bring back Interfaces, as NWBDataInterface

core/nwb.base.yaml

@@ -7,14 +7,17 @@ datasets:
   neurodata_type_def: NWBData
 groups:
 - attributes:
-  - doc: Short description of what this type of Interface contains.
+  - doc: Short description of what this type of NWBContainer contains.
     dtype: text
     name: help
   - doc: Path to the origin of the data represented in this interface.
     dtype: text
     name: source
   doc: The attributes specified here are included in all interfaces.
   neurodata_type_def: NWBContainer
+- doc: An abstract data type for differentiating experimental data from metadata
+  neurodata_type_inc: NWBContainer
+  neurodata_type_def: NWBDataInterface
 - attributes:
   - default_value: no comments
     doc: Human-readable comments about the TimeSeries. This second descriptive field
@@ -131,7 +134,7 @@ groups:
     name: sync
     quantity: '?'
   neurodata_type_def: TimeSeries
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Description of Module
     dtype: text
@@ -145,7 +148,23 @@ groups:
     to a particular type of data.
   groups:
   - doc: Interface objects containing data output from processing steps
-    neurodata_type_inc: NWBContainer
+    neurodata_type_inc: NWBDataInterface
     quantity: '*'
   neurodata_type_def: ProcessingModule
   neurodata_type_inc: NWBContainer
+- attributes:
+  - doc: Description of images in this container
+    dtype: text
+    name: description
+  - doc: Value is 'A collection of images that have some meaningful relationship'
+    dtype: text
+    name: help
+    value: A collection of images that have some meaningful relationship
+  datasets:
+    - doc: Images stored in this NWBDataInterface
+      neurodata_type_inc: Image
+      quantity: '+'
+  default_name: Images
+  doc: A NWBDataInterface for storing images that have some relationship
+  neurodata_type_def: Images
+  neurodata_type_inc: NWBDataInterface

core/nwb.behavior.yaml

@@ -63,7 +63,7 @@ groups:
     quantity: '*'
   default_name: BehavioralEpochs
   neurodata_type_def: BehavioralEpochs
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Position data, whether along the x, xy or xyz axis'
     dtype: text
@@ -77,7 +77,7 @@ groups:
     quantity: '*'
   default_name: BehavioralEvents
   neurodata_type_def: BehavioralEvents
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'General container for storing continuously sampled behavioral data.'
     dtype: text
@@ -91,7 +91,7 @@ groups:
     quantity: '*'
   default_name: BehavioralTimeSeries
   neurodata_type_def: BehavioralTimeSeries
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Eye-tracking data, representing pupil size'
     dtype: text
@@ -104,7 +104,7 @@ groups:
     quantity: +
   default_name: PupilTracking
   neurodata_type_def: PupilTracking
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Eye-tracking data, representing direction of gaze'
     dtype: text
@@ -117,7 +117,7 @@ groups:
     quantity: '*'
   default_name: EyeTracking
   neurodata_type_def: EyeTracking
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Direction as measured radially. Spatial series reference frame
       should indicate which direction corresponds to zero and what is the direction
@@ -137,7 +137,7 @@ groups:
     quantity: '*'
   default_name: CompassDirection
   neurodata_type_def: CompassDirection
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Position data, whether along the x, xy or xyz axis'
     dtype: text
@@ -150,7 +150,7 @@ groups:
     quantity: +
   default_name: Position
   neurodata_type_def: Position
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Image stacks whose frames have been shifted (registered) to account
       for motion'
@@ -185,4 +185,4 @@ groups:
     quantity: +
   default_name: MotionCorrection
   neurodata_type_def: MotionCorrection
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface

core/nwb.ecephys.yaml

@@ -116,7 +116,7 @@ groups:
     target_type: Clustering
   default_name: ClusterWaveforms
   neurodata_type_def: ClusterWaveforms
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Clustered spike data, whether from automatic clustering tools (eg,
       klustakwik) or as a result of manual sorting'
@@ -156,7 +156,7 @@ groups:
     or as a result of manual sorting.
   default_name: Clustering
   neurodata_type_def: Clustering
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Container for salient features of detected events'
     dtype: text
@@ -195,7 +195,7 @@ groups:
     SpikeEvent TimeSeries or other source.
   default_name: FeatureExtraction
   neurodata_type_def: FeatureExtraction
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Detected spike events from voltage trace(s)'
     dtype: text
@@ -238,7 +238,7 @@ groups:
     target_type: ElectricalSeries
   default_name: EventDetection
   neurodata_type_def: EventDetection
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Waveform of detected extracellularly recorded spike events'
     dtype: text
@@ -253,7 +253,7 @@ groups:
     quantity: '*'
   default_name: EventWaveform
   neurodata_type_def: EventWaveform
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Ephys data from one or more channels that is subjected to filtering,
       such as for gamma or theta oscillations (LFP has its own interface). Filter
@@ -278,7 +278,7 @@ groups:
     quantity: +
   default_name: FilteredEphys
   neurodata_type_def: FilteredEphys
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'LFP data from one or more channels. Filter properties should be
       noted in the ElectricalSeries'
@@ -295,7 +295,7 @@ groups:
     quantity: +
   default_name: LFP
   neurodata_type_def: LFP
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Metadata about a physical grouping of channels'
     dtype: str

