From 5657292eeb1ce1a7a5bbfe2afe752e86a5b3f4e6 Mon Sep 17 00:00:00 2001
From: "TORBEN-XPS\\torben" <torben.cshl@gmail.com>
Date: Tue, 1 May 2018 20:25:07 -0400
Subject: [PATCH 1/2] Cellbase-specific preferences are now saved in
 PREFERENCES variable in Cellbase mat-file. New functions: setcbpref,
 getcbpref, default_preferences, import_preferences. Updated set/get calls in
 other functions.

---
 .../plotting/plot_mclust_projections.m        |  4 +-
 .../optical_tagging/lightcluster.m            |  6 +--
 .../spike_clusters/LRatio.m                   |  4 +-
 .../spike_clusters/LRatio2.m                  |  4 +-
 .../spike_clusters/check_channel_validity.m   |  2 +-
 .../spike_clusters/plot_mclust_projections2.m |  4 +-
 .../MakeTrialEvents2_gonogo.m                 |  2 +-
 .../extractSpikeWaveforms.m                   |  2 +-
 .../database_functions/analyses/addanalysis.m |  2 +-
 .../database_functions/analyses/delanalysis.m |  4 +-
 .../database_functions/analyses/insertdata.m  |  2 +-
 .../database_functions/analyses/setvalue.m    |  4 +-
 .../cellbase/default_preferences.m            | 33 ++++++++++++
 .../database_functions/cellbase/getcbpref.m   | 40 ++++++++++++++
 .../cellbase/import_preferences.m             | 30 +++++++++++
 .../database_functions/cellbase/initcb.m      | 28 +++++-----
 .../database_functions/cellbase/loadcb.m      |  8 +--
 .../database_functions/cellbase/mountcb.m     | 14 +++--
 .../database_functions/cellbase/setcbpref.m   | 31 +++++++++++
 .../database_functions/cellbase/upgradecb.m   |  7 ++-
 .../database_functions/cells/addcell.m        |  4 +-
 .../database_functions/cells/addnewcells.m    |  2 +-
 .../database_functions/cells/delcell.m        |  4 +-
 .../database_functions/cells/findallcells.m   |  8 +--
 .../conversion/cellid2fnames.m                | 22 ++++----
 .../conversion/fname2cellid.m                 |  2 +-
 CellBase_R2013a/Help/CellBase_functions.html  |  4 ++
 .../Help/MakeTrialEvents2_gonogo.html         |  2 +-
 CellBase_R2013a/Help/default_preferences.html | 49 +++++++++++++++++
 CellBase_R2013a/Help/getcbpref.html           | 49 +++++++++++++++++
 CellBase_R2013a/Help/import_preferences.html  | 52 +++++++++++++++++++
 CellBase_R2013a/Help/setcbpref.html           | 49 +++++++++++++++++
 32 files changed, 408 insertions(+), 70 deletions(-)
 create mode 100644 CellBase_R2013a/Functions/database_functions/cellbase/default_preferences.m
 create mode 100644 CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m
 create mode 100644 CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m
 create mode 100644 CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m
 create mode 100644 CellBase_R2013a/Help/default_preferences.html
 create mode 100644 CellBase_R2013a/Help/getcbpref.html
 create mode 100644 CellBase_R2013a/Help/import_preferences.html
 create mode 100644 CellBase_R2013a/Help/setcbpref.html

diff --git a/CellBase_R2013a/AddOns/AnalysisFcn_AK_SPR/plotting/plot_mclust_projections.m b/CellBase_R2013a/AddOns/AnalysisFcn_AK_SPR/plotting/plot_mclust_projections.m
index fcb2440..6899b1a 100644
--- a/CellBase_R2013a/AddOns/AnalysisFcn_AK_SPR/plotting/plot_mclust_projections.m
+++ b/CellBase_R2013a/AddOns/AnalysisFcn_AK_SPR/plotting/plot_mclust_projections.m
@@ -8,7 +8,7 @@ function plot_mclust_projections(cellid)
 % Only the first light evoked spike is selected for plotting. To account
 % for drift, only spikes during the stimulation protocol are selected for
 % plotting.
-% SPR 2011-12-28
+% SPR 2011-12-28, TO 5/2018
 
 if nargin < 1,
     help plot_mclust_projections
@@ -47,7 +47,7 @@ function plot_mclust_projections(cellid)
 prop = 'Energy.fd';
 % prop = 'Peak.fd';
 
-propfn = [getpref('cellbase','cell_pattern') num2str(t) '_' prop];
+propfn = [getcbpref('Spikes_cell_pattern') num2str(t) '_' prop];
 propfn_path = [cellid2fnames(cellid,'sess') filesep propfn];
 wf_prop = load(propfn_path,'-mat');
 wf_prop1 = wf_prop.FeatureData(:,1);
diff --git a/CellBase_R2013a/Functions/analysis_functions/optical_tagging/lightcluster.m b/CellBase_R2013a/Functions/analysis_functions/optical_tagging/lightcluster.m
index 0d8e386..d58de13 100644
--- a/CellBase_R2013a/Functions/analysis_functions/optical_tagging/lightcluster.m
+++ b/CellBase_R2013a/Functions/analysis_functions/optical_tagging/lightcluster.m
@@ -21,7 +21,7 @@
 %   balazs.cshl@gmail.com
 %   09-May-2012
 
-%   Edit log: BH 5/9/12, 6/20/12 
+%   Edit log: BH 5/9/12, 6/20/12, TO 5/2018
 
 % Input arguments
 prs = inputParser;
@@ -40,7 +40,7 @@
 % Load spikes from Ntt file.
 Nttfn = cellid2fnames(cellid,'Ntt');
 all_spikes = LoadTT_NeuralynxNT(Nttfn);
-TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
 all_spikes = all_spikes * TIMEFACTOR;
 spk = loadcb(cellid,'Spikes');
 
@@ -71,7 +71,7 @@
 valid_channels = check_channel_validity(cellid);   % valid channels
 X = [];
 for k = 1:length(g.feature_names)
-    basename = [getpref('cellbase','cell_pattern') num2str(t)];
+    basename = [getcbpref('Spikes_cell_pattern') num2str(t)];
     propfn = [basename '_' g.feature_names{k}];   % name of feature file (e.g. TT1_Amplitude)
     sessionpath = cellid2fnames(cellid,'sess');
     propfn_path = [sessionpath filesep 'FD'];   % where the feature file can be found
diff --git a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio.m b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio.m
index 2e6fb47..827f630 100644
--- a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio.m
+++ b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio.m
@@ -28,7 +28,7 @@
 % Load Ntt file
 Nttfn = cellid2fnames(cellid,'Ntt');
 all_spikes = LoadTT_NeuralynxNT(Nttfn);
-TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
 all_spikes = all_spikes * TIMEFACTOR;
 spk = loadcb(cellid,'Spikes');
 n = length(all_spikes);   % avoid subsampling of spikes due to rounding errors
@@ -43,7 +43,7 @@
 % Feature matrix
 X = [];
 for k = 1:length(feature_names)
-    basename = [getpref('cellbase','cell_pattern') num2str(t)];
+    basename = [getcbpref('Spikes_cell_pattern') num2str(t)];
     propfn = [basename '_' feature_names{k}];   % name of feature file (e.g. TT1_Amplitude)
     sessionpath = cellid2fnames(cellid,'sess');
     propfn_path = [sessionpath filesep 'FD'];   % where the feature file can be found
diff --git a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio2.m b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio2.m
index c27b50f..11cefb4 100644
--- a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio2.m
+++ b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/LRatio2.m
@@ -36,7 +36,7 @@
 % Load Ntt file
 Nttfn = cellid2fnames(cellid,'Ntt');
 all_spikes = LoadTT_NeuralynxNT(Nttfn);
-TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
 all_spikes = all_spikes * TIMEFACTOR;
 spk = loadcb(cellid,'Spikes');
 n = length(all_spikes);
@@ -49,7 +49,7 @@
 % Feature matrix
 X = [];
 for k = 1:length(g.feature_names)
-    basename = [getpref('cellbase','cell_pattern') num2str(t)];
+    basename = [getcbpref('Spikes_cell_pattern') num2str(t)];
     propfn = [basename '_' g.feature_names{k}];   % name of feature file (e.g. TT1_Amplitude)
     sessionpath = cellid2fnames(cellid,'sess');
     propfn_path = [sessionpath filesep 'FD'];   % where the feature file can be found
diff --git a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/check_channel_validity.m b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/check_channel_validity.m
index edcee56..f907f90 100644
--- a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/check_channel_validity.m
+++ b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/check_channel_validity.m
@@ -13,7 +13,7 @@
 [r,s,t,u] = cellid2tags(cellid);
 
