562 lines
20 KiB
Python
562 lines
20 KiB
Python
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# -*- coding: utf-8 -*-
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# imageio is distributed under the terms of the (new) BSD License.
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""" Read/Write TIFF files.
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Backend: internal
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Provides support for a wide range of Tiff images using the tifffile
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backend.
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Parameters for reading
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----------------------
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offset : int
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Optional start position of embedded file. By default this is
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the current file position.
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size : int
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Optional size of embedded file. By default this is the number
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of bytes from the 'offset' to the end of the file.
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multifile : bool
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If True (default), series may include pages from multiple files.
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Currently applies to OME-TIFF only.
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multifile_close : bool
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If True (default), keep the handles of other files in multifile
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series closed. This is inefficient when few files refer to
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many pages. If False, the C runtime may run out of resources.
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Parameters for saving
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---------------------
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bigtiff : bool
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If True, the BigTIFF format is used.
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byteorder : {'<', '>'}
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The endianness of the data in the file.
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By default this is the system's native byte order.
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software : str
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Name of the software used to create the image.
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Saved with the first page only.
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Metadata for reading
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--------------------
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planar_configuration : {'contig', 'planar'}
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Specifies if samples are stored contiguous or in separate planes.
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By default this setting is inferred from the data shape.
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'contig': last dimension contains samples.
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'planar': third last dimension contains samples.
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resolution_unit : int
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The resolution unit stored in the TIFF tag. Usually 1 means no/unknown unit,
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2 means dpi (inch), 3 means dpc (centimeter).
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resolution : (float, float, str)
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A tuple formatted as (X_resolution, Y_resolution, unit). The unit is a
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string representing one of the following units::
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NONE # No unit or unit unknown
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INCH # dpi
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CENTIMETER # cpi
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MILLIMETER
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MICROMETER
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compression : int
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Value indicating the compression algorithm used, e.g. 5 is LZW,
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7 is JPEG, 8 is deflate.
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If 1, data are uncompressed.
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predictor : int
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Value 2 indicates horizontal differencing was used before compression,
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while 3 indicates floating point horizontal differencing.
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If 1, no prediction scheme was used before compression.
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orientation : {'top_left', 'bottom_right', ...}
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Oriented of image array.
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is_rgb : bool
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True if page contains a RGB image.
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is_contig : bool
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True if page contains a contiguous image.
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is_tiled : bool
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True if page contains tiled image.
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is_palette : bool
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True if page contains a palette-colored image and not OME or STK.
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is_reduced : bool
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True if page is a reduced image of another image.
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is_shaped : bool
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True if page contains shape in image_description tag.
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is_fluoview : bool
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True if page contains FluoView MM_STAMP tag.
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is_nih : bool
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True if page contains NIH image header.
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is_micromanager : bool
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True if page contains Micro-Manager metadata.
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is_ome : bool
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True if page contains OME-XML in image_description tag.
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is_sgi : bool
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True if page contains SGI image and tile depth tags.
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is_mdgel : bool
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True if page contains md_file_tag tag.
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is_mediacy : bool
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True if page contains Media Cybernetics Id tag.
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is_stk : bool
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True if page contains UIC2Tag tag.
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is_lsm : bool
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True if page contains LSM CZ_LSM_INFO tag.
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description : str
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Image description
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description1 : str
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Additional description
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is_imagej : None or str
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ImageJ metadata
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software : str
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Software used to create the TIFF file
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datetime : datetime.datetime
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Creation date and time
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Metadata for writing
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--------------------
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photometric : {'minisblack', 'miniswhite', 'rgb'}
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The color space of the image data.
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By default this setting is inferred from the data shape.
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planarconfig : {'contig', 'planar'}
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Specifies if samples are stored contiguous or in separate planes.
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By default this setting is inferred from the data shape.
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'contig': last dimension contains samples.
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'planar': third last dimension contains samples.
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resolution : (float, float) or ((int, int), (int, int))
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X and Y resolution in dots per inch as float or rational numbers.
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description : str
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The subject of the image. Saved with the first page only.
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compress : int
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Values from 0 to 9 controlling the level of zlib (deflate) compression.
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If 0, data are written uncompressed (default).
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compression : str, (int, int)
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Compression scheme used while writing the image. If omitted (default) the
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image is not uncompressed. Compression cannot be used to write contiguous
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series. Compressors may require certain data shapes, types or value ranges.
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For example, JPEG compression requires grayscale or RGB(A), uint8 or 12-bit
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uint16. JPEG compression is experimental. JPEG markers and TIFF tags may not
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match. Only a limited set of compression schemes are implemented. 'ZLIB' is
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short for ADOBE_DEFLATE. The value is written to the Compression tag.
