Develop (#236)

* HOTFIX updated alyx-matlab submodule

* Scale cleanup (#220)

* #219 fix for scale cleanup on error

* Update to CHANGELOG

* Support for remote error IDs

* Added test for StimulusControl and fixed err id in expServer test

* Mpep bind server test (#209)

* Started expServer tests

* Added more tests; bug fix for older versions

* Removed validation functions for old MATLAB versions; added documentation

* More coverage, documentation

* Draws text to screen during calibration #128

* Fix for #4

* Added structAssign test; rewardId tests

* Typo fix in structAssign_test

* Finished tests for expServer

* #156

* Returned listener delete to cleanup

* Stricter tolerance in AlyxPanel_test; bug fix for rounding negative numbers

* Update alyx-matlab submodule

* Minor changes to documentation

* Update CHANGELOG.md

* Added tests for tl.bindMpepServer and pnet spy

* Fixture path fix

* Moved audioDevices default to devices mock

* Assertion added #204

* paths template consistent with new cortexlab servers (#224)

* single-character change to README.md to test if I still have permission to push to dev (hopefully I don't)

* modified paths_template to be consistent with current cortexlab server settings

* Changes to server name vars in paths template

* ExpPanel updates (#221)

* Returned access restriction; started docs; Hiding info fields and comments box; cleaner subclassing

* Rethrow Signals update mismatch as warning, #72

* SqueakExpPanel -> SignalsExpPanel

* Removed code for very specific experiment that is no longer used

* Completed using_ExpPanel docs

* Formatting docs

* Issue #79

* Cleaned up UpdatesFilter

* documentation; changed plot colours

* Signals exp test (#231)

* Tiny changes to appease MATLAB

* Started installation section

* Added matlabdomain extension

* Added infomation for remote location in reposPath

* Started a setup page

* Added parameters walkthrough

* HOTFIX changed Alyx Panel login timer to 90 mins

* 2.3 <- 2.2.1 (#198)

* updated signals submodule

* updated signals submodule (eb71b1f)

* Added test for ensureCell

* Fix'd typo in ensureCell_test

* Future-proofing runall to ignore tests with specific hardware requirements

* Added tests for nop, iff and emptyElems

* Added tests for cellsprintf and num2cellstr; bug fix in num2cellstr

* Submodule update

* mapToCell test

* Removed complete todos

* Added test for dat.expExists

* Restore changes made in commit
247060a

* Expanded test for dispWaterReq

* assert -> verifyMatches

* Added catStructs test

* Added tabulateArgs test

* superSave test added

* added an informative error message in the case that dat.paths is missing

* Attempting to construct a branch that doesn't differ from dev in its submodules

* Revert "Attempting to construct a branch that doesn't differ from dev in its submodules"
Reverting a commit that should have been to dev_kevin, not to dev

* Revert "added an informative error message in the case that dat.paths is missing"
Reverting a commit that should have been to dev_kevin, not to dev
This reverts commit a492bd2.

* Added file package test

* Added test for pick

* Added test for namedArg

* Added varName test

* Added back tolerance change

* Dev kevin (#192)

* added an informative error message when dat.paths is not present

* added an identifier to the error message

* Added warnings and errors to deal with the case that hardware.mat is not found

* fixed identifier

* Changed error identifiers following Miles' suggestion of module:package:function:error

* added more info to error for empty rig

* added more info to no dat.paths error

* Bug fix in namedArg test

* Removed old function -> now a method of Alyx

* Started +fun package test; added fileFunction test

* No longer using 'which' to assert function existence

* Bug fixes for tests

* Bug fix for wiringInfo method

* Added KeyedSeq test

* Added docs for apply and applyForce

* Added loadVar test

* Issue #168

* Added mergeStructs test

* Added performance tests; reorganized tests; updated changelog

* Added parameters walkthrough

* Added timeline walkthrough; bug fix for wiringInfo in Timeline

* added informative error messages to calibration code

* Added documentation for setting up Window; documentation for Window class; Minor bug fixes

