Merge pull request #482 from NeurodataWithoutBorders/enh/analysis

final changes before minor release

Author: ajtritt

docs/gallery/domain/ophys.py

@@ -47,13 +47,13 @@
 
 
 optical_channel = OpticalChannel('my_optchan', 'Ca2+ imaging example',
-                                 'pi wavelength', '3.14')
+                                 'pi wavelength', 500.)
 imaging_plane = nwbfile.create_imaging_plane('my_imgpln',
                                              'Ca2+ imaging example',
                                              optical_channel,
                                              'a very interesting part of the brain',
                                              'imaging_device_1',
-                                             '6.28', '2.718', 'GFP', 'my favorite brain location',
+                                             600., '2.718', 'GFP', 'my favorite brain location',
                                              (1, 2, 1, 2, 3), 4.0, 'manifold unit', 'A frame to refer to')
 
 

docs/gallery/general/linking_data.py

@@ -252,5 +252,5 @@
 #
 # External links are convenient but to share data we may want to hand a single file with all the
 # data to our collaborator rather than having to collect all relevant files. To do this,
-# :py:class:`~pynwb.from.backends.hdf5.h5tools.HDF5IO` (and in turn :py:class:`~pynwb.NWBHDF5IO`)
-# provide the convenience function :py:func:`~pynwb.from.backends.hdf5.h5tools.HDF5IO.copy_file`
+# :py:class:`~pynwb.form.backends.hdf5.h5tools.HDF5IO` (and in turn :py:class:`~pynwb.NWBHDF5IO`)
+# provide the convenience function :py:func:`~pynwb.form.backends.hdf5.h5tools.HDF5IO.copy_file`

src/pynwb/data/nwb.file.yaml

@@ -59,6 +59,10 @@ groups:
       end users. Such data should be placed in the analysis group. The analysis data
       should be documented so that it is sharable with other labs'
     name: analysis
+    groups:
+    - doc: Custom analysis results
+      neurodata_type_inc: NWBContainer
+      quantity: '*'
   - doc: "Experimental intervals, whether that be logically distinct sub-experiments\
     \ having a particular scientific goal, trials during an experiment, or epochs\
     \ deriving from analysis of data.  COMMENT: Epochs provide pointers to time\

src/pynwb/data/nwb.ophys.yaml

@@ -227,7 +227,7 @@ groups:
     dtype: text
     name: device
   - doc: Excitation wavelength
-    dtype: text
+    dtype: float
     name: excitation_lambda
   - doc: Rate images are acquired, in Hz.
     dtype: text
@@ -283,7 +283,7 @@ groups:
       dtype: text
       name: description
     - doc: Emission lambda for channel
-      dtype: text
+      dtype: float
       name: emission_lambda
     doc: 'One of possibly many groups storing channel-specific data COMMENT: Name
       is arbitrary but should be meaningful'

src/pynwb/file.py

@@ -81,6 +81,12 @@ class NWBFile(MultiContainerInterface):
             'type': NWBDataInterface,
             'get': 'get_acquisition'
         },
+        {
+            'attr': 'analysis',
+            'add': 'add_analysis',
+            'type': NWBContainer,
+            'get': 'get_analysis'
+        },
         {
             'attr': 'stimulus',
             'add': 'add_stimulus',

src/pynwb/form/container.py

@@ -9,7 +9,10 @@ class Container(with_metaclass(abc.ABCMeta, object)):
             {'name': 'parent', 'type': 'Container', 'doc': 'the Container that holds this Container', 'default': None},
             {'name': 'container_source', 'type': str, 'doc': 'the source of this container', 'default': None})
     def __init__(self, **kwargs):
-        self.__name = getargs('name', kwargs)
+        name = getargs('name', kwargs)
+        if '/' in name:
+            raise ValueError("name '" + name + "' cannot contain '/'")
+        self.__name = name
         self.__parent = getargs('parent', kwargs)
         self.__container_source = getargs('container_source', kwargs)
         self.__children = list()

