# -*- coding: utf-8 -*- # imageio is distributed under the terms of the (new) BSD License. """ Storage of image data in tiff format. """ import datetime from .. import formats from ..core import Format import numpy as np _tifffile = None # Defer loading to lib() function. def load_lib(): global _tifffile try: import tifffile as _tifffile except ImportError: from . import _tifffile return _tifffile TIFF_FORMATS = (".tif", ".tiff", ".stk", ".lsm") WRITE_METADATA_KEYS = ( "photometric", "planarconfig", "resolution", "description", "compress", "predictor", "volume", "writeshape", "extratags", "datetime", ) READ_METADATA_KEYS = ( "planar_configuration", "is_fluoview", "is_nih", "is_contig", "is_micromanager", "is_ome", "is_lsm" "is_palette", "is_reduced", "is_rgb", "is_sgi", "is_shaped", "is_stk", "is_tiled", "is_mdgel" "resolution_unit", "compression", "predictor", "is_mediacy", "orientation", "description", "description1", "is_imagej", "software", ) class TiffFormat(Format): """ 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 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. """ def _can_read(self, request): # We support any kind of image data return request.extension in self.extensions def _can_write(self, request): # We support any kind of image data return request.extension in self.extensions # -- reader class Reader(Format.Reader): def _open(self, **kwargs): if not _tifffile: load_lib() # Allow loading from http; tifffile uses seek, so download first if self.request.filename.startswith(("http://", "https://")): self._f = f = open(self.request.get_local_filename(), "rb") else: self._f = None f = self.request.get_file() self._tf = _tifffile.TiffFile(f, **kwargs) # metadata is the same for all images self._meta = {} def _close(self): self._tf.close() if self._f is not None: self._f.close() def _get_length(self): if self.request.mode[1] in "vV": return 1 # or can there be pages in pages or something? else: return len(self._tf.pages) def _get_data(self, index): if self.request.mode[1] in "vV": # Read data as single 3D (+ color channels) array if index != 0: raise IndexError('Tiff support no more than 1 "volume" per file') im = self._tf.asarray() # request as singleton image meta = self._meta else: # Read as 2D image if index < 0 or index >= self._get_length(): raise IndexError("Index out of range while reading from tiff file") im = self._tf.pages[index].asarray() meta = self._meta or self._get_meta_data(index) # Return array and empty meta data return im, meta def _get_meta_data(self, index): page = self._tf.pages[index or 0] for key in READ_METADATA_KEYS: try: self._meta[key] = getattr(page, key) except Exception: pass # tifffile <= 0.12.1 use datetime, newer use DateTime for key in ("datetime", "DateTime"): try: self._meta["datetime"] = datetime.datetime.strptime( page.tags[key].value, "%Y:%m:%d %H:%M:%S" ) break except Exception: pass return self._meta # -- writer class Writer(Format.Writer): def _open(self, bigtiff=None, byteorder=None, software=None): if not _tifffile: load_lib() try: self._tf = _tifffile.TiffWriter( self.request.get_file(), bigtiff, byteorder, software=software ) self._software = None except TypeError: # In tifffile >= 0.15, the `software` arg is passed to # TiffWriter.save self._tf = _tifffile.TiffWriter( self.request.get_file(), bigtiff, byteorder ) self._software = software self._meta = {} def _close(self): self._tf.close() def _append_data(self, im, meta): if meta: self.set_meta_data(meta) # No need to check self.request.mode; tifffile figures out whether # this is a single page, or all page data at once. if self._software is None: self._tf.save(np.asanyarray(im), **self._meta) else: # tifffile >= 0.15 self._tf.save(np.asanyarray(im), software=self._software, **self._meta) def set_meta_data(self, meta): self._meta = {} for (key, value) in meta.items(): if key in WRITE_METADATA_KEYS: # Special case of previously read `predictor` int value # 1(=NONE) translation to False expected by TiffWriter.save if key == "predictor" and not isinstance(value, bool): self._meta[key] = value > 1 else: self._meta[key] = value # Register format = TiffFormat("tiff", "TIFF format", TIFF_FORMATS, "iIvV") formats.add_format(format)