 % Load Energy
-propfn = [getpref('cellbase','cell_pattern') num2str(t) '_Energy'];
+propfn = [getcbpref('Spikes_cell_pattern') num2str(t) '_Energy'];
 propfn_path = [cellid2fnames(cellid,'sess') filesep 'FD'];
 if ~isdir(propfn_path)
     propfn_path = cellid2fnames(cellid,'sess');
diff --git a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/plot_mclust_projections2.m b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/plot_mclust_projections2.m
index cce15b5..e906748 100644
--- a/CellBase_R2013a/Functions/analysis_functions/spike_clusters/plot_mclust_projections2.m
+++ b/CellBase_R2013a/Functions/analysis_functions/spike_clusters/plot_mclust_projections2.m
@@ -66,7 +66,7 @@
 % Load spikes from Ntt file.
 Nttfn = cellid2fnames(cellid,'Ntt');
 all_spikes = LoadTT_NeuralynxNT(Nttfn);
-TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
 all_spikes = all_spikes * TIMEFACTOR;
 val_spk_i = [find(all_spikes >= pon(1),1,'first') ...
     find(all_spikes <= pon(end),1,'last')]; % consider spikes only within the stimulation protocol to account for drift
@@ -101,7 +101,7 @@
 [r,s,t] = cellid2tags(cellid);
 for k = 1:length(g.feature_names)
     prop = [g.feature_names{k} '.fd'];
-    propfn = [getpref('cellbase','cell_pattern') num2str(t) '_' prop];
+    propfn = [getcbpref('Spikes_cell_pattern') num2str(t) '_' prop];
     sessionpath = cellid2fnames(cellid,'sess');
     propfn_path = [sessionpath filesep 'FD'];   % where the feature file can be found
     if ~isdir(propfn_path)
diff --git a/CellBase_R2013a/Functions/data_processing_functions/MakeTrialEvents2_gonogo.m b/CellBase_R2013a/Functions/data_processing_functions/MakeTrialEvents2_gonogo.m
index a31c370..fe9963c 100644
--- a/CellBase_R2013a/Functions/data_processing_functions/MakeTrialEvents2_gonogo.m
+++ b/CellBase_R2013a/Functions/data_processing_functions/MakeTrialEvents2_gonogo.m
@@ -9,7 +9,7 @@ function MakeTrialEvents2_gonogo(sessionpath,varargin)
 %	file becomes the primary store of behavioral data for a particular
 %	session; it is retrieved by LOADCB via CELLID2FNAMES. This default
 %	file name is one of the preference settings of CellBase - type 
-%   getpref('cellbase','session_filename');
+%   getcbpref('TrialEvents_filename');
 %
 %   MAKETRIALEVENTS2_GONOGO(SESSIONPATH,'StimNttl',TTL) specifies the TTL
 %   channel which serves as the basis for synchronization.
diff --git a/CellBase_R2013a/Functions/data_processing_functions/extractSpikeWaveforms.m b/CellBase_R2013a/Functions/data_processing_functions/extractSpikeWaveforms.m
index c1c1af1..dafaf73 100644
--- a/CellBase_R2013a/Functions/data_processing_functions/extractSpikeWaveforms.m
+++ b/CellBase_R2013a/Functions/data_processing_functions/extractSpikeWaveforms.m
@@ -37,7 +37,7 @@
 
 % Load waveform data (Ntt file)
 Nttfile = cellid2fnames(cellid,'ntt');
-TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
 [all_spikes all_waves] = LoadTT_NeuralynxNT(Nttfile);
 [junk junk2 evoked_inx] = intersect(SpikeTimes,all_spikes*TIMEFACTOR);
 if ~isequal(junk,SpikeTimes)   % internal check for spike times
diff --git a/CellBase_R2013a/Functions/database_functions/analyses/addanalysis.m b/CellBase_R2013a/Functions/database_functions/analyses/addanalysis.m
index 19210a8..b9509cc 100644
--- a/CellBase_R2013a/Functions/database_functions/analyses/addanalysis.m
+++ b/CellBase_R2013a/Functions/database_functions/analyses/addanalysis.m
@@ -163,7 +163,7 @@ function  addanalysis(funhandle,varargin)
 copyfile(cb,backup_name)    % make backup before overwriting
 
 % SAVE CELLBASE
-save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST')
+save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')
 
 % -------------------------------------------------------------------------
 function  ts = timestamp
diff --git a/CellBase_R2013a/Functions/database_functions/analyses/delanalysis.m b/CellBase_R2013a/Functions/database_functions/analyses/delanalysis.m
index 4ad53ac..9dcea4c 100644
--- a/CellBase_R2013a/Functions/database_functions/analyses/delanalysis.m
+++ b/CellBase_R2013a/Functions/database_functions/analyses/delanalysis.m
@@ -9,7 +9,7 @@ function  delanalysis(funhandle)
 %
 %   See also ADDANALYSIS and FINDANALYSIS.
 
-%   Edit log: BH 6/21/12
+%   Edit log: BH 6/21/12, TO 5/2018
 
 % Load CellBase
 load(getpref('cellbase','fname'));
@@ -73,4 +73,4 @@ function  delanalysis(funhandle)
 dsr = regexprep(dsr,':','_');
 backup_name = fullfile(pth,[fnm '_' dsr ext]);
 copyfile(cb,backup_name)    % make backup before overwriting
-save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST')   
\ No newline at end of file
+save(getpref('cellbase','fname'),'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')   
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/analyses/insertdata.m b/CellBase_R2013a/Functions/database_functions/analyses/insertdata.m
index 6422b5b..0f841e3 100644
--- a/CellBase_R2013a/Functions/database_functions/analyses/insertdata.m
+++ b/CellBase_R2013a/Functions/database_functions/analyses/insertdata.m
@@ -1 +1 @@
-function varargout = insertdata(varargin)
%INSERTDATA   Insert data into CellBase directly.
%   NF = INSERTDATA(DATA,PARAM,VALUE) inserts DATA into TheMatrix
%   and ANALYSES (see CellBase documentation). It optionally returns the
%   list of entries in DATA which did not provide a match with CELLIDLIST
%   (NF).
%   Input arguments:
%       DATA - Either a Matlab variable or a full pathname to a .mat or an
%           Excel file. It can optionally contain a header row with
%           'property_names' in the first column and corresponding property
%           names for data columns. First column should contain cellIDs. If
%           property names are added as both input argument and data
%           header, the user is forced to choose which one to use.
%       'TYPE', T - Parameter indicating whether an analysis or a set of
%           properties are added. T should start with the letter 'a' or 'p'
%           accordingly.
%       'NAME', NM - Name of the analysis or properti(es). For analysis: 
%           it should be the name of a valid m file. For properties: either
%           a character array (one property) or a cell array of strings
%           (multiple properties).
%       'INPUT_ARGUMENTS', LS1 - Input arguments for analysis, cell array.
%       'OUTPUT_ARGUMENTS', LS2 - Names of output arguments for analysis, 
%           cell array of strings. This determines the property names when
%           an analysis is added.
%
%   The number of properties or output arguments (in case of adding values
%   to an analysis) must match the number of data columns (number of all
%   columns minus one) in DATA.
%
%   Missing input arguments are asked for interactively. If DATA is empty,
%   the user has to browse for the data file. If 'Cancel' is selected for
%   browsing result, data values will interactively be prompted for
%   according to a selected tag type (animal, session, tetrode or cell).
%
%   If a property or an analysis is already added to CellBase, the user is
%   asked whether to overwrite previous data. An analysis is only
%   considered the same if the name of the m file and both the list of 
%   input and output arguments are the same. If the data is overwritten,
%   the timestamp property in ANALYSES is updated.
%
%   New data is inserted into TheMatrix and ANALYSES according to the
%   corresponding cellIDs. A backup of the previous cellbase file is stored
%   before overwriting.
%
%   Examples:
%   insertdata(data,'type','analysis','name','LRatio','input_arguments',...
%       {{'Amplitude','Energy'}},'output_arguments',{'ID_amp','Lr_amp'})
%   not_found = insertdata([],'type','prop','name','validity');
%   insertdata('c:\Balazs\_analysis\NB\tagging\validity.xls','type',...
%       'prop','name','validity')
%   insertdata('c:\Balazs\_analysis\NB\tagging2\spikeshapecorr.xls','type',...
%       'analysis','name','spikeshapecorr')
%
%   See also ADDANALYSIS and RUNANALYSIS.

