Update tutorials to use dot notation for accessing data objects from Sets and Container types

tutorials/private/mcode/behavior.m

@@ -52,15 +52,15 @@
 % |SpatialSeries|> objects.
 
 position = types.core.Position();
-position.spatialseries.set('SpatialSeries', position_spatial_series);
+position.add('SpatialSeries', position_spatial_series);
 %% Create a Behavior Processing Module
 % Create a processing module called "behavior" for storing behavioral data in 
 % the NWBFile, then add the <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/Position.html 
 % |Position|> object to the processing module.
 
 behavior_processing_module = types.core.ProcessingModule('description', 'stores behavioral data.');
-behavior_processing_module.nwbdatainterface.set("Position", position);
-nwb.processing.set("behavior", behavior_processing_module);
+behavior_processing_module.add("Position", position);
+nwb.processing.add("behavior", behavior_processing_module);
 %% CompassDirection: Storing view angle measured over time
 % Analogous to how position can be stored, we can create a <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/SpatialSeries.html 
 % |SpatialSeries|> object for representing the view angle of the subject.
@@ -77,13 +77,13 @@
     'data_unit', 'radians' ...
     );
 direction = types.core.CompassDirection();
-direction.spatialseries.set('spatial_series', direction_spatial_series);
+direction.add('SpatialSeries', direction_spatial_series);
 %% 
 % We can add a <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/CompassDirection.html 
 % |CompassDirection|> object to the behavior processing module the same way we 
 % have added the position data.
 
-behavior_processing_module.nwbdatainterface.set('CompassDirection', direction);
+behavior_processing_module.add('CompassDirection', direction);
 %% BehaviorTimeSeries: Storing continuous behavior data
 % <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/BehavioralTimeSeries.html 
 % |BehavioralTimeSeries|> is an interface for storing continuous behavior data, 
@@ -100,10 +100,10 @@
     );
 
 behavioral_time_series = types.core.BehavioralTimeSeries();
-behavioral_time_series.timeseries.set('speed', speed_time_series);
+behavioral_time_series.add('speed', speed_time_series);
 
 % Add behavioral_time_series to the processing module
-behavior_processing_module.nwbdatainterface.set('BehavioralTimeSeries', behavioral_time_series);
+behavior_processing_module.add('BehavioralTimeSeries', behavioral_time_series);
 %% BehavioralEvents: Storing behavioral events
 % <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/BehavioralEvents.html 
 % |BehavioralEvents|> is an interface for storing behavioral events. We can use 
@@ -121,10 +121,10 @@
     );
 
 behavioral_events = types.core.BehavioralEvents();
-behavioral_events.timeseries.set('lever_presses', time_series);
+behavioral_events.add('lever_presses', time_series);
 
 % Add behavioral_events to the processing module
-behavior_processing_module.nwbdatainterface.set('BehavioralEvents', behavioral_events);
+behavior_processing_module.add('BehavioralEvents', behavioral_events);
 %% 
 % Storing only the timestamps of the events is possible with the ndx-events 
 % NWB extension. You can also add labels associated with the events with this 
@@ -146,7 +146,7 @@
     );
 
 behavioral_epochs = types.core.BehavioralEpochs();
-behavioral_epochs.intervalseries.set('running', run_intervals);
+behavioral_epochs.add('running', run_intervals);
 %% 
 % You can add more than one <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/IntervalSeries.html 
 % |IntervalSeries|> to a <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/BehavioralEpochs.html 
@@ -157,10 +157,10 @@
     'data', [1, -1, 1, -1], ...
     'timestamps', [15.0, 30.0, 60.0, 95.0] ...
     );
-behavioral_epochs.intervalseries.set('sleeping', sleep_intervals);
+behavioral_epochs.add('sleeping', sleep_intervals);
 
 % Add behavioral_epochs to the processing module
-behavior_processing_module.nwbdatainterface.set('BehavioralEpochs', behavioral_epochs);
+behavior_processing_module.add('BehavioralEpochs', behavioral_epochs);
 % Another approach: TimeIntervals
 % Using <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/TimeIntervals.html 
 % |TimeIntervals|> to represent time intervals is often preferred over <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/BehavioralEpochs.html 
@@ -179,7 +179,7 @@
 sleep_intervals.addRow('start_time', 0.7, 'stop_time', 0.9, 'stage', 2);
 sleep_intervals.addRow('start_time', 1.3, 'stop_time', 3.0, 'stage', 3);
 
-nwb.intervals.set('sleep_intervals', sleep_intervals);
+nwb.intervals.add('sleep_intervals', sleep_intervals);
 %% EyeTracking: Storing continuous eye-tracking data of gaze direction
 % <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/EyeTracking.html 
 % |EyeTracking|> is for storing eye-tracking data which represents direction of 
@@ -209,10 +209,10 @@
     );
 
 eye_tracking = types.core.EyeTracking();
-eye_tracking.spatialseries.set('right_eye_position', right_eye_position);
-eye_tracking.spatialseries.set('left_eye_position', left_eye_position);
+eye_tracking.add('right_eye_position', right_eye_position);
+eye_tracking.add('left_eye_position', left_eye_position);
 
-behavior_processing_module.nwbdatainterface.set('EyeTracking', eye_tracking);
+behavior_processing_module.add('EyeTracking', eye_tracking);
 %% PupilTracking: Storing continuous eye-tracking data of pupil size
 % <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/PupilTracking.html 
 % |PupilTracking|> is for storing eye-tracking data which represents pupil size. 
@@ -230,9 +230,9 @@
     );
 
 pupil_tracking = types.core.PupilTracking();
-pupil_tracking.timeseries.set('pupil_diameter', pupil_diameter);
+pupil_tracking.add('pupil_diameter', pupil_diameter);
 
