o :ήc8@sdZddlZddlmZddlZddlmZddlmZddlmZddl Z ddl m Z m ZeeedkrDdd lmZed d d dd lmZgdZddZddZddZGdddeZddZGdddeZdS)zEData structures to hold collections of images, with optional caching.N)glob)Sequence)copy)version)Image __version__z8.1.2)warnzYour installed pillow version is < 8.1.2. Several security issues (CVE-2021-27921, CVE-2021-25290, CVE-2021-25291, CVE-2021-25293, and more) have been fixed in pillow 8.1.2 or higher. We recommend to upgrade this library.) stacklevel)TiffFile) MultiImageImageCollectionconcatenate_imagesimread_collection_wrappercCs6dd|D}zt|}W|Stytdw)auConcatenate all images in the image collection into an array. Parameters ---------- ic : an iterable of images The images to be concatenated. Returns ------- array_cat : ndarray An array having one more dimension than the images in `ic`. See Also -------- ImageCollection.concatenate, MultiImage.concatenate Raises ------ ValueError If images in `ic` don't have identical shapes. Notes ----- ``concatenate_images`` receives any iterable object containing images, including ImageCollection and MultiImage, and returns a NumPy array. cSsg|] }|tjdfqS).)npnewaxis).0imager:z&concatenate_images..zImage dimensions must agree.)r concatenate ValueError)ic all_images array_catrrrrs  rcCsddtd|D}|S)aAConvert string to list of strings and ints that gives intuitive sorting. Parameters ---------- s : string Returns ------- k : a list of strings and ints Examples -------- >>> alphanumeric_key('z23a') ['z', 23, 'a'] >>> filenames = ['f9.10.png', 'e10.png', 'f9.9.png', 'f10.10.png', ... 'f10.9.png'] >>> sorted(filenames) ['e10.png', 'f10.10.png', 'f10.9.png', 'f9.10.png', 'f9.9.png'] >>> sorted(filenames, key=alphanumeric_key) ['e10.png', 'f9.9.png', 'f9.10.png', 'f10.9.png', 'f10.10.png'] cSs g|] }|r t|n|qSr)isdigitint)rcrrrrXs z$alphanumeric_key..z([0-9]+))resplit)skrrralphanumeric_keyBsr$cCsPt|to tj|v}t|t }t|t}tdd|D}|p%|o%|o%|}|S)zlHelping function. Returns True if pattern contains a tuple, list, or a string separated with os.pathsep.css|]}t|tVqdSN) isinstancestr)rpatrrr dsz#_is_multipattern..)r&r'ospathseprall) input_patternhas_str_ospathsep not_a_string has_iterable has_stringsis_multipatternrrr_is_multipattern\s   r3c@steZdZdZdddZeddZedd Zd d Zd d Z ddZ ddZ ddZ ddZ dddZddZdS)r aLoad and manage a collection of image files. Parameters ---------- load_pattern : str or list of str Pattern string or list of strings to load. The filename path can be absolute or relative. conserve_memory : bool, optional If True, `ImageCollection` does not keep more than one in memory at a specific time. Otherwise, images will be cached once they are loaded. Other parameters ---------------- load_func : callable ``imread`` by default. See notes below. Attributes ---------- files : list of str If a pattern string is given for `load_pattern`, this attribute stores the expanded file list. Otherwise, this is equal to `load_pattern`. Notes ----- Note that files are always returned in alphanumerical order. Also note that slicing returns a new ImageCollection, *not* a view into the data. ImageCollection can be modified to load images from an arbitrary source by specifying a combination of `load_pattern` and `load_func`. For an ImageCollection ``ic``, ``ic[5]`` uses ``load_func(load_pattern[5])`` to load the image. Imagine, for example, an ImageCollection that loads every third frame from a video file:: video_file = 'no_time_for_that_tiny.gif' def vidread_step(f, step): vid = imageio.get_reader(f) seq = [v for v in vid.iter_data()] return seq[::step] ic = ImageCollection(video_file, load_func=vidread_step, step=3) ic # is an ImageCollection object of length 1 because there is 1 file x = ic[0] # calls vidread_step(video_file, step=3) x[5] # is the sixth element of a list of length 8 (24 / 3) Another use of ``load_func`` would be to convert all images to ``uint8``:: def imread_convert(f): return imread(f).astype(np.uint8) ic = ImageCollection('/tmp/*.png', load_func=imread_convert) Examples -------- >>> import skimage.io as io >>> from skimage import data_dir >>> coll = io.ImageCollection(data_dir + '/chess*.png') >>> len(coll) 2 >>> coll[0].shape (200, 200) >>> ic = io.ImageCollection(['/tmp/work/*.png', '/tmp/other/*.jpg']) TNcKsg|_t|r t|tr|tj}|D] }|jt|qnt|tr.|jt|nt dt |jt d|_|durMddl m }||_||_n ||_t|j|_d|_|r^d}n|j}||_d|_||_tj|td|_dS)z'Load and manage a collection of images.zInvalid pattern as input.)keyNimreaddtype)_filesr3r&r'r!r*r+extendr TypeErrorsortedr$_ior7 load_func _find_images _numframeslen _frame_index_conserve_memory_cachedload_func_kwargsremptyobjectdata)self load_patternconserve_memoryr?rFpatternr7 memory_slotsrrr__init__s2      zImageCollection.