%   Edit log: AK,SPR 5/10; BH 5/3/12

% Input arguments
prs = inputParser;
addOptional(prs,'data',[],@(s)isempty(s)||iscell(s)||ischar(s))
addParamValue(prs,'type','',@(s)ismember(s(1),{'p','a'})) % property or analysis
addParamValue(prs,'name',{},@(s)ischar(s)||iscell(s))  % name of properties or analysis function
addParamValue(prs,'input_arguments',{},@iscell) % name of input arguments for analysis function
addParamValue(prs,'output_arguments',{},@(s)ischar(s)||iscell(s)) % name of output arguments for analysis function - used for proporty names if type=analysis
parse(prs,varargin{:})
g = prs.Results;

% If no options specified, ask everything
% Property or analysis?
if isempty(g.type)
    pora = '';
    while ~ismember(pora,{'p','a'})
        pora = input('\n Do you want to insert a property or an analysis? p/a ','s');
    end
else
    pora = g.type(1);
end

% Property names or mfile name
switch pora
    case 'p'    % property names
        if isempty(g.name)
            tinp = input('\n Please enter the property names you want to add. ','s');
            propnames = strread(tinp,'%s','delimiter',', ')';
        else
            propnames = g.name;
        end
        if ischar(propnames) % convert to cell if there's only one property
            propnames = {propnames};
        end
        funhandle = @insertdata;    % for properties, the function handle is 'insertdata'
        arglist = {};   % a property does not have arguments 
                        % (except for manually entered properties, where it is the 'option', see below)
            
    case 'a'    % mfile name
        if isempty(g.name)
            wi = 0;
            while ~wi
                mfile = input('\n Please enter the name of the analysis function. ','s');
                funhandle = str2func(mfile);    % check analysis function
                funinfo = functions(funhandle);
                if ~isempty(funinfo.file)
                    fprintf('\n%s\n','Analysis file was loacated: ')
                    disp(funinfo.file)
                    wi = 1;
                else
                    fprintf('\n%s\n','INSERTDATA: Function is not valid.')
                end
            end
        else
            mfile = g.name;
            funhandle = str2func(mfile);
        end
        if isempty(g.input_arguments)     % mfile input arguments
            tinp = input(['\n Please enter the list of input arguments for '...
                mfile ',\n or press Enter for no arguments. ']);
            arglist = tinp;
        else
            arglist = g.input_arguments;
        end
        if isempty(g.output_arguments)     % mfile output arguments (properties)
            tinp = input(['\n Please enter the list of output arguments for '...
                mfile '. '],'s');
            propnames = strread(tinp,'%s','delimiter',', ')';
        else
            propnames = g.output_arguments;
        end
        if ischar(propnames) % convert to cell if there's only one output argument
            propnames = {propnames};
        end
end

% Load data
if isempty(g.data)
    [filename, pathname] = uigetfile( ...
        {'*.mat;*.xls;*.xlsx','Supported formats (*.mat,*.xls,*.xlsx)';...
        '*.mat','MAT-files (*.mat)'; ...
        '*.xls;*.xlsx','Excel files (*.xls,*.xlsx)'; ...
        '*.*',  'All Files (*.*)'}, ...
        'Select Datafile');     % select data file
    fullpth = fullfile(pathname,filename);
    vardata = read_data(fullpth);
else
    if ischar(g.data)
        vardata = read_data(g.data);
    else
        vardata = g.data;
    end
end

% Load CellBase
load(getpref('cellbase','fname'));

% Check data
if ~isempty(vardata)
    if isequal(vardata{1,1},'property_names')   % property names in data header
        newpropnames = vardata(1,2:end);
        vardata = vardata(2:end,:);
        if isempty(propnames)
            propnames = newpropnames;
            fprintf('\n%s','Using property names detected in data header:')
            disp(propnames)
        end
        if ~isequal(propnames,newpropnames)   % optionally overwrite input argument with header
            useheader = input('\nUse property/argument names of data header? (y/n) ','s');
            while ~ismember(useheader,{'y','n'})
                useheader = input('\nUse property/argument names of data header? (y/n) ','s');
            end
            if isequal(useheader,'y')
                propnames = newpropnames;
                fprintf('\n%s','Using property names detected in data header:')
                disp(propnames)
            end
        end
    end
    infinx = cellfun(@(s)isequal('Inf',s),vardata);    % convert 'Inf' to Inf
    vardata(infinx) = {Inf};
    infinx = cellfun(@(s)isequal('-Inf',s),vardata);
    vardata(infinx) = {-Inf};
    naninx = cellfun(@(s)isequal('NaN',s),vardata);   % convert 'NaN' to NaN
    vardata(naninx) = {NaN};
    if ~isequal(length(propnames),size(vardata,2)-1)
        error('INSERTDATA: Data does not match the number of properties.')
    end
end

% If no data, add values one by one
if isempty(vardata)
    option = input(['\nYou will be prompted to add values manually. \n'...
        'Would you like to add separate value for each \n'...
        'animal/session/tetrode/cell? '],'s');
    if ~(strncmp(option,'ani',3) || strncmp(option,'rat',3) || ...
            strncmp(option,'ses',3) || strncmp(option,'tet',3) || ...
            strncmp(option,'cel',3))
        error('INSERTDATA: unknown option.');
    else
        arglist = {option};     % store the chosen option in the argument field
    end
    
    % Add values for each properties
    vardata = {};  % initalize
    for prp = 1:length(propnames)
        propname = propnames{prp};
        lastcellpos = 0;
        
        % Create list to display
        list = listtag(option);      % find all relevant cell classes
        if strncmp(option,'session',3)
            list2add = strcat(char(list(:,1)),'_',char(list(:,2)));
        elseif strncmp(option,'tetrode',3)
            list2add = strcat(char(list(:,1)),'_',char(list(:,2)),'_',char(list(:,3)));
        else  % option = rat or cell
            list2add = char(list);
        end
        
