Merge pull request #42 from NovelaNeuro/user/acwikla/data_acq_device

User/acwikla/data acq device

Author: MarcinAtNovela

README.md

@@ -60,4 +60,12 @@ Representation of Probe object in NWB <br>
     **contact_size**  `float`: value of contact size as float <br>
     **shanks**  `object`: shanks in the probe <br>
 
+#### DataAcqDevice
+Representation of DataAcqDevice object in NWB <br>
+**Attributes:** <br>
+    **system**  `string`: system of device <br>
+    **amplifier**  `string`: amplifier (default: '') <br>
+    **adc_circuit**  `string`: adc_circuit (default: '') <br>
+
+
 This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).

spec/ndx-franklab-novela.extensions.yaml

@@ -52,6 +52,19 @@ groups:
   - neurodata_type_inc: Shank
     doc: shank in the probe
     quantity: '*'
+- neurodata_type_def: DataAcqDevice
+  neurodata_type_inc: Device
+  doc: A custom Device interface
+  attributes:
+  - name: system
+    dtype: text
+    doc: system of device
+  - name: amplifier
+    dtype: text
+    doc: amplifier
+  - name: adc_circuit
+    dtype: text
+    doc: adc_circuit
 - neurodata_type_def: HeaderDevice
   neurodata_type_inc: Device
   doc: metadata from global configuration from header

spec/ndx-franklab-novela.namespace.yaml

@@ -12,4 +12,4 @@ namespaces:
     - Device
     - NWBDataInterface
   - source: ndx-franklab-novela.extensions.yaml
-  version: 0.0.004
+  version: 0.0.005

src/pynwb/ndx_franklab_novela/data_acq_device.py

@@ -0,0 +1,28 @@
+from hdmf import docval
+from hdmf.utils import get_docval, call_docval_func
+from pynwb import register_class
+from pynwb.device import Device
+
+
+@register_class('DataAcqDevice', 'ndx-franklab-novela')
+class DataAcqDevice(Device):
+    ''' Representation of Probe object in NWB '''
+
+    @docval(*get_docval(Device.__init__) + (
+            {'name': 'system', 'type': 'str', 'doc': 'system of device'},
+            {'name': 'amplifier', 'type': 'str', 'doc': 'amplifier', 'default': ''},
+            {'name': 'adc_circuit', 'type': 'str', 'doc': 'adc_circuit', 'default': ''},
+    ))
+    def __init__(self, **kwargs):
+        super().__init__(**{kwargs_item: kwargs[kwargs_item]
+                            for kwargs_item in kwargs.copy()
+                            if kwargs_item != 'system'
+                            if kwargs_item != 'amplifier'
+                            if kwargs_item != 'adc_circuit'
+                            })
+        call_docval_func(super(DataAcqDevice, self).__init__, kwargs)
+        self.system = kwargs['system']
+        self.amplifier = kwargs['amplifier']
+        self.adc_circuit = kwargs['adc_circuit']
+
+    __nwbfields__ = ('system', 'amplifier', 'adc_circuit')

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

@@ -52,6 +52,19 @@ groups:
   - neurodata_type_inc: Shank
     doc: shank in the probe
     quantity: '*'
+- neurodata_type_def: DataAcqDevice
+  neurodata_type_inc: Device
+  doc: A custom Device interface
+  attributes:
+  - name: system
+    dtype: text
+    doc: system of device
+  - name: amplifier
+    dtype: text
+    doc: amplifier
+  - name: adc_circuit
+    dtype: text
+    doc: adc_circuit
 - 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

@@ -12,4 +12,4 @@ namespaces:
     - Device
     - NWBDataInterface
   - source: ndx-franklab-novela.extensions.yaml
-  version: 0.0.004
+  version: 0.0.005

