Ejk;dZddlmZddlmZmZmZmZddlZddl Z ddl Z ddl m Z mZmZddlmZmZddlmZd e j(d eeeffd ZGd d eZy)aRead/Write TIFF files using tifffile. .. note:: To use this plugin you need to have `tifffile `_ installed:: pip install tifffile This plugin wraps tifffile, a powerful library to manipulate TIFF files. It superseeds our previous tifffile plugin and aims to expose all the features of tifffile. The plugin treats individual TIFF series as ndimages. A series is a sequence of TIFF pages that, when combined describe a meaningful unit, e.g., a volumetric image (where each slice is stored on an individual page) or a multi-color staining picture (where each stain is stored on an individual page). Different TIFF flavors/variants use series in different ways and, as such, the resulting reading behavior may vary depending on the program used while creating a particular TIFF file. Methods ------- .. note:: Check the respective function for a list of supported kwargs and detailed documentation. .. autosummary:: :toctree: TifffilePlugin.read TifffilePlugin.iter TifffilePlugin.write TifffilePlugin.properties TifffilePlugin.metadata Additional methods available inside the :func:`imopen ` context: .. autosummary:: :toctree: TifffilePlugin.iter_pages )BytesIO)AnyDictOptionalcastN) URI_BYTESInitializationErrorRequest)ImagePropertiesPluginV3) ArrayLikepagereturnc|i} |jdjj|d< |jdj}|jdj}|d|dz |d|dz f|d<|S#t$r|cYSwxYw#t$rY|St$rt j dt Y|SwxYw) Ni(resolution_unitiir resolutionzPIgnoring resolution metadata because at least one direction has a 0 denominator.)tagsvalueKeyErrorZeroDivisionErrorwarningswarnRuntimeWarning)rmetadata resolution_x resolution_ys Y/root/workspace/ytshorts/venv/lib/python3.12/site-packages/imageio/plugins/tifffile_v3.py_get_resolutionr :sH&*iin&:&:&@&@"#  yy~++ yy~++  Ol1o - Ol1o -"  O-     O      O s)&A8A B 8 BB B;"B;:B;c eZdZdZdeddffd Zddddededejfd Z dejfd Z d d d e de de efdZeddddedede deeeffdZddddededefdZdfd ZddZxZS)TifffilePluginaSupport for tifffile as backend. Parameters ---------- request : iio.Request A request object that represents the users intent. It provides a standard interface for a plugin to access the various ImageResources. Check the docs for details. kwargs : Any Additional kwargs are forwarded to tifffile's constructor, i.e. to ``TiffFile`` for reading or ``TiffWriter`` for writing. requestrNc dt||d|_|jjdk(r+ t j |jfi||_yt j|jfi||_y#t j j$r tdwxYw)Nrz Tifffile can not read this file.) super__init___fhmodeio_modetifffileTiffFileget_file TiffFileErrorr TiffWriter)selfr#kwargs __class__s rr'zTifffilePlugin.__init__gs ! <<  3 & N#,,W-=-=-?J6J **7+;+;+=HHDH$$22 N)*LMM Ns )B)B/)indexrr3rc hd|vr||d<n | td|d|vr tdd|vr|jd}n|nd}|tur7|5tj|j di|Dcgc]}|c}}|S|turdn|}|j jdd|i|}|Scc}w)aRead a ndimage or page. The ndimage returned depends on the value of both ``index`` and ``page``. ``index`` selects the series to read and ``page`` allows selecting a single page from the selected series. If ``index=None``, ``page`` is understood as a flat index, i.e., the selection ignores individual series inside the file. If both ``index`` and ``page`` are ``None``, then all the series are read and returned as a batch. Parameters ---------- index : int If ``int``, select the ndimage (series) located at that index inside the file and return ``page`` from it. If ``None`` and ``page`` is ``int`` read the page located at that (flat) index inside the file. If ``None`` and ``page=None``, read all ndimages from the file and return them as a batch. page : int If ``None`` return the full selected ndimage. If ``int``, read the page at the selected index and return it. kwargs : Any Additional kwargs are forwarded to TiffFile's ``as_array`` method. Returns ------- ndarray : np.ndarray The decoded ndimage or page. keyNz,Can't use `page` and `key` at the same time.seriesz0Can't use `series` and `index` at the same time.r) ValueErrorpopEllipsisnpstackiterr(asarray)r0r3rr1xndimages rreadzTifffilePlugin.readws<   F5M  KL L  V!3OP P  JJx(E   E H hh9499+>v+>?a?