U a+d8@sdZddlmZddlmZmZmZmZddlZddl Z ddl Z ddl Z ddl mZmZmZddlmZmZddlmZd d Zd d ZGd ddeZdS)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 powerfull 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) ArrayLikecCsi}d|jkr |jdjj|d<d|jkrd|jkrd|jkr|jdj}|jdj}|ddksn|ddkr|tdtn$|d|d|d|df|d<|S) z,Get the resolution in a py3.7 compatible wayi(Zresolution_unitiirzQIgnoring resulution metadata, because at least one direction has a 0 denominator. resolution)tagsvaluewarningswarnRuntimeWarning)pagemetadataZ resolution_xZ resolution_yr?/tmp/pip-unpacked-wheel-xbmu82vq/imageio/plugins/tifffile_v3.py_get_resolution;s   rcCs<i}ztj|jdjd|d<Wntk r6YnX|S)z/Get the datetime in a python 3.7 compatible wayi2z%Y:%m:%d %H:%M:%Sdatetime)rstrptimerrKeyError)rrrrr _get_datatimeZs  rcseZdZdZeddfdd Zdddeeejddd Z ejd d d Z d de e e edddZedddeee eeefdddZdddeeedddZdd fdd ZdddZZS)TifffilePluginaSupport for tifffile as backend. Parameters ---------- request : iio.Request A request object that represents the users intent. It provides a standard interface for a plugin to access the various ImageResources. Check the docs for details. kwargs : Any Additional kwargs are forwarded to tifffile's constructor, i.e. to ``TiffFile`` for reading or ``TiffWriter`` for writing. N)requestreturnc srt|d|_|jjdkrZztj|f||_Wqntjjk rVt dYqnXntj |f||_dS)Nrz Tifffile can not read this file.) super__init___fhmodeZio_modetifffileZTiffFileget_fileZ TiffFileErrorr Z TiffWriter)selfrkwargs __class__rrr#{s  zTifffilePlugin.__init__)indexr)r,rr cKsd|kr||d<n|dk r"td|dk rsz'TifffilePlugin.read..) ValueErrorpopEllipsisnpstackiterr$asarray)r(r,rr)ndimagerrrreads    zTifffilePlugin.read)r cks |jjD]}|jf|VqdS)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. N)r$r.r8)r(r)sequencerrrr7s zTifffilePlugin.iterF)is_batch)r9r<r cKsf|st|dddf}|D]}|jj|f|q|jjtkrb|jtt |j }| SdS)a_Save a ndimage as TIFF. Parameters ---------- ndimage : ArrayLike The ndimage to encode and write to the ImageResource. is_batch : bool If True, the first dimension of the given ndimage is treated as a batch dimension and each element will create a new series. kwargs : Any Additional kwargs are forwarded to TiffWriter's ``write`` method. Returns ------- encoded_image : bytes If the ImageResource is ``""``, return the encoded bytes. Otherwise write returns None. Notes ----- Incremental writing is supported. Subsequent calls to ``write`` will create new series unless ``contiguous=True`` is used, in which case the call to write will append to the current series. N) r5r8r$write_requestZ _uri_typercloserrr'getvalue)r(r9r<r)imagefilerrrr=s  zTifffilePlugin.writeT)r,rexclude_applied)r,rrCr c CsJ|tk r$|dk r$|jj|j|}nF|tk rH|dkrH|jj|jd}n"|tkrf|dk rf|jj|}nd}i}|dkr|jj|d<tjjD]h}t|jd|}||d|<|rt |j|drt|j|d}t |t r| |dq| |qnP|j }| dd|jD| |j|j|jd|j|j|jdt|t||S) asFormat-Specific TIFF metadata. The metadata returned depends 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) metadata is returned. Parameters ---------- index : int Select the series of which to extract metadata from. If Ellipsis, treat page as a flat index into the file's pages. page : int If not None, select the page of which to extract metadata from. If None, read series-level metadata or, if ``index=...`` global, file-level metadata. exclude_applied : bool For API compatibility. Currently ignored. Returns ------- metadata : dict A dictionary with information regarding the tiff flavor (file-level) or tiff tags (page-level). Nr byteorderis_ _metadatacSsi|]}|j|jqSr)namer)r/tagrrr 8sz+TifffilePlugin.metadata..)Zplanar_configuration compression predictorZ orientation description1 descriptionsoftware)r4r$r.pagesrDr&ZTIFFZ FILE_FLAGSgetattrhasattr isinstancetupleupdateZkeyframerZ planarconfigrJrKrLrMrNrr) r(r,rrCtargetrflag flag_valueZflavor_metadatarrrrsD     zTifffilePlugin.metadatacCs|pd}|pd}|tkr&|jj|}n|jj|j|}|tkrx|dkrxt|jj}t|f|j|jdt|dd}nt|j|jdt|dd}|S)aStandardized metadata. The properties returned depend on the value of both ``index`` and ``page``. ``index`` selects a series and ``page`` allows selecting a single page from the selected series. If ``index=Ellipsis``, ``page`` is understood as a flat index, i.e., the selection ignores individual series inside the file. If ``index=Ellipsis`` and ``page=None`` then global (file-level) properties is returned. Parameters ---------- index : int If ``int``, select the ndimage (series) located at that index inside the file. If ``Ellipsis`` and ``page`` is ``int`` extract the properties of the page located at that (flat) index inside the file. If ``Ellipsis`` and ``page=None``, return the properties for the batch of all ndimages in the file. page : int If ``None`` return the properties of the full ndimage. If ``int``, return the properties of the page at the selected index only. Returns ------- image_properties : ImageProperties The standardized metadata (properties) of the selected ndimage or series. rNTr)shapedtyper<spacingF) r4r$rOr.lenr rXrYr)r(r,rZpage_idxZ target_pageZn_seriespropsrrr propertiesJs(    zTifffilePlugin.propertiescs"|jdk r|jtdS)N)r$r?r")r(r*rrr?s  zTifffilePlugin.close.cks:|tkr|jj}n |jj|}|D]}|jf|Vq"dS)a7Yield pages from a TIFF file. This generator walks over the flat index of the pages inside an ImageResource and yields them in order. Parameters ---------- index : int The index of the series to yield pages from. If Ellipsis, walk over the file's flat index (and ignore individual series). kwargs : Any Additional kwargs are passed to TiffPage's ``as_array`` method. Yields ------ page : np.ndarray A page stored inside the TIFF file. N)r4r$rOr.r8)r(r,r)rOrrrr iter_pagess   zTifffilePlugin.iter_pages).)__name__ __module__ __qualname____doc__r r#intr5Zndarrayr:r7r boolrbytesr=r4rstrrrr r]r?r^ __classcell__rrr*rrls,6 ) O6 r)rbiortypingrrrrrrZnumpyr5r&Z core.requestrr r Zcore.v3_plugin_apir r r rrrrrrrs-