def test_init(self):
corrected = ImageSeries(name='corrected',
data=np.ones((1000, 100, 100)),
unit='na',
format='raw',
starting_time=0.0,
rate=1.0)
xy_translation = TimeSeries(
name='xy_translation',
data=np.ones((1000, 2)),
unit='pixels',
starting_time=0.0,
rate=1.0,
)
ip = create_imaging_plane()
image_series = TwoPhotonSeries(name='TwoPhotonSeries1',
data=np.ones((1000, 100, 100)),
imaging_plane=ip,
rate=1.0,
unit='normalized amplitude')
corrected_image_stack = CorrectedImageStack(
corrected=corrected,
original=image_series,
xy_translation=xy_translation,
)
motion_correction = MotionCorrection(
corrected_image_stacks=[corrected_image_stack])
self.assertEqual(
motion_correction.corrected_image_stacks['CorrectedImageStack'],
corrected_image_stack)
def setUpContainer(self):
""" Return the test ImagingPlane to read/write """
self.device, self.optical_channel, self.imaging_plane = make_imaging_plane(
)
self.two_photon_series = TwoPhotonSeries(
name='TwoPhotonSeries',
data=np.ones((1000, 100, 100)),
imaging_plane=self.imaging_plane,
rate=1.0,
unit='normalized amplitude')
corrected = ImageSeries(name='corrected',
data=np.ones((1000, 100, 100)),
unit='na',
format='raw',
starting_time=0.0,
rate=1.0)
xy_translation = TimeSeries(
name='xy_translation',
data=np.ones((1000, 2)),
unit='pixels',
starting_time=0.0,
rate=1.0,
)
corrected_image_stack = CorrectedImageStack(
corrected=corrected,
original=self.two_photon_series,
xy_translation=xy_translation,
)
return MotionCorrection(corrected_image_stacks=[corrected_image_stack])
def cicada_create_motion_correction(self):
""" class pynwb.ophys.MotionCorrection(corrected_images_stacks={}, name='MotionCorrection')
"""
# Nom du module où récupérer les infos de métadonnée
name_module = "motion_correction_"
corrected_images_stacks = {}
self.motion_correction = MotionCorrection(
corrected_images_stacks=corrected_images_stacks,
name="MotionCorrection")
self.mod.add_data_interface(self.motion_correction)
def test_init(self):
MotionCorrection(list())
def test_init(self):
mc = MotionCorrection('test_mc', list())
self.assertEqual(mc.source, 'test_mc')
xy_translation = TimeSeries(
name='xy_translation',
data=np.ones((1000, 2)),
unit='pixels',
starting_time=0.0,
rate=1.0,
)
corrected_image_stack = CorrectedImageStack(
corrected=corrected,
original=image_series1,
xy_translation=xy_translation,
)
motion_correction = MotionCorrection(
corrected_image_stacks=[corrected_image_stack])
####################
# We will create a :py:class:`~pynwb.base.ProcessingModule` named "ophys" to store optical
# physiology data and add the motion correction data to the :py:class:`~pynwb.file.NWBFile`.
#
ophys_module = nwbfile.create_processing_module(
name='ophys', description='optical physiology processed data')
ophys_module.add(motion_correction)
####################
# Plane Segmentation
# ---------------------------------
#