make MotionCorrection test (#1374)

* attempt to make MotionCorrection test. I don't understand why it's failing

* Fix CorrectedImageStack nwbfields

* Fix tests

* Fix test

* Fix flake8

* Fix test

Co-authored-by: Ryan Ly <[email protected]>

src/pynwb/ophys.py

@@ -161,8 +161,8 @@ class CorrectedImageStack(NWBDataInterface):
     assumed to be 2-D (has only x & y dimensions).
     """
 
-    __nwbfields__ = ({'name': 'corrected', 'child': True},
-                     {'name': 'xy_translation', 'child': True},
+    __nwbfields__ = ({'name': 'corrected', 'child': True, 'required_name': 'corrected'},
+                     {'name': 'xy_translation', 'child': True, 'required_name': 'xy_translation'},
                      'original')
 
     @docval({'name': 'name', 'type': str,
@@ -193,7 +193,7 @@ class MotionCorrection(MultiContainerInterface):
         'get': 'get_corrected_image_stack',
         'create': 'create_corrected_image_stack',
         'type': CorrectedImageStack,
-        'attr': 'corrected_images_stacks'
+        'attr': 'corrected_image_stacks'
     }
 
 

tests/integration/hdf5/test_ophys.py

@@ -1,19 +1,46 @@
 from copy import deepcopy
 from abc import ABCMeta
 
+import numpy as np
 from pynwb.ophys import (
     ImagingPlane,
     OpticalChannel,
     PlaneSegmentation,
     ImageSegmentation,
     TwoPhotonSeries,
-    RoiResponseSeries
+    RoiResponseSeries,
+    MotionCorrection,
+    CorrectedImageStack,
 )
+from pynwb.base import TimeSeries
 from pynwb.image import ImageSeries
 from pynwb.device import Device
 from pynwb.testing import NWBH5IOMixin, AcquisitionH5IOMixin, TestCase
 
 
+def make_imaging_plane():
+    """ Make an ImagingPlane and related objects """
+    device = Device(name='dev1')
+    optical_channel = OpticalChannel(
+        name='optchan1',
+        description='a fake OpticalChannel',
+        emission_lambda=500.
+    )
+    imaging_plane = ImagingPlane(
+        name='imgpln1',
+        optical_channel=optical_channel,
+        description='a fake ImagingPlane',
+        device=device,
+        excitation_lambda=600.,
+        imaging_rate=300.,
+        indicator='GFP',
+        location='somewhere in the brain',
+        reference_frame='unknown'
+    )
+
+    return device, optical_channel, imaging_plane
+
+
 class TestImagingPlaneIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):
@@ -50,31 +77,69 @@ def getContainer(self, nwbfile):
         return nwbfile.get_imaging_plane(self.container.name)
 
 
-class TestTwoPhotonSeriesIO(AcquisitionH5IOMixin, TestCase):
+class TestMotionCorrection(NWBH5IOMixin, TestCase):
 
-    def make_imaging_plane(self):
-        """ Make an ImagingPlane and related objects """
-        self.device = Device(name='dev1')
-        self.optical_channel = OpticalChannel(
-            name='optchan1',
-            description='a fake OpticalChannel',
-            emission_lambda=500.
+    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'
         )
-        self.imaging_plane = ImagingPlane(
-            name='imgpln1',
-            optical_channel=self.optical_channel,
-            description='a fake ImagingPlane',
-            device=self.device,
-            excitation_lambda=600.,
-            imaging_rate=300.,
-            indicator='GFP',
-            location='somewhere in the brain',
-            reference_frame='unknown'
+
+        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 addContainer(self, nwbfile):
+        """ Add the test ImagingPlane and Device to the given NWBFile """
+
+        nwbfile.add_device(self.device)
+        nwbfile.add_imaging_plane(self.imaging_plane)
+        nwbfile.add_acquisition(self.two_photon_series)
+
+        ophys_module = nwbfile.create_processing_module(
+            name='ophys',
+            description='optical physiology processed data'
         )
+        ophys_module.add(self.container)
+
+    def getContainer(self, nwbfile):
+        """ Return the test ImagingPlane from the given NWBFile """
+        return nwbfile.processing['ophys'].data_interfaces['MotionCorrection']
+
+
+class TestTwoPhotonSeriesIO(AcquisitionH5IOMixin, TestCase):
 
     def setUpContainer(self):
         """ Return the test TwoPhotonSeries to read/write """
-        self.make_imaging_plane()
+        self.device, self.optical_channel, self.imaging_plane = make_imaging_plane()
         data = [[[1., 1.] * 2] * 2]
         timestamps = list(map(lambda x: x/10, range(10)))
         fov = [2.0, 2.0, 5.0]

tests/unit/test_ophys.py

@@ -200,13 +200,47 @@ def test_init(self):
 
 class MotionCorrectionConstructor(TestCase):
     def test_init(self):
-        MotionCorrection(list())
+        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)
 
 
 class CorrectedImageStackConstructor(TestCase):
     def test_init(self):
         is1 = ImageSeries(
-            name='is1',
+            name='corrected',
             data=np.ones((2, 2, 2)),
             unit='unit',
             external_file=['external_file'],
@@ -216,7 +250,6 @@ def test_init(self):
         )
         is2 = ImageSeries(
             name='is2',
-            data=np.ones((2, 2, 2)),
             unit='unit',
             external_file=['external_file'],
             starting_frame=[1, 2, 3],
@@ -225,7 +258,7 @@ def test_init(self):
         )
         tstamps = np.arange(1.0, 100.0, 0.1, dtype=np.float)
         ts = TimeSeries(
-            name="test_ts",
+            name='xy_translation',
             data=list(range(len(tstamps))),
             unit='unit',
             timestamps=tstamps