src/pynwb/tests/test_dataAcqDevice.py

@@ -0,0 +1,47 @@
+import unittest
+
+from src.pynwb.ndx_franklab_novela.data_acq_device import DataAcqDevice
+
+
+class TestDataAcqDevice(unittest.TestCase):
+
+    def test_data_acq_device_successfully_created_with_optional_data(self):
+
+        data_acq_device = DataAcqDevice(
+            name='DataAcqDevice1',
+            system='System1',
+            amplifier='Amplifier1',
+            adc_circuit='adc_circuit1',
+        )
+
+        self.assertIsInstance(data_acq_device, DataAcqDevice)
+
+        self.assertIsInstance(data_acq_device.name, str)
+        self.assertIsInstance(data_acq_device.system, str)
+        self.assertIsInstance(data_acq_device.amplifier, str)
+        self.assertIsInstance(data_acq_device.adc_circuit, str)
+
+        self.assertEqual(data_acq_device.name, 'DataAcqDevice1')
+        self.assertEqual(data_acq_device.system, 'System1')
+        self.assertEqual(data_acq_device.amplifier, 'Amplifier1')
+        self.assertEqual(data_acq_device.adc_circuit, 'adc_circuit1')
+
+    def test_data_acq_device_successfully_created_without_optional_data(self):
+
+        data_acq_device = DataAcqDevice(
+            name='DataAcqDevice1',
+            system='System1'
+        )
+
+        self.assertIsInstance(data_acq_device, DataAcqDevice)
+        
+        self.assertIsInstance(data_acq_device.name, str)
+        self.assertIsInstance(data_acq_device.system, str)
+        self.assertIsInstance(data_acq_device.amplifier, str)
+        self.assertIsInstance(data_acq_device.adc_circuit, str)
+
+        self.assertEqual(data_acq_device.name, 'DataAcqDevice1')
+        self.assertEqual(data_acq_device.system, 'System1')
+        self.assertEqual(data_acq_device.amplifier, '')
+        self.assertEqual(data_acq_device.adc_circuit, '')
+

src/pynwb/tests/test_read_nwb.py

@@ -9,6 +9,7 @@
 from pynwb.device import Device
 from pynwb.testing import TestCase
 
+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.probe import Probe, Shank, ShanksElectrode
@@ -95,6 +96,26 @@ def test_read_nwb_probe_successfully(self):
 
         self.delete_nwb('probe')
 
+    def test_read_nwb_data_acq_device_successfully(self):
+        data_acq_device = DataAcqDevice(
+            name='DataAcqDevice1',
+            system='System1',
+            amplifier='Amplifier1',
+            adc_circuit='adc_circuit1'
+        )
+        self.nwb_file_content.add_device(data_acq_device)
+
+        nwb_file_handler = NWBHDF5IO('data_acq_device.nwb', mode='w')
+        nwb_file_handler.write(self.nwb_file_content)
+        nwb_file_handler.close()
+
+        self.assertTrue(os.path.exists('data_acq_device.nwb'))
+        with pynwb.NWBHDF5IO('data_acq_device.nwb', 'r',  load_namespaces=True) as nwb_file_handler:
+            nwb_file = nwb_file_handler.read()
+            self.assertContainerEqual(nwb_file.devices['DataAcqDevice1'], data_acq_device)
+
+        self.delete_nwb('data_acq_device')
+
     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

@@ -118,6 +118,29 @@ def main():
         ]
     )
 
+    data_acq_device = NWBGroupSpec(
+        doc='A custom Device interface',
+        neurodata_type_def='DataAcqDevice',
+        neurodata_type_inc='Device',
+        attributes=[
+            NWBAttributeSpec(
+                name='system',
+                doc='system of device',
+                dtype='text'
+            ),
+            NWBAttributeSpec(
+                name='amplifier',
+                doc='amplifier',
+                dtype='text'
+            ),
+            NWBAttributeSpec(
+                name='adc_circuit',
+                doc='adc_circuit',
+                dtype='text'
+            ),
+        ]
+    )
+
     associated_files = NWBGroupSpec(
         neurodata_type_def='AssociatedFiles',
         neurodata_type_inc='NWBDataInterface',
@@ -277,7 +300,9 @@ def main():
         ]
     )
 
-    new_data_types = [shanks_electrode, shanks, probe, header_device, associated_files, nwb_electrode_group]
+    new_data_types = [
+        shanks_electrode, shanks, probe, data_acq_device, header_device, associated_files, nwb_electrode_group
+    ]
 
     # export the spec to yaml files in the spec folder
     output_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..', 'spec'))