Fix calibrations

+dat/addLogEntry.m

@@ -26,6 +26,7 @@
 %% create and store entry
 e = entry(nextidx);
 log(nextidx) = e;
+% Store an instance of Alyx for narrative registration
 if nargin > 5; e.AlyxInstance = AlyxInstance; end
 
 %% store updated log to *all* repos locations

+dat/delParamProfile.m

@@ -8,7 +8,7 @@ function delParamProfile(expType, profileName)
 
 %path to repositories
 fn = 'parameterProfiles.mat';
-repos = fullfile(dat.reposPath('expInfo'), fn);
+repos = fullfile(dat.reposPath('main'), fn);
 
 %load existing profiles for specified expType
 profiles = dat.loadParamProfiles(expType);

+dat/expExists.m

@@ -1,6 +1,9 @@
 function b = expExists(expRef)
 %DAT.EXPEXISTS Confirm existence of experiment(s) with reference
-%   b = DAT.EXPEXISTS(expRef) TODO
+%   b = DAT.EXPEXISTS(expRef) Returns true is expRef exists, where expRef
+%   is an experiment reference string or cell array thereof.
+%
+% See Also DAT.LISTEXPS, DAT.PATHS
 %
 % Part of Rigbox
 
@@ -14,7 +17,7 @@
 
   function b = check(expRef)
     % ensure the standard folder given the reference exists
-    b = file.exists(dat.expPath(expRef, 'expInfo', 'master'));
+    b = file.exists(dat.expPath(expRef, 'main', 'master'));
   end
 
 end

+dat/expFilePath.m

@@ -7,105 +7,117 @@
 %   e.g. to get the paths for an experiments 2 photon TIFF movie:
 %   DAT.EXPFILEPATH('mouse1', datenum(2013, 01, 01), 1, '2p-raw');
 %
-%   [full, filename] = expFilePath(ref, type, [reposlocation])
+%   [full, filename] = expFilePath(ref, type, [reposlocation, ext])
 %
-%   [full, filename] = expFilePath(subject, date, seq, type, [reposlocation])
+%   [full, filename] = expFilePath(subject, date, seq, type, [reposlocation, ext])
 %
 %   Options for reposlocation are: 'local' or 'master'
 %   Many options for type, e.g. 'block', '2p-raw', 'eyetracking', etc
+%   If ext is specified, the path returned has the extention ext, otherwise
+%   the default for that type is used.
 %
 % Part of Rigbox
 
 % 2013-03 CB created
 
-if nargin == 3 || nargin == 5
-  % repos argument was passed, save the value and remove from varargin
-  location = varargin(end);
-  varargin(end) = [];
-elseif nargin < 2
-  error('Not enough arguments supplied.');
-else
-  % repos argument not passed
-  location = {};
+assert(length(varargin) > 1, 'Error: Not enough arguments supplied.')
+
+parsed = catStructs(regexp(varargin{1}, dat.expRefRegExp, 'names'));
+if isempty(parsed) % Subject, not ref
+  if nargin > 4
+    location = varargin{5};
+    varargin(5) = [];
+  else
+    location = {};
+  end
+  typeIdx = 4;
+else % Ref, not subject
+  typeIdx = 2;
+  if nargin > 2
+    location = varargin{3};
+    varargin(3) = [];
+  else
+    location = {};
+  end
 end
 
 % tabulate the args to get complete rows
 [varargin{1:end}, singleArgs] = tabulateArgs(varargin{:});
 
-% last argument is the file type
-fileType = varargin{end};
+fileType = varargin{typeIdx};
+extention = iff(any(numel(varargin) == [3,5]), varargin{end},...
+  cell(1,length(varargin{1})));
+if any(numel(varargin) == [3,5]); varargin(end) = []; end
+
 % convert file types to file suffixes
-[repos, suffix, dateLevel] = mapToCell(@typeInfo, fileType);
+[repos, suffix, dateLevel] = mapToCell(@typeInfo, fileType(:), extention(:));
 
 reposArgs = cat(2, {repos}, location);
 
 % and the rest are for the experiment reference
 [expPath, expRef] = dat.expPath(varargin{1:end - 1}, reposArgs{:});
 
