0-PhPdZddlZddlmZddlmZmZddlZddl Z ddl Z n"#e $re j deddlm Z YnwxYwd Zd Zd ZGd d eZdS)a Read/Write TIFF files. Backend: internal Provides support for a wide range of Tiff images using the tifffile backend. Parameters for reading ---------------------- 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. multifile_close : bool If True (default), keep the handles of other files in multifile series closed. This is inefficient when few files refer to many pages. If False, the C runtime may run out of resources. Parameters for saving --------------------- 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. software : str Name of the software used to create the image. Saved with the first page only. Metadata for reading -------------------- planar_configuration : {'contig', 'planar'} Specifies if samples are stored contiguous or in separate planes. By default this setting is inferred from the data shape. 'contig': last dimension contains samples. 'planar': third last dimension contains samples. resolution_unit : int The resolution unit stored in the TIFF tag. Usually 1 means no/unknown unit, 2 means dpi (inch), 3 means dpc (centimeter). resolution : (float, float, str) A tuple formatted as (X_resolution, Y_resolution, unit). The unit is a string representing one of the following units:: NONE # No unit or unit unknown INCH # dpi CENTIMETER # cpi MILLIMETER MICROMETER compression : int Value indicating the compression algorithm used, e.g. 5 is LZW, 7 is JPEG, 8 is deflate. If 1, data are uncompressed. predictor : int Value 2 indicates horizontal differencing was used before compression, while 3 indicates floating point horizontal differencing. If 1, no prediction scheme was used before compression. orientation : {'top_left', 'bottom_right', ...} Oriented of image array. is_rgb : bool True if page contains a RGB image. is_contig : bool True if page contains a contiguous image. is_tiled : bool True if page contains tiled image. is_palette : bool True if page contains a palette-colored image and not OME or STK. is_reduced : bool True if page is a reduced image of another image. is_shaped : bool True if page contains shape in image_description tag. is_fluoview : bool True if page contains FluoView MM_STAMP tag. is_nih : bool True if page contains NIH image header. is_micromanager : bool True if page contains Micro-Manager metadata. is_ome : bool True if page contains OME-XML in image_description tag. is_sgi : bool True if page contains SGI image and tile depth tags. is_mdgel : bool True if page contains md_file_tag tag. is_mediacy : bool True if page contains Media Cybernetics Id tag. is_stk : bool True if page contains UIC2Tag tag. is_lsm : bool True if page contains LSM CZ_LSM_INFO tag. description : str Image description description1 : str Additional description is_imagej : None or str ImageJ metadata software : str Software used to create the TIFF file datetime : datetime.datetime Creation date and time Metadata for writing -------------------- photometric : {'minisblack', 'miniswhite', 'rgb'} The color space of the image data. By default this setting is inferred from the data shape. planarconfig : {'contig', 'planar'} Specifies if samples are stored contiguous or in separate planes. By default this setting is inferred from the data shape. 'contig': last dimension contains samples. 'planar': third last dimension contains samples. resolution : (float, float) or ((int, int), (int, int)) X and Y resolution in dots per inch as float or rational numbers. description : str The subject of the image. Saved with the first page only. compress : int Values from 0 to 9 controlling the level of zlib (deflate) compression. If 0, data are written uncompressed (default). compression : str, (int, int) Compression scheme used while writing the image. If omitted (default) the image is not uncompressed. Compression cannot be used to write contiguous series. Compressors may require certain data shapes, types or value ranges. For example, JPEG compression requires grayscale or RGB(A), uint8 or 12-bit uint16. JPEG compression is experimental. JPEG markers and TIFF tags may not match. Only a limited set of compression schemes are implemented. 'ZLIB' is short for ADOBE_DEFLATE. The value is written to the Compression tag. compressionargs: Extra arguments passed to compression codec, e.g., compression level. Refer to the Imagecodecs implementation for supported arguments. predictor : bool If True, horizontal differencing is applied before compression. Note that using an int literal 1 actually means no prediction scheme will be used. volume : bool If True, volume data are stored in one tile (if applicable) using the SGI image_depth and tile_depth tags. Image width and depth must be multiple of 16. Few software can read this format, e.g. MeVisLab. writeshape : bool If True, write the data shape to the image_description tag if necessary and no other description is given. 