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compressionargs:
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Extra arguments passed to compression codec, e.g., compression level. Refer
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to the Imagecodecs implementation for supported arguments.
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predictor : bool
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If True, horizontal differencing is applied before compression.
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Note that using an int literal 1 actually means no prediction scheme
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will be used.
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volume : bool
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If True, volume data are stored in one tile (if applicable) using
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the SGI image_depth and tile_depth tags.
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Image width and depth must be multiple of 16.
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Few software can read this format, e.g. MeVisLab.
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writeshape : bool
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If True, write the data shape to the image_description tag
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if necessary and no other description is given.
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extratags: sequence of tuples
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Additional tags as [(code, dtype, count, value, writeonce)].
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code : int
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The TIFF tag Id.
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dtype : str
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Data type of items in 'value' in Python struct format.
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One of B, s, H, I, 2I, b, h, i, f, d, Q, or q.
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count : int
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Number of data values. Not used for string values.
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value : sequence
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'Count' values compatible with 'dtype'.
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writeonce : bool
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If True, the tag is written to the first page only.
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Notes
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-----
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Global metadata is stored with the first frame in a TIFF file.
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Thus calling :py:meth:`Format.Writer.set_meta_data` after the first frame
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was written has no effect. Also, global metadata is ignored if metadata is
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provided via the `meta` argument of :py:meth:`Format.Writer.append_data`.
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If you have installed tifffile as a Python package, imageio will attempt
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to use that as backend instead of the bundled backend. Doing so can
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provide access to new performance improvements and bug fixes.
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"""
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import datetime
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from ..core import Format
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from ..core.request import URI_BYTES, URI_FILE
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import numpy as np
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import warnings
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try:
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import tifffile as _tifffile
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except ImportError:
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warnings.warn(
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"ImageIO's vendored tifffile backend is deprecated and will be"
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" removed in ImageIO v3. Install the tifffile directly:"
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" `pip install imageio[tifffile]`",
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DeprecationWarning,
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)
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from . import _tifffile
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TIFF_FORMATS = (".tif", ".tiff", ".stk", ".lsm")
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WRITE_METADATA_KEYS = (
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"photometric",
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"planarconfig",
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"resolution",
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"description",
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"compress",
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"compression",
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"compressionargs",
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"predictor",
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"volume",
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"writeshape",
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"extratags",
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"datetime",
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)
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READ_METADATA_KEYS = (
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"planar_configuration",
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"is_fluoview",
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"is_nih",
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"is_contig",
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"is_micromanager",
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"is_ome",
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"is_lsm",
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"is_palette",
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"is_reduced",
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"is_rgb",
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"is_sgi",
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"is_shaped",
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"is_stk",
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"is_tiled",
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"is_mdgel",
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"resolution_unit",
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"compression",
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"predictor",
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"is_mediacy",
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"orientation",
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"description",
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"description1",
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"is_imagej",
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"software",
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)
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class TiffFormat(Format):
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"""Provides support for a wide range of Tiff images using the tifffile
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backend.
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Images that contain multiple pages can be read using ``imageio.mimread()``
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to read the individual pages, or ``imageio.volread()`` to obtain a
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single (higher dimensional) array.
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Note that global metadata is stored with the first frame in a TIFF file.
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Thus calling :py:meth:`Format.Writer.set_meta_data` after the first frame
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was written has no effect. Also, global metadata is ignored if metadata is
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provided via the `meta` argument of :py:meth:`Format.Writer.append_data`.
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If you have installed tifffile as a Python package, imageio will attempt
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to use that as backend instead of the bundled backend. Doing so can
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provide access to new performance improvements and bug fixes.
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Parameters for reading
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----------------------
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offset : int
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Optional start position of embedded file. By default this is
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the current file position.
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size : int
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Optional size of embedded file. By default this is the number
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of bytes from the 'offset' to the end of the file.
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multifile : bool
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If True (default), series may include pages from multiple files.
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Currently applies to OME-TIFF only.
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multifile_close : bool
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If True (default), keep the handles of other files in multifile
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series closed. This is inefficient when few files refer to
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many pages. If False, the C runtime may run out of resources.
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Parameters for saving
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---------------------
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bigtiff : bool
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If True, the BigTIFF format is used.
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byteorder : {'<', '>'}
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The endianness of the data in the file.
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By default this is the system's native byte order.
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software : str
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Name of the software used to create the image.
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Saved with the first page only.
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Metadata for reading
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--------------------
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planar_configuration : {'contig', 'planar'}
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Specifies if samples are stored contiguous or in separate planes.
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By default this setting is inferred from the data shape.
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'contig': last dimension contains samples.
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'planar': third last dimension contains samples.
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resolution_unit : (float, float) or ((int, int), (int, int))
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X and Y resolution in dots per inch as float or rational numbers.
