460 lines
14 KiB
Python
460 lines
14 KiB
Python
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"""Data structures to hold collections of images, with optional caching."""
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import os
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from glob import glob
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import re
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from collections.abc import Sequence
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from copy import copy
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import numpy as np
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from PIL import Image, __version__ as pil_version
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# Check CVE-2020-10379
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from distutils.version import LooseVersion
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if LooseVersion(pil_version) < LooseVersion('7.1.0'):
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from warnings import warn
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warn('Your installed pillow version is < 7.1.0. '
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'Several security issues (CVE-2020-11538, '
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'CVE-2020-10379, CVE-2020-10994, CVE-2020-10177) '
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'have been fixed in pillow 7.1.0 or higher. '
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'We recommend to upgrade this library.',
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stacklevel=2)
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from tifffile import TiffFile
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__all__ = ['MultiImage', 'ImageCollection', 'concatenate_images',
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'imread_collection_wrapper']
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def concatenate_images(ic):
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"""Concatenate all images in the image collection into an array.
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Parameters
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----------
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ic : an iterable of images
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The images to be concatenated.
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Returns
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-------
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array_cat : ndarray
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An array having one more dimension than the images in `ic`.
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See Also
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--------
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ImageCollection.concatenate, MultiImage.concatenate
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Raises
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------
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ValueError
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If images in `ic` don't have identical shapes.
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Notes
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-----
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``concatenate_images`` receives any iterable object containing images,
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including ImageCollection and MultiImage, and returns a NumPy array.
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"""
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all_images = [image[np.newaxis, ...] for image in ic]
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try:
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array_cat = np.concatenate(all_images)
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except ValueError:
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raise ValueError('Image dimensions must agree.')
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return array_cat
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def alphanumeric_key(s):
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"""Convert string to list of strings and ints that gives intuitive sorting.
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Parameters
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----------
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s : string
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Returns
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-------
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k : a list of strings and ints
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Examples
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--------
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>>> alphanumeric_key('z23a')
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['z', 23, 'a']
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>>> filenames = ['f9.10.png', 'e10.png', 'f9.9.png', 'f10.10.png',
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... 'f10.9.png']
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>>> sorted(filenames)
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['e10.png', 'f10.10.png', 'f10.9.png', 'f9.10.png', 'f9.9.png']
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>>> sorted(filenames, key=alphanumeric_key)
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['e10.png', 'f9.9.png', 'f9.10.png', 'f10.9.png', 'f10.10.png']
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"""
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k = [int(c) if c.isdigit() else c for c in re.split('([0-9]+)', s)]
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return k
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def _is_multipattern(input_pattern):
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"""Helping function. Returns True if pattern contains a tuple, list, or a
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string separated with os.pathsep."""
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# Conditions to be accepted by ImageCollection:
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has_str_ospathsep = (isinstance(input_pattern, str)
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and os.pathsep in input_pattern)
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not_a_string = not isinstance(input_pattern, str)
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has_iterable = isinstance(input_pattern, Sequence)
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has_strings = all(isinstance(pat, str) for pat in input_pattern)
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is_multipattern = (has_str_ospathsep or
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(not_a_string
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and has_iterable
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and has_strings))
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return is_multipattern
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class ImageCollection(object):
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"""Load and manage a collection of image files.
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Parameters
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----------
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load_pattern : str or list of str
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Pattern string or list of strings to load. The filename path can be
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absolute or relative.
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conserve_memory : bool, optional
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If True, `ImageCollection` does not keep more than one in memory at a
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specific time. Otherwise, images will be cached once they are loaded.
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Other parameters
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----------------
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load_func : callable
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``imread`` by default. See notes below.
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Attributes
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----------
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files : list of str
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If a pattern string is given for `load_pattern`, this attribute
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stores the expanded file list. Otherwise, this is equal to
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`load_pattern`.
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Notes
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-----
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Note that files are always returned in alphanumerical order. Also note
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that slicing returns a new ImageCollection, *not* a view into the data.
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ImageCollection can be modified to load images from an arbitrary
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source by specifying a combination of `load_pattern` and
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`load_func`. For an ImageCollection ``ic``, ``ic[5]`` uses
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``load_func(load_pattern[5])`` to load the image.