        % Type values
        fprintf('\n%s%s%s\n','Insert values for ',propname,'.')
        for i = 1:size(list2add,1)
            value = prompt_for_value(list2add(i,:));
            if strncmp(option,'session',3)
                pos = findcellpos('rat',list(i,1),'session',list(i,2));
            elseif strncmp(option,'tetrode',3)
                pos = findcellpos('rat',list(i,1),'session',list(i,2),'tetrode',list(i,3));
            elseif strncmp(option,'rat',3)
                pos = findcellpos('rat',list(i));
            elseif strncmp(option,'animal',3)
                pos = findcellpos('animal',list(i));
            else
                pos = findcellpos(list(i));
            end
            
            cells2add = CELLIDLIST(pos);  % add cellid and value for each new cell
            nws = length(cells2add);
            vardata(lastcellpos+1:lastcellpos+nws,1)=cells2add';
            vardata(lastcellpos+1:lastcellpos+nws,prp+1)={value}; %#ok<AGROW>
            lastcellpos = lastcellpos + nws;
        end
    end
end

% Time stamp
timestamp = {gettimestamp};

% Insert data
% Find the position to insert to
NumCol = length(propnames);
NumCell = size(vardata,1);
NumAnal = length(ANALYSES);  %#ok<NODEF>
if NumAnal == 0
    lastcolumn = 0;
else
    lastcolumn = ANALYSES(NumAnal).columns(end);
end
columns = lastcolumn+1:lastcolumn+NumCol;
isoverwrite = false;    % changed later if previous data is overwritten

% Add to ANALYSES
switch pora
    case 'p'   % properties are added one by one
        for i = 1:NumCol
            [prevanal anum] = findanalysis(propnames{i});
            if prevanal  % give an option to overwrite
                str = sprintf('\nINSERTDATA: Analysis already exists for %s at position %d.',propnames{i},prevanal);
                disp(str)
                co = input('Overwrite previous data? overwrite/cancel [c] ','s');
                if ~strncmp(co,'overwrite',4)
                    fprintf('\n%s\n','INSERTDATA: Action cancelled. No data inserted.')
                    return
                end
                columns(i) = prevanal;
                ANALYSES(anum(1)).timestamp = timestamp; %#ok<AGROW>
                ANALYSES(anum(1)).varargin = arglist; %#ok<AGROW>
            else
                ANALYSES(NumAnal+i).funhandle = funhandle; %#ok<AGROW>
                ANALYSES(NumAnal+i).varargin = arglist; %#ok<AGROW>
                ANALYSES(NumAnal+i).propnames = propnames(i); %#ok<AGROW>
                ANALYSES(NumAnal+i).columns = columns(i); %#ok<AGROW>
                ANALYSES(NumAnal+i).timestamp = timestamp; %#ok<AGROW>
            end
        end
        
    case 'a'    % output arguments of an analysis are added as a single entry
        [cols anum] = findanalysis(funhandle);
        mts = length(anum);   % multiple matches with different arguments are possible
        isfound = nan(1:mts);
        for aa = 1:mts
            isfound(aa) = ~isequal(cols,0) & isequal(ANALYSES(anum(aa)).varargin,arglist)...
                & isequal(ANALYSES(anum(aa)).propnames,propnames); % consider the same if the analysis name, input and output parameters are the same
        end
        if any(isfound)  % give an option to overwrite
            anum = anum(logical(isfound));
            columns = ANALYSES(anum).columns;
            str = sprintf('\nINSERTDATA: Analysis already exists at position %d.',cols);
            disp(str)
            co = input('Overwrite previous data? overwrite/cancel [c] ','s');
            if ~strncmp(co,'overwrite',4)
                fprintf('\n%s\n','INSERTDATA: Action cancelled. No data inserted.')
                return
            else
                isoverwrite = true;
            end
            ANALYSES(anum).timestamp = timestamp;
        else
            ANALYSES(NumAnal+1).funhandle = funhandle;
            ANALYSES(NumAnal+1).varargin = arglist;
            ANALYSES(NumAnal+1).propnames = propnames;
            ANALYSES(NumAnal+1).columns = columns;
            ANALYSES(NumAnal+1).timestamp = timestamp;
        end
end

% Add to TheMatrix
[cmn inxa inxb] = intersect(CELLIDLIST,vardata(:,1)); %#ok<*ASGLU>
if iscell(TheMatrix) %#ok<NODEF>
    TheMatrix(inxa,columns) = vardata(inxb,2:end);   % TheMatrix is a cell in the updated CellBase
else
    if ~isoverwrite
        TheMatrix(:,columns) = NaN;   % initialize with NaNs to avoid padding with zeros
    end
    TheMatrix(inxa,columns) = cell2mat(vardata(inxb,2:end));  % keep it compatible with the old version
end
notfound_list = setdiff(vardata(:,1),CELLIDLIST);
NotFound = length(notfound_list);

% Return changed variables to workspace & save all
assignin('base','TheMatrix',TheMatrix)
assignin('base','ANALYSES',ANALYSES)
cb = getpref('cellbase','fname');
[pth fnm ext] = fileparts(cb);
dsr = datestr(now);
dsr = regexprep(dsr,':','_');
backup_name = fullfile(pth,[fnm '_' dsr ext]);
copyfile(cb,backup_name)    % make backup before overwriting
save(cb,'TheMatrix','ANALYSES','CELLIDLIST')

% Feedback
if NotFound
    donestr = sprintf('INSERTDATA done.\nData added to %d cells creating/updating %d properti(es).\n %d cellids not found.\n',NumCell,NumCol,NotFound);
else
    donestr = sprintf('INSERTDATA done.\nData added to %d cells creating/updating %d properti(es).\n',NumCell,NumCol);
end
disp(donestr);
if nargout > 0
    varargout{1} = notfound_list;
end

% -------------------------------------------------------------------------
function value = prompt_for_value(tag,varargin)

value = [];
question = sprintf('Enter value for %s    ',tag);
if nargin == 1
	while isempty(value)
        value = input(question);
	end
elseif strcmpi(varargin{1},'NaN')
    value = input(question);
    if isempty(value)
        value = NaN;
    end   
end

% -------------------------------------------------------------------------
function  ts = gettimestamp

% Now
c = clock;
ts = sprintf('%d/%d/%d %.2d:%.2d',c(2),c(3),c(1),c(4),c(5));

% -------------------------------------------------------------------------
function vardata = read_data(fullpth)

% Decompose path name
[pth fnm ext] = fileparts(fullpth);