-  function [repos, suff, dateLevel] = typeInfo(type)
+  function [repos, suff, dateLevel] = typeInfo(type, newExt)
     % whether this repository is at the date level or otherwise deeper at the sequence
-    % level (default)
+    % level (default). FIXME: Date level doesn't work, perhaps this should
+    % be modified to work with deeper sequences also? E.g.
+    % default\2018-05-04\1\2
     dateLevel = false;
+    repos = 'main';
+    ext = '.mat'; 
     switch lower(type)
       case 'block' % MAT-file with info about each set of trials
-        repos = 'expInfo';
-        suff = '_Block.mat';
+        suff = '_Block';
       case 'hw-info' % MAT-file with info about the hardware used for an experiment
-        repos = 'expInfo';
-        suff = '_hardwareInfo.mat';
+        suff = '_hardwareInfo';
       case '2p-raw' % TIFF with 2-photon raw fluorescence movies
-        repos = 'twoPhoton';
         suff = '_2P.tif';
+        ext = '.tif';
       case 'calcium-preview'
-        repos = 'twoPhoton';
-        suff = '_2P_CalciumPreview.tif';
+        suff = '_2P_CalciumPreview';
+        ext = '.tif';
       case 'calcium-reg'
-        repos = 'twoPhoton';
         suff = '_2P_CalciumReg';
+        ext = '';
       case 'calcium-regframe'
-        repos = 'twoPhoton';
-        suff = '_2P_CalciumRegFrame.tif';
+        suff = '_2P_CalciumRegFrame';
+        ext = '.tif';
       case 'timeline' % MAT-file with acquired timing information
-        repos = 'expInfo';
-        suff = '_Timeline.mat';
+        suff = '_Timeline';
       case 'calcium-roi'
-        repos = 'twoPhoton';
-        suff = '_ROI.mat';
+        suff = '_ROI';
       case 'calcium-fc' % minimally filtered fractional change frames
-        repos = 'twoPhoton';
         suff = '_2P_CalciumFC';
+        ext = '';
       case 'calcium-ffc' % ROI filtered fractional change frames
-        repos = 'twoPhoton';
         suff = '_2P_CalciumFFC';
+        ext = '';
       case 'calcium-widefield-svd'
-        repos = 'widefield';
         suff = '_SVD';
+        ext = '';
       case 'eyetracking'
-        repos = 'eyeTracking';
         suff = '_eye';
+        ext = '';
       case 'parameters' % MAT-file with parameters used for experiment
-        repos = 'expInfo';
-        suff = '_parameters.mat';
+        suff = '_parameters';
       case 'lasermanip'
-        repos = 'expInfo';
-        suff = '_laserManip.mat';
+        suff = '_laserManip';
       case 'img-info'
-        repos = 'twoPhoton';
-        suff = '_imgInfo.mat';
+        suff = '_imgInfo';
       case 'tmaze'
-        repos = 'expInfo';
-        suff = '_TMaze.mat';
+        suff = '_TMaze';
       case 'expdeffun'
-        repos = 'expInfo';
-        suff = '_expDef.m';
+        suff = '_expDef';
+        ext = '.m';
       case 'svdspatialcomps'
         dateLevel = true;
-        %               expPath = mapToCell(@fileparts, expPath);
-        %                 repos = 'expInfo';
-        %                 suff = '_expDef.m';
       otherwise
         error('"%s" is not a valid file type', type);
     end
+    % Append extention to suffix
+    ext = iff(isempty(newExt)&&~ischar(newExt), ext, newExt);
+    suff = iff((isempty(ext)&&ischar(ext))||(~isempty(ext)&&ext(1)=='.'),...
+      [suff, ext], [suff, '.', ext]);
   end
 
 % generate a filename for each experiment
@@ -120,5 +132,4 @@
   filename = filename{1};
 end
 
-end
-
+end

+dat/expLogRequest.m

@@ -6,7 +6,7 @@
 
 if nargin < 2
   args = struct;
-elseif nargin == 2 && isstruct(varargin{1});  
+elseif nargin == 2 && isstruct(varargin{1})
 else
   args = varargin2struct(varargin{:});
 end

+dat/expPath.m

@@ -9,10 +9,10 @@
 %   sames as the above, but returns paths for an experiment with a
 %   specified 'subject', on a particular 'date', and numbered 'seq'.
 %
-% e.g. to get the paths for the 'expInfo' repository, for the first
+% e.g. to get the paths for the 'main' repository, for the first
 % experiment of the day for 'SUBJECTA':
 % 
-% paths = DAT.EXPPATH('SUBJECTA', now, 1, 'expInfo');
+% paths = DAT.EXPPATH('SUBJECTA', now, 1, 'main');
 %
 % Part of Rigbox
 