@G "X-D5E&dhh&&>e>v>G @s1 B/c+jK|jjD]}|jdi|yw)a!Yield ndimages from the TIFF. Parameters ---------- kwargs : Any Additional kwargs are forwarded to the TiffPageSeries' ``as_array`` method. Yields ------ ndimage : np.ndarray A decoded ndimage. Nr7)r(r6r>)r0r1sequences rr=zTifffilePlugin.iters5 -H"("",V, , -s13F)is_batchr@rDc |stj|dddf}|D]}t|}tj|}|jdk\r$|jddvr|j ddnD|jdk\r5|jddvr$|j dd|j dd |j j|fi||jjtk(rR|j jtt|jj}|jSy) aCSave a ndimage as TIFF. Parameters ---------- ndimage : ArrayLike The ndimage to encode and write to the ImageResource. is_batch : bool If True, the first dimension of the given ndimage is treated as a batch dimension and each element will create a new series. kwargs : Any Additional kwargs are forwarded to TiffWriter's ``write`` method. Returns ------- encoded_image : bytes If the ImageResource is ``""``, return the encoded bytes. Otherwise write returns None. Notes ----- Incremental writing is supported. Subsequent calls to ``write`` will create new series unless ``contiguous=True`` is used, in which case the call to write will append to the current series. When ``photometric`` / ``planarconfig`` are omitted, ImageIO sets defaults for common RGB layouts so tifffile does not emit deprecation warnings about ambiguous channel-axis interpretation: - channel-last arrays (shape ``(..., 3)`` or ``(..., 4)``): ``photometric="rgb"`` - channel-first arrays (shape ``(3, ...)`` or ``(4, ...)`` on the third-to-last axis): ``photometric="rgb"`` and ``planarconfig="separate"`` N)rF photometricrgb planarconfigseparate)r;r>dictndimshape setdefaultr(write_request _uri_typer closerrr-getvalue)r0r@rDr1image write_kwargsarrfiles rrRzTifffilePlugin.writes Ljj)$'2G 2E  T%5XX__U+11$7F ( "t|XX__U+11!4F h 4#3XX^^D)FF >$(HH$6$6H[ ! 00 9$TXXut|< )3&'$((D;4F"G&-dhh{8J&KO!/59 (:; 8 9:#__F OOFKKHSSXXsyy0H I OO,2,?,?#)#5#5!'!1!1#'$*$7$7#)#5#5 & &f-   Is9Hc |xsd}|dtfvrdn|}|tur|jj|}n&|jj|j|}|turc|at |jj}t |g|j |j|dt|jd}|S|turi|turat |jj}t |g|j |j|dt|jd}|St |j |jdt|jd}|S)aStandardized metadata. The properties returned depend on the value of both ``index`` and ``page``. ``index`` selects a series and ``page`` allows selecting a single page from the selected series. If ``index=Ellipsis``, ``page`` is understood as a flat index, i.e., the selection ignores individual series inside the file. If ``index=Ellipsis`` and ``page=None`` then global (file-level) properties are returned. If ``index=Ellipsis`` and ``page=...``, file-level properties for the flattened index are returned. Parameters ---------- index : int If ``int``, select the ndimage (series) located at that index inside the file. If ``Ellipsis`` and ``page`` is ``int`` extract the properties of the page located at that (flat) index inside the file. If ``Ellipsis`` and ``page=None``, return the properties for the batch of all ndimages in the file. page : int If ``None`` return the properties of the full ndimage. If ``...`` return the properties of the flattened index. If ``int``, return the properties of the page at the selected index only. Returns ------- image_properties : ImageProperties The standardized metadata (properties) of the selected ndimage or series. rNTr)rPdtypen_imagesrDspacingF)rPryrDr{) r:r(rir6lenr rPryr get)r0r3rpage_idx target_pagen_seriespropsn_pagess r propertieszTifffilePlugin.propertiesEs[> x 001d H ((..2K((//%066x@K H 488??+H#4+"3"34!''!' 488F E0 #h 48#3$((..)G#3!2!23!'' ' 488F E $!''!''' 488F E r[cn|j|jjt|y)N)r(rUr&)r0r2s rrUzTifffilePlugin.closes$ 88  HHNN   r[c+K|tur|jj}n|jj|}|D]}|jdi|yw)a7Yield pages from a TIFF file. This generator walks over the flat index of the pages inside an ImageResource and yields them in order. Parameters ---------- index : int The index of the series to yield pages from. If Ellipsis, walk over the file's flat index (and ignore individual series). kwargs : Any Additional kwargs are passed to TiffPage's ``as_array`` method. Yields ------ page : np.ndarray A page stored inside the TIFF file. Nr7)r:r(rir6r>)r0r3r1rirs r iter_pageszTifffilePlugin.iter_pagessR* H HHNNEHHOOE*E )D$,,(( ( )sAA)rN).)__name__ __module__ __qualname____doc__r r'intr;ndarrayrAr=rboolrbytesrRr:rstrrrr rrUr __classcell__)r2s@rr"r"Xs  I Id I $(T4S4s4 4l- -&7<6# 6#/36# %6#r'DRVLL.1LKOL c3hL\*.4A3ASAOAF)r[r")riortypingrrrrrnumpyr;r+ core.requestr r r core.v3_plugin_apir r rTiffPagerr r"r7r[rrsZ+Z,,BB:(++S#X