% Read the data for supported formats
switch ext
    case {'.xls' '.xlsx'}
        [t0 t1 vardata] = xlsread(fullpth);     % Excel
    case '.mat'
        pvd = load(fullpth);    % Matlab
        fld = fieldnames(pvd);
        vardata = pvd.(fld{1});
    otherwise
        vardata = [];
end
\ No newline at end of file
+function varargout = insertdata(varargin)
%INSERTDATA   Insert data into CellBase directly.
%   NF = INSERTDATA(DATA,PARAM,VALUE) inserts DATA into TheMatrix
%   and ANALYSES (see CellBase documentation). It optionally returns the
%   list of entries in DATA which did not provide a match with CELLIDLIST
%   (NF).
%   Input arguments:
%       DATA - Either a Matlab variable or a full pathname to a .mat or an
%           Excel file. It can optionally contain a header row with
%           'property_names' in the first column and corresponding property
%           names for data columns. First column should contain cellIDs. If
%           property names are added as both input argument and data
%           header, the user is forced to choose which one to use.
%       'TYPE', T - Parameter indicating whether an analysis or a set of
%           properties are added. T should start with the letter 'a' or 'p'
%           accordingly.
%       'NAME', NM - Name of the analysis or properti(es). For analysis: 
%           it should be the name of a valid m file. For properties: either
%           a character array (one property) or a cell array of strings
%           (multiple properties).
%       'INPUT_ARGUMENTS', LS1 - Input arguments for analysis, cell array.
%       'OUTPUT_ARGUMENTS', LS2 - Names of output arguments for analysis, 
%           cell array of strings. This determines the property names when
%           an analysis is added.
%
%   The number of properties or output arguments (in case of adding values
%   to an analysis) must match the number of data columns (number of all
%   columns minus one) in DATA.
%
%   Missing input arguments are asked for interactively. If DATA is empty,
%   the user has to browse for the data file. If 'Cancel' is selected for
%   browsing result, data values will interactively be prompted for
%   according to a selected tag type (animal, session, tetrode or cell).
%
%   If a property or an analysis is already added to CellBase, the user is
%   asked whether to overwrite previous data. An analysis is only
%   considered the same if the name of the m file and both the list of 
%   input and output arguments are the same. If the data is overwritten,
%   the timestamp property in ANALYSES is updated.
%
%   New data is inserted into TheMatrix and ANALYSES according to the
%   corresponding cellIDs. A backup of the previous cellbase file is stored
%   before overwriting.
%
%   Examples:
%   insertdata(data,'type','analysis','name','LRatio','input_arguments',...
%       {{'Amplitude','Energy'}},'output_arguments',{'ID_amp','Lr_amp'})
%   not_found = insertdata([],'type','prop','name','validity');
%   insertdata('c:\Balazs\_analysis\NB\tagging\validity.xls','type',...
%       'prop','name','validity')
%   insertdata('c:\Balazs\_analysis\NB\tagging2\spikeshapecorr.xls','type',...
%       'analysis','name','spikeshapecorr')
%
%   See also ADDANALYSIS and RUNANALYSIS.

%   Edit log: AK,SPR 5/10; BH 5/3/12, TO 5/2018

% Input arguments
prs = inputParser;
addOptional(prs,'data',[],@(s)isempty(s)||iscell(s)||ischar(s))
addParamValue(prs,'type','',@(s)ismember(s(1),{'p','a'})) % property or analysis
addParamValue(prs,'name',{},@(s)ischar(s)||iscell(s))  % name of properties or analysis function
addParamValue(prs,'input_arguments',{},@iscell) % name of input arguments for analysis function
addParamValue(prs,'output_arguments',{},@(s)ischar(s)||iscell(s)) % name of output arguments for analysis function - used for proporty names if type=analysis
parse(prs,varargin{:})
g = prs.Results;

% If no options specified, ask everything
% Property or analysis?
if isempty(g.type)
    pora = '';
    while ~ismember(pora,{'p','a'})
        pora = input('\n Do you want to insert a property or an analysis? p/a ','s');
    end
else
    pora = g.type(1);
end

% Property names or mfile name
switch pora
    case 'p'    % property names
        if isempty(g.name)
            tinp = input('\n Please enter the property names you want to add. ','s');
            propnames = strread(tinp,'%s','delimiter',', ')';
        else
            propnames = g.name;
        end
        if ischar(propnames) % convert to cell if there's only one property
            propnames = {propnames};
        end
        funhandle = @insertdata;    % for properties, the function handle is 'insertdata'
        arglist = {};   % a property does not have arguments 
                        % (except for manually entered properties, where it is the 'option', see below)
            
    case 'a'    % mfile name
        if isempty(g.name)
            wi = 0;
            while ~wi
                mfile = input('\n Please enter the name of the analysis function. ','s');
                funhandle = str2func(mfile);    % check analysis function
                funinfo = functions(funhandle);
                if ~isempty(funinfo.file)
                    fprintf('\n%s\n','Analysis file was loacated: ')
                    disp(funinfo.file)
                    wi = 1;
                else
                    fprintf('\n%s\n','INSERTDATA: Function is not valid.')
                end
            end
        else
            mfile = g.name;
            funhandle = str2func(mfile);
        end
        if isempty(g.input_arguments)     % mfile input arguments
            tinp = input(['\n Please enter the list of input arguments for '...
                mfile ',\n or press Enter for no arguments. ']);
            arglist = tinp;
        else
            arglist = g.input_arguments;
        end
        if isempty(g.output_arguments)     % mfile output arguments (properties)
            tinp = input(['\n Please enter the list of output arguments for '...
                mfile '. '],'s');
            propnames = strread(tinp,'%s','delimiter',', ')';
        else
            propnames = g.output_arguments;
        end
        if ischar(propnames) % convert to cell if there's only one output argument
            propnames = {propnames};
        end
end

% Load data
if isempty(g.data)
    [filename, pathname] = uigetfile( ...
        {'*.mat;*.xls;*.xlsx','Supported formats (*.mat,*.xls,*.xlsx)';...
        '*.mat','MAT-files (*.mat)'; ...
        '*.xls;*.xlsx','Excel files (*.xls,*.xlsx)'; ...
        '*.*',  'All Files (*.*)'}, ...
        'Select Datafile');     % select data file
    fullpth = fullfile(pathname,filename);
    vardata = read_data(fullpth);
else
    if ischar(g.data)
        vardata = read_data(g.data);
    else
        vardata = g.data;
    end
end

% Load CellBase
load(getpref('cellbase','fname'));

% Check data
if ~isempty(vardata)
    if isequal(vardata{1,1},'property_names')   % property names in data header
        newpropnames = vardata(1,2:end);
        vardata = vardata(2:end,:);
        if isempty(propnames)
            propnames = newpropnames;
            fprintf('\n%s','Using property names detected in data header:')
            disp(propnames)
        end
        if ~isequal(propnames,newpropnames)   % optionally overwrite input argument with header
            useheader = input('\nUse property/argument names of data header? (y/n) ','s');
            while ~ismember(useheader,{'y','n'})
                useheader = input('\nUse property/argument names of data header? (y/n) ','s');
            end
            if isequal(useheader,'y')
                propnames = newpropnames;
                fprintf('\n%s','Using property names detected in data header:')
                disp(propnames)
            end
        end
    end
    infinx = cellfun(@(s)isequal('Inf',s),vardata);    % convert 'Inf' to Inf
    vardata(infinx) = {Inf};
    infinx = cellfun(@(s)isequal('-Inf',s),vardata);
    vardata(infinx) = {-Inf};
    naninx = cellfun(@(s)isequal('NaN',s),vardata);   % convert 'NaN' to NaN
    vardata(naninx) = {NaN};
    if ~isequal(length(propnames),size(vardata,2)-1)
        error('INSERTDATA: Data does not match the number of properties.')
    end
end

% If no data, add values one by one
if isempty(vardata)
    option = input(['\nYou will be prompted to add values manually. \n'...
        'Would you like to add separate value for each \n'...
        'animal/session/tetrode/cell? '],'s');
    if ~(strncmp(option,'ani',3) || strncmp(option,'rat',3) || ...
            strncmp(option,'ses',3) || strncmp(option,'tet',3) || ...
            strncmp(option,'cel',3))
        error('INSERTDATA: unknown option.');
    else
        arglist = {option};     % store the chosen option in the argument field
    end
    
    % Add values for each properties
    vardata = {};  % initalize
    for prp = 1:length(propnames)
        propname = propnames{prp};
        lastcellpos = 0;
        
        % Create list to display
        list = listtag(option);      % find all relevant cell classes
        if strncmp(option,'session',3)
            list2add = strcat(char(list(:,1)),'_',char(list(:,2)));
        elseif strncmp(option,'tetrode',3)
            list2add = strcat(char(list(:,1)),'_',char(list(:,2)),'_',char(list(:,3)));
        else  % option = rat or cell
            list2add = char(list);
        end
        
