Merge pull request #204 from NeurodataWithoutBorders/schema_2.2.4

Update to Schema 2.2.4

Author: lawrence-mbf

+tests/+system/ElectrodeGroupIOTest.m

@@ -1,7 +1,8 @@
 classdef ElectrodeGroupIOTest < tests.system.PyNWBIOTest
     methods
         function addContainer(testCase, file) %#ok<INUSL>
-            dev = types.core.Device();
+            % Device description is for pynwb compatibility
+            dev = types.core.Device('description', 'dev1 description');
             file.general_devices.set('dev1', dev);
             eg = types.core.ElectrodeGroup( ...
                 'description', 'a test ElectrodeGroup', ...

+tests/+system/ImagingPlaneIOTest.m

@@ -1,7 +1,7 @@
 classdef ImagingPlaneIOTest < tests.system.PyNWBIOTest
     methods
         function addContainer(testCase, file) %#ok<INUSL>
-            dev = types.core.Device();
+            dev = types.core.Device('description', 'dev1 description');
             oc = types.core.OpticalChannel( ...
                 'description', 'a fake OpticalChannel', ...
                 'emission_lambda', 3.14);

+tests/+system/PhotonSeriesIOTest.m

@@ -1,7 +1,7 @@
 classdef PhotonSeriesIOTest < tests.system.PyNWBIOTest & tests.system.AmendTest
     methods
         function addContainer(testCase, file) %#ok<INUSL>
-            dev = types.core.Device();
+            dev = types.core.Device('description', 'dev1 description');
 
             oc = types.core.OpticalChannel( ...
                 'description', 'a fake OpticalChannel', ...

+tests/+system/PyNWBIOTest.py

@@ -148,8 +148,16 @@ class ImagingPlaneIOTest(PyNWBIOTest):
     def addContainer(self, file):
         dev1 = file.create_device('imaging_device_1', 'dev1 description')
         oc = OpticalChannel('optchan1', 'a fake OpticalChannel', 3.14)
-        ip = file.create_imaging_plane('imgpln1', oc, 'a fake ImagingPlane',
-                                       dev1, 6.28, 2.718, 'GFP', 'somewhere in the brain')
+        ip = file.create_imaging_plane(
+            'imgpln1',
+            oc,
+            description = 'a fake ImagingPlane',
+            device = dev1,
+            excitation_lambda = 6.28,
+            indicator = 'GFP',
+            location = 'somewhere in the brain',
+            imaging_rate = 2.718)
+            
         return ip
 
     def getContainer(self, file):
@@ -160,8 +168,15 @@ class PhotonSeriesIOTest(PyNWBIOTest):
     def addContainer(self, file):
         dev1 = file.create_device('dev1', 'dev1 description')
         oc = OpticalChannel('optchan1', 'a fake OpticalChannel', 3.14)
-        ip = file.create_imaging_plane('imgpln1', oc, 'a fake ImagingPlane',
-                                       dev1, 6.28, 2.718, 'GFP', 'somewhere in the brain')
+        ip = file.create_imaging_plane(
+            'imgpln1',
+            oc,
+            description = 'a fake ImagingPlane',
+            device = dev1,
+            excitation_lambda = 6.28,
+            indicator = 'GFP',
+            location = 'somewhere in the brain',
+            imaging_rate = 2.718)
         data = np.ones((3, 3, 3))
         timestamps = list(range(10))
         fov = [2.0, 2.0, 5.0]

doc/+types/+core/ImagingPlane.html

@@ -70,7 +70,7 @@
          </tr>
          <tr class="summary-item">
             <td class="name">imaging_rate</td>
-            <td class="m-help">Rate that images are acquired, in Hz.&nbsp;</td>
+            <td class="m-help">Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.&nbsp;</td>
          </tr>
          <tr class="summary-item">
             <td class="name">indicator</td>

doc/+types/+core/LabMetaData.html

@@ -16,7 +16,7 @@
          </tr>
       </table>
       <div class="title">types.core.LabMetaData</div>
-      <div class="helptext"><pre><!--helptext -->  <span class="helptopic">LabMetaData</span> Place-holder than can be extended so that lab-specific meta-data can be placed in /general.</pre></div><!--after help -->
+      <div class="helptext"><pre><!--helptext -->  <span class="helptopic">LabMetaData</span> Lab-specific meta-data.</pre></div><!--after help -->
       <!--Class-->
       <div class="sectiontitle">Class Details</div>
       <table class="class-details">