* Added a few examples to hardware docs

* Added Viewing model walkthrough and expanded FAQ

* Updated changelog

* Updates to docs

* Added test for +hw/calibrate.m

* deleted exp.construct

* Added documentation for calibration test

* Updated docs; added services guide

* Updates docs

* Fix for Communicator WTF mode; increased test coverage for iff

* Update to changelog and signals

* HOTFIX changed Alyx Panel login timer to 90 mins

* Removed readthedocs, updated submodules

* Update Shields

* HOTFIX: Correct location of docs in README; Stronger wording in install instructions

* Added issue templates (#179)

* Added troubleshooting docs and error id list

* Using signals error handling branch; added troubleshooting doc

* Re-factoring SignalsExp for test subclassing

* Started expServer tests

* Added more tests; bug fix for older versions

* Removed validation functions for old MATLAB versions; added documentation

* More coverage, documentation

* Draws text to screen during calibration #128

* Fix for #4

* Added structAssign test; rewardId tests

* Typo fix in structAssign_test

* Finished tests for expServer

* #156

* Returned listener delete to cleanup

* Stricter tolerance in AlyxPanel_test; bug fix for rounding negative numbers

* Update alyx-matlab submodule

* Minor changes to documentation

* Update CHANGELOG.md

* Added tests for tl.bindMpepServer and pnet spy

* Fixture path fix

* Moved audioDevices default to devices mock

* WIP

* #100 #202

* Updated tests with share fixtures; added pause/resume to SignalsExp; added further tests for SignalsExp; updated tests README; SessionURL fetched from database when necessary

* Added better update of keyboard input signal

* Potential fix for #213

* Updates to submodules

* Update to alyx-matlab

* Context menu for hiding event updates in ExpPenel

* trialCondition index can be reset with signal

* Improvements to test UI

* Documentation

* README for +eui package (#156)

* WIP

* Removed warning from updateLogEntry when Alyx deactivated #202

* Added hide option for ExpPanel; ExpPanel guide in docs

* Added utils; started docs

* #218

* Support for ids in errOnFail

* Removed old commented-out code

* Scale port closed on errors

* Added brief PTB install instructions (#228)

* cleanup

* Documentation; #229

* More flags for addRigboxPaths

* started updating README after Anwar's comments

* updated some instructions in README

* Revert "started updating README after Anwar's comments"

This reverts commit 9f5a456.

* Updated documentation

* Removed PTBDebug call and added example to docstring

* Update to CHANGELOG and signals

* #205 - refactored

* Update to tests

* Warning supression in tests

* CHANGELOG

Co-authored-by: Jai Bhagat <[email protected]>

* Fix for eui.ExpPanel/live input parse error and tests added (#239)

* Fix for eui.ExpPanel/live input parse error and tests added

* Updated CHANGELOG and tests Contents file

* Better handling of ExpDefs; Documentation updates

* Fix for selecting expDef from uigetfile

* Use erase instead of strrep (#238)

* Bug fix for updateParams on edit; update submodules

* Documentation (#237)

* Added troubleshooting to index

* Fixed external links in index

* Updated index version number

* Documented stimulusControllers and typo fix in MockDialog

* Documented tabulateArgs

* README and CONTRIBUTING

* Updated badges

* Ignore todos in html

* Param profiles test (#244)

* tests and documentation for *paramProfile functions; repos created when none exist

* CHANGELOG

* Info label format (#246)

* Added label format option to SignalsExpPanel

* CHANGELOG

* Documentation (#261)

* Typo fix; added acknowledgement; mentioned 2PCs in software req

* Generic paths template

* added more steering wheel setup details

* Merge from master and updates to README, addRigboxPaths

Co-authored-by: Jai Bhagat <[email protected]>
Co-authored-by: Kevin Miller <[email protected]>

+dat/constructExpRef.m

@@ -1,6 +1,6 @@
 function ref = constructExpRef(subjectRef, expDate, expSequence)
 %DAT.CONSTRUCTEXPREF Constructs an experiment reference string
-%   ref = DAT.CONSTRUCTEXPREF(subject, dat, seq) constructs and returns a
+%   ref = DAT.CONSTRUCTEXPREF(subject, date, seq) constructs and returns a
 %   standard format string reference, for the experiment using the 'subject',
 %   the 'date' of the experiment (a MATLAB datenum), and the daily sequence
 %   number of the experiment, 'seq' (must be an integer).