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compression : int
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Value indicating the compression algorithm used, e.g. 5 is LZW,
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7 is JPEG, 8 is deflate.
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If 1, data are uncompressed.
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predictor : int
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Value 2 indicates horizontal differencing was used before compression,
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while 3 indicates floating point horizontal differencing.
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If 1, no prediction scheme was used before compression.
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orientation : {'top_left', 'bottom_right', ...}
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Oriented of image array.
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is_rgb : bool
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True if page contains a RGB image.
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is_contig : bool
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True if page contains a contiguous image.
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is_tiled : bool
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True if page contains tiled image.
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is_palette : bool
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True if page contains a palette-colored image and not OME or STK.
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is_reduced : bool
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True if page is a reduced image of another image.
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is_shaped : bool
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True if page contains shape in image_description tag.
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is_fluoview : bool
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True if page contains FluoView MM_STAMP tag.
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is_nih : bool
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True if page contains NIH image header.
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is_micromanager : bool
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True if page contains Micro-Manager metadata.
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is_ome : bool
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True if page contains OME-XML in image_description tag.
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is_sgi : bool
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True if page contains SGI image and tile depth tags.
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is_stk : bool
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True if page contains UIC2Tag tag.
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is_mdgel : bool
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True if page contains md_file_tag tag.
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is_mediacy : bool
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True if page contains Media Cybernetics Id tag.
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is_stk : bool
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True if page contains UIC2Tag tag.
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is_lsm : bool
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True if page contains LSM CZ_LSM_INFO tag.
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description : str
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Image description
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description1 : str
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Additional description
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is_imagej : None or str
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ImageJ metadata
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software : str
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Software used to create the TIFF file
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datetime : datetime.datetime
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Creation date and time
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||
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Metadata for writing
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|
--------------------
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photometric : {'minisblack', 'miniswhite', 'rgb'}
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The color space of the image data.
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|
By default this setting is inferred from the data shape.
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planarconfig : {'contig', 'planar'}
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Specifies if samples are stored contiguous or in separate planes.
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By default this setting is inferred from the data shape.
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'contig': last dimension contains samples.
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'planar': third last dimension contains samples.
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resolution : (float, float) or ((int, int), (int, int))
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X and Y resolution in dots per inch as float or rational numbers.
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description : str
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The subject of the image. Saved with the first page only.
|
||
|
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compress : int
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|
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Values from 0 to 9 controlling the level of zlib (deflate) compression.
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If 0, data are written uncompressed (default).
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|
