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Use tifffile 0.3.2, which passes doctests

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This commit is contained in:
Steven Silvester
2014-10-16 05:05:37 -05:00
parent b5da90e4c7
commit 17a3b50a5e
1 changed files with 40 additions and 40 deletions
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skimage/external/tifffile/tifffile_local.py
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+40 -40
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@@ -116,13 +116,13 @@ References
Examples
--------
>> data = numpy.random.rand(5, 301, 219)
>> imsave('temp.tif', data)
>>> data = numpy.random.rand(5, 301, 219)
>>> imsave('temp.tif', data)
>> image = imread('temp.tif')
>> numpy.testing.assert_array_equal(image, data)
>>> image = imread('temp.tif')
>>> numpy.testing.assert_array_equal(image, data)
>> with TiffFile('temp.tif') as tif:
>>> with TiffFile('temp.tif') as tif:
... images = tif.asarray()
... for page in tif:
... for tag in page.tags.values():
@@ -153,7 +153,7 @@ import numpy
from . import _tifffile
__version__ = '0.3.1'
__version__ = '0.3.2'
__docformat__ = 'restructuredtext en'
__all__ = ('imsave', 'imread', 'imshow', 'TiffFile', 'TiffWriter',
'TiffSequence')
@@ -180,9 +180,9 @@ def imsave(filename, data, **kwargs):
Examples
--------
>> data = numpy.random.rand(2, 5, 3, 301, 219)
>> description = u'{"shape": %s}' % str(list(data.shape))
>> imsave('temp.tif', data, compress=6,
>>> data = numpy.random.rand(2, 5, 3, 301, 219)
>>> description = u'{"shape": %s}' % str(list(data.shape))
>>> imsave('temp.tif', data, compress=6,
... extratags=[(270, 's', 0, description, True)])
"""
@@ -209,8 +209,8 @@ class TiffWriter(object):
Examples
--------
>> data = numpy.random.rand(2, 5, 3, 301, 219)
>> with TiffWriter('temp.tif', bigtiff=True) as tif:
>>> data = numpy.random.rand(2, 5, 3, 301, 219)
>>> with TiffWriter('temp.tif', bigtiff=True) as tif:
... for i in range(data.shape[0]):
... tif.save(data[i], compress=6)
@@ -663,12 +663,12 @@ def imread(files, **kwargs):
Examples
--------
>> im = imread('test.tif', key=0)
>> im.shape
(256, 256, 4)
>> ims = imread(['test.tif', 'test.tif'])
>> ims.shape
(2, 256, 256, 4)
>>> im = imread('temp.tif', key=0)
>>> im.shape
(3, 301, 219)
>>> ims = imread(['temp.tif', 'temp.tif'])
>>> ims.shape
(2, 10, 3, 301, 219)
"""
kwargs_file = {}
@@ -733,10 +733,10 @@ class TiffFile(object):
Examples
--------
>> with TiffFile('test.tif') as tif:
>>> with TiffFile('temp.tif') as tif:
... data = tif.asarray()
... data.shape
(256, 256, 4)
(5, 301, 219)
"""
def __init__(self, arg, name=None, offset=None, size=None,
@@ -2215,11 +2215,11 @@ class TiffSequence(object):
Examples
--------
>> tifs = TiffSequence("test.oif.files/*.tif")
>> tifs.shape, tifs.axes
>>> tifs = TiffSequence("test.oif.files/*.tif") # doctest: +SKIP
>>> tifs.shape, tifs.axes # doctest: +SKIP
((2, 100), 'CT')
>> data = tifs.asarray()
>> data.shape
>>> data = tifs.asarray() # doctest: +SKIP
>>> data.shape # doctest: +SKIP
(2, 100, 256, 256)
"""
@@ -3316,12 +3316,12 @@ def unpackrgb(data, dtype='<B', bitspersample=(5, 6, 5), rescale=True):
Examples
--------
>> data = struct.pack('BBBB', 0x21, 0x08, 0xff, 0xff)
>> print(unpackrgb(data, '<B', (5, 6, 5), False))
>>> data = struct.pack('BBBB', 0x21, 0x08, 0xff, 0xff)
>>> print(unpackrgb(data, '<B', (5, 6, 5), False))
[ 1 1 1 31 63 31]
>> print(unpackrgb(data, '<B', (5, 6, 5)))
>>> print(unpackrgb(data, '<B', (5, 6, 5)))
[ 8 4 8 255 255 255]
>> print(unpackrgb(data, '<B', (5, 5, 5)))
>>> print(unpackrgb(data, '<B', (5, 5, 5)))
[ 16 8 8 255 255 255]
"""
@@ -3381,7 +3381,7 @@ def squeeze_axes(shape, axes, skip='XY'):
Remove unused dimensions unless their axes are listed in 'skip'.