nwb-schema/core/nwb.file.yaml

@@ -7,7 +7,7 @@ groups:
   attributes:
   - name: nwb_version
     dtype: text
-    value: 2.2.2
+    value: 2.2.4
     doc: File version string. Use semantic versioning, e.g. 1.2.1. This will be the
       name of the format with trailing major, minor and patch numbers.
   datasets:
@@ -93,14 +93,9 @@ groups:
       doc: Any one-off tables
       quantity: '*'
     datasets:
-    - neurodata_type_def: ScratchData
-      neurodata_type_inc: NWBData
+    - neurodata_type_inc: ScratchData
       doc: Any one-off datasets
       quantity: '*'
-      attributes:
-      - name: notes
-        doc: 'Any notes the user has about the dataset being stored'
-        dtype: text
   - name: processing
     doc: "The home for ProcessingModules. These modules perform intermediate analysis\
       \ of data that is necessary to perform before scientific analysis. Examples\
@@ -248,8 +243,7 @@ groups:
         date made, injection location, volume, etc.
       quantity: '?'
     groups:
-    - neurodata_type_def: LabMetaData
-      neurodata_type_inc: NWBContainer
+    - neurodata_type_inc: LabMetaData
       doc: Place-holder than can be extended so that lab-specific meta-data can be
         placed in /general.
       quantity: '*'
@@ -261,46 +255,10 @@ groups:
       - neurodata_type_inc: Device
         doc: Data acquisition devices.
         quantity: '*'
-    - neurodata_type_def: Subject
-      neurodata_type_inc: NWBContainer
-      name: subject
+    - name: subject
+      neurodata_type_inc: Subject
       doc: Information about the animal or person from which the data was measured.
       quantity: '?'
-      datasets:
-      - name: age
-        dtype: text
-        doc: Age of subject. Can be supplied instead of 'date_of_birth'.
-        quantity: '?'
-      - name: date_of_birth
-        dtype: isodatetime
-        doc: Date of birth of subject. Can be supplied instead of 'age'.
-        quantity: '?'
-      - name: description
-        dtype: text
-        doc: Description of subject and where subject came from (e.g., breeder, if
-          animal).
-        quantity: '?'
-      - name: genotype
-        dtype: text
-        doc: Genetic strain. If absent, assume Wild Type (WT).
-        quantity: '?'
-      - name: sex
-        dtype: text
-        doc: Gender of subject.
-        quantity: '?'
-      - name: species
-        dtype: text
-        doc: Species of subject.
-        quantity: '?'
-      - name: subject_id
-        dtype: text
-        doc: ID of animal/person used/participating in experiment (lab convention).
-        quantity: '?'
-      - name: weight
-        dtype: text
-        doc: Weight at time of experiment, at time of surgery and at other important
-          times.
-        quantity: '?'
     - name: extracellular_ephys
       doc: Metadata related to extracellular electrophysiology.
       quantity: '?'
@@ -427,3 +385,55 @@ groups:
     neurodata_type_inc: Units
     doc: Data about sorted spike units.
     quantity: '?'
+
+- neurodata_type_def: LabMetaData
+  neurodata_type_inc: NWBContainer
+  doc: Lab-specific meta-data.
+
+- neurodata_type_def: Subject
+  neurodata_type_inc: NWBContainer
+  doc: Information about the animal or person from which the data was measured.
+  datasets:
+  - name: age
+    dtype: text
+    doc: Age of subject. Can be supplied instead of 'date_of_birth'.
+    quantity: '?'
+  - name: date_of_birth
+    dtype: isodatetime
+    doc: Date of birth of subject. Can be supplied instead of 'age'.
+    quantity: '?'
+  - name: description
+    dtype: text
+    doc: Description of subject and where subject came from (e.g., breeder, if
+      animal).
+    quantity: '?'
+  - name: genotype
+    dtype: text
+    doc: Genetic strain. If absent, assume Wild Type (WT).
+    quantity: '?'
+  - name: sex
+    dtype: text
+    doc: Gender of subject.
+    quantity: '?'
+  - name: species
+    dtype: text
+    doc: Species of subject.
+    quantity: '?'
+  - name: subject_id
+    dtype: text
+    doc: ID of animal/person used/participating in experiment (lab convention).
+    quantity: '?'
+  - name: weight
+    dtype: text
+    doc: Weight at time of experiment, at time of surgery and at other important
+      times.
+    quantity: '?'
+
+datasets:
+- neurodata_type_def: ScratchData
+  neurodata_type_inc: NWBData
+  doc: Any one-off datasets
+  attributes:
+  - name: notes
+    doc: 'Any notes the user has about the dataset being stored'
+    dtype: text

nwb-schema/core/nwb.namespace.yaml

@@ -57,4 +57,4 @@ namespaces:
   - doc: This source module contains neurodata_type for retinotopy data.
     source: nwb.retinotopy.yaml
     title: Retinotopy
-  version: 2.2.2
+  version: 2.2.4