Merge pull request #1 from t-b/first-steps

First steps

.gitattributes

@@ -0,0 +1 @@
+*.yaml eol=lf text

setup.py

@@ -21,7 +21,7 @@
     readme = ""
 
 setup_args = {
-    'name': 'ndx-MIES',
+    'name': 'ndx-mies',
     'version': '0.1.0',
     'description': 'An NWB:N extension for data and metadata from the Multichannel Igor Electrophysiology Suite (MIES)',
     'long_description': readme,
@@ -31,13 +31,13 @@
     'url': '',
     'license': 'BSD 3-Clause',
     'install_requires': [
-        'pynwb>=1.1.2'
+        'pynwb>=1.3.0'
     ],
     'packages': find_packages('src/pynwb'),
     'package_dir': {'': 'src/pynwb'},
     'package_data': {'ndx_mies': [
-        'spec/ndx-MIES.namespace.yaml',
-        'spec/ndx-MIES.extensions.yaml',
+        'spec/ndx-mies.namespace.yaml',
+        'spec/ndx-mies.extensions.yaml',
     ]},
     'classifiers': [
         "Intended Audience :: Developers",
@@ -48,8 +48,8 @@
 
 
 def _copy_spec_files(project_dir):
-    ns_path = os.path.join(project_dir, 'spec', 'ndx-MIES.namespace.yaml')
-    ext_path = os.path.join(project_dir, 'spec', 'ndx-MIES.extensions.yaml')
+    ns_path = os.path.join(project_dir, 'spec', 'ndx-mies.namespace.yaml')
+    ext_path = os.path.join(project_dir, 'spec', 'ndx-mies.extensions.yaml')
 
     dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_mies', 'spec')
     if not os.path.exists(dst_dir):

spec/ndx-mies.extensions.yaml

@@ -0,0 +1,208 @@
+datasets:
+- neurodata_type_def: UserCommentString
+  neurodata_type_inc: NWBData
+  doc: device specific user text notes
+- 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.'
+- neurodata_type_def: GeneratedBy
+  neurodata_type_inc: NWBData
+  shape:
+  - null
+  - 2
+  doc: Software provenance information as key (first column) value (second column)
+    pairs.
+- neurodata_type_def: TestpulseRawData
+  neurodata_type_inc: NWBData
+  shape:
+  - null
+  doc: Raw AD testpulse data
+- 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: 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.
+- 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: StimulusSetReferencedWaveform
+  doc: Additional stimulus set waveform data. Some epoch types for stimulus sets allow
+    to include arbitrary waveform data. These waveforms are stored in a tree structure
+    here. The stimulus set parameter referencing these waveforms has the path to these
+    entries with colons (:) separated.
+groups:
+- neurodata_type_def: UserComment
+  doc: Free form text notes from the experimenter
+  groups:
+  - neurodata_type_inc: UserCommentDevice
+    doc: Device for the user text notes
+- neurodata_type_def: UserCommentDevice
+  neurodata_type_inc: Device
+  doc: Device for the user text notes
+  datasets:
+  - neurodata_type_inc: UserCommentString
+    doc: device specific user text notes
+- neurodata_type_def: Testpulse
+  doc: Testpulse data
+  groups:
+  - neurodata_type_inc: TestpulseDevice
+    doc: Device for the testpulse data
+- neurodata_type_def: TestpulseDevice
+  doc: Device for the testpulse data
+  datasets:
+  - neurodata_type_inc: TestpulseMetadata
+    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_inc: TestpulseRawData
+    doc: Raw AD testpulse data
+    quantity: '*'
+- neurodata_type_def: LabNotebook
+  doc: Labnotebooks
+  groups:
+  - neurodata_type_inc: LabNotebookDevice
+    doc: Device for the labnotebooks
+- neurodata_type_def: StimulusSets
+  doc: 'Stimulus Sets: Parameter waves, referenced custom waves and third-party stimsets'
+  datasets:
+  - neurodata_type_inc: StimulusSetWavebuilderSegmentTypes
+    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.
+    quantity: '*'
+  - neurodata_type_inc: StimulusSetWavebuilderParameterText
+    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.
+    quantity: '*'
+  - neurodata_type_inc: StimulusSetWavebuilderParameter
+    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.
+    quantity: '*'
+  - neurodata_type_inc: StimulusSetWaveform
+    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: '*'
+  groups:
+  - neurodata_type_inc: StimulusSetReferenced
+    doc: Additional stimulus set waveform data is store here in tree structure.
+- neurodata_type_def: StimulusSetReferenced
+  doc: Additional stimulus set waveform data is store here in tree structure.
+  groups:
+  - neurodata_type_inc: StimulusSetReferencedFolder
+    doc: Folder
+    quantity: '*'
+- neurodata_type_def: StimulusSetReferencedFolder
+  doc: Folder
+  datasets:
+  - neurodata_type_inc: StimulusSetReferencedWaveform
+    doc: Additional stimulus set waveform data. Some epoch types for stimulus sets
+      allow to include arbitrary waveform data. These waveforms are stored in a tree
+      structure here. The stimulus set parameter referencing these waveforms has the
+      path to these entries with colons (:) separated.
+    quantity: '*'
+  groups:
+  - neurodata_type_inc: StimulusSetReferencedFolder
+    doc: Nested Folder
+    quantity: '*'
+- neurodata_type_def: LabNotebookDevice
+  neurodata_type_inc: Device
+  doc: Device for the labnotebooks
+  datasets:
+  - neurodata_type_inc: LabNotebookNumericalValues
+    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_inc: LabNotebookNumericalKeys
+    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_inc: LabNotebookTextualKeys
+    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_inc: LabNotebookTextualValues
+    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: MIESMetaData
+  neurodata_type_inc: LabMetaData
+  doc: Additional data and metadata from MIES
+  datasets:
+  - neurodata_type_inc: GeneratedBy
+    doc: Software provenance information as key (first column) value (second column)
+      pairs.
+  groups:
+  - neurodata_type_inc: UserComment
+    doc: Free form text notes from the experimenter
+  - neurodata_type_inc: Testpulse
+    doc: Testpulse data
+    quantity: '?'
+  - neurodata_type_inc: LabNotebook
+    doc: Labnotebooks
+  - neurodata_type_inc: StimulusSets
+    doc: 'Stimulus Sets: Parameter waves, referenced custom waves and third-party
+      stimsets'
+    quantity: '?'

spec/ndx-MIES.namespace.yaml → spec/ndx-mies.namespace.yaml

@@ -5,10 +5,8 @@ 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
+  - source: ndx-mies.extensions.yaml
   version: 0.1.0