mirror of
https://github.com/wassname/scikit-image.git
synced 2026-07-15 11:25:53 +08:00
Finish merging multiimage capability into collections
This commit is contained in:
Steven Silvester
committed by
Stefan van der Walt
Stefan van der Walt
parent
b4838c3bd9
commit
76fc909b62
+106
-167
@@ -75,167 +75,6 @@ def alphanumeric_key(s):
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return k
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class MultiImage(object):
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"""A class containing a single multi-frame image.
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Parameters
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----------
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filename : str
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The complete path to the image file.
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conserve_memory : bool, optional
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Whether to conserve memory by only caching a single frame. Default is
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True.
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Notes
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-----
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If ``conserve_memory=True`` the memory footprint can be reduced, however
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the performance can be affected because frames have to be read from file
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more often.
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The last accessed frame is cached, all other frames will have to be read
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from file.
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The current implementation makes use of PIL.
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Examples
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--------
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>>> from skimage import data_dir
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>>> img = MultiImage(data_dir + '/multipage.tif') # doctest: +SKIP
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>>> len(img) # doctest: +SKIP
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2
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>>> for frame in img: # doctest: +SKIP
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... print(frame.shape) # doctest: +SKIP
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(15, 10)
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(15, 10)
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"""
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def __init__(self, filename, conserve_memory=True, dtype=None):
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"""Load a multi-img."""
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self._filename = filename
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self._conserve_memory = conserve_memory
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self._dtype = dtype
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self._cached = None
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if filename.lower().endswith(('.tiff', '.tif')):
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self.tif_img = img = TiffFile(self._filename)
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else:
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img = Image.open(self._filename)
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self.tif_img = None
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if self._conserve_memory:
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self._numframes = self._find_numframes(img)
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else:
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self._frames = self._getallframes()
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# TODO: this is not correct
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self._numframes = self._frames.shape[0]
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if not self.tif_img:
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img.fp.close()
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@property
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def filename(self):
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return self._filename
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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_numframes(self, img):
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"""Find the number of frames in the multi-img."""
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if self.tif_img:
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return len(img.pages)
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else:
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i = 0
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while True:
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i += 1
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try:
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img.seek(i)
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except EOFError:
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break
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return i
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def _getframe(self, framenum):
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"""Open the image and extract the frame."""
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if self.tif_img:
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return self.tif_img[framenum].asarray()
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else:
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from ._io import imread
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return imread(self.filename, self._dtype, img_num=framenum)
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def _getallframes(self):
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"""Extract all frames from the multi-img."""
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if self.tif_img:
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return self.tif_img.asarray()
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else:
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from ._io import imread
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return imread(self.filename, self._dtype)
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def __getitem__(self, n):
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"""Return the n-th frame as an array.
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Parameters
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----------
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n : int
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Number of the required frame.
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Returns
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-------
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frame : ndarray
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The n-th frame.
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"""
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numframes = self._numframes
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if -numframes <= n < numframes:
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n = n % numframes
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else:
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raise IndexError("There are only %s frames in the image"
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% numframes)
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if self.conserve_memory:
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if not self._cached == n:
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frame = self._getframe(n)
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self._cached = n
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self._cachedframe = frame
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return self._cachedframe
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else:
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return self._frames[n]
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def __iter__(self):
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"""Iterate over the frames."""
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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.filename) + ' [%s frames]' % self._numframes
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def concatenate(self):
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"""Concatenate all images in the multi-image 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 `MultiImage` don't have identical shapes.
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"""
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return concatenate_images(self)
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class ImageCollection(object):
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"""Load and manage a collection of image files.
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@@ -295,6 +134,9 @@ class ImageCollection(object):
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ic = ImageCollection('/tmp/*.png', load_func=imread_convert)
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For files with multiple images, the images will be flattened into a list
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and added to the list of available images.
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Examples
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--------
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>>> import skimage.io as io
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@@ -317,13 +159,16 @@ class ImageCollection(object):
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for pattern in load_pattern:
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self._files.extend(glob(pattern))
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self._files = sorted(self._files, key=alphanumeric_key)
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self._numframes = self._find_images()
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else:
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self._files = load_pattern
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self._numframes = len(load_pattern)
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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 = len(self._files)
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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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@@ -344,6 +189,32 @@ class ImageCollection(object):
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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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img = TiffFile(fname)
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index += [(fname, i) for i in range(len(img.pages))]
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else:
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im = Image.open(fname)
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try:
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# this will raise an IOError if the file is not readable
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im.getdata()[0]
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except IOError:
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site = "http://pillow.readthedocs.org/en/latest/installation.html#external-libraries"
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raise ValueError('Could not load "%s"\nPlease see documentation at: %s' % (fname, site))
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else:
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i = 0
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while True:
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i += 1
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index.append((fname, i))
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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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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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@@ -374,7 +245,12 @@ class ImageCollection(object):
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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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self.data[idx] = self.load_func(self.files[n])
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if self._frame_index:
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fname, img_num = self._frame_index[idx]
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print('loading function')
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self.data[idx] = self.load_func(fname, img_num=img_num)
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else:
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self.data[idx] = self.load_func(self.files[n])
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self._cached = n
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return self.data[idx]
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@@ -383,9 +259,17 @@ class ImageCollection(object):
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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(len(self.files))[n]
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fidx = range(self._numframes)[n]
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new_ic = copy(self)
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new_ic._files = [self.files[i] for i in fidx]
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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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@@ -398,7 +282,7 @@ class ImageCollection(object):
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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 = len(self.files)
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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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@@ -413,7 +297,7 @@ class ImageCollection(object):
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def __len__(self):
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"""Number of images in collection."""
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return len(self.files)
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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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@@ -474,3 +358,58 @@ def imread_collection_wrapper(imread):
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return ImageCollection(load_pattern, conserve_memory=conserve_memory,
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load_func=imread)
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return imread_collection
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class MultiImage(ImageCollection):
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"""A class containing a single multi-frame image.
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Parameters
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----------
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filename : str
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The complete path to the image file.
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conserve_memory : bool, optional
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Whether to conserve memory by only caching a single frame. Default is
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True.
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Notes
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-----
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If ``conserve_memory=True`` the memory footprint can be reduced, however
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the performance can be affected because frames have to be read from file
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more often.
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The last accessed frame is cached, all other frames will have to be read
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from file.
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The current implementation makes use of ``tifffile`` for Tiff files and
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PIL otherwise.
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Examples
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--------
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>>> from skimage import data_dir
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>>> img = MultiImage(data_dir + '/multipage.tif') # doctest: +SKIP
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>>> len(img) # doctest: +SKIP
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2
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>>> for frame in img: # doctest: +SKIP
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... print(frame.shape) # doctest: +SKIP
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(15, 10)
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(15, 10)
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"""
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def __init__(self, filename, conserve_memory=True, dtype=None):
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"""Load a multi-img."""
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from ._io import imread
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def load_func(fname, **kwargs):
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kwargs.setdefault('dtype', dtype)
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return imread(fname, **kwargs)
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self._filename = filename
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super(MultiImage, self).__init__(filename, conserve_memory,
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load_func=load_func)
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@property
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def filename(self):
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return self._filename
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