# -*- coding: utf-8 -*- # imageio is distributed under the terms of the (new) BSD License. """ Storage of image data in tiff format. """ from __future__ import absolute_import, print_function, division import sys import datetime from .. import formats from ..core import Format import numpy as np _tifffile = None # Defer loading to lib() function. def load_lib(): if sys.version_info < (3,): try: import enum # noqa - needs enum34 import concurrent.futures # noqa - needs futures except ImportError: raise ImportError( "The Imageio TIFF format has extra dependencies " "on Python 2.7. Install these using e.g. " '"pip install enum34 futures".' ) 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", "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", "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 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. """ 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; tiffile 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_local_filename(), 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_local_filename(), 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; tiffile 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: self._meta[key] = value # Register format = TiffFormat("tiff", "TIFF format", TIFF_FORMATS, "iIvV") formats.add_format(format)