+dat/expFilePath.m

@@ -20,25 +20,36 @@
 
 % 2013-03 CB created
 
-assert(length(varargin) > 1, 'Error: Not enough arguments supplied.')
+assert(length(varargin) > 1, 'Rigbox:dat:expFilePath:NotEnoughInputs',...
+  'Not enough input arguments.')
 
 parsed = catStructs(regexp(varargin{1}, dat.expRefRegExp, 'names'));
 if isempty(parsed) % Subject, not ref
-  if nargin > 4
+  if nargin < 3
+    error('Rigbox:dat:expFilePath:NotEnoughInputs', ...
+      ['Not enough input arguments; check expRef formatted correcly ' ...
+      'or enter subject, date and sequence as separate arguments'])
+  elseif nargin == 3
+    error('Rigbox:dat:expFilePath:NotEnoughInputs', ...
+      'Not enough input arguments; missing file type')
+  elseif nargin > 4
     location = varargin{5};
     varargin(5) = [];
   else
     location = {};
   end
   typeIdx = 4;
 else % Ref, not subject
-  typeIdx = 2;
-  if nargin > 2
+  if nargin < 2
+    error('Rigbox:dat:expFilePath:NotEnoughInputs', ...
+      'Not enough input arguments; missing file type')
+  elseif nargin > 2
     location = varargin{3};
     varargin(3) = [];
   else
     location = {};
   end
+  typeIdx = 2;
 end
 
 % tabulate the args to get complete rows

+dat/expPath.m

@@ -23,6 +23,9 @@
   reposArgs = varargin(end);
   varargin = varargin(1:end - 1);
 else
+  % Check for minimum inputs
+  assert(nargin > 2, ...
+    'Rigbox:dat:expPath:NotEnoughInputs', 'Must provide repo location')
   reposArgs = varargin((end - 1):end);
   varargin = varargin(1:end - 2);
 end

+dat/loadParamProfiles.m

@@ -1,6 +1,24 @@
 function p = loadParamProfiles(expType)
 %DAT.LOADPARAMPROFILES Loads the parameter sets for given experiment type
-%   TODO
+%   Loads a struct of parameter structures from a MAT file called
+%   'parameterProfiles'. Each field of this struct is a parameter set name
+%   for a given expType.  Parameters of a given expType can be saved using
+%   the DAT.SAVEPARAMPROFILE function.
+%
+%   Input:
+%     expType (char): The name of the experiment type, e.g. ChoiceWorld.
+%
+%   Output:
+%     p (struct): a scalar struct of parameter sets for the given
+%       experiment type.  Each fieldname holds a different parameter
+%       structure.  The fields are sorted in ASCII dictionary order.
+%
+%   Example:
+%     dat.saveParamProfile('ChoiceWorld', 'defSet', exp.choiceWorldParams)
+%     profiles = dat.loadParamProfiles('ChoiceWorld');
+%     p = exp.Parameters(profiles.defSet);
+%   
+% See also DAT.SAVEPARAMPROFILE, DAT.PATHS
 %
 % Part of Rigbox
 

