σ ;c›]c@`sΓdZddlmZmZmZddlZddlZddlmZddl m Z ddl Z dad„Zd.Zd/Zd0Zd)e fd*„ƒYZed+d,ed-ƒZejeƒdS(1s' Storage of image data in tiff format. i(tabsolute_importtprint_functiontdivisionNi(tformats(tFormatcC`s†tjdkrNyddl}ddl}WqNtk rJtdƒ‚qNXnyddlaWn!tk rddlmanXtS(NiistThe Imageio TIFF format has extra dependencies on Python 2.7. Install these using e.g. "pip install enum34 futures".i(t _tifffile(i(tsyst version_infotenumtconcurrent.futurest ImportErrorttifffileRt(Rt concurrent((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pytload_libs   s.tifs.tiffs.stks.lsmt photometrict planarconfigt resolutiont descriptiontcompresstvolumet writeshapet extratagstdatetimetplanar_configurationt is_fluoviewtis_niht is_contigtis_micromanagertis_ometis_lsmis_palettet is_reducedtis_rgbtis_sgit is_shapedtis_stktis_tiledtis_mdgelresolution_unitt compressiont is_mediacyt orientationt description1t is_imagejtsoftwaret TiffFormatcB`sReZdZd„Zd„Zdejfd„ƒYZdejfd„ƒYZRS(s™ Provides support for a wide range of Tiff images. 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. 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 Values from 0 to 9 indicating the level of zlib compression. If 0, data is uncompressed. 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 compression. If 0, data are written uncompressed (default). 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. cC`s|j|jkS(N(t extensiont extensions(tselftrequest((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt _can_readΡscC`s|j|jkS(N(R-R.(R/R0((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt _can_writeΥstReadercB`s5eZd„Zd„Zd„Zd„Zd„ZRS(cK`ststƒn|jjjdƒrGt|jjƒdƒ|_}nd|_|jj ƒ}tj |||_ i|_ dS(Nshttp://shttps://trb(shttp://shttps://( RRR0tfilenamet startswithtopentget_local_filenamet_ftNonetget_filetTiffFilet_tft_meta(R/tkwargstf((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt_openάs " cC`s0|jjƒ|jdk r,|jjƒndS(N(R=tcloseR9R:(R/((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt_closeκs cC`s.|jjddkrdSt|jjƒSdS(NitvV(R0tmodetlenR=tpages(R/((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt _get_lengthοscC`s±|jjddkrL|dkr1tdƒ‚n|jjƒ}|j}n[|dksj||jƒkrytdƒ‚n|jj|jƒ}|jp€|j|ƒ}||fS(NiRDis-Tiff support no more than 1 "volume" per files/Index out of range while reading from tiff file( R0REt IndexErrorR=tasarrayR>RHRGt_get_meta_data(R/tindextimtmeta((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt _get_dataυs  cC`s¬|jj|pd}x<tD]4}yt||ƒ|j|t ExceptionRtstrptimettagstvalue(R/RLtpagetkey((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyRKs     (t__name__t __module__RARCRHRORK(((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyR3Ϋs     tWritercB`s5eZdddd„Zd„Zd„Zd„ZRS(cC`ststƒny4tj|jjƒ||d|ƒ|_d|_Wn;tk rtj|jjƒ||ƒ|_||_nXi|_ dS(NR+( RRt TiffWriterR0R;R=R:t _softwaret TypeErrorR>(R/tbigtifft byteorderR+((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyRAs !   cC`s|jjƒdS(N(R=RB(R/((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyRC.scC`ss|r|j|ƒn|jdkrG|jjtj|ƒ|jn(|jjtj|ƒd|j|jdS(NR+(t set_meta_dataR]R:R=tsavetnpt asanyarrayR>(R/RMRN((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyt _append_data1s "cC`sFi|_x6|jƒD](\}}|tkr||j|titemstWRITE_METADATA_KEYS(R/RNRXRV((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyRa<s  N(RYRZR:RARCReRa(((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyR[s  (RYRZt__doc__R1R2RR3R[(((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pyR,Ms ‚  ?ttiffs TIFF formattiIvV(s.tifs.tiffs.stks.lsm( RRRRRRRRR(RRRRRRRRR R!R"R#R$R%R&R'R(RR)R*R+(Rht __future__RRRRRR RtcoreRtnumpyRcR:RRt TIFF_FORMATSRgRQR,tformatt add_format(((s7lib/python2.7/site-packages/imageio/plugins/tifffile.pytsT    χ