From b6c69508d72218e0f082f1b493eb39a62a6ae943 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Wed, 20 Apr 2022 09:40:37 -0400 Subject: [PATCH 1/4] make spatial series shape more restrictive (#510) --- core/nwb.behavior.yaml | 12 ++++++++++-- docs/format/source/format_release_notes.rst | 4 ++++ 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/core/nwb.behavior.yaml b/core/nwb.behavior.yaml index 53bbc905..1a951b2f 100644 --- a/core/nwb.behavior.yaml +++ b/core/nwb.behavior.yaml @@ -16,11 +16,19 @@ groups: dims: - - num_times - - num_times - - num_features + - x + - - num_times + - x,y + - - num_times + - x,y,z shape: - - null - - null - - null + - 1 + - - null + - 2 + - - null + - 3 doc: 1-D or 2-D array storing position or direction relative to some reference frame. attributes: - name: unit diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 39b07a35..2547b23d 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -10,6 +10,10 @@ Minor changes ^^^^^^^^^^^^^ - Added an ``offset`` attribute to all ``TimeSeries`` objects to allow enhanced translation to scientific units. +Major changes +^^^^^^^^^^^^^ +- Shape of SpatialSeries.data is more restrictive to prevent > 3 columns. + 2.4.0 (Aug. 11, 2021) --------------------- From abd367600955d910aea9b102a0a3187a8fd22041 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 21 Apr 2022 08:08:27 -0700 Subject: [PATCH 2/4] Update nwb.ophys.yaml (#513) --- core/nwb.ophys.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.ophys.yaml b/core/nwb.ophys.yaml index bdf27acb..ab049e73 100644 --- a/core/nwb.ophys.yaml +++ b/core/nwb.ophys.yaml @@ -217,7 +217,7 @@ groups: default_value: 1.0 doc: Scalar to multiply each element in data to convert it to the specified 'unit'. If the data are stored in acquisition system units or other units - that require a conversion to be interpretable, multiply the data by 'conversion' and add 'offset' + that require a conversion to be interpretable, multiply the data by 'conversion' to convert the data to the specified 'unit'. e.g. if the data acquisition system stores values in this object as pixels from x = -500 to 499, y = -500 to 499 that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get From 150157b9180019042a03ace9171b4a40e967ebad Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 21 Apr 2022 13:36:33 -0400 Subject: [PATCH 3/4] add cell_id to IntracellularElectrode (#512) * add cell_id to IntracellularElectrode * Update core/nwb.icephys.yaml Co-authored-by: Oliver Ruebel * Update format_release_notes.rst * Update format_release_notes.rst Co-authored-by: Oliver Ruebel --- core/nwb.icephys.yaml | 4 ++++ docs/format/source/format_release_notes.rst | 3 ++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/core/nwb.icephys.yaml b/core/nwb.icephys.yaml index 40bf20ef..7f717315 100644 --- a/core/nwb.icephys.yaml +++ b/core/nwb.icephys.yaml @@ -199,6 +199,10 @@ groups: neurodata_type_inc: NWBContainer doc: An intracellular electrode and its metadata. datasets: + - name: cell_id + dtype: text + doc: unique ID of the cell + quantity: '?' - name: description dtype: text doc: Description of electrode (e.g., whole-cell, sharp, etc.). diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 2547b23d..6b029c66 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -9,10 +9,11 @@ Release Notes Minor changes ^^^^^^^^^^^^^ - Added an ``offset`` attribute to all ``TimeSeries`` objects to allow enhanced translation to scientific units. +- Added ``cell_id`` field to ``IntracellularElectrode``. (#512) Major changes ^^^^^^^^^^^^^ -- Shape of SpatialSeries.data is more restrictive to prevent > 3 columns. +- Shape of SpatialSeries.data is more restrictive to prevent > 3 columns. (#510) 2.4.0 (Aug. 11, 2021) From 4cc938f7dd69b6b92c209b084e15aa0c40656b20 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Thu, 21 Apr 2022 14:16:50 -0700 Subject: [PATCH 4/4] Improve documentation for some electrodes table columns (#498) Co-authored-by: Ben Dichter --- core/nwb.file.yaml | 3 ++- docs/format/source/format_release_notes.rst | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index fc3ac7eb..e35ba165 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -325,7 +325,8 @@ groups: - name: reference neurodata_type_inc: VectorData dtype: text - doc: Description of the reference used for this electrode. + doc: Description of the reference electrode and/or reference scheme used for this electrode, e.g., + "stainless steel skull screw" or "online common average referencing". quantity: '?' - name: intracellular_ephys doc: Metadata related to intracellular electrophysiology. diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 6b029c66..6f10fde2 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -9,6 +9,7 @@ Release Notes Minor changes ^^^^^^^^^^^^^ - Added an ``offset`` attribute to all ``TimeSeries`` objects to allow enhanced translation to scientific units. +- Clarified the doc string for the ``reference`` column of the electrodes table. (#498) - Added ``cell_id`` field to ``IntracellularElectrode``. (#512) Major changes