        % Type values
        fprintf('\n%s%s%s\n','Insert values for ',propname,'.')
        for i = 1:size(list2add,1)
            value = prompt_for_value(list2add(i,:));
            if strncmp(option,'session',3)
                pos = findcellpos('rat',list(i,1),'session',list(i,2));
            elseif strncmp(option,'tetrode',3)
                pos = findcellpos('rat',list(i,1),'session',list(i,2),'tetrode',list(i,3));
            elseif strncmp(option,'rat',3)
                pos = findcellpos('rat',list(i));
            elseif strncmp(option,'animal',3)
                pos = findcellpos('animal',list(i));
            else
                pos = findcellpos(list(i));
            end
            
            cells2add = CELLIDLIST(pos);  % add cellid and value for each new cell
            nws = length(cells2add);
            vardata(lastcellpos+1:lastcellpos+nws,1)=cells2add';
            vardata(lastcellpos+1:lastcellpos+nws,prp+1)={value}; %#ok<AGROW>
            lastcellpos = lastcellpos + nws;
        end
    end
end

% Time stamp
timestamp = {gettimestamp};

% Insert data
% Find the position to insert to
NumCol = length(propnames);
NumCell = size(vardata,1);
NumAnal = length(ANALYSES);  %#ok<NODEF>
if NumAnal == 0
    lastcolumn = 0;
else
    lastcolumn = ANALYSES(NumAnal).columns(end);
end
columns = lastcolumn+1:lastcolumn+NumCol;
isoverwrite = false;    % changed later if previous data is overwritten

% Add to ANALYSES
switch pora
    case 'p'   % properties are added one by one
        for i = 1:NumCol
            [prevanal anum] = findanalysis(propnames{i});
            if prevanal  % give an option to overwrite
                str = sprintf('\nINSERTDATA: Analysis already exists for %s at position %d.',propnames{i},prevanal);
                disp(str)
                co = input('Overwrite previous data? overwrite/cancel [c] ','s');
                if ~strncmp(co,'overwrite',4)
                    fprintf('\n%s\n','INSERTDATA: Action cancelled. No data inserted.')
                    return
                end
                columns(i) = prevanal;
                ANALYSES(anum(1)).timestamp = timestamp; %#ok<AGROW>
                ANALYSES(anum(1)).varargin = arglist; %#ok<AGROW>
            else
                ANALYSES(NumAnal+i).funhandle = funhandle; %#ok<AGROW>
                ANALYSES(NumAnal+i).varargin = arglist; %#ok<AGROW>
                ANALYSES(NumAnal+i).propnames = propnames(i); %#ok<AGROW>
                ANALYSES(NumAnal+i).columns = columns(i); %#ok<AGROW>
                ANALYSES(NumAnal+i).timestamp = timestamp; %#ok<AGROW>
            end
        end
        
    case 'a'    % output arguments of an analysis are added as a single entry
        [cols anum] = findanalysis(funhandle);
        mts = length(anum);   % multiple matches with different arguments are possible
        isfound = nan(1:mts);
        for aa = 1:mts
            isfound(aa) = ~isequal(cols,0) & isequal(ANALYSES(anum(aa)).varargin,arglist)...
                & isequal(ANALYSES(anum(aa)).propnames,propnames); % consider the same if the analysis name, input and output parameters are the same
        end
        if any(isfound)  % give an option to overwrite
            anum = anum(logical(isfound));
            columns = ANALYSES(anum).columns;
            str = sprintf('\nINSERTDATA: Analysis already exists at position %d.',cols);
            disp(str)
            co = input('Overwrite previous data? overwrite/cancel [c] ','s');
            if ~strncmp(co,'overwrite',4)
                fprintf('\n%s\n','INSERTDATA: Action cancelled. No data inserted.')
                return
            else
                isoverwrite = true;
            end
            ANALYSES(anum).timestamp = timestamp;
        else
            ANALYSES(NumAnal+1).funhandle = funhandle;
            ANALYSES(NumAnal+1).varargin = arglist;
            ANALYSES(NumAnal+1).propnames = propnames;
            ANALYSES(NumAnal+1).columns = columns;
            ANALYSES(NumAnal+1).timestamp = timestamp;
        end
end

% Add to TheMatrix
[cmn inxa inxb] = intersect(CELLIDLIST,vardata(:,1)); %#ok<*ASGLU>
if iscell(TheMatrix) %#ok<NODEF>
    TheMatrix(inxa,columns) = vardata(inxb,2:end);   % TheMatrix is a cell in the updated CellBase
else
    if ~isoverwrite
        TheMatrix(:,columns) = NaN;   % initialize with NaNs to avoid padding with zeros
    end
    TheMatrix(inxa,columns) = cell2mat(vardata(inxb,2:end));  % keep it compatible with the old version
end
notfound_list = setdiff(vardata(:,1),CELLIDLIST);
NotFound = length(notfound_list);

% Return changed variables to workspace & save all
assignin('base','TheMatrix',TheMatrix)
assignin('base','ANALYSES',ANALYSES)
cb = getpref('cellbase','fname');
[pth fnm ext] = fileparts(cb);
dsr = datestr(now);
dsr = regexprep(dsr,':','_');
backup_name = fullfile(pth,[fnm '_' dsr ext]);
copyfile(cb,backup_name)    % make backup before overwriting
save(cb,'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')

% Feedback
if NotFound
    donestr = sprintf('INSERTDATA done.\nData added to %d cells creating/updating %d properti(es).\n %d cellids not found.\n',NumCell,NumCol,NotFound);
else
    donestr = sprintf('INSERTDATA done.\nData added to %d cells creating/updating %d properti(es).\n',NumCell,NumCol);
end
disp(donestr);
if nargout > 0
    varargout{1} = notfound_list;
end

% -------------------------------------------------------------------------
function value = prompt_for_value(tag,varargin)

value = [];
question = sprintf('Enter value for %s    ',tag);
if nargin == 1
	while isempty(value)
        value = input(question);
	end
elseif strcmpi(varargin{1},'NaN')
    value = input(question);
    if isempty(value)
        value = NaN;
    end   
end

% -------------------------------------------------------------------------
function  ts = gettimestamp

% Now
c = clock;
ts = sprintf('%d/%d/%d %.2d:%.2d',c(2),c(3),c(1),c(4),c(5));

% -------------------------------------------------------------------------
function vardata = read_data(fullpth)

% Decompose path name
[pth fnm ext] = fileparts(fullpth);

% Read the data for supported formats
switch ext
    case {'.xls' '.xlsx'}
        [t0 t1 vardata] = xlsread(fullpth);     % Excel
    case '.mat'
        pvd = load(fullpth);    % Matlab
        fld = fieldnames(pvd);
        vardata = pvd.(fld{1});
    otherwise
        vardata = [];
end
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/analyses/setvalue.m b/CellBase_R2013a/Functions/database_functions/analyses/setvalue.m
index 4c45189..c230e71 100644
--- a/CellBase_R2013a/Functions/database_functions/analyses/setvalue.m
+++ b/CellBase_R2013a/Functions/database_functions/analyses/setvalue.m
@@ -6,7 +6,7 @@
 %
 %   See also GETVALUE.
 
