Remove NwbImageSeries type (#2)

Author: rly

README.md

@@ -85,9 +85,4 @@ Representation of CameraDevice object in NWB <br>
     **lens**  `string`: info about lens in this camera <br>
     **camera_name**  `string`: name of this camera <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).

requirements.txt

@@ -1,3 +1,4 @@
-hdmf_docutils
-hdmf
-pynwb
+# pinned dependencies to reproduce a working development environment
+hdmf_docutils==0.4.4
+hdmf==3.1.1
+pynwb==2.0.0

setup.py

@@ -34,7 +34,8 @@
     'url': '',
     'license': 'BSD 3-Clause',
     'install_requires': [
-        'pynwb'
+        'hdmf>=3.1.1,<4',
+        'pynwb>=2.0.0,<3'
     ],
     'packages': find_packages('src/pynwb'),
     'package_dir': {'': 'src/pynwb'},

spec/ndx-franklab-novela.extensions.yaml

@@ -81,13 +81,6 @@ groups:
   - name: lens
     dtype: text
     doc: lens info
-- 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

@@ -1,16 +1,22 @@
 namespaces:
 - author:
   - NovelaDevops
+  - Loren Frank
+  - Eric Denovellis
+  - Ryan Ly
   contact:
   - [email protected]
-  doc: NovelaNeurotechnologies Namespaces
+  - [email protected]
+  - [email protected]
+  - [email protected]
+  doc: NWB extension to store additional metadata and data types for Loren Frank's
+    Lab
   name: ndx-franklab-novela
   schema:
   - namespace: core
     neurodata_types:
     - ElectrodeGroup
     - Device
     - NWBDataInterface
-    - ImageSeries
   - source: ndx-franklab-novela.extensions.yaml
-  version: 0.0.011.36
+  version: 0.1.0

src/pynwb/ndx_franklab_novela/__init__.py

@@ -28,5 +28,4 @@
 from .data_acq_device import DataAcqDevice
 from .header_device import HeaderDevice
 from .nwb_electrode_group import NwbElectrodeGroup
-from .nwb_image_series import NwbImageSeries
 from .probe import Probe, Shank, ShanksElectrode

src/pynwb/ndx_franklab_novela/nwb_image_series.py

@@ -5,15 +5,13 @@
 from dateutil.tz import tzlocal
 from pynwb import NWBFile
 from pynwb import NWBHDF5IO, ProcessingModule
-from pynwb.behavior import BehavioralEvents
 from pynwb.device import Device
 from pynwb.testing import TestCase
 
 from src.pynwb.ndx_franklab_novela import CameraDevice, AssociatedFiles
 from src.pynwb.ndx_franklab_novela import DataAcqDevice
 from src.pynwb.ndx_franklab_novela import HeaderDevice
 from src.pynwb.ndx_franklab_novela import NwbElectrodeGroup
-from src.pynwb.ndx_franklab_novela import NwbImageSeries
 from src.pynwb.ndx_franklab_novela import Probe, Shank, ShanksElectrode
 
 
@@ -140,43 +138,6 @@ def test_read_nwb_camera_device_successfully(self):
 
         self.delete_nwb('camera_device')
 
-    def test_read_nwb_nwb_image_series_successfully(self):
-        device_1 = Device('device1')
-        device_2 = Device('device2')
-        mock_timestamps = [1, 2, 3]
-        mock_external_file = ['some file']
-
-        nwb_image_series = NwbImageSeries(
-            name='NwbImageSeries1',
-            timestamps=mock_timestamps,
-            external_file=mock_external_file,
-            devices=[device_1, device_2]
-        )
-
-        behavioral_time_series = BehavioralEvents(name="BehavioralTimeSeries")
-        behavioral_time_series.add_timeseries(nwb_image_series)
-        processing_module = ProcessingModule(name='ProcessingModule', description='')
-        processing_module.add_data_interface(behavioral_time_series)
-        self.nwb_file_content.add_processing_module(processing_module)
-
-        self.nwb_file_content.add_stimulus_template(nwb_image_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()
-            self.assertContainerEqual(nwb_file.stimulus_template['NwbImageSeries1'], nwb_image_series)
-            self.assertContainerEqual(
-                nwb_file.processing['ProcessingModule'].data_interfaces['BehavioralTimeSeries'].
-                    time_series['NwbImageSeries1'],
-                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/pynwb/tests/test_nwbImageSeries.py

@@ -8,13 +8,11 @@
 def main():
     # these arguments were auto-generated from your cookiecutter inputs
     ns_builder = NWBNamespaceBuilder(
-        doc="""NovelaNeurotechnologies Namespaces""",
+        doc="""NWB extension to store additional metadata and data types for Loren Frank's Lab""",
         name="""ndx-franklab-novela""",
-
-        version="""0.0.011.36""",
-
-        author=list(map(str.strip, """NovelaDevops""".split(','))),
-        contact=list(map(str.strip, """[email protected]""".split(',')))
+        version="""0.1.0""",
+        author=["NovelaDevops", "Loren Frank", "Eric Denovellis", "Ryan Ly"],
+        contact=["[email protected]", "[email protected]", "[email protected]", "[email protected]"]
     )
 
     # # as in which namespace they are found
@@ -23,7 +21,6 @@ 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
@@ -195,19 +192,6 @@ 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',
@@ -350,7 +334,14 @@ def main():
     )
 
     new_data_types = [
-        shanks_electrode, shanks, probe, data_acq_device, camera_device, nwb_image_series, header_device, associated_files, nwb_electrode_group
+        shanks_electrode,
+        shanks,
+        probe,
+        data_acq_device,
+        camera_device,
+        header_device,
+        associated_files,
+        nwb_electrode_group
     ]
 
     # export the spec to yaml files in the spec folder