src/pynwb/ophys.py

@@ -23,7 +23,7 @@ class OpticalChannel(NWBContainer):
     @docval({'name': 'name', 'type': str, 'doc': 'the name of this electrode'},
             {'name': 'source', 'type': str, 'doc': 'the source of the data'},
             {'name': 'description', 'type': str, 'doc': 'Any notes or comments about the channel.'},
-            {'name': 'emission_lambda', 'type': str, 'doc': 'Emission lambda for channel.'},
+            {'name': 'emission_lambda', 'type': float, 'doc': 'Emission lambda for channel.'},
             {'name': 'parent', 'type': 'NWBContainer',
              'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
@@ -57,11 +57,11 @@ class ImagingPlane(NWBContainer):
              'doc': 'One of possibly many groups storing channelspecific data.'},
             {'name': 'description', 'type': str, 'doc': 'Description of this ImagingPlane.'},
             {'name': 'device', 'type': str, 'doc': 'Name of device in /general/devices'},
-            {'name': 'excitation_lambda', 'type': str, 'doc': 'Excitation wavelength.'},
+            {'name': 'excitation_lambda', 'type': float, 'doc': 'Excitation wavelength.'},
             {'name': 'imaging_rate', 'type': str, 'doc': 'Rate images are acquired, in Hz.'},
             {'name': 'indicator', 'type': str, 'doc': 'Calcium indicator'},
             {'name': 'location', 'type': str, 'doc': 'Location of image plane.'},
-            {'name': 'manifold', 'type': Iterable, 'doc': 'Physical position of each pixel. height, weight, x, y, z.',
+            {'name': 'manifold', 'type': Iterable, 'doc': 'Physical position of each pixel. height, weight, xyz.',
              'default': None},
             {'name': 'conversion', 'type': float,
              'doc': 'Multiplier to get from stored values to specified unit (e.g., 1e-3 for millimeters)',

tests/integration/ui_write/test_ophys.py

@@ -23,9 +23,9 @@ class TestImagingPlaneIO(base.TestMapRoundTrip):
 
     def setUpContainer(self):
         self.optical_channel = OpticalChannel('optchan1', 'unit test TestImagingPlaneIO',
-                                              'a fake OpticalChannel', '3.14')
+                                              'a fake OpticalChannel', 500.)
         return ImagingPlane('imgpln1', 'unit test TestImagingPlaneIO', self.optical_channel,
-                            'a fake ImagingPlane', 'imaging_device_1', '6.28', '2.718', 'GFP', 'somewhere in the brain')
+                            'a fake ImagingPlane', 'imaging_device_1', 600., '2.718', 'GFP', 'somewhere in the brain')
 
     def setUpBuilder(self):
         optchan_builder = GroupBuilder(
@@ -37,7 +37,7 @@ def setUpBuilder(self):
                 'source': 'unit test TestImagingPlaneIO'},
             datasets={
                 'description': DatasetBuilder('description', 'a fake OpticalChannel'),
-                'emission_lambda': DatasetBuilder('emission_lambda', '3.14')},
+                'emission_lambda': DatasetBuilder('emission_lambda', 500.)},
         )
         return GroupBuilder(
             'imgpln1',
@@ -49,7 +49,7 @@ def setUpBuilder(self):
             datasets={
                 'description': DatasetBuilder('description', 'a fake ImagingPlane'),
                 'device': DatasetBuilder('device', 'imaging_device_1'),
-                'excitation_lambda': DatasetBuilder('excitation_lambda', '6.28'),
+                'excitation_lambda': DatasetBuilder('excitation_lambda', 600.),
                 'imaging_rate': DatasetBuilder('imaging_rate', '2.718'),
                 'indicator': DatasetBuilder('indicator', 'GFP'),
                 'location': DatasetBuilder('location', 'somewhere in the brain')},
@@ -70,10 +70,10 @@ def getContainer(self, nwbfile):
 class TestTwoPhotonSeries(base.TestDataInterfaceIO):
 
     def make_imaging_plane(self, source):
-        self.optical_channel = OpticalChannel('optchan1', source, 'a fake OpticalChannel', '3.14')
+        self.optical_channel = OpticalChannel('optchan1', source, 'a fake OpticalChannel', 500.)
         self.imaging_plane = ImagingPlane('imgpln1', source, self.optical_channel,
                                           'a fake ImagingPlane',
-                                          'imaging_device_1', '6.28', '2.718', 'GFP', 'somewhere in the brain')
+                                          'imaging_device_1', 600., '2.718', 'GFP', 'somewhere in the brain')
 
