def setUp(self):
_skip_if_no_imread()
self.filepath = os.path.join(path, 'image_sequence3d')
self.filenames = [
'file_t001_z001_c1.png', 'file_t001_z001_c2.png',
'file_t001_z002_c1.png', 'file_t001_z002_c2.png',
'file_t002_z001_c1.png', 'file_t002_z001_c2.png',
'file_t002_z002_c1.png', 'file_t002_z002_c2.png',
'file_t003_z001_c1.png', 'file_t003_z001_c2.png',
'file_t003_z002_c1.png', 'file_t003_z002_c2.png'
]
shape = (10, 11)
frames = save_dummy_png(self.filepath, self.filenames, shape)
self.filename = os.path.join(self.filepath, '*.png')
self.frame0 = np.array([frames[0], frames[2]])
self.frame1 = np.array([frames[4], frames[6]])
self.klass = pims.ImageSequenceND
self.kwargs = dict(axes_identifiers='tzc')
self.v = self.klass(self.filename, **self.kwargs)
self.v.default_coords['c'] = 0
self.expected_len = 3
self.expected_Z = 2
self.expected_C = 2
self.expected_shape = (self.expected_Z, ) + shape
def setUp(self):
_skip_if_no_skimage()
self.filepath = os.path.join(path, 'image_sequence')
self.filenames = [
'T76S3F00001.png', 'T76S3F00002.png', 'T76S3F00003.png',
'T76S3F00004.png', 'T76S3F00005.png'
]
shape = (10, 11)
frames = save_dummy_png(self.filepath, self.filenames, shape)
self.filename = os.path.join(self.filepath, '*.png')
self.frame0 = frames[0]
self.frame1 = frames[1]
self.kwargs = dict(plugin='matplotlib')
self.klass = pims.ImageSequence
self.v = self.klass(self.filename, **self.kwargs)
self.expected_shape = shape
self.expected_len = 5
def setUp(self):
_skip_if_no_imread()
self.filepath = os.path.join(path, 'image_sequence3d')
self.filenames = [
'file001.png', 'file002.png', 'file003.png', 'file004.png'
]
shape = (10, 11, 3)
frames = save_dummy_png(self.filepath, self.filenames, shape)
self.filename = os.path.join(self.filepath, '*.png')
self.frame0 = frames[0]
self.frame1 = frames[1]
self.klass = pims.ReaderSequence
self.kwargs = dict(reader_cls=pims.ImageReaderND, axis_name='t')
self.v = self.klass(self.filename, **self.kwargs)
self.v.bundle_axes = 'yxc'
self.v.iter_axes = 't'
self.expected_len = 4
self.expected_C = 3
self.expected_shape = (10, 11, 3)
def setUp(self):
_skip_if_no_skimage()
self.filepath = os.path.join(path, 'image_sequence')
self.filenames = [
'T76S3F00001.png', 'T76S3F00002.png', 'T76S3F00003.png',
'T76S3F00004.png', 'T76S3F00005.png'
]
shape = (10, 11)
frames = save_dummy_png(self.filepath, self.filenames, shape)
self.filename = os.path.join(self.filepath, '*.png')
self.frame0 = frames[0]
self.frame1 = frames[1]
self.kwargs = dict(plugin='pil')
self.klass = pims.ImageSequence
self.v = self.klass(self.filename, **self.kwargs)
self.expected_shape = shape
self.expected_len = 5
self.tempdir = tempfile.mkdtemp()
self.tempfile = os.path.join(self.tempdir, 'test.zip')
with zipfile.ZipFile(self.tempfile, 'w') as archive:
for fn in self.filenames:
archive.write(os.path.join(self.filepath, fn))