nwb_image_series

Author: aleksandercwikla

README.md

@@ -72,4 +72,9 @@ Representation of CameraDevice object in NWB <br>
 **Attributes:** <br>
     **meters_per_pixel**  `float`: meter per pixel <br>
 
+#### NbwTimeSeries
+Extension of ImageSeries object in NWB <br>
+**Attributes:** <br>
+    **devices**  `list of Device`: devices used to record video <br>
+
 This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).

spec/ndx-franklab-novela.extensions.yaml

@@ -72,6 +72,13 @@ groups:
   - name: meters_per_pixel
     dtype: float
     doc: meters per pixel
+- neurodata_type_def: NwbImageSeries
+  neurodata_type_inc: ImageSeries
+  doc: Extension of ImageSeries object in NWB
+  groups:
+  - neurodata_type_inc: Device
+    doc: devices used to record video
+    quantity: '*'
 - neurodata_type_def: HeaderDevice
   neurodata_type_inc: Device
   doc: metadata from global configuration from header

spec/ndx-franklab-novela.namespace.yaml

@@ -11,5 +11,6 @@ namespaces:
     - ElectrodeGroup
     - Device
     - NWBDataInterface
+    - ImageSeries
   - source: ndx-franklab-novela.extensions.yaml
   version: 0.0.007

src/pynwb/ndx_franklab_novela/nwb_image_series.py

@@ -0,0 +1,31 @@
+from hdmf import docval
+from hdmf.utils import get_docval, call_docval_func
+from pynwb import register_class
+from pynwb.core import MultiContainerInterface
+from pynwb.device import Device
+from pynwb.image import ImageSeries
+
+
+@register_class('NwbImageSeries', 'ndx-franklab-novela')
+class NwbImageSeries(ImageSeries, MultiContainerInterface):
+    ''' Extension of ImageSeries object in NWB '''
+
+    @docval(*get_docval(ImageSeries .__init__) + (
+            {'name': 'devices', 'type': (list, tuple), 'doc': 'devices used to record video', 'default': list()},
+    ))
+    def __init__(self, **kwargs):
+        super().__init__(**{kwargs_item: kwargs[kwargs_item]
+                            for kwargs_item in kwargs.copy()
+                            if kwargs_item != 'devices'
+                            })
+        call_docval_func(super(NwbImageSeries, self).__init__, kwargs)
+        self.devices = kwargs['devices']
+
+    __clsconf__ = [
+        {
+            'attr': 'devices',
+            'type': Device,
+            'add': 'add_device',
+            'get': 'get_device'
+        }
+    ]

src/pynwb/ndx_franklab_novela/spec/ndx-franklab-novela.extensions.yaml

@@ -72,6 +72,13 @@ groups:
   - name: meters_per_pixel
     dtype: float
     doc: meters per pixel
+- neurodata_type_def: NwbImageSeries
+  neurodata_type_inc: ImageSeries
+  doc: Extension of ImageSeries object in NWB
+  groups:
+  - neurodata_type_inc: Device
+    doc: devices used to record video
+    quantity: '*'
 - neurodata_type_def: HeaderDevice
   neurodata_type_inc: Device
   doc: metadata from global configuration from header

src/pynwb/ndx_franklab_novela/spec/ndx-franklab-novela.namespace.yaml

@@ -11,5 +11,6 @@ namespaces:
     - ElectrodeGroup
     - Device
     - NWBDataInterface
+    - ImageSeries
   - source: ndx-franklab-novela.extensions.yaml
   version: 0.0.007

src/pynwb/tests/test_nwbImageSeries.py

@@ -0,0 +1,30 @@
+from unittest import TestCase
+from unittest.mock import Mock
+
+from pynwb.device import Device
+
+from src.pynwb.ndx_franklab_novela.nwb_image_series import NwbImageSeries
+
+
+class TestNwbImageSeries(TestCase):
+
+    def test_nwb_image_series_created_successfully(self):
+        mock_device_1 = Mock(spec=Device)
+        mock_device_2 = Mock(spec=Device)
+        mock_timestamps = [1, 2, 3]
+        mock_external_file = []
+
+        nwb_image_series = NwbImageSeries(
+            name='NwbImageSeries1',
+            timestamps=mock_timestamps,
+            external_file=mock_external_file,
+            devices=[mock_device_1, mock_device_2]
+        )
+
+        self.assertEqual(nwb_image_series.name, 'NwbImageSeries1')
+        self.assertEqual(nwb_image_series.timestamps, mock_timestamps)
+        self.assertEqual(nwb_image_series.external_file, mock_external_file)
+        self.assertEqual(nwb_image_series.devices, {
+            mock_device_1.name: mock_device_1,
+            mock_device_2.name: mock_device_2
+        })

src/pynwb/tests/test_read_nwb.py

@@ -1,17 +1,21 @@
 import os
+from unittest.mock import Mock
 
 import pynwb
-from pynwb import NWBHDF5IO
+from pynwb import NWBHDF5IO, ProcessingModule
 
 from datetime import datetime
 from dateutil.tz import tzlocal
 from pynwb import NWBFile
+from pynwb.behavior import BehavioralTimeSeries
 from pynwb.device import Device
 from pynwb.testing import TestCase
 