+dat/reposPath.m

@@ -4,21 +4,26 @@
 %   repository specified by 'name'.
 %
 %   Each repository can have multiple locations with one location being the
-%   "master" copy and others considered backups (e.g. copies on local
-%   machines). Users of this function wanting to *save* data should do so
-%   in all locations. To *load* data, the master may be the only location
-%   containing all data (i.e. because local copies will only be on specific
-%   machines). The optional 'location' parameter specifies one or more
-%   locations, with "all" being the default that returns all locations for
-%   that repository, and "master" will return the path to the master
-%   location.
+%   'master' copy and others considered backups or archives (e.g. copies on
+%   local machines). Users of this function wanting to *save* data should
+%   do so in all locations (i.e. master and local). To *load* data, the
+%   remote locations (i.e. master and archives) should be used (i.e.
+%   because local copies will only be on specific machines). The optional
+%   'location' parameter specifies one or more locations, with 'all' being
+%   the default that returns the master and local locations for that
+%   repository, 'master' will return the path to the master location, and
+%   'remote' will return the master and archive/alternate paths (in that
+%   order).
 %
-%   e.g. to get all paths you should save to for the "main" repository:
-%   savePaths = DAT.REPOSPATH('main') % savePaths is a string cell array
+%   e.g. to get all paths you should save to for the 'main' repository:
+%   savePaths = DAT.REPOSPATH('main') % savePaths is a cell string
 %
-%   To get the master location for the "main" repository:
+%   To get the master location for the 'main' repository:
 %   loadPath = DAT.REPOSPATH('main', 'master') % loadPath is a string
 %
+%   When data are spread across multiple remote locations such as archives:
+%   loadPath = DAT.REPOSPATH('main', 'remote') % loadPath is a cell string
+%
 % Part of Rigbox
 
 % 2013-03 CB created

+dat/saveParamProfile.m

@@ -1,38 +1,49 @@
 function saveParamProfile(expType, profileName, params)
 %DAT.SAVEPARAMPROFILE Stores the named parameters for experiment type
-%   TODO
-%     - Figure out how to save struct without for-loop in 2016b!
+%   Saves a parameter structure in a MAT file called 'parameterProfiles'.
+%   Each field of this struct is an expType, and each nested field
+%   is the set name.  Parameters of a given expType can be loaded using the
+%   DAT.LOADPARAMPROFILES function.
+%
+%   Inputs:
+%     expType (char): The name of the experiment type, e.g. ChoiceWorld.
+%     profileName (char): The name of the parameter set being saved.  If
+%       the name already exists in the file for a given expType, it is
+%       overwritten.
+%     params (struct): A parameter structure to be saved.
+%
+%   Example:
+%     dat.saveParamProfile('ChoiceWorld', 'defSet', exp.choiceWorldParams)
+%     profiles = dat.loadParamProfiles('ChoiceWorld');
+%     p = exp.Parameters(profiles.defSet);
+%   
+% See also DAT.LOADPARAMPROFILES, DAT.PATHS
+%
 % Part of Rigbox
 
 % 2013-07 CB created
 % 2017-02 MW adapted to work in 2016b
 
-%path to repositories
+% If main repo folders don't exist yet, create them
+repos = dat.reposPath('main');
+cellfun(@mkdir, repos(~file.exists(repos)))
+
+% Path to repository files
 fn = 'parameterProfiles.mat';
-repos = fullfile(dat.reposPath('main'), fn);
+repos = fullfile(repos, fn);
 
-%load existing profiles for specified expType
+% Load existing profiles for specified expType
 profiles = dat.loadParamProfiles(expType);
-%add (or replace) the params with a field named by profile
+% Add (or replace) the params with a field named by profile
 profiles.(profileName) = params;
-%wrap in a struct for saving
+% Wrap in a struct for saving
 set = struct;
 set.(expType) = profiles;
 
-%save the updated set of profiles to each repos
-%where files exist already, append
-% cellfun(@(p) save(p, '-struct', 'set', '-append'),
-% file.filterExists(repos, true)); % Had to change her to a for loop, sorry
-% Chris!
-p = file.filterExists(repos, true);
-for i = 1:length(p)
-    save(p{i}, '-struct', 'set', '-append')
-end
-%and any that don't we should create from scratch
-p = file.filterExists(repos, false);
-for i = 1:length(p)
-    save(p{i}, '-struct', 'set')
-end
-% cellfun(@(p) save(p, '-struct', 'set'), file.filterExists(repos, false));
+% Save the updated set of profiles to each repos where files exist already,
+% append
+saveFn = @(p,name,varargin) save(p, '-struct', 'name', varargin{:});
+cellfun(@(p) saveFn(p, set, '-append') , file.filterExists(repos, true));
 
