Merge pull request #40 from NovelaNeuro/user/acwikla/remove_num_shanks_field

Author: wbodo

README.md

@@ -56,7 +56,6 @@ Representation of Probe object in NWB <br>
     **probe_type**  `string`: type of probe <br>
     **units**  `string`: units in device <br>
     **probe_description**  `string`: probe_description of probe <br>
-    **num_shanks**  `int`: number of shanks associated with probe <br>
     **contact_side_numbering**  `bool`: is contact_side_numbering enabled <br>
     **contact_size**  `float`: value of contact size as float <br>
     **shanks**  `object`: shanks in the probe <br>

spec/ndx-franklab-novela.extensions.yaml

@@ -42,9 +42,6 @@ groups:
   - name: probe_description
     dtype: text
     doc: description of the probe
-  - name: num_shanks
-    dtype: int
-    doc: number of shanks in probe
   - name: contact_side_numbering
     dtype: bool
     doc: is contact_side_numbering enabled

src/pynwb/ndx_franklab_novela/probe.py

@@ -52,7 +52,6 @@ class Probe(Device, MultiContainerInterface):
             {'name': 'probe_type', 'type': 'str', 'doc': 'type of probe'},
             {'name': 'units', 'type': 'str', 'doc': 'units in device'},
             {'name': 'probe_description', 'type': 'str', 'doc': 'description of the probe'},
-            {'name': 'num_shanks', 'type': 'int', 'doc': 'number of shanks associated with probe'},
             {'name': 'contact_side_numbering', 'type': 'bool', 'doc': 'is contact_side_numbering enabled'},
             {'name': 'contact_size', 'type': 'float', 'doc': 'value of contact size as float'},
             {'name': 'shanks', 'type': (list, tuple), 'doc': 'shanks in probe', 'default': list()}
@@ -64,7 +63,6 @@ def __init__(self, **kwargs):
                             if kwargs_item != 'probe_type'
                             if kwargs_item != 'units'
                             if kwargs_item != 'probe_description'
-                            if kwargs_item != 'num_shanks'
                             if kwargs_item != 'contact_side_numbering'
                             if kwargs_item != 'contact_size'
                             if kwargs_item != 'shanks'
@@ -74,12 +72,11 @@ def __init__(self, **kwargs):
         self.probe_type = kwargs['probe_type']
         self.units = kwargs['units']
         self.probe_description = kwargs['probe_description']
-        self.num_shanks = kwargs['num_shanks']
         self.contact_side_numbering = kwargs['contact_side_numbering']
         self.contact_size = kwargs['contact_size']
         self.shanks = kwargs['shanks']
 
-    __nwbfields__ = ('id', 'probe_type', 'units', 'probe_description', 'num_shanks', 'contact_side_numbering',
+    __nwbfields__ = ('id', 'probe_type', 'units', 'probe_description', 'contact_side_numbering',
                      'contact_size')
 
     __clsconf__ = [

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

@@ -42,9 +42,6 @@ groups:
   - name: probe_description
     dtype: text
     doc: description of the probe
-  - name: num_shanks
-    dtype: int
-    doc: number of shanks in probe
   - name: contact_side_numbering
     dtype: bool
     doc: is contact_side_numbering enabled

src/pynwb/tests/test_probe.py

@@ -67,7 +67,6 @@ def test_probe_successfully_created(self):
             probe_type='type_1',
             units='um',
             probe_description='sample description',
-            num_shanks=2,
             contact_side_numbering=True,
             contact_size=1.0,
         )
@@ -81,7 +80,6 @@ def test_probe_successfully_created(self):
         self.assertIsInstance(probe.probe_type, str)
         self.assertIsInstance(probe.units, str)
         self.assertIsInstance(probe.probe_description, str)
-        self.assertIsInstance(probe.num_shanks, int)
         self.assertIsInstance(probe.contact_side_numbering, bool)
         self.assertIsInstance(probe.contact_size, float)
         self.assertIsInstance(probe.shanks, dict)
@@ -91,7 +89,6 @@ def test_probe_successfully_created(self):
         self.assertEqual(probe.probe_type, 'type_1')
         self.assertEqual(probe.units, 'um')
         self.assertEqual(probe.probe_description, 'sample description')
-        self.assertEqual(probe.num_shanks, 2)
         self.assertEqual(probe.contact_side_numbering, True)
         self.assertEqual(probe.contact_size, 1.0)
         self.assertEqual(probe.shanks, {

src/pynwb/tests/test_read_nwb.py

@@ -78,7 +78,6 @@ def test_read_nwb_probe_successfully(self):
             id=1,
             probe_type='type_1',
             probe_description='2',
-            num_shanks=3,
             contact_size=1.0,
             contact_side_numbering=False
         )

src/spec/create_extension_spec.py

@@ -105,11 +105,6 @@ def main():
                 doc='description of the probe',
                 dtype='text'
             ),
-            NWBAttributeSpec(
-                name='num_shanks',
-                doc='number of shanks in probe',
-                dtype='int'
-            ),
             NWBAttributeSpec(
                 name='contact_side_numbering',
                 doc='is contact_side_numbering enabled',