+dat/listExps.m

@@ -7,15 +7,15 @@
 
 % 2013-03 CB created
 
-% The master 'expInfo' repository is the reference for the existence of
+% The master 'main' repository is the reference for the existence of
 % experiments, as given by the folder structure
-expInfoPath = dat.reposPath('expInfo', 'master');
+mainPath = dat.reposPath('main', 'master');
 
   function [expRef, expDate, expSeq] = subjectExps(subject)
     % finds experiments for individual subjects
     % experiment dates correpsond to date formated folders in subject's
     % folder
-    subjectPath = fullfile(expInfoPath, subject);
+    subjectPath = fullfile(mainPath, subject);
     subjectDirs = file.list(subjectPath, 'dirs');
     dateRegExp = '^(?<year>\d\d\d\d)\-?(?<month>\d\d)\-?(?<day>\d\d)$';
     dateMatch = regexp(subjectDirs, dateRegExp, 'names');

+dat/listSubjects.m

@@ -1,17 +1,43 @@
-function subjects = listSubjects()
+function subjects = listSubjects(varargin)
 %DAT.LISTSUBJECTS Lists recorded subjects
-%   subjects = DAT.LISTSUBJECTS() Lists the experimental subjects present
-%   in experiment info repository ('expInfo').
+%   subjects = DAT.LISTSUBJECTS([alyxInstance]) Lists the experimental subjects present
+%   in experiment info repository ('main').
+%
+% Optional input argument of an alyx instance will enable generating this
+% list from alyx rather than from the directory structure on zserver
 %
 % Part of Rigbox
 
 % 2013-03 CB created
+% 2018-01 NS added Alyx compatibility
 
-% The master 'expInfo' repository is the reference for the existence of
-% experiments, as given by the folder structure
-expInfoPath = dat.reposPath('expInfo', 'master');
-
-dirs = file.list(expInfoPath, 'dirs');
-subjects = setdiff(dirs, {'misc'}); %exclude the misc directory
-
+if nargin>0 && ~isempty(varargin{1}) % user provided an alyx instance
+    ai = varargin{1}; % an alyx instance
+
+    % get list of all living, non-stock mice from alyx
+    s = alyx.getData(ai, 'subjects?stock=False&alive=True');
+
+    % determine the user for each mouse
+    respUser = cellfun(@(x)x.responsible_user, s, 'uni', false);
+
+    % get cell array of subject names
+    subjNames = cellfun(@(x)x.nickname, s, 'uni', false);
+
+    % determine which subjects belong to this user
+    thisUserSubs = sort(subjNames(strcmp(respUser, ai.username)));
+
+    % all the subjects
+    otherUserSubs = sort(subjNames(~strcmp(respUser, ai.username)));
+
+    % the full, ordered list
+    subjects = [{'default'}, thisUserSubs, otherUserSubs]';
+else
+
+    % The master 'main' repository is the reference for the existence of
+    % experiments, as given by the folder structure
+    mainPath = dat.reposPath('main', 'master');
+
+    dirs = file.list(mainPath, 'dirs');
+    subjects = dirs(~cellfun(@(d)startsWith(d, '@'), dirs)); % exclude misc directories
+end
 end

+dat/loadParamProfiles.m

@@ -8,7 +8,7 @@
 % 2017-02 MW Param struct now sorted in ASCII dictionary order
 
 fn = 'parameterProfiles.mat';
-masterPath = fullfile(dat.reposPath('expInfo', 'master'), fn);
+masterPath = fullfile(dat.reposPath('main', 'master'), fn);
 
 p = struct; %default is to return an empty struct
 
@@ -18,7 +18,8 @@
   loaded = load(masterPath, expType); %load profiles for specific experiment type
   warning(origState);
   if isfield(loaded, expType)
-    p = orderfields(loaded.(expType)); %extract those profiles to return
+    [~, I] = sort(lower(fieldnames(loaded.(expType))));
+    p = orderfields(loaded.(expType), I); %extract those profiles to return
   end
 end
 

+dat/logPath.m

@@ -10,8 +10,8 @@
 
 %ensure the subject exists
 assert(dat.subjectExists(subject), 'Subject "%s" does not exist', subject);
-% get path(s) to expInfo repository
-reposPath = dat.reposPath('expInfo', varargin{:});
+% get path(s) to main repository
+reposPath = dat.reposPath('main', varargin{:});
 
 filename = sprintf('%s_log.mat', subject);
 subjectPath = file.mkPath(reposPath, subject);