     def setUpContainer(self):
         self.make_imaging_plane('unit test TestTwoPhotonSeries')
@@ -95,7 +95,7 @@ def setUpBuilder(self):
                  'source': 'unit test TestTwoPhotonSeries'},
             datasets={
                  'description': DatasetBuilder('description', 'a fake OpticalChannel'),
-                 'emission_lambda': DatasetBuilder('emission_lambda', '3.14')},
+                 'emission_lambda': DatasetBuilder('emission_lambda', 500.)},
         )
         imgpln_builder = GroupBuilder(
             'imgpln1',
@@ -107,7 +107,7 @@ def setUpBuilder(self):
             datasets={
                 'description': DatasetBuilder('description', 'a fake ImagingPlane'),
                 'device': DatasetBuilder('device', 'imaging_device_1'),
-                'excitation_lambda': DatasetBuilder('excitation_lambda', '6.28'),
+                'excitation_lambda': DatasetBuilder('excitation_lambda', 600.),
                 'imaging_rate': DatasetBuilder('imaging_rate', '2.718'),
                 'indicator': DatasetBuilder('indicator', 'GFP'),
                 'location': DatasetBuilder('location', 'somewhere in the brain')},
@@ -167,13 +167,13 @@ def buildPlaneSegmentation(self):
                                         starting_frame=[1, 2, 3], format='tiff', timestamps=list())
 
         self.optical_channel = OpticalChannel('test_optical_channel', 'optical channel source',
-                                              'optical channel description', '3.14')
+                                              'optical channel description', 500.)
         self.imaging_plane = ImagingPlane('test_imaging_plane',
                                           'ophys integration tests',
                                           self.optical_channel,
                                           'imaging plane description',
                                           'imaging_device_1',
-                                          '6.28', '2.718', 'GFP', 'somewhere in the brain',
+                                          600., '2.718', 'GFP', 'somewhere in the brain',
                                           (1, 2, 1, 2, 3), 4.0, 'manifold unit', 'A frame to refer to')
 
         self.img_mask = deepcopy(img_mask)
@@ -195,7 +195,7 @@ def get_plane_segmentation_builder(self):
                 'source': 'optical channel source'},
             datasets={
                 'description': DatasetBuilder('description', 'optical channel description'),
-                'emission_lambda': DatasetBuilder('emission_lambda', '3.14')},
+                'emission_lambda': DatasetBuilder('emission_lambda', 500.)},
         )
         self.imgpln_builder = GroupBuilder(
             'imgpln1',
@@ -207,7 +207,7 @@ def get_plane_segmentation_builder(self):
             datasets={
                 'description': DatasetBuilder('description', 'imaging plane description'),
                 'device': DatasetBuilder('device', 'imaging_device_1'),
-                'excitation_lambda': DatasetBuilder('excitation_lambda', '6.28'),
+                'excitation_lambda': DatasetBuilder('excitation_lambda', 600.),
                 'imaging_rate': DatasetBuilder('imaging_rate', '2.718'),
                 'indicator': DatasetBuilder('indicator', 'GFP'),
                 'manifold': DatasetBuilder('manifold', (1, 2, 1, 2, 3),

tests/unit/form_tests/test_container.py

@@ -0,0 +1,52 @@
+import unittest2 as unittest
+
+from pynwb.form.container import Container
+
+
+class MyTestClass(Container):
+
+    def __init__(self, src, name, parent=None):
+        super(MyTestClass, self).__init__(src, name, parent=parent)
+
+    def basic_add(self, **kwargs):
+        return kwargs
+
+    def basic_add2(self, **kwargs):
+        return kwargs
+
+    def basic_add2_kw(self, **kwargs):
+        return kwargs
+
+
+class MyTestSubclass(MyTestClass):
+
+    def basic_add(self, **kwargs):
+        return kwargs
+
+    def basic_add2_kw(self, **kwargs):
+        return kwargs
+
+
+class TestNWBContainer(unittest.TestCase):
+
+    def test_constructor(self):
+        """Test that constructor properly sets parent
+        """
+        parent_obj = MyTestClass('test source', 'obj1')
+        child_obj = MyTestSubclass('test source', 'obj2', parent=parent_obj)
+        self.assertIs(child_obj.parent, parent_obj)
+
+    def test_set_parent_parent(self):
+        """Test that parent setter  properly sets parent
+        """
+        parent_obj = MyTestClass('test source', 'obj1')
+        child_obj = MyTestSubclass('test source', 'obj2')
+        child_obj.parent = parent_obj
+        self.assertIs(child_obj.parent, parent_obj)
+
+    def test_slash_restriction(self):
+        self.assertRaises(ValueError, Container, 'bad/name')
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/unit/pynwb_tests/test_ophys.py