-end
+% Any that don't we should create from scratch
+cellfun(@(p) saveFn(p, set), file.filterExists(repos, false));

+dat/updateLogEntry.m

@@ -10,7 +10,7 @@ function updateLogEntry(subject, id, newEntry)
 
 % 2013-03 CB created
 
-if isfield(newEntry, 'AlyxInstance')
+if isfield(newEntry, 'AlyxInstance') && ~isempty(getOr(dat.paths, 'databaseURL'))
   % Update session narrative on Alyx
   if ~isempty(newEntry.comments) && ~strcmp(subject, 'default')
     try

+eui/ChoiceExpPanel.m

@@ -95,7 +95,7 @@ function refresh(obj)
     end
   end
 
-  methods %(Access = protected)
+  methods (Access = protected)
     function newTrial(obj, num, condition)
       %attempt num is red when on higher than third
       attemptColour = iff(condition.repeatNum > 3, [1 0 0], [0 0 0]);

+eui/ConditionPanel.m

@@ -105,7 +105,7 @@ function onEdit(obj, src, eventData)
       % See also FILLCONDITIONTABLE, EUI.PARAMEDITOR/UPDATE
       row = eventData.Indices(1);
       col = eventData.Indices(2);
-      assert(all(cellfun(@strcmpi, strrep(obj.ConditionTable.ColumnName, ' ', ''), ...
+      assert(all(cellfun(@strcmpi, erase(obj.ConditionTable.ColumnName, ' '), ...
         obj.ParamEditor.Parameters.TrialSpecificNames)), 'Unexpected condition names')
       paramName = obj.ParamEditor.Parameters.TrialSpecificNames{col};
       newValue = obj.ParamEditor.update(paramName, eventData.NewData, row);

+eui/Contents.m

@@ -0,0 +1,32 @@
+% +EUI Experiment UI package
+%
+% This +eui package contains all code pertaining to graphical user
+% interfaces in Rigbox. There are five base classes in this folder:
+% 
+% 1. MControl - The class behind the Master Control (MC) GUI.  
+% 2. ExpPanel - The superclass for UI panels that process and plot remote
+%    experiment event updates (i.e. the panels under the Current
+%    Experiments tab of MC).
+% 3. Log - UI control for viewing experiment log entries (the table under
+%    the Log tab of MC).
+% 4. AlyxPanel - UI for interacting with the Alyx database (the Alyx panel
+%    in the New Experiments tab of MC).  Can be run as a stand-alone GUI.
+% 5. ParamEditor - UI for viewing and editing parameters (the Parameter
+%    panel in the New Experiments table of MC).  Can be run as a
+%    stand-alone GUI.
+%
+% Files
+%   AlyxPanel       - A GUI for interating with the Alyx database
+%   ChoiceExpPanel  - UI control for monitoring a 2AFC experiment
+%   ConditionPanel  - Deals with formatting trial conditions UI table
+%   ExpPanel        - Basic UI control for monitoring an experiment
+%   FieldPanel      - Deals with formatting global parameter UI elements
+%   Log             - UI control for viewing experiment log entries
+%   MappingExpPanel - Preliminary UI for monitoring a mapping experiment
+%   MControl        - GUI for the control of experiments
+%   ParamEditor     - GUI for visualizing and editing experiment parameters
+%   SignalsTest     - A GUI for testing SignalsExp experiment definitions
+%   SqueakExpPanel  - Basic UI control for monitoring a Signals experiment
+%
+% See Also
+%   docs/html/using_mc.m, docs/html/using_ParamEditor.m