core/nwb.file.yaml

@@ -45,32 +45,9 @@ groups:
       group, the data can exist in a separate HDF5 file that is linked to by the file
       being used for processing and analysis.'
     groups:
-    - datasets:
-      - attributes:
-        - doc: 'Human description of image. COMMENT: If image is of slice data, include
-            slice thickness and orientation, and reference to appropriate entry in
-            /general/slices'
-          dtype: text
-          name: description
-        - doc: 'Format of the image.  COMMENT: eg, jpg, png, mpeg'
-          dtype: text
-          name: format
-        doc: 'Photograph of experiment or experimental setup (video also OK). COMMENT:
-          Name is arbitrary.  Data is stored as a single binary object (HDF5 opaque
-          type).'
-        dtype: binary
-        neurodata_type_def: Image
-        quantity: '*'
-      doc: Acquired images
-      name: images
-    - doc: 'Acquired TimeSeries.COMMENT: When importing acquisition data to an NWB
-        file, all acquisition/tracking/stimulus data must already be aligned to a
-        common time frame. It is assumed that this task has already been performed.'
-      groups:
-      - doc: TimeSeries object containing data generated during data acquisition
-        neurodata_type_inc: TimeSeries
-        quantity: '*'
-      name: timeseries
+    - doc: Any objects representing acquired data
+      neurodata_type_inc: NWBDataInterface
+      quantity: '*'
     name: acquisition
   - doc: 'Lab-specific and custom scientific analysis of data. There is no defined
       format for the content of this group - the format is up to the individual user/lab.

core/nwb.misc.yaml

@@ -132,6 +132,9 @@ groups:
       dtype: text
       name: help
       value: Times for a particular UnitTime object
+    - doc: Description of the unit (eg, cell type).
+      dtype: text
+      name: unit_description
     datasets:
     - dims:
       - num_events
@@ -140,13 +143,10 @@ groups:
       name: times
       shape:
       - null
-    - doc: Description of the unit (eg, cell type).
-      dtype: text
-      name: unit_description
     doc: Group storing times for <unit_N>.
     neurodata_type_def: SpikeUnit
-    neurodata_type_inc: NWBContainer
+    neurodata_type_inc: NWBDataInterface
     quantity: +
   default_name: UnitTimes
   neurodata_type_def: UnitTimes
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface

core/nwb.ophys.yaml

@@ -4,15 +4,6 @@ groups:
     dtype: text
     name: help
     value: Image stack recorded from 2-photon microscope
-  datasets:
-  - dims:
-    - width|height|depth
-    doc: Width, height and depth of image, or imaged area (meters).
-    dtype: float32
-    name: field_of_view
-    quantity: '?'
-    shape:
-    - 3
   - doc: Photomultiplier gain
     dtype: float32
     name: pmt_gain
@@ -23,6 +14,15 @@ groups:
     dtype: float32
     name: scan_line_rate
     quantity: '?'
+  datasets:
+  - dims:
+    - width|height|depth
+    doc: Width, height and depth of image, or imaged area (meters).
+    dtype: float32
+    name: field_of_view
+    quantity: '?'
+    shape:
+    - 3
   doc: A special case of optical imaging.
   links:
   - doc: link to ImagingPlane group from which this TimeSeries data was generated
@@ -78,7 +78,7 @@ groups:
     quantity: '*'
   default_name: DfOverF
   neurodata_type_def: DfOverF
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Fluorescence over time of one or more ROIs. TimeSeries names should
       correspond to imaging plane names'
@@ -95,7 +95,7 @@ groups:
     quantity: +
   default_name: Fluorescence
   neurodata_type_def: Fluorescence
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Stores groups of pixels that define regions of interest from one
       or more imaging planes'
@@ -176,7 +176,7 @@ groups:
     quantity: '*'
   default_name: ImageSegmentation
   neurodata_type_def: ImageSegmentation
-  neurodata_type_inc: NWBContainer
+  neurodata_type_inc: NWBDataInterface
 - attributes:
   - doc: Value is 'Metadata about an imaging plane'
     dtype: text