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Imagine, for example, an ImageCollection that loads every third
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frame from a video file::
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video_file = 'no_time_for_that_tiny.gif'
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def vidread_step(f, step):
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vid = imageio.get_reader(f)
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seq = [v for v in vid.iter_data()]
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return seq[::step]
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ic = ImageCollection(video_file, load_func=vidread_step, step=3)
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ic # is an ImageCollection object of length 1 because there is 1 file
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x = ic[0] # calls vidread_step(video_file, step=3)
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x[5] # is the sixth element of a list of length 8 (24 / 3)
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Another use of ``load_func`` would be to convert all images to ``uint8``::
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def imread_convert(f):
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return imread(f).astype(np.uint8)
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ic = ImageCollection('/tmp/*.png', load_func=imread_convert)
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Examples
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--------
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>>> import skimage.io as io
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>>> from skimage import data_dir
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>>> coll = io.ImageCollection(data_dir + '/chess*.png')
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>>> len(coll)
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2
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>>> coll[0].shape
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(200, 200)
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>>> ic = io.ImageCollection(['/tmp/work/*.png', '/tmp/other/*.jpg'])
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"""
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def __init__(self, load_pattern, conserve_memory=True, load_func=None,
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**load_func_kwargs):
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"""Load and manage a collection of images."""
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self._files = []
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if _is_multipattern(load_pattern):
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if isinstance(load_pattern, str):
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load_pattern = load_pattern.split(os.pathsep)
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for pattern in load_pattern:
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self._files.extend(glob(pattern))
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elif isinstance(load_pattern, str):
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self._files.extend(glob(load_pattern))
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else:
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raise TypeError('Invalid pattern as input.')
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self._files = sorted(self._files, key=alphanumeric_key)
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if load_func is None:
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from ._io import imread
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self.load_func = imread
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self._numframes = self._find_images()
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else:
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self.load_func = load_func
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self._numframes = len(self._files)
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self._frame_index = None
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if conserve_memory:
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memory_slots = 1
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else:
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memory_slots = self._numframes
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self._conserve_memory = conserve_memory
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self._cached = None
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self.load_func_kwargs = load_func_kwargs
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self.data = np.empty(memory_slots, dtype=object)
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@property
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def files(self):
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return self._files
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@property
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def conserve_memory(self):
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return self._conserve_memory
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def _find_images(self):
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index = []
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for fname in self._files:
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if fname.lower().endswith(('.tiff', '.tif')):
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with open(fname, 'rb') as f:
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img = TiffFile(f)
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index += [(fname, i) for i in range(len(img.pages))]
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else:
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try:
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im = Image.open(fname)
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im.seek(0)
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except (IOError, OSError):
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continue
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i = 0
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while True:
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try:
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im.seek(i)
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except EOFError:
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break
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index.append((fname, i))
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i += 1
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if hasattr(im, 'fp') and im.fp:
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im.fp.close()
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self._frame_index = index
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return len(index)
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def __getitem__(self, n):
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"""Return selected image(s) in the collection.
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Loading is done on demand.
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Parameters
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----------
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n : int or slice
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The image number to be returned, or a slice selecting the images
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and ordering to be returned in a new ImageCollection.
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Returns
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-------
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img : ndarray or ImageCollection.
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The `n`-th image in the collection, or a new ImageCollection with
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the selected images.
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"""
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if hasattr(n, '__index__'):
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n = n.__index__()
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if type(n) not in [int, slice]:
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raise TypeError('slicing must be with an int or slice object')
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if type(n) is int:
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n = self._check_imgnum(n)
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idx = n % len(self.data)
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if ((self.conserve_memory and n != self._cached) or
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(self.data[idx] is None)):
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kwargs = self.load_func_kwargs
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if self._frame_index:
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fname, img_num = self._frame_index[n]
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if img_num is not None:
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kwargs['img_num'] = img_num
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try:
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self.data[idx] = self.load_func(fname, **kwargs)
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# Account for functions that do not accept an img_num kwarg
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except TypeError as e:
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if "unexpected keyword argument 'img_num'" in str(e):
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del kwargs['img_num']
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self.data[idx] = self.load_func(fname, **kwargs)
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else:
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raise
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else:
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self.data[idx] = self.load_func(self.files[n], **kwargs)
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self._cached = n
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return self.data[idx]
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else:
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# A slice object was provided, so create a new ImageCollection
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# object. Any loaded image data in the original ImageCollection
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# will be copied by reference to the new object. Image data
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# loaded after this creation is not linked.