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, f, d, Q, or q. count : int Number of data values. Not used for string values. value : sequence 'Count' values compatible with 'dtype'. writeonce : bool If True, the tag is written to the first page only. Notes ----- Global metadata is stored with the first frame in a TIFF file. Thus calling :py:meth:`Format.Writer.set_meta_data` after the first frame was written has no effect. Also, global metadata is ignored if metadata is provided via the `meta` argument of :py:meth:`Format.Writer.append_data`. If you have installed tifffile as a Python package, imageio will attempt to use that as backend instead of the bundled backend. Doing so can provide access to new performance improvements and bug fixes. N)Format) URI_BYTESURI_FILEzImageIO's vendored tifffile backend is deprecated and will be removed in ImageIO v3. Install the tifffile directly: `pip install imageio[tifffile]`) _tifffile)z.tifz.tiffz.stkz.lsm) photometric planarconfig resolution descriptioncompress compressioncompressionargs predictorvolume writeshape extratagsdatetime)planar_configuration is_fluoviewis_nih is_contigis_micromanageris_omeis_lsm is_palette is_reducedis_rgbis_sgi is_shapedis_stkis_tiledis_mdgelresolution_unitrr is_mediacy orientationr description1 is_imagejsoftwarecjeZdZdZdZdZGddejZGddejZdS) TiffFormataProvides support for a wide range of Tiff images using the tifffile backend. Images that contain multiple pages can be read using ``imageio.mimread()`` to read the individual pages, or ``imageio.volread()`` to obtain a single (higher dimensional) array. Note that global metadata is stored with the first frame in a TIFF file. Thus calling :py:meth:`Format.Writer.set_meta_data` after the first frame was written has no effect. Also, global metadata is ignored if metadata is provided via the `meta` argument of :py:meth:`Format.Writer.append_data`. If you have installed tifffile as a Python package, imageio will attempt to use that as backend instead of the bundled backend. Doing so can provide access to new performance improvements and bug fixes. Parameters for reading ---------------------- 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. multifile_close : bool If True (default), keep the handles of other files in multifile series closed. This is inefficient when few files refer to many pages. If False, the C runtime may run out of resources. Parameters for saving --------------------- 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. software : str Name of the software used to create the image. Saved with the first page only. Metadata for reading -------------------- planar_configuration : {'contig', 'planar'} Specifies if samples are stored contiguous or in separate planes. By default this setting is inferred from the data shape. 'contig': last dimension contains samples. 'planar': third last dimension contains samples. resolution_unit : (float, float) or ((int, int), (int, int)) X and Y resolution in dots per inch as float or rational numbers. compression : int Value indicating the compression algorithm used, e.g. 5 is LZW, 7 is JPEG, 8 is deflate. If 1, data are uncompressed. predictor : int Value 2 indicates horizontal differencing was used before compression, while 3 indicates floating point horizontal differencing. If 1, no prediction scheme was used before compression. orientation : {'top_left', 'bottom_right', ...} Oriented of image array. is_rgb : bool True if page contains a RGB image. is_contig : bool True if page contains a contiguous image. is_tiled : bool True if page contains tiled image. is_palette : bool True if page contains a palette-colored image and not OME or STK. is_reduced : bool True if page is a reduced image of another image. is_shaped : bool True if page contains shape in image_description tag. is_fluoview : bool True if page contains FluoView MM_STAMP tag. is_nih : bool True if page contains NIH image header. is_micromanager : bool True if page contains Micro-Manager metadata. is_ome : bool True if page contains OME-XML in image_description tag. is_sgi : bool True if page contains SGI image and tile depth tags. is_stk : bool True if page contains UIC2Tag tag. is_mdgel : bool True if page contains md_file_tag tag. is_mediacy : bool True if page contains Media Cybernetics Id tag. is_stk : bool True if page contains UIC2Tag tag. is_lsm : bool True if page contains LSM CZ_LSM_INFO tag. description : str Image description description1 : str Additional description is_imagej : None or str ImageJ metadata software : str Software used to create the TIFF file datetime : datetime.datetime Creation date and time Metadata for writing -------------------- photometric : {'minisblack', 'miniswhite', 'rgb'} The color space of the image data. By default this setting is inferred from the data shape. planarconfig : {'contig', 'planar'} Specifies if samples are stored contiguous or in separate planes. By default this setting is inferred from the data shape. 