2?jk;dZddlmZddlmZmZmZmZddlZddl Z ddl Z ddl m Z mZmZddlmZmZddlmZd e jd eeeffd ZGd d eZdS)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) ArrayLikepagereturncfi} |jdjj|d<n#t$r|cYSwxYw |jdj}|jdj}|d|dz |d|dz f|d<n5#t$rYn)t$rt jdt YnwxYw|S) Ni(resolution_unitiir resolutionzPIgnoring resolution metadata because at least one direction has a 0 denominator.)tagsvalueKeyErrorZeroDivisionErrorwarningswarnRuntimeWarning)rmetadata resolution_x resolution_ys LC:\Projects\Historical\venv\Lib\site-packages\imageio/plugins/tifffile_v3.py_get_resolutionr :sH&*in&:&@"##  y~+ y~+  Ol1o - Ol1o -"                    Os$ ..A A<< 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 pt|d|_|jjdkrS t j|fi||_dS#t jj$rtdwxYwt j |fi||_dS)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-=-=-?-?JJ6JJ$2 N N N)*LMMM N *7+;+;+=+=HHHHDHHHs )A&&$B )indexrr3rc Pd|vr||d<n|td|d|vrtdd|vr|d}n|nd}|tur,|*tjd|jdi|D}n!|turdn|}|jjdd|i|}|S) 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.rcg|]}|Sr8).0xs r z'TifffilePlugin.read..s???a???r8) ValueErrorpopEllipsisnpstackiterr(asarray)r0r3rr1ndimages rreadzTifffilePlugin.readws<    F5MM  KLL L  V!3!3OPP P   JJx((EE   E H  h??949+>+>v+>+>???@@GG!X--DD5E&dh&>>e>v>>Gr<c+FK|jjD]}|jdi|VdS)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. Nr8)r(r6rC)r0r1sequences rrBzTifffilePlugin.itersG - -H"(",,V,, , , , , - -r<F)is_batchrDrHc |stj|dddf}|D]}t|}tj|}|jdkr&|jddvr|ddnF|jdkr;|jddvr,|dd|dd |jj|fi||jj tkrY|j tt|j}|SdS) 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)rJ photometricrgb planarconfigseparate)r@rCdictndimshape setdefaultr(write_request _uri_typer closerrr-getvalue)r0rDrHr1image write_kwargsarrfiles rrVzTifffilePlugin.writesAL 3j))$'2G 2 2E<z+TifffilePlugin.metadata..4sHHHSSXsyHHHr<)planar_configuration compression predictor orientation description1 descriptionsoftwaredatetime)r?r(r6pagesrar+TIFF FILE_FLAGSgetattrhasattr isinstancetupleupdatekeyframerrPrirjrlrmrnr ro) r0r3rr_targetrflag flag_valueflavor_metadatas rrzTifffilePlugin.metadatas>  T%5X_U+1$7FF ( " "t|X_U+1!4FF h  4#3X^D)FFF >$(H$6H[ ! 0 9 9$TXut|<< )3&9'$(D;4F"G"G9&-dh{8J&K&KO!/5999 (:;;;; 888 9_F OOHHFKHHH I I I OO,2,?#)#5!'!1#'$*$7#)#5 &  &f--      r<c |pd}|dtfvrdn|}|tur|jj|}n|jj|j|}|tur^|\t |jj}t |g|jR|j|dt| d}n|ture|tur\t |jj}t |g|jR|j|dt| d}n=t |j|jdt| d}|S)aStandardized metadata. The properties returned depend on the value of both ``index`` and ``page``. ``index`` selects a series and ``page`` allows selecting a single page from the selected series. If ``index=Ellipsis``, ``page`` is understood as a flat index, i.e., the selection ignores individual series inside the file. If ``index=Ellipsis`` and ``page=None`` then global (file-level) properties are returned. If ``index=Ellipsis`` and ``page=...``, file-level properties for the flattened index are returned. Parameters ---------- index : int If ``int``, select the ndimage (series) located at that index inside the file. If ``Ellipsis`` and ``page`` is ``int`` extract the properties of the page located at that (flat) index inside the file. If ``Ellipsis`` and ``page=None``, return the properties for the batch of all ndimages in the file. page : int If ``None`` return the properties of the full ndimage. If ``...`` return the properties of the flattened index. If ``int``, return the properties of the page at the selected index only. Returns ------- image_properties : ImageProperties The standardized metadata (properties) of the selected ndimage or series. rNTr)rTdtypen_imagesrHspacingF)rTr~rHr) r?r(rpr6lenr rTr~r get)r0r3rpage_idx target_pagen_seriespropsn_pagess r propertieszTifffilePlugin.propertiesEs{> x 00011d H  (.2KK(/%06x@K H  48?++H#4+"344!'!' 4488FF EEh  48#3#3$(.))G#3!233!' ' 4488FF EE$!'!'' 4488FF E r<c|j|jtdS)N)r(rYr&)r0r2s rrYzTifffilePlugin.closes2 8  HNN     r<.c+K|tur |jj}n|jj|}|D]}|jdi|VdS)a7Yield pages from a TIFF file. This generator walks over the flat index of the pages inside an ImageResource and yields them in order. Parameters ---------- index : int The index of the series to yield pages from. If Ellipsis, walk over the file's flat index (and ignore individual series). kwargs : Any Additional kwargs are passed to TiffPage's ``as_array`` method. Yields ------ page : np.ndarray A page stored inside the TIFF file. Nr8)r?r(rpr6rC)r0r3r1rprs r iter_pageszTifffilePlugin.iter_pagessf* H  HNEEHOE*E ) )D$,(((( ( ( ( ( ) )r<)rN).)__name__ __module__ __qualname____doc__r r'intr@ndarrayrErBrboolrbytesrVr?rstrrrr rrYr __classcell__)r2s@rr"r"Xs   I Id I I I I I I $(T444S4s4 4444l- ----&7<6#6#6# 6#/36# %6#6#6#6#r'DRVLLLL.1LKOL c3hLLLL\*.4AAA3ASAOAAAAF))))))))r<r")riortypingrrrrrnumpyr@r+ core.requestr r r core.v3_plugin_apir r rTiffPagerr r"r8r<rrs++Z,,,,,,,,,,,,BBBBBBBBBB::::::::(+S#X