-%   Edit log: BH 4/16/2013
+%   Edit log: BH 4/16/2013, TO 5/2018
 
 % Load CellBase
 load(getpref('cellbase','fname')); 
@@ -37,7 +37,7 @@
 dsr = regexprep(dsr,':','_');
 backup_name = fullfile(pth,[fnm '_' dsr ext]);
 copyfile(cb,backup_name)    % make backup before overwriting
-save(cb,'TheMatrix','ANALYSES','CELLIDLIST')
+save(cb,'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')
 
 % Feedback
 status = true;
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/default_preferences.m b/CellBase_R2013a/Functions/database_functions/cellbase/default_preferences.m
new file mode 100644
index 0000000..5b3ca57
--- /dev/null
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/default_preferences.m
@@ -0,0 +1,33 @@
+function PREFERENCES = default_preferences()
+% DEFAULT_PREFERENCES creates a struct PREFERENCES containing default
+% parameters specific to a cellbase. Note than cellbase-general preferences
+% (cellbase name, data folder, cellbase file) are manipulated with
+% getpref('cellbase')/setpref('cellbase',...).
+%
+% See also import_preferences(), setcbpref(name,value), getcbpref(name), initcb()
+%
+% TO 05/2018
+
+cb_path = which('initcb');
+cb_path=fileparts(fileparts(fileparts(fileparts(cb_path))));
+
+PREFERENCES = struct();
+
+%TrialEvents parameters
+PREFERENCES.TrialEvents_fname = 'TrialEvents.mat';
+PREFERENCES.TrialEvents_fun = fullfile(cb_path,'Templates','MakeTrialEvents.m');
+PREFERENCES.TrialEvents_defineEventEpochs = fullfile(cb_path,'Templates','defineEventEpochs.m');
+
+%StimEvents parameters
+PREFERENCES.StimEvents_fname = 'StimEvents.mat';
+PREFERENCES.StimEvents_fun = fullfile(cb_path,'Templates','MakeStimEvents.m');
+
+%Spike times parameters
+PREFERENCES.Spikes_cell_pattern = 'TT';
+PREFERENCES.Spikes_timefactor = 1;
+PREFERENCES.Spikes_create_fun = '';
+
+%Database parameters
+PREFERENCES.session_separator = '';
+
+
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m b/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m
new file mode 100644
index 0000000..a89f887
--- /dev/null
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m
@@ -0,0 +1,40 @@
+function val = getcbpref(name)
+% GETCBPREF() returns current cellbase's preference value for preference name STR.
+% Cellbase-specific preferences are stored in cellbase file
+% (getpref('cellbase','fname')). Note than cellbase-general preferences
+% (cellbase name, data folder, cellbase file) are manipulated with
+% getpref('cellbase')/setpref('cellbase',...).
+%
+% Returns VAL, the value of preference NAME. Returns FALSE if n preference
+% with NAME exists.
+%
+% See also: setcbpref(name,value), default_preferences()
+%
+% TO 05/2018
+
+if any(strcmp({'datapath','name','fname','filesep','cellbases'},name)) %global settings
+    warning('Please use getpref to get global cellbase settings.');
+    val = getpref('cellbase',name);
+else %correct use for cellbase-specific parameters
+    if exist(fullfile(getpref('cellbase','fname')),'file')==2
+        P = load(fullfile(getpref('cellbase','fname')),'PREFERENCES');
+        fields = fieldnames(P);
+        if ~isempty(fields)
+            P=P.PREFERENCES;
+            if isfield(P,name)
+                val=P.(name);
+            else %no parameter in PREFERENCES with that name
+                val = false;
+                warning('getcbpref: no parameter with the specified name found. Try setcbpref() first.');
+            end
+        else %no preference file
+            import_preferences();
+            val=getcbpref(name);
+        end
+        
+    else %no cellbase
+        error('getcbpref: No Cellbase database found. Check cellbase filename.');
+    end
+end
+
+end
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m b/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m
new file mode 100644
index 0000000..2f08abc
--- /dev/null
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m
@@ -0,0 +1,30 @@
+function import_preferences()
+% IMPORT_PREFERENCES creates a struct PREFERENCES containing default parameters
+% or loads preferences from getpref('cellbase'). This is a
+% convenience function to maintain backwards compatibility to cellbase
+% 5fbf007 (12 Sep 2017) and prior.
+
+% See also default_preferences(), setcbpref(name,value), getcbpref(name), initcb()
+%
+% TO 05/2018
+
+str = 'No PREFERENCE variable found. Likely due to use of older cellbase version. Please choose if you want to use default parameters or import from getpref("cellbase"). ';
+str=strcat(str,'Preferences can be manipulated using getpref and setpref and are stored in your cellbase file.');
+
+A = questdlg(str,'convert_preferences','Default','Import','Default');
+
+PREFERENCES = default_preferences();
+
+switch A
+    case 'Default'
+        %
+    case 'Import'
+        PREFERENCES.TrialEvents_fname = getpref('cellbase','TrialEvents_filename');
+        PREFERENCES.StimEvents_fname = getpref('cellbase','StimEvents_filename');
+        PREFERENCES.Spikes_cell_pattern = getpref('cellbase','cell_pattern');
+        PREFERENCES.Spikes_timefactor = getpref('cellbase','timefactor');
+end
+
+CB = load(fullfile(getpref('cellbase','fname')));
+CB.PREFERENCES=PREFERENCES;
+save(fullfile(getpref('cellbase','fname')),'-struct','CB')
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/initcb.m b/CellBase_R2013a/Functions/database_functions/cellbase/initcb.m
index 2698b33..00c0cea 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/initcb.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/initcb.m
@@ -9,7 +9,8 @@ function initcb(cb_name)
 %
 %   See also LOADCB, CHOOSECB, DELETECB and ADDNEWCELLS.
 
-%   Edit log: AK 3/04, 10/06; BH 3/18/11, 5/30/11, 4/26/12, 5/7/12, 8/20/13
+%   Edit log: AK 3/04, 10/06; BH 3/18/11, 5/30/11, 4/26/12, 5/7/12,
+%   8/20/13, TO 5/2018
 
 % Check input arguments
 error(nargchk(0,1,nargin))
@@ -51,24 +52,23 @@ function initcb(cb_name)
 disp(['File name is ' fname])
 disp(['CellBase name is ' cb_name])
 
+% cellbase-specific preferences
+
 % Timestamp conversion
 tsc = questdlg('I''m going convert timestamps to seconds in','Timestamp conversion',...
-    'CellBase','MClust','CellBase');
+    'CellBase (factor=10^-4)','MClust (factor=1)','CellBase (factor=10^-4)');
 switch tsc
-    case 'CellBase'
+    case 'CellBase (factor=10^-4)'
         timefactor = 1e-4;  % TT*.mat files will reflect the timestamps of the Ntt files;
                             % loadcb will convert them to seconds
-    case 'MClust'
+    case 'MClust (factor=1)'
         timefactor = 1;     % timestamps in TT*.mat files will already be converted to seconds
 end
 
 % Set other preferences (persistent and maintain their values between MATLAB sessions)
-setpref('cellbase','session_filename','TrialEvents.mat');
-setpref('cellbase','TrialEvents_filename','TrialEvents.mat');
-setpref('cellbase','StimEvents_filename','StimEvents.mat');
-setpref('cellbase','cell_pattern','TT');
-setpref('cellbase','filesep',filesep);
-setpref('cellbase','timefactor',timefactor);
+
+PREFERENCES = default_preferences();
+PREFERENCES.Spikes_timefactor=timefactor;
 
 % Store cellbases to allow multiple instances
 if ispref('cellbase','cellbases')
@@ -82,18 +82,19 @@ function initcb(cb_name)
 end
 cellbases{end+1} = gp;
 setpref('cellbase','cellbases',cellbases)
+setpref('cellbase','filesep',filesep);
 
 % Open main database file
 QuestionStr = sprintf('\n %s already exists. \n\n Do you want to delete it? \n',fname);
-fid = fopen(fname);
-if ( fid == -1) || strcmp(questdlg(QuestionStr,...
+
+if exist(fname,'file')~=2 || strcmp(questdlg(QuestionStr,...
         'InitCB','Yes','No','No'),'Yes') %file doesn't exist or to be deleted !   
     