'contig': last dimension contains samples. 'planar': third last dimension contains samples. resolution : (float, float) or ((int, int), (int, int)) X and Y resolution in dots per inch as float or rational numbers. description : str The subject of the image. Saved with the first page only. compress : int Values from 0 to 9 controlling the level of zlib (deflate) compression. If 0, data are written uncompressed (default). predictor : bool If True, horizontal differencing is applied before compression. Note that using an int literal 1 actually means no prediction scheme will be used. volume : bool If True, volume data are stored in one tile (if applicable) using the SGI image_depth and tile_depth tags. Image width and depth must be multiple of 16. Few software can read this format, e.g. MeVisLab. writeshape : bool If True, write the data shape to the image_description tag if necessary and no other description is given. 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, f, d, Q, or q. count : int Number of data values. Not used for string values. value : sequence 'Count' values compatible with 'dtype'. writeonce : bool If True, the tag is written to the first page only. c tj|fi|jnp#t$r+Y|ddStj$r+Y|ddSwxYw |dn,#|dwxYwdS)NrFT)rTiffFileget_filekwargs ValueErrorseek TiffFileErrorselfrequests X/var/www/html/test/jupyter/venv/lib/python3.11/site-packages/imageio/plugins/tifffile.py _can_readzTiffFormat._can_reads  '  w//11 D DW^ D D D D         # #A & & & & & &         # #A & & & & &   E      # #A & & & &G     # #A & & & &ts1),C BC B.CBC)C.c2|jttfvrn|j|jvrdS t j|fi|jnp#t$r+Y| ddSt j $r+Y| ddSwxYw | dn,#| dwxYwdS)NFrT) _uri_typerr extension extensionsr TiffWriterr.r/r0r1r2r3s r6 _can_writezTiffFormat._can_writes8  9 5 5 5   do 5 55 '  !1!1!3!3 F Fw~ F F F F         # #A & & & & & &         # #A & & & & &   G      # #A & & & &G     # #A & & & &ts5)AC+ B?C+B?C+>B??C++)Dc,eZdZdZdZdZdZdZdS)TiffFormat.Readerc |jjdr/t|jdx|_}n d|_|j}tj|fi||_ dS)N)zhttp://zhttps://rb) r5filename startswithopenget_local_filename_fr.rr-_tf)r4r/fs r6_openzTiffFormat.Reader._opens||$//0GHH ,"4<#B#B#D#DdKKK!!L))++ )!66v66DHHHc||j|j|jdSdSN)rGcloserFr4s r6_closezTiffFormat.Reader._closes7 HNN   w" #"rJc4t|jjSrL)lenrGseriesrNs r6 _get_lengthzTiffFormat.Reader._get_lengthstx'' 'rJc|dks||krtd|j|}||}||fS)Nrz/Index out of range while reading from tiff file)rR)rS IndexErrorrGasarray_get_meta_data)r4indeximmetas r6 _get_datazTiffFormat.Reader._get_datasdqyyET%5%5%7%777 !RSSS!!!//B&&u--Dt8OrJci}|jj|pd}tD]&} t||||<#t$rY#wxYwdD]G} t j|j|jd|d<n#t$rYDwxYwd|jvr|jdjj|d<d|jvrd|jvrd|jvr|jdj}|jdj}|d dks |d dkrtj d tn;|d|d z |d|d z |jdjj f|d <|S) Nr)rDateTimez%Y:%m:%d %H:%M:%Sri(r$iirzQIgnoring resolution metadata, because at least one direction has a 0 denominator.r ) rGpagesREAD_METADATA_KEYSgetattr ExceptionrstrptimetagsvaluewarningswarnRuntimeWarningname)r4rXrZpagekey resolution_x resolution_ys r6rWz TiffFormat.Reader._get_meta_datasD8>%*1-D)   'c 2 2DII D0  '/'8'A'A #,.A((D$E Ddi*.)C.*>*D&'diC49$4$4 9I9I#y~3 #y~3 ?a''<?a+?+?MN&%Q,q/9$Q,q/9 #,1*D& Ks!5 AA 3A?? B  B N)__name__ __module__ __qualname__rIrOrSr[rWrJr6Readerr?s_ 7 7 7    ( ( (   & & & & & rJrqc>eZdZddZdZdZedZdZdS)TiffFormat.WriterNc0 tj|j||||_d|_nJ#t $r=tj|j|||_||_YnwxYwi|_d|_dS)N)bigtiff byteorderr))rurvr) rr<r5r.rG _software TypeError_meta_frames_written)r4rurvr)s r6rIzTiffFormat.Writer._opens *$/L))++#'%  "& * * *%/L))++W "*  *DJ#$D s;>ABBc8|jdSrL)rGrMrNs r6rOzTiffFormat.Writer._closes HNN     rJcD|||}n|jdkr|jni}|j|jdkr |j|d< |jj}n#t $r|jj}YnwxYw|tj |fddi||xjdz c_dS)Nrr) contiguousFr) _sanitize_metarzryrwrGwriteAttributeErrorsavenp asanyarray)r4rYrZ write_meths r6 _append_datazTiffFormat.Writer._append_datas**400&*%9Q%>%>tzzB~)d.Ba.G.G#'>Z  +!X^ ! + + +!X]  + Jr}R(( C CU Cd C C C  A % s AA0/A0c:i}|D]\}}|tvru|dkrt|ts |dk||<3|dkrE|dkr?t jdt tjdkrd|f|d<qd |d<d |i|d <~|||<|S) Nrrr rzUThe use of `compress` is deprecated. Use `compression` and `compressionargs` instead.2022rzliblevelr) itemsWRITE_METADATA_KEYS isinstanceboolrerfDeprecationWarningr __version__)rZretrjrds r6r~z TiffFormat.Writer._sanitize_metasC"jjll ) ) U---k))*UD2I2I)#(19C **uzz s. %069923UC ..17C .6=u5EC 122#(CJrJc:|||_dSrL)r~ry)r4rZs r6 set_meta_datazTiffFormat.Writer.set_meta_data0s,,T22DJJJrJ)NNN) rmrnrorIrOr staticmethodr~rrprJr6Writerrssp % % % %(    & & &$     . 3 3 3 3 3rJrN) rmrnro__doc__r7r=rrqrrprJr6r+r+sTTl   (AAAAAAAAHC3C3C3C3C3C3C3C3C3C3rJr+)rrcorer core.requestrrnumpyrretifffiler ImportErrorrfr TIFF_FORMATSrr_r+rprJr6rskkZ........      HM +   1  8@3@3@3@3@3@3@3@3@3@3s#AA