Add NWB extension for MIES specific data and metadata

spec/ndx-MIES.extensions.yaml

@@ -1,8 +1,124 @@
 groups:
-- neurodata_type_def: TetrodeSeries
-  neurodata_type_inc: ElectricalSeries
-  doc: An extension of ElectricalSeries to include the tetrode ID for each time series.
-  attributes:
-  - name: trode_id
-    dtype: int32
-    doc: The tetrode ID.
+- neurodata_type_def: MIESMetaData
+  neurodata_type_inc: LabMetaData
+  doc: Additional data and metadata from MIES
+  datasets:
+  - neurodata_type_def: GeneratedBy
+    neurodata_type_inc: NWBData
+    shape:
+    - null
+    - 2
+    doc: Software provenance information as key (first column) value (second column)
+      pairs.
+  groups:
+  - neurodata_type_def: UserComment
+    doc: Free form text notes from the experimenter
+    groups:
+    - neurodata_type_def: UserCommentDevice
+      neurodata_type_inc: Device
+      doc: Device for the user text notes
+      datasets:
+      - neurodata_type_def: UserCommentString
+        neurodata_type_inc: NWBData
+        doc: device specific user text notes
+  - neurodata_type_def: Testpulse
+    doc: Testpulse data
+    quantity: '?'
+    groups:
+    - neurodata_type_def: TestpulseDevice
+      neurodata_type_inc: Device
+      doc: Device for the testpulse data
+      datasets:
+      - neurodata_type_def: TestpulseMetadata
+        neurodata_type_inc: NWBData
+        shape:
+        - null
+        - null
+        - null
+        doc: 'Metadata about the Testpulse: Rows are the running index, Columns are
+          active AD channels (up to version <= 7) or headstages (version >= 8), the
+          data is in the Layers.'
+        quantity: '*'
+      - neurodata_type_def: TestpulseRawData
+        neurodata_type_inc: NWBData
+        doc: Raw AD testpulse data
+        quantity: '*'
+  - neurodata_type_def: LabNotebook
+    doc: Labnotebooks
+    groups:
+    - neurodata_type_def: LabNotebookDevice
+      neurodata_type_inc: Device
+      doc: Device for the labnotebooks
+      datasets:
+      - neurodata_type_def: LabNotebookNumericalValues
+        neurodata_type_inc: NWBData
+        shape:
+        - null
+        - null
+        - null
+        doc: 'Numerical labnotebook values: Rows are the running index, Columns hold
+          the different entry names, Layers (up to nine) hold the headstage dependent
+          data in the first 8 and the headstage independent data in the 9th layer.
+          See also https://alleninstitute.github.io/MIES/labnotebook-docs.html.'
+      - neurodata_type_def: LabNotebookNumericalKeys
+        neurodata_type_inc: NWBData
+        shape:
+        - 3
+        - null
+        doc: 'Numerical labnotebook keys: First row is the name, second row is the
+          unit and third row is the tolerance. Columns are the running index. See
+          also https://alleninstitute.github.io/MIES/labnotebook-docs.html.'
+      - neurodata_type_def: LabNotebookTextualValues
+        neurodata_type_inc: NWBData
+        shape:
+        - null
+        - null
+        - null
+        doc: 'Textual labnotebook values: Rows are the running index, Columns hold
+          the different entry names, Layers (up to nine) hold the headstage dependent
+          data in the first 8 and the headstage independent data in the 9th layer.
+          See also https://alleninstitute.github.io/MIES/labnotebook-docs.html.'
+      - neurodata_type_def: LabNotebookTextualKeys
+        neurodata_type_inc: NWBData
+        shape:
+        - 3
+        - null
+        doc: 'Textual labnotebook keys: First row is the name, second row is the unit
+          and third row is the tolerance. Columns are the running index. See also
+          https://alleninstitute.github.io/MIES/labnotebook-docs.html.'
+  - neurodata_type_def: StimulusSets
+    doc: 'Stimulus Sets: Parameter waves, referenced custom waves and third-party
+      stimsets'
+    datasets:
+    - neurodata_type_def: StimulusSetWavebuilderParameter
+      neurodata_type_inc: NWBData
+      shape:
+      - null
+      - 100
+      - 9
+      doc: Numerical part of the stimulus set parameter waves for recreating the stimset
+        in MIES. Rows are the data entries, Columns are the index of the segment/epoch
+        and Layers hold different stimulus waveform types. See also https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html#_CPPv423GetWaveBuilderWaveParamv.
+    - neurodata_type_def: StimulusSetWavebuilderParameterText
+      neurodata_type_inc: NWBData
+      shape:
+      - null
+      - 100
+      - 9
+      doc: Textual part of the stimulus set parameter waves for recreating the stimset
+        in MIES. Rows are the data entries, Columns are the index of the segment/epoch
+        (last index holds settings for the full set) and Layers hold different stimulus
+        waveform types. See also https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html#_CPPv427GetWaveBuilderWaveTextParamv.
+    - neurodata_type_def: StimulusSetWavebuilderSegmentTypes
+      neurodata_type_inc: NWBData
+      shape:
+      - 102
+      doc: Stimulus set parameters for the full set. See also https://alleninstitute.github.io/MIES/file/_m_i_e_s___wave_data_folder_getters_8ipf.html#_CPPv418GetSegmentTypeWavev.
+    - neurodata_type_def: StimulusSetWaveform
+      neurodata_type_inc: NWBData
+      shape:
+      - null
+      - null
+      doc: Stimulus set waveform data. This is only present if not all three parameter
+        waves could be found or a third-party stimset was used. One column per sweep.
+      quantity: '?'

spec/ndx-MIES.namespace.yaml

@@ -5,10 +5,30 @@ namespaces:
   - thomas.braun@byte-physics.de
   doc: An NWB:N extension for data and metadata from the Multichannel Igor Electrophysiology
     Suite (MIES)
-  name: ndx-MIES
+  name: ndx-mies
   schema:
   - namespace: core
     neurodata_types:
-    - ElectricalSeries
-  - source: ndx-MIES.extensions.yaml
+    - NWBData
+    - NWBDataInterface
+    - NWBFile
+    - NWBContainer
+    - LabMetaData
+    - Units
+    - ProcessingModule
+    - TimeSeries
+    - Subject
+    - Device
+    - SweepTable
+    - VectorData
+    - VectorIndex
+    - Index
+    - ElementIdentifiers
+    - IntracellularElectrode
+  - namespace: hdmf-common
+    neurodata_types:
+    - Data
+    - Container
+    - DynamicTable
+  - source: ndx-mies.extensions.yaml
   version: 0.1.0