From 9d46daa5c3f07f04a55c9b810904ef71478417e1 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Thu, 7 Dec 2023 14:55:53 -0500 Subject: [PATCH 1/8] propose more stimulus types --- core/nwb.file.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 682a5844..d3df715d 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -131,6 +131,12 @@ groups: - neurodata_type_inc: TimeSeries doc: TimeSeries objects containing data of presented stimuli. quantity: '*' + - neurodata_type_inc: DynamicTable + doc: DynamicTable objects containing data of presented stimuli. + quantity: '*' + - neurodata_type_inc: NWBDataInterface + doc: Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. + quantity: '*' - name: templates doc: 'Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are From bd8694682f696b33e6022cdc431a987d6eeafbe4 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Sat, 13 Jan 2024 00:37:06 -0800 Subject: [PATCH 2/8] Update core/nwb.file.yaml --- core/nwb.file.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 98b5f817..638f2814 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -137,6 +137,9 @@ groups: - neurodata_type_inc: NWBDataInterface doc: Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. quantity: '*' + # even though TimeSeries is a NWBDataInterface, we do not remove TimeSeries + # in order to maintain backwards compatibility in the APIs that + # use the neurodata_type_inc from the schema to set the variable name - name: templates doc: 'Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are From c7de87a6963f7b6b1d172fd6fc23db58652a6f2e Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Sat, 13 Jan 2024 00:37:27 -0800 Subject: [PATCH 3/8] Update core/nwb.file.yaml --- core/nwb.file.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 638f2814..35df14ea 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -137,7 +137,7 @@ groups: - neurodata_type_inc: NWBDataInterface doc: Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. quantity: '*' - # even though TimeSeries is a NWBDataInterface, we do not remove TimeSeries + # even though TimeSeries is a child type of NWBDataInterface, we do not remove TimeSeries # in order to maintain backwards compatibility in the APIs that # use the neurodata_type_inc from the schema to set the variable name - name: templates From e1275d3cfec912d134683fb96808a240204fd769 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 5 Feb 2024 10:43:44 -0800 Subject: [PATCH 4/8] Update nwb.file.yaml --- core/nwb.file.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 35df14ea..1c58c71a 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -128,15 +128,15 @@ groups: - name: presentation doc: Stimuli presented during the experiment. groups: - - neurodata_type_inc: TimeSeries - doc: TimeSeries objects containing data of presented stimuli. + # - neurodata_type_inc: TimeSeries + # doc: TimeSeries objects containing data of presented stimuli. + # quantity: '*' + - neurodata_type_inc: NWBDataInterface + doc: Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. quantity: '*' - neurodata_type_inc: DynamicTable doc: DynamicTable objects containing data of presented stimuli. quantity: '*' - - neurodata_type_inc: NWBDataInterface - doc: Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. - quantity: '*' # even though TimeSeries is a child type of NWBDataInterface, we do not remove TimeSeries # in order to maintain backwards compatibility in the APIs that # use the neurodata_type_inc from the schema to set the variable name From e7d4fb64f7de6319382b7a980a96b65eee0f2b66 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 5 Feb 2024 10:44:46 -0800 Subject: [PATCH 5/8] Update nwb.file.yaml --- core/nwb.file.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 1c58c71a..18d5b986 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -132,7 +132,8 @@ groups: # doc: TimeSeries objects containing data of presented stimuli. # quantity: '*' - neurodata_type_inc: NWBDataInterface - doc: Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. + doc: 'TimeSeries objects or generic NWB data interfaces, usually from an extension, ' + 'containing data of presented stimuli.' quantity: '*' - neurodata_type_inc: DynamicTable doc: DynamicTable objects containing data of presented stimuli. From 738ba3e8139118413c683051ba114d8f5fea92cf Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 5 Feb 2024 10:45:58 -0800 Subject: [PATCH 6/8] Update nwb.file.yaml --- core/nwb.file.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 18d5b986..fc158007 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -128,11 +128,11 @@ groups: - name: presentation doc: Stimuli presented during the experiment. groups: - # - neurodata_type_inc: TimeSeries - # doc: TimeSeries objects containing data of presented stimuli. - # quantity: '*' + - neurodata_type_inc: TimeSeries + doc: TimeSeries objects containing data of presented stimuli. + quantity: '*' - neurodata_type_inc: NWBDataInterface - doc: 'TimeSeries objects or generic NWB data interfaces, usually from an extension, ' + doc: 'Generic NWB data interfaces, usually from an extension, ' 'containing data of presented stimuli.' quantity: '*' - neurodata_type_inc: DynamicTable From 82da898b331dbccd97e26aedc92c9f9ead330e9d Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 5 Feb 2024 11:03:36 -0800 Subject: [PATCH 7/8] Update nwb.file.yaml --- core/nwb.file.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index fc158007..c3da4afc 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -132,8 +132,8 @@ groups: doc: TimeSeries objects containing data of presented stimuli. quantity: '*' - neurodata_type_inc: NWBDataInterface - doc: 'Generic NWB data interfaces, usually from an extension, ' - 'containing data of presented stimuli.' + doc: 'Generic NWB data interfaces, usually from an extension, + containing data of presented stimuli.' quantity: '*' - neurodata_type_inc: DynamicTable doc: DynamicTable objects containing data of presented stimuli. From a7247881b5c1162184f04f57752e0323885de2a0 Mon Sep 17 00:00:00 2001 From: Ryan Ly Date: Mon, 5 Feb 2024 13:50:53 -0800 Subject: [PATCH 8/8] Update format_release_notes.rst --- docs/format/source/format_release_notes.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index 99d96d42..b9fc0df7 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -9,9 +9,10 @@ Release Notes Minor changes ^^^^^^^^^^^^^ - Fixed typos in docstrings. (#560) -- Deprecated `ImagingRetinotopy` neurodata type. (#565) -- Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. (#564) +- Deprecated ``ImagingRetinotopy`` neurodata type. (#565) +- Modified ``OptogeneticSeries`` to allow 2D data, primarily in extensions of ``OptogeneticSeries``. (#564) - Added optional ``stimulus_template`` column to ``IntracellularStimuliTable`` as part of the ``IntracellularRecordingsTable``. (#545) +- Added support for ``NWBDataInterface`` and ``DynamicTable`` in ``NWBFile.stimulus``. (#559) 2.6.0 (January 17, 2023) -----------------------