@@ -17,8 +17,8 @@ def CreatePlaneSegmentation():
     iSS = ImageSeries(name='test_iS', source='a hypothetical source', data=list(), unit='unit',
                       external_file=['external_file'], starting_frame=[1, 2, 3], format='tiff', timestamps=list())
 
-    oc = OpticalChannel('test_optical_channel', 'test_source', 'description', 'emission_lambda')
-    ip = ImagingPlane('test_imaging_plane', 'test_source', oc, 'description', 'device', 'excitation_lambda',
+    oc = OpticalChannel('test_optical_channel', 'test_source', 'description', 500.)
+    ip = ImagingPlane('test_imaging_plane', 'test_source', oc, 'description', 'device', 600.,
                       'imaging_rate', 'indicator', 'location', (1, 2, 1, 2, 3), 4.0, 'unit', 'reference_frame')
 
     pS = PlaneSegmentation('test source', 'description', ip, 'test_name', iSS)
@@ -29,19 +29,19 @@ def CreatePlaneSegmentation():
 
 class TwoPhotonSeriesConstructor(unittest.TestCase):
     def test_init(self):
-        oc = OpticalChannel('test_name', 'test_source', 'description', 'emission_lambda')
+        oc = OpticalChannel('test_name', 'test_source', 'description', 500.)
         self.assertEqual(oc.description, 'description')
-        self.assertEqual(oc.emission_lambda, 'emission_lambda')
+        self.assertEqual(oc.emission_lambda, 500.)
 
-        ip = ImagingPlane('test_imaging_plane', 'test source', oc, 'description', 'device', 'excitation_lambda',
-                          'imaging_rate', 'indicator', 'location', (1, 2, 1, 2, 3), 4.0, 'unit', 'reference_frame')
+        ip = ImagingPlane('test_imaging_plane', 'test source', oc, 'description', 'device', 600.,
+                          'imaging_rate', 'indicator', 'location', (50, 100, 3), 4.0, 'unit', 'reference_frame')
         self.assertEqual(ip.optical_channel[0], oc)
         self.assertEqual(ip.device, 'device')
-        self.assertEqual(ip.excitation_lambda, 'excitation_lambda')
+        self.assertEqual(ip.excitation_lambda, 600.)
         self.assertEqual(ip.imaging_rate, 'imaging_rate')
         self.assertEqual(ip.indicator, 'indicator')
         self.assertEqual(ip.location, 'location')
-        self.assertEqual(ip.manifold, (1, 2, 1, 2, 3))
+        self.assertEqual(ip.manifold, (50, 100, 3))
         self.assertEqual(ip.conversion, 4.0)
         self.assertEqual(ip.unit, 'unit')
         self.assertEqual(ip.reference_frame, 'reference_frame')
@@ -145,8 +145,8 @@ def test_init(self):
         iSS = ImageSeries(name='test_iS', source='a hypothetical source', data=list(), unit='unit',
                           external_file=['external_file'], starting_frame=[1, 2, 3], format='tiff', timestamps=list())
 
-        oc = OpticalChannel('test_optical_channel', 'test_source', 'description', 'emission_lambda')
-        ip = ImagingPlane('test_imaging_plane', 'test_source', oc, 'description', 'device', 'excitation_lambda',
+        oc = OpticalChannel('test_optical_channel', 'test_source', 'description', 500.)
+        ip = ImagingPlane('test_imaging_plane', 'test_source', oc, 'description', 'device', 600.,
                           'imaging_rate', 'indicator', 'location', (1, 2, 1, 2, 3), 4.0, 'unit', 'reference_frame')
 
         pS = PlaneSegmentation('test source', 'description', ip, 'test_name', iSS)