6{   ! !D 4yy6ii\fk\*eW4tVGqLMM7JJKK Jr@cB|d}|t|trd}nd}t|}|}g}|D]}|||t|}||kr||F|} | | dkr|} nAdt | cxkrdkr'nn$t tj|| z} | dkr | |z } | dkrd} |dks ||dzkrC| dkr||| d||d|| dkr%|||||z dz$| |ks ||dzkr%||d||z |zX||z |z} | | dzz } | | z} ||d| |z|| dzt|trd |Sd |S) zcReturn string cut to specified length. >>> snipstr('abcdefghijklmnop', 8) 'abc...op' N?ru…rDr%rrrr4) rKrrSr r[rrrrr) rn r;r"r#r r rzrrlinelenrwsplitlenr'r(s r>rDrD.s~~ fe $ $ HHH MME""$$JF D D < MM( # # # d)) e   MM& ! ! !  =EQJJEE U    a      7U?3344E 199 W Eqyy A::**zz feVWWo.... fVeVn---- aZZ MM(VEEMNN%;; < < < < g  !2!2 MM&%%-08; < < < <.H8q=(D(?D MM&$-(2VDEE]B C C C C&%  "zz&!!! 99V  r@c6|j}|t|}|S)z4Return short string representation of Enum instance.)r,rL)r r,s r>rnrn,/s 9D |4yy Kr@c ||S#t$r> ||cYS#t$rtd|wxYwwxYw)zReturn enum member from its name or value. >>> enumarg(TIFF.PHOTOMETRIC, 2) >>> enumarg(TIFF.PHOTOMETRIC, 'RGB') zinvalid argument )rfrrO)r r/s r>rr4/s8tCyy 888 8 $ $ $ $ 8 8 866677 7 88s A4AAAci}|D]}||vr||||<||=|D]\}}||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)rUr\ keyvaluesrzr7rs r>r!r!F/sF &== +F3Ks oo''  U &== +F3Ks F3KK Mr@c L|D]\}}||vr|||<dS)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)rUrIr7rs r>r r a/s@ oo''  U f  F3K  r@c`ddl}|tj|g|Ri|dS)zLog message with level WARNING.r%N)logging getLoggerrwarning)r3r*rUrLs r>rro/sBNNN'Gh'=d===f=====r@cPddl}|dg}|d}|||ddg}d|vry|D]f}|}|dr9|dd}|D]}||vrn t |dSedSdS) 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. 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Return figure, subplot and plot axis. Requires pyplot already imported C{from matplotlib import pyplot}. Parameters ---------- data : nd array The image data. photometric : {'MINISWHITE', 'MINISBLACK', 'RGB', or 'PALETTE'} The color space of the image data. planarconfig : {'CONTIG' or 'SEPARATE'} Defines how components of each pixel are stored. bitspersample : int Number of bits per channel in integer RGB images. interpolation : str The image interpolation method used in matplotlib.imshow. By default, 'nearest' will be used for image dimensions <= 512, else 'bilinear'. cmap : str or matplotlib.colors.Colormap The colormap maps non-RGBA scalar data to colors. vmin, vmax : scalar Data range covered by the colormap. By default, the complete range of the data is covered. figure : matplotlib.figure.Figure Matplotlib figure to use for plotting. title : str Window and subplot title. subplot : int A matplotlib.pyplot.subplot axis. maxdim : int Maximum image width and length. kwargs : dict Additional arguments for matplotlib.pyplot.imshow. 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