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fidx = range(self._numframes)[n]
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new_ic = copy(self)
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if self._frame_index:
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new_ic._files = [self._frame_index[i][0] for i in fidx]
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new_ic._frame_index = [self._frame_index[i] for i in fidx]
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else:
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new_ic._files = [self._files[i] for i in fidx]
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new_ic._numframes = len(fidx)
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if self.conserve_memory:
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if self._cached in fidx:
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new_ic._cached = fidx.index(self._cached)
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new_ic.data = np.copy(self.data)
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else:
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new_ic.data = np.empty(1, dtype=object)
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else:
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new_ic.data = self.data[fidx]
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return new_ic
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def _check_imgnum(self, n):
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"""Check that the given image number is valid."""
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num = self._numframes
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if -num <= n < num:
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n = n % num
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else:
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raise IndexError("There are only %s images in the collection"
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% num)
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return n
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def __iter__(self):
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"""Iterate over the images."""
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for i in range(len(self)):
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yield self[i]
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def __len__(self):
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"""Number of images in collection."""
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return self._numframes
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def __str__(self):
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return str(self.files)
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def reload(self, n=None):
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"""Clear the image cache.
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Parameters
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----------
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n : None or int
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Clear the cache for this image only. By default, the
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entire cache is erased.
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"""
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self.data = np.empty_like(self.data)
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def concatenate(self):
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"""Concatenate all images in the collection into an array.
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Returns
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-------
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ar : np.ndarray
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An array having one more dimension than the images in `self`.
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See Also
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--------
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concatenate_images
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Raises
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------
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ValueError
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If images in the `ImageCollection` don't have identical shapes.
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"""
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return concatenate_images(self)
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def imread_collection_wrapper(imread):
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def imread_collection(load_pattern, conserve_memory=True):
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"""Return an `ImageCollection` from files matching the given pattern.
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Note that files are always stored in alphabetical order. Also note that
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slicing returns a new ImageCollection, *not* a view into the data.
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See `skimage.io.ImageCollection` for details.
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Parameters
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----------
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load_pattern : str or list
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Pattern glob or filenames to load. The path can be absolute or
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relative. Multiple patterns should be separated by a colon,
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e.g. ``/tmp/work/*.png:/tmp/other/*.jpg``. Also see
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implementation notes below.
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conserve_memory : bool, optional
|
||
|
|
If True, never keep more than one in memory at a specific
|
||
|
|
time. Otherwise, images will be cached once they are loaded.
|
||
|
|
|
||
|
|
"""
|
||
|
|
return ImageCollection(load_pattern, conserve_memory=conserve_memory,
|
||
|
|
load_func=imread)
|
||
|
|
return imread_collection
|
||
|
|
|
||
|
|
|
||
|
|
class MultiImage(ImageCollection):
|
||
|
|
|
||
|
|
"""A class containing all frames from multi-frame images.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
load_pattern : str or list of str
|
||
|
|
Pattern glob or filenames to load. The path can be absolute or
|
||
|
|
relative.
|
||
|
|
conserve_memory : bool, optional
|
||
|
|
Whether to conserve memory by only caching a single frame. Default is
|
||
|
|
True.
|
||
|
|
|
||
|
|
Other parameters
|
||
|
|
----------------
|
||
|
|
load_func : callable
|
||
|
|
``imread`` by default. See notes below.
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
If ``conserve_memory=True`` the memory footprint can be reduced, however
|
||
|
|
the performance can be affected because frames have to be read from file
|
||
|
|
more often.
|
||
|
|
|
||
|
|
The last accessed frame is cached, all other frames will have to be read
|
||
|
|
from file.
|
||
|
|
|
||
|
|
The current implementation makes use of ``tifffile`` for Tiff files and
|
||
|
|
PIL otherwise.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> from skimage import data_dir
|
||
|
|
|
||
|
|
>>> img = MultiImage(data_dir + '/multipage.tif') # doctest: +SKIP
|
||
|
|
>>> len(img) # doctest: +SKIP
|
||
|
|
2
|
||
|
|
>>> for frame in img: # doctest: +SKIP
|
||
|
|
... print(frame.shape) # doctest: +SKIP
|
||
|
|
(15, 10)
|
||
|
|
(15, 10)
|
||
|
|
|
||
|
|
"""
|
||
|
|
|
||
|
|
def __init__(self, filename, conserve_memory=True, dtype=None,
|
||
|
|
**imread_kwargs):
|
||
|
|
"""Load a multi-img."""
|
||
|
|
from ._io import imread
|
||
|
|
|
||
|
|
self._filename = filename
|
||
|
|
super(MultiImage, self).__init__(filename, conserve_memory,
|
||
|
|
load_func=imread, **imread_kwargs)
|
||
|
|
|
||
|
|
@property
|
||
|
|
def filename(self):
|
||
|
|
return self._filename
|