__init__cC|jSr%r:rJrrrfileszImageCollection.filescCrPr%)rDrRrrrrLrTzImageCollection.conserve_memoryc s g}|jD]xdr8td}t|}|fddtt|jD7}Wdn1s2wYqz t}| dWn t t fyOYqwd} z| |Wn t ycYn w| |f|d7}qSt|dr}|jr}|jq||_t|S) N)z.tiffz.tifrbcsg|]}|fqSrrrifnamerrrsz0ImageCollection._find_images..rTr5fp)r:lowerendswithopenr rangerBpagesrseekIOErrorOSErrorEOFErrorappendhasattrrZcloserC)rJindexfimgimrWrrXrr@s:  "   zImageCollection._find_imagesc st|dr |}t|ttfvrtdt|tur|}|tj}j r/|j ks6j|durj }j rj |\}}|durK||d<zj |fi|j|<Wn8ty}zdt|vrw|d=j |fi|j|<nWYd}~nd}~wwj j|fi|j|<|_ j|Stj|}t}j rfdd|D|_fdd|D|_ n fd d|D|_t||_j rj |vr|j |_ tj|_|Stjd td |_|Sj||_|S) aReturn selected image(s) in the collection. Loading is done on demand. Parameters ---------- n : int or slice The image number to be returned, or a slice selecting the images and ordering to be returned in a new ImageCollection. Returns ------- img : ndarray or ImageCollection. The `n`-th image in the collection, or a new ImageCollection with the selected images. __index__z+slicing must be with an int or slice objectNimg_numz%unexpected keyword argument 'img_num'csg|] }j|dqS)rrCrVrRrrr3rz/ImageCollection.__getitem__..cg|]}j|qSrrmrVrRrrr4crnrrQrVrRrrr6ror5r8)rerktyperslicer< _check_imgnumrBrIrLrErFrCr?r'rSr^rArr:rgrrGrH) rJnidxkwargsrYrlefidxnew_icrrRr __getitem__sX          zImageCollection.__getitem__cCs8|j}| |kr|krnn||}|Std|)z+Check that the given image number is valid.z*There are only %s images in the collection)rA IndexError)rJrsnumrrrrrDszImageCollection._check_imgnumccs"tt|D]}||VqdS)zIterate over the images.N)r^rB)rJrWrrr__iter__Ns zImageCollection.__iter__cCrP)zNumber of images in collection.)rArRrrr__len__SrTzImageCollection.__len__cCs t|jSr%)r'rSrRrrr__str__Ws zImageCollection.__str__cCst|j|_dS)zClear the image cache. Parameters ---------- n : None or int Clear the cache for this image only. By default, the entire cache is erased. N)r empty_likerI)rJrsrrrreloadZs zImageCollection.reloadcCst|S)aConcatenate all images in the collection into an array. Returns ------- ar : np.ndarray An array having one more dimension than the images in `self`. See Also -------- concatenate_images Raises ------ ValueError If images in the `ImageCollection` don't have identical shapes. )rrRrrrrfszImageCollection.concatenateTNr%)__name__ __module__ __qualname____doc__rOpropertyrSrLr@ryrrr|r}r~rrrrrrr ms F$  J   r csdfdd }|S)NTcst||dS)aReturn an `ImageCollection` from files matching the given pattern. Note that files are always stored in alphabetical order. Also note that slicing returns a new ImageCollection, *not* a view into the data. See `skimage.io.ImageCollection` for details. Parameters ---------- load_pattern : str or list Pattern glob or filenames to load. The path can be absolute or relative. Multiple patterns should be separated by a colon, e.g. ``/tmp/work/*.png:/tmp/other/*.jpg``. Also see implementation notes below. conserve_memory : bool, optional If True, never keep more than one in memory at a specific time. Otherwise, images will be cached once they are loaded. )rLr?)r )rKrLr6rrimread_collection{sz4imread_collection_wrapper..imread_collection)Tr)r7rrr6rrzsrcs.eZdZdZdfdd ZeddZZS) r aqA class containing all frames from multi-frame images. Parameters ---------- load_pattern : str or list of str Pattern glob or filenames to load. The path can be absolute or relative. conserve_memory : bool, optional Whether to conserve memory by only caching a single frame. Default is True. Other parameters ---------------- load_func : callable ``imread`` by default. See notes below. Notes ----- If ``conserve_memory=True`` the memory footprint can be reduced, however the performance can be affected because frames have to be read from file more often. The last accessed frame is cached, all other frames will have to be read from file. The current implementation makes use of ``tifffile`` for Tiff files and PIL otherwise. Examples -------- >>> from skimage import data_dir >>> img = MultiImage(data_dir + '/multipage.tif') # doctest: +SKIP >>> len(img) # doctest: +SKIP 2 >>> for frame in img: # doctest: +SKIP ... print(frame.shape) # doctest: +SKIP (15, 10) (15, 10) TNc s4ddlm}||_tt|j||fd|i|dS)zLoad a multi-img.r5r6r?N)r>r7 _filenamesuperr rO)rJfilenamerLr9 imread_kwargsr7 __class__rrrOs  zMultiImage.__init__cCrPr%)rrRrrrrrTzMultiImage.filenamer)rrrrrOrr __classcell__rrrrr s * r )rr*rr collections.abcrr packagingrnumpyrPILrr pil_versionparsewarningsrtifffiler __all__rr$r3rHr rr rrrrs0      #