def open(sequence, **kwargs):
"""Read a filename, list of filenames, or directory of image files into an
iterable that returns images as numpy arrays.
Parameters
----------
sequence : string, list of strings, or glob
The sequence you want to load. This can be a directory containing
images, a glob ('/path/foo*.png') pattern of images,
a video file, or a tiff stack
kwargs :
All keyword arguments will be passed to the reader.
Examples
--------
>>> video = open('path/to/images/*.png') # or *.tif, or *.jpg
>>> imshow(video[0]) # Show the first frame.
>>> imshow(video[-1]) # Show the last frame.
>>> imshow(video[1][0:10, 0:10]) # Show one corner of the second frame.
>>> for frame in video[:]:
... # Do something with every frame.
>>> for frame in video[10:20]:
... # Do something with frames 10-20.
>>> for frame in video[[5, 7, 13]]:
... # Do something with frames 5, 7, and 13.
>>> frame_count = len(video) # Number of frames in video
>>> frame_shape = video.frame_shape # Pixel dimensions of video
"""
files = glob.glob(sequence)
if len(files) > 1:
# todo: test if ImageSequence can read the image type,
# delegate to subclasses as needed
return ImageSequence(sequence, **kwargs)
_, ext = os.path.splitext(sequence)
if ext is None or len(ext) < 2:
raise UnknownFormatError(
"Could not detect your file type because it did not have an "
"extension. Try specifying a loader class, e.g. "
"Video({0})".format(sequence))
ext = ext.lower()[1:]
# list all readers derived from the pims baseclasses
all_handlers = chain(_recursive_subclasses(FramesSequence),
_recursive_subclasses(FramesSequenceND))
# keep handlers that support the file ext. use set to avoid duplicates.
eligible_handlers = set(h for h in all_handlers
if ext and ext in map(_drop_dot, h.class_exts()))
if len(eligible_handlers) < 1:
raise UnknownFormatError(
"Could not autodetect how to load a file of type {0}. "
"Try manually "
"specifying a loader class, e.g. Video({1})".format(ext, sequence))
def sort_on_priority(handlers):
# This uses optional priority information from subclasses
# > 10 means that it will be used instead of than built-in subclasses
def priority(cls):
try:
return cls.class_priority
except AttributeError:
return 10
return sorted(handlers, key=priority, reverse=True)
exceptions = ''
for handler in sort_on_priority(eligible_handlers):
try:
return handler(sequence, **kwargs)
except Exception as e:
message = '{0} errored: {1}'.format(str(handler), str(e))
warn(message)
exceptions += message + '\n'
raise UnknownFormatError("All handlers returned exceptions:\n" + exceptions)
def open(sequence, process_func=None, dtype=None, as_grey=False, plugin=None):
"""Read a directory of sequentially numbered image files into an
iterable that returns images as numpy arrays.
Parameters
----------
sequence : string, list of strings, or glob
The sequence you want to load. This can be a directory containing
images, a glob ('/path/foo*.png') pattern of images,
a video file, or a tiff stack
process_func : function, optional
callable with signalture `proc_img = process_func(img)`,
which will be applied to the data from each frame
dtype : numpy datatype, optional
Image arrays will be converted to this datatype.
as_grey : boolean, optional
Convert color images to greyscale. False by default.
May not be used in conjection with process_func.
plugin : string
Passed on to skimage.io.imread if scikit-image is available.
If scikit-image is not available, this will be ignored and a warning
will be issued.
Examples
--------
>>> video = open('path/to/images/*.png') # or *.tif, or *.jpg
>>> imshow(video[0]) # Show the first frame.
>>> imshow(video[-1]) # Show the last frame.
>>> imshow(video[1][0:10, 0:10]) # Show one corner of the second frame.
>>> for frame in video[:]:
... # Do something with every frame.
>>> for frame in video[10:20]:
... # Do something with frames 10-20.
>>> for frame in video[[5, 7, 13]]:
... # Do something with frames 5, 7, and 13.
>>> frame_count = len(video) # Number of frames in video
>>> frame_shape = video.frame_shape # Pixel dimensions of video
"""
files = glob.glob(sequence)
if len(files) > 1:
# todo: test if ImageSequence can read the image type,
# delegate to subclasses as needed
return ImageSequence(sequence, process_func, dtype, as_grey, plugin)
# We are now not in an image sequence, so warn if plugin is specified,
# since we will not be able to use it
if plugin is not None:
warn("scikit-image plugin specification ignored because such plugins "
"only apply when loading a sequence of image files. ")
_, ext = os.path.splitext(sequence)
if ext is None or len(ext) < 2:
raise UnknownFormatError(
"Could not detect your file type because it did not have an "
"extension. Try specifying a loader class, e.g. "
"Video({1})".format(sequence))
ext = ext.lower()[1:]
all_handlers = _recursive_subclasses(FramesSequence)
eligible_handlers = [
h for h in all_handlers if ext and ext in h.class_exts()
]
if len(eligible_handlers) < 1:
raise UnknownFormatError(
"Could not autodetect how to load a file of type {0}. "
"Try manually "
"specifying a loader class, e.g. Video({1})".format(ext, sequence))
def sort_on_priority(handlers):
# TODO make this use optional information from subclasses
# give any user-defined (non-build-in) subclasses priority
return handlers
handler = sort_on_priority(eligible_handlers)[0]
# TODO maybe we should wrap this in a try and loop to try all the
# handlers if early ones throw exceptions
return handler(sequence,
process_func=process_func,
dtype=dtype,
as_grey=as_grey)