Add lab meta data (#751)

You can now write zero or more lab extensions and put them in /general/ by making them inherit from LabMetaData and calling nwbfile.add_lab_meta_data

tests were also added

Author: bendichter

src/pynwb/data/nwb.file.yaml

@@ -223,6 +223,10 @@ groups:
         date made, injection location, volume, etc.
       quantity: '?'
     groups:
+    - neurodata_type_def: LabMetaData
+      neurodata_type_inc: NWBContainer
+      doc: 'place-holder than can be extended so that lab-specific meta-data can be placed in /general'
+      quantity: '*'
     - name: devices
       doc: 'Description of hardware devices used during experiment. COMMENT: Eg, monitors,
         ADC boards, microscopes, etc'

src/pynwb/file.py

@@ -28,6 +28,12 @@ class SpecFile(Container):
     pass
 
 
+@register_class('LabMetaData', CORE_NAMESPACE)
+class LabMetaData(NWBContainer):
+    def __init__(self, **kwargs):
+        super(LabMetaData, self).__init__(kwargs['name'])
+
+
 @register_class('Subject', CORE_NAMESPACE)
 class Subject(NWBContainer):
 
@@ -141,6 +147,13 @@ class NWBFile(MultiContainerInterface):
             'create': 'create_time_intervals',
             'get': 'get_time_intervals'
         },
+        {
+            'attr': 'lab_meta_data',
+            'add': 'add_lab_meta_data',
+            'type': LabMetaData,
+            'create': 'create_lab_meta_data',
+            'get': 'get_lab_meta_data'
+        }
     ]
 
     __nwbfields__ = ('timestamps_reference_time',

src/pynwb/io/file.py

@@ -47,6 +47,7 @@ def __init__(self, spec):
 
         self.map_spec('subject', general_spec.get_group('subject'))
         self.map_spec('devices', general_spec.get_group('devices').get_neurodata_type('Device'))
+        self.map_spec('lab_meta_data', general_spec.get_neurodata_type('LabMetaData'))
 
     @ObjectMapper.constructor_arg('session_start_time')
     def dateconversion(self, builder, manager):

tests/unit/pynwb_tests/test_core.py

@@ -309,6 +309,7 @@ def test_print_file(self):
   epoch_tags: """ + empty_set_str + """
   ic_electrodes: { }
   imaging_planes: { }
+  lab_meta_data: { }
   modules: { }
   ogen_sites: { }
   stimulus: { }

tests/unit/pynwb_tests/test_extension.py

@@ -1,13 +1,16 @@
-import unittest2 as unittest
 import os
-from tempfile import gettempdir
 import random
 import string
+from datetime import datetime
+from dateutil.tz import tzlocal
+from tempfile import gettempdir
 
-from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec, NWBDatasetSpec
+import unittest2 as unittest
+from pynwb import get_type_map, TimeSeries, NWBFile, register_class, docval, load_namespaces, popargs
 from pynwb.form.spec.spec import RefSpec
-from pynwb import get_type_map, TimeSeries
 from pynwb.form.utils import get_docval
+from pynwb.spec import NWBNamespaceBuilder, NWBGroupSpec, NWBAttributeSpec, NWBDatasetSpec
+from pynwb.file import LabMetaData
 
 
 def id_generator(N=10):
@@ -80,6 +83,35 @@ def test_load_namespace_with_reftype_attribute_check_autoclass_const(self):
         self.assertIsNotNone(docval)
         self.assertEqual(docval['type'], TimeSeries)
 
+    def test_lab_meta(self):
+        ns_builder = NWBNamespaceBuilder('Extension for use in my Lab', self.prefix)
+        test_meta_ext = NWBGroupSpec(
+            neurodata_type_def='MyTestMetaData',
+            neurodata_type_inc='LabMetaData',
+            doc='my test meta data',
+            attributes=[
+                NWBAttributeSpec(name='test_attr', dtype='float', doc='test_dtype')])
+        ns_builder.add_spec(self.ext_source, test_meta_ext)
+        ns_builder.export(self.ns_path, outdir=self.tempdir)
+        ns_abs_path = os.path.join(self.tempdir, self.ns_path)
+
+        load_namespaces(ns_abs_path)
+
+        @register_class('MyTestMetaData', self.prefix)
+        class MyTestMetaData(LabMetaData):
+            __nwbfields__ = ('test_attr',)
+
+            @docval({'name': 'name', 'type': str, 'doc': 'name'},
+                    {'name': 'test_attr', 'type': float, 'doc': 'test attribute'})
+            def __init__(self, **kwargs):
+                test_attr = popargs('test_attr', kwargs)
+                super(MyTestMetaData, self).__init__(**kwargs)
+                self.test_attr = test_attr
+
+        nwbfile = NWBFile("a file with header data", "NB123A",  datetime(2017, 5, 1, 12, 0, 0, tzinfo=tzlocal()))
+
+        nwbfile.add_lab_meta_data(MyTestMetaData(name='test_name', test_attr=5.))
+
 
 class TestCatchDupNS(unittest.TestCase):