+from src.pynwb.ndx_franklab_novela.camera_device import CameraDevice
 from src.pynwb.ndx_franklab_novela.data_acq_device import DataAcqDevice
 from src.pynwb.ndx_franklab_novela.header_device import HeaderDevice
 from src.pynwb.ndx_franklab_novela.nwb_electrode_group import NwbElectrodeGroup
+from src.pynwb.ndx_franklab_novela.nwb_image_series import NwbImageSeries
 from src.pynwb.ndx_franklab_novela.probe import Probe, Shank, ShanksElectrode
 
 
@@ -116,6 +120,54 @@ def test_read_nwb_data_acq_device_successfully(self):
 
         self.delete_nwb('data_acq_device')
 
+    def test_read_nwb_camera_device_successfully(self):
+        camera_device = CameraDevice(
+            name='CameraDevice1',
+            meters_per_pixel=0.20
+        )
+        self.nwb_file_content.add_device(camera_device)
+
+        nwb_file_handler = NWBHDF5IO('camera_device.nwb', mode='w')
+        nwb_file_handler.write(self.nwb_file_content)
+        nwb_file_handler.close()
+
+        self.assertTrue(os.path.exists('camera_device.nwb'))
+        with pynwb.NWBHDF5IO('camera_device.nwb', 'r',  load_namespaces=True) as nwb_file_handler:
+            nwb_file = nwb_file_handler.read()
+            self.assertContainerEqual(nwb_file.devices['CameraDevice1'], camera_device)
+
+        self.delete_nwb('camera_device')
+
+    def test_read_nwb_nwb_image_series_successfully(self):
+        mock_device_1 = Mock(spec=Device)
+        mock_device_2 = Mock(spec=Device)
+        mock_timestamps = [1, 2, 3]
+        mock_external_file = []
+
+        nwb_image_series = NwbImageSeries(
+            name='NwbImageSeries1',
+            timestamps=mock_timestamps,
+            external_file=mock_external_file,
+            devices=[mock_device_1, mock_device_2]
+        )
+        behavioral_time_series = BehavioralTimeSeries(name="ImageSeries")
+        behavioral_time_series.add_timeseries(nwb_image_series)
+        processing_module = ProcessingModule(name='PM_ImageSeries', description='')
+        self.nwb_file_content.add_processing_module(processing_module)
+        self.nwb_file_content.processing['PM_ImageSeries'].add(behavioral_time_series)
+
+        nwb_file_handler = NWBHDF5IO('nwb_image_series.nwb', mode='w')
+        nwb_file_handler.write(self.nwb_file_content)
+        # nwb_file_handler.close()
+        #
+        # self.assertTrue(os.path.exists('nwb_image_series.nwb'))
+        # with pynwb.NWBHDF5IO('nwb_image_series.nwb', 'r',  load_namespaces=True) as nwb_file_handler:
+        #     nwb_file = nwb_file_handler.read()
+        #     print(nwb_file.processing['PM_ImageSeries'])
+        #     self.assertContainerEqual(nwb_file.processing['PM_ImageSeries'], nwb_image_series)
+        #
+        # self.delete_nwb('nwb_image_series')
+
     def test_read_nwb_nwb_electrode_group_successfully(self):
         device = Device('device_0')
         self.nwb_file_content.add_device(device)

src/spec/create_extension_spec.py

@@ -21,6 +21,7 @@ def main():
     ns_builder.include_type('ElectrodeGroup', namespace='core')
     ns_builder.include_type('Device', namespace='core')
     ns_builder.include_type('NWBDataInterface', namespace='core')
+    ns_builder.include_type('ImageSeries', namespace='core')
 
     # see https://pynwb.readthedocs.io/en/latest/extensions.html#extending-nwb
     # for more information
@@ -172,6 +173,19 @@ def main():
         ]
     )
 
+    nwb_image_series = NWBGroupSpec(
+        neurodata_type_def='NwbImageSeries',
+        neurodata_type_inc='ImageSeries',
+        doc='Extension of ImageSeries object in NWB',
+        groups=[
+            NWBGroupSpec(
+                neurodata_type_inc='Device',
+                doc='devices used to record video',
+                quantity='*'
+            )
+        ],
+    )
+
     header_device = NWBGroupSpec(
         doc='metadata from global configuration from header',
         neurodata_type_def='HeaderDevice',
@@ -314,7 +328,7 @@ def main():
     )
 
     new_data_types = [
-        shanks_electrode, shanks, probe, data_acq_device, camera_device, header_device, associated_files, nwb_electrode_group
+        shanks_electrode, shanks, probe, data_acq_device, camera_device, nwb_image_series, header_device, associated_files, nwb_electrode_group
     ]
 
     # export the spec to yaml files in the spec folder