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# -*- 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)