>> squeeze_axes((5, 1, 2, 1, 1), 'TZYXC')
>>> squeeze_axes((5, 1, 2, 1, 1), 'TZYXC')
((5, 2, 1), 'TYX')
"""
@@ -3397,7 +3397,7 @@ def transpose_axes(data, axes, asaxes='CTZYX'):
A view is returned if possible.
>> transpose_axes(numpy.zeros((2, 3, 4, 5)), 'TYXC', asaxes='CTZYX').shape
>>> transpose_axes(numpy.zeros((2, 3, 4, 5)), 'TYXC', asaxes='CTZYX').shape
(5, 2, 1, 3, 4)
"""
@@ -3448,7 +3448,7 @@ def stripnull(string):
Clean NULL terminated C strings.
>> stripnull(b'string\\x00')
>>> stripnull(b'string\\x00')
b'string'
"""
@@ -3461,9 +3461,9 @@ def stripascii(string):
Clean NULL separated and terminated TIFF strings.
>> stripascii(b'string\\x00string\\n\\x01\\x00')
>>> stripascii(b'string\\x00string\\n\\x01\\x00')
b'string\\x00string\\n'
>> stripascii(b'\\x00')
>>> stripascii(b'\\x00')
b''
"""
@@ -3490,9 +3490,9 @@ def format_size(size):
def sequence(value):
"""Return tuple containing value if value is not a sequence.
>> sequence(1)
>>> sequence(1)
(1,)
>> sequence([1])
>>> sequence([1])
[1]
"""
@@ -3508,9 +3508,9 @@ def product(iterable):
Equivalent of functools.reduce(operator.mul, iterable, 1).
>> product([2**8, 2**30])
>>> product([2**8, 2**30])
274877906944
>> product([])
>>> product([])
1
"""
@@ -3525,7 +3525,7 @@ def natural_sorted(iterable):
E.g. for sorting file names.
>> natural_sorted(['f1', 'f2', 'f10'])
>>> natural_sorted(['f1', 'f2', 'f10'])
['f1', 'f2', 'f10']
"""
@@ -3540,7 +3540,7 @@ def excel_datetime(timestamp, epoch=datetime.datetime.fromordinal(693594)):
Convert LSM time stamps.
>> excel_datetime(40237.029999999795)
>>> excel_datetime(40237.029999999795)
datetime.datetime(2010, 2, 28, 0, 43, 11, 999982)
"""
@@ -3552,7 +3552,7 @@ def julian_datetime(julianday, milisecond=0):
Convert Julian dates according to MetaMorph.
>> julian_datetime(2451576, 54362783)
>>> julian_datetime(2451576, 54362783)
datetime.datetime(2000, 2, 2, 15, 6, 2, 783)
"""
@@ -3586,7 +3586,7 @@ def test_tifffile(directory='testimages', verbose=True):
Print error message on failure.
>> test_tifffile(verbose=False)
>>> test_tifffile(verbose=False)
"""
successful = 0