-behavior_processing_module.nwbdatainterface.set('PupilTracking', pupil_tracking);
+behavior_processing_module.add('PupilTracking', pupil_tracking);
 %% Writing the behavior data to an NWB file
 % All of the above commands build an NWBFile object in-memory. To write this 
 % file, use <https://matnwb.readthedocs.io/en/latest/pages/functions/nwbExport.html 

tutorials/private/mcode/intro.m

@@ -113,7 +113,7 @@
 );
 
 % Add the AnnotationSeries to the NWBFile's stimulus group
-nwb.stimulus_presentation.set('Airpuffs', annotations)
+nwb.stimulus_presentation.add('Airpuffs', annotations)
 %% Behavior
 % SpatialSeries and Position
 % Many types of data have special data types in NWB. To store the spatial position 
@@ -170,10 +170,10 @@
 
 % add the Position object (that holds the SpatialSeries object) to the module 
 % and name the Position object "Position"
-behavior_module.nwbdatainterface.set('Position', position);
+behavior_module.add('Position', position);
 
 % add the processing module to the NWBFile object, and name the processing module "behavior"
-nwb.processing.set('behavior', behavior_module);
+nwb.processing.add('behavior', behavior_module);
 % Trials
 % Trials are stored in a <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/TimeIntervals.html 
 % |*TimeIntervals*|> object which is a subclass of <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/hdmf_common/DynamicTable.html 
@@ -207,7 +207,7 @@
 
 % If you have multiple trials tables, you will need to use custom names for
 % each one:
-nwb.intervals.set('custom_intervals_table_name', trials);
+nwb.intervals.add('custom_intervals_table_name', trials);
 %% Write
 % Now, to write the NWB file that we have built so far:
 
@@ -229,8 +229,7 @@
 % |*Position*|> object contains our <https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/SpatialSeries.html 
 % |*SpatialSeries*|> object named |'SpatialSeries'|.
 
-read_spatial_series = read_nwbfile.processing.get('behavior'). ...
-    nwbdatainterface.get('Position').spatialseries.get('SpatialSeries')
+read_spatial_series = read_nwbfile.processing.behavior.Position.SpatialSeries
 % Reading Data
 % Counter to normal MATLAB workflow, data arrays are read passively from the 
 % file. Calling |*read_spatial_series.data*| does not read the data values, but 

tutorials/private/mcode/read_demo_dandihub.m

@@ -14,10 +14,14 @@
 % <https://nwb-overview.readthedocs.io/en/latest/file_read/file_read.html#reading-with-matnwb 
 % NWB Overview Documentation>
 %% Download the Dataset
-% Use the pre-installed |dandi| Python package to download the dataset to the 
-% user-local dandisets folder:
+% Use the |dandi| Python package to download the dataset to the user-local dandisets 
+% folder. If you are running this livescript on DandiHub, the |dandi| package 
+% is already pre-installed. On a local environment, you need to install the |dandi| 
+% package in the python environment returned by running |pyenv()| in MATLAB. For 
+% more details on using Python from MATLAB, please refer to the <https://se.mathworks.com/help/matlab/matlab_external/install-supported-python-implementation.html 
+% MATLAB documentation>.
 
-environment = "Local";
+environment = "Local"; % Local or DandiHub
 switch environment
     case "DandiHub"
         targetFolder = "/home/jovyan/dandisets/000004";
@@ -36,18 +40,19 @@
 
 nwb.stimulus_presentation
 %% 
-% This results shows us that |nwb.stimulus_presentation| is a |Set| object that 
-% contains a single data object called |StimulusPresentation|, which is an |OpticalSeries| 
-% neurodata type. Use the |get| method to return this |OpticalSeries|. |Set| objects 
-% store a collection of other NWB objects.
+% This result shows that |nwb.stimulus_presentation| is a |Set| object. In MatNWB, 
+% a |Set| object stores a collection of other NWB objects. In this case, the |Set| 
+% contains a single data object named |StimulusPresentation|, which is of the 
+% |OpticalSeries| neurodata type. You can use dot notation of the form |Set.objectName| 
+% to access this |OpticalSeries|:
 
-nwb.stimulus_presentation.get('StimulusPresentation')
+nwb.stimulus_presentation.StimulusPresentation
 %% 
 % |OpticalSeries| is a neurodata type that stores information about visual stimuli 
 % presented to subjects. This print out shows all of the attributes in the |OpticalSeries| 
 % object named |StimulusPresentation|. The images are stored in |StimulusPresentation.data|
 
-StimulusImageData = nwb.stimulus_presentation.get('StimulusPresentation').data
+StimulusImageData = nwb.stimulus_presentation.StimulusPresentation.data
 %% 
 % When calling a data object directly, the data is not read but instead a |DataStub| 
 % is returned. This is because data is read "lazily" in MatNWB. Instead of reading 
@@ -73,7 +78,7 @@
 % arguments. We will use this approach to read all of the image display timestamps 
 % into memory.
 
-stimulus_times = nwb.stimulus_presentation.get('StimulusPresentation').timestamps.load();
+stimulus_times = nwb.stimulus_presentation.StimulusPresentation.timestamps.load();
 %% Quick PSTH and raster
 % Here, I will pull out spike times of a particular unit, align them to the 
 % image display times, and finally display the results.