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predictor : bool
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If True, horizontal differencing is applied before compression.
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Note that using an int literal 1 actually means no prediction scheme
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|
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will be used.
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||
|
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volume : bool
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||
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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.
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||
|
|
Few software can read this format, e.g. MeVisLab.
|
||
|
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writeshape : bool
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||
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If True, write the data shape to the image_description tag
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||
|
|
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):
|
||
|
|
try:
|
||
|
|
_tifffile.TiffFile(request.get_file(), **request.kwargs)
|
||
|
|
except ValueError:
|
||
|
|
# vendored backend raises value exception
|
||
|
|
return False
|
||
|
|
except _tifffile.TiffFileError: # pragma: no-cover
|
||
|
|
# current version raises custom exception
|
||
|
|
return False
|
||
|
|
finally:
|
||
|
|
request.get_file().seek(0)
|
||
|
|
|
||
|
|
return True
|
||
|
|
|
||
|
|
def _can_write(self, request):
|
||
|
|
if request._uri_type in [URI_FILE, URI_BYTES]:
|
||
|
|
pass # special URI
|
||
|
|
elif request.extension not in self.extensions:
|
||
|
|
return False
|
||
|
|
|
||
|
|
try:
|
||
|
|
_tifffile.TiffWriter(request.get_file(), **request.kwargs)
|
||
|
|
except ValueError:
|
||
|
|
# vendored backend raises value exception
|
||
|
|
return False
|
||
|
|
except _tifffile.TiffFileError: # pragma: no-cover
|
||
|
|
# current version raises custom exception
|
||
|
|
return False
|
||
|
|
finally:
|
||
|
|
request.get_file().seek(0)
|
||
|
|
return True
|
||
|
|
|
||
|
|
# -- reader
|
||
|
|
|
||
|
|
class Reader(Format.Reader):
|
||
|
|
def _open(self, **kwargs):
|
||
|
|
# 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)
|
||
|
|
|
||
|
|
def _close(self):
|
||
|
|
self._tf.close()
|
||
|
|
if self._f is not None:
|
||
|
|
self._f.close()
|
||
|
|
|
||
|
|
def _get_length(self):
|
||
|
|
return len(self._tf.series)
|
||
|
|
|
||
|
|
def _get_data(self, index):
|
||
|
|
if index < 0 or index >= self._get_length():
|
||
|
|
raise IndexError("Index out of range while reading from tiff file")
|
||
|
|
|
||
|
|
im = self._tf.asarray(series=index)
|
||
|
|
meta = self._get_meta_data(index)
|
||
|
|
|
||
|
|
return im, meta
|
||
|
|
|
||
|
|
def _get_meta_data(self, index):
|
||
|
|
meta = {}
|
||
|
|
page = self._tf.pages[index or 0]
|
||
|
|
for key in READ_METADATA_KEYS:
|
||
|
|
try:
|
||
|
|
meta[key] = getattr(page, key)
|
||
|
|
except Exception:
|
||
|
|
pass
|
||
|
|
|
||
|
|
# tifffile <= 0.12.1 use datetime, newer use DateTime
|
||
|
|
for key in ("datetime", "DateTime"):
|
||
|
|
try:
|
||
|
|
meta["datetime"] = datetime.datetime.strptime(
|
||
|
|
page.tags[key].value, "%Y:%m:%d %H:%M:%S"
|
||
|
|
)
|
||
|
|
break
|
||
|
|
except Exception:
|
||
|
|
pass
|
||
|
|
|
||
|
|
if 296 in page.tags:
|
||
|
|
meta["resolution_unit"] = page.tags[296].value.value
|
||
|
|
|
||
|
|
if 282 in page.tags and 283 in page.tags and 296 in page.tags:
|
||
|
|
resolution_x = page.tags[282].value
|
||
|
|
resolution_y = page.tags[283].value
|
||
|
|
if resolution_x[1] == 0 or resolution_y[1] == 0:
|
||
|
|
warnings.warn(
|
||
|
|
"Ignoring resolution metadata, "
|
||
|
|
"because at least one direction has a 0 denominator.",
|
||
|
|
RuntimeWarning,
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
meta["resolution"] = (
|
||
|
|
resolution_x[0] / resolution_x[1],
|
||
|
|
resolution_y[0] / resolution_y[1],
|
||
|
|
page.tags[296].value.name,
|
||
|
|
)
|
||
|
|
|
||
|
|
return meta
|
||
|
|
|
||
|
|
# -- writer
|
||
|
|
class Writer(Format.Writer):
|
||
|
|
def _open(self, bigtiff=None, byteorder=None, software=None):
|
||
|
|
try:
|
||
|
|
self._tf = _tifffile.TiffWriter(
|
||
|
|
self.request.get_file(),
|
||
|
|
bigtiff=bigtiff,
|
||
|
|
byteorder=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=bigtiff, byteorder=byteorder
|
||
|
|
)
|
||
|
|
self._software = software
|
||
|
|
|
||
|
|
self._meta = {}
|
||
|
|
self._frames_written = 0
|
||
|
|
|
||
|
|
def _close(self):
|
||
|
|
self._tf.close()
|
||
|
|
|
||
|
|
def _append_data(self, im, meta):
|
||
|
|
if meta is not None:
|
||
|
|
meta = self._sanitize_meta(meta)
|
||
|
|
else:
|
||
|
|
# Use global metadata for first frame
|
||
|
|
meta = self._meta if self._frames_written == 0 else {}
|
||
|
|
if self._software is not None and self._frames_written == 0:
|
||
|
|
meta["software"] = self._software
|
||
|
|
# No need to check self.request.mode; tifffile figures out whether
|
||
|
|
# this is a single page, or all page data at once.
|
||
|
|
try:
|
||
|
|
# TiffWriter.save has been deprecated in version 2020.9.30
|
||
|
|
write_meth = self._tf.write
|
||
|
|
except AttributeError:
|
||
|
|
write_meth = self._tf.save
|
||
|
|
write_meth(np.asanyarray(im), contiguous=False, **meta)
|
||
|
|
self._frames_written += 1
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def _sanitize_meta(meta):
|
||
|
|
ret = {}
|
||
|
|
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):
|
||
|
|
ret[key] = value > 1
|
||
|
|
elif key == "compress" and value != 0:
|
||
|
|
warnings.warn(
|
||
|
|
"The use of `compress` is deprecated. Use `compression` and `compressionargs` instead.",
|
||
|
|
DeprecationWarning,
|
||
|
|
)
|
||
|
|
|
||
|
|
if _tifffile.__version__ < "2022":
|
||
|
|
ret["compression"] = (8, value)
|
||
|
|
else:
|
||
|
|
ret["compression"] = "zlib"
|
||
|
|
ret["compressionargs"] = {"level": value}
|
||
|
|
else:
|
||
|
|
ret[key] = value
|
||
|
|
return ret
|
||
|
|
|
||
|
|
def set_meta_data(self, meta):
|
||
|
|
self._meta = self._sanitize_meta(meta)
|