     % Save empty CellBase
     TheMatrix = [];
     ANALYSES  = [];
     CELLIDLIST = [];
-    save(fname,'TheMatrix','ANALYSES','CELLIDLIST');
+    save(fname,'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES');
     
     % Convert TrialEvents & Sessions
     NUM_CELLS = addnewcells;
@@ -112,7 +113,6 @@ function initcb(cb_name)
         warndlg('Something went wrong.','InitCB');
     end
 else
-    fclose(fid);
     welcomestr = sprintf('\n %s already exists. Delete it if you need a rebuild.\n',fname);
     msgbox(welcomestr,'Welcome to CellBase','warn');
 end
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/loadcb.m b/CellBase_R2013a/Functions/database_functions/cellbase/loadcb.m
index 6b51e89..4c3e434 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/loadcb.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/loadcb.m
@@ -1,6 +1,6 @@
 function  varargout = loadcb(varargin)
 %LOADCB   Load the CellBase files.
-%   LOADCB loads CellBase (CELLIDLIST, ANALYSES, TheMatrix) into the caller
+%   LOADCB loads CellBase (CELLIDLIST, ANALYSES, TheMatrix, PREFERENCES) into the caller
 %   function's workspace.
 %
 %   OUT = LOADCB(CELLID,FILETYPE) loads the specified file (FILETYPE) of
@@ -10,7 +10,7 @@
 %
 %   See also INITCB and CELLID2FNAMES.
 
-% Edit log: AK 3/04, 11/06, 4/10; BH 7/6/12
+% Edit log: AK 3/04, 11/06, 4/10; BH 7/6/12, TO 5/2018
 
 % Without input arguments, load the entire database
 if nargin == 0
@@ -33,7 +33,7 @@
     
     % Filename to load
     fname = cellid2fnames(cellid,filetype);
-    TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+    TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
     
     if nargout == 1     % if we are loading into a variable
         if strncmpi(filetype,'Spikes',5)
@@ -44,7 +44,7 @@
             
             % Load waveform data (Ntt file)
             Nttfile = cellid2fnames(cellid,'ntt');
-            TIMEFACTOR = getpref('cellbase','timefactor');    % scaling factor to convert spike times into seconds
+            TIMEFACTOR = getcbpref('Spikes_timefactor');    % scaling factor to convert spike times into seconds
             [all_spikes all_waves] = LoadTT_NeuralynxNT(Nttfile);
             [junk junk2 evoked_inx] = intersect(SpikeTimes,all_spikes*TIMEFACTOR);
             if ~isequal(junk,SpikeTimes)   % internal check for spike times
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/mountcb.m b/CellBase_R2013a/Functions/database_functions/cellbase/mountcb.m
index 9b1f53b..00c44bf 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/mountcb.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/mountcb.m
@@ -9,7 +9,7 @@ function mountcb(cb_name)
 %
 %   See also INITCB, LOADCB, CHOOSECB and DELETECB.
 
-%   Edit log: TL 10/21/2015
+%   Edit log: TL 10/21/2015, TO 5/2018
 
 % Check input arguments
 narginchk(0,1)
@@ -48,13 +48,7 @@ function mountcb(cb_name)
         timefactor = 1;     % timestamps in TT*.mat files will already be converted to seconds
 end
 
-% Set other preferences (persistent and maintain their values between MATLAB sessions)
-setpref('cellbase','session_filename','TrialEvents.mat');
-setpref('cellbase','TrialEvents_filename','TrialEvents.mat');
-setpref('cellbase','StimEvents_filename','StimEvents.mat');
-setpref('cellbase','cell_pattern','TT');
-setpref('cellbase','filesep',filesep);
-setpref('cellbase','timefactor',timefactor);
+
 
 % Store cellbases to allow multiple instances
 if ispref('cellbase','cellbases')
@@ -68,6 +62,10 @@ function mountcb(cb_name)
 end
 cellbases{end+1} = gp;  % adds the new CellBase to 'cellbases' 
 setpref('cellbase','cellbases',cellbases)
+setpref('cellbase','filesep',filesep);
+
+%other preferences should be present in cellbase or will be queried when
+%required (TO 5/2018)
 
 % Feedback
 welcomestr = sprintf('New CellBase named %s was successfully mounted.\n',cb_name);
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m b/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m
new file mode 100644
index 0000000..ad4f47e
--- /dev/null
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m
@@ -0,0 +1,31 @@
+function setcbpref(name,val)
+% SETCBPREF() sets current cellbase's preference value for preference NAME
+% to VAL.
+% Cellbase-specific preferences are stored in cellbase file
+% (getpref('cellbase','fname')). Note than cellbase-general preferences
+% (cellbase name, data folder, cellbase file) are manipulated with
+% getpref('cellbase')/setpref('cellbase',...).
+%
+% See also: getcbpref(name), default_preferences()
+%
+% TO 05/2018
+
+if any(strcmp({'datapath','name','fname','filesep','cellbases'},name)) %global settings
+    warning('Please use setpref to set global cellbase settings.');
+    setpref('cellbase',name,val);
+else %correct use for cellbase-specific parameters
+    if exist(fullfile(getpref('cellbase','fname')),'file')==2
+        CB = load(fullfile(getpref('cellbase','fname')));
+        fields = fieldnames(CB);
+        if ~isempty(fields)
+            CB.PREFERENCES.(name)=val;
+            save(fullfile(getpref('cellbase','fname')),'-struct','CB')
+        else %no preference file
+            import_preferences();
+            setcbpref(name,val);
+        end
+        
+    else %no cellbase
+        error('setcbpref: No Cellbase database found. Check cellbase filename.');
+    end
+end
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/upgradecb.m b/CellBase_R2013a/Functions/database_functions/cellbase/upgradecb.m
index 7c4ba0c..b51aa81 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/upgradecb.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/upgradecb.m
@@ -35,6 +35,9 @@
 cellbases{end+1} = gp;
 
 % Set preferences (persistent and maintain their values between MATLAB sessions)
-setpref('cellbase','timefactor',timefactor);
+% globale preferences
 setpref('cellbase','cellbases',cellbases);
-setpref('cellbase','name',cb_name);
\ No newline at end of file
+setpref('cellbase','name',cb_name);
+
+%cellbase specific preferences
+setcbpref('cellbase','timefactor',timefactor);
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cells/addcell.m b/CellBase_R2013a/Functions/database_functions/cells/addcell.m
index ef852a1..d18233d 100644
--- a/CellBase_R2013a/Functions/database_functions/cells/addcell.m
+++ b/CellBase_R2013a/Functions/database_functions/cells/addcell.m
@@ -28,7 +28,7 @@
 end
 
 % Load cellbase
-clear global CELLIDLIST ANALYSES TheMatrix
+clear global CELLIDLIST ANALYSES TheMatrix PREFERENCES
 cellbase_fname = getpref('cellbase','fname');
 load(cellbase_fname);
 
@@ -115,5 +115,5 @@
 % Save cellbase
 assignin('base','TheMatrix',TheMatrix)
 assignin('base','CELLIDLIST',CELLIDLIST)
-save(cellbase_fname,'TheMatrix','ANALYSES','CELLIDLIST')
+save(cellbase_fname,'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES')
 OK = 1;
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cells/addnewcells.m b/CellBase_R2013a/Functions/database_functions/cells/addnewcells.m
index bbfcf53..0ef3c7b 100644
--- a/CellBase_R2013a/Functions/database_functions/cells/addnewcells.m
+++ b/CellBase_R2013a/Functions/database_functions/cells/addnewcells.m
@@ -26,7 +26,7 @@
 g = prs.Results;
 
 % Get CellBase preferences
-clear global CELLIDLIST ANALYSES TheMatrix   % refresh the globals
+clear global CELLIDLIST ANALYSES TheMatrix PREFERENCES   % refresh the globals
 cellbase_datapath = getpref('cellbase','datapath');
 
 % Find all cells and sort the new ones
diff --git a/CellBase_R2013a/Functions/database_functions/cells/delcell.m b/CellBase_R2013a/Functions/database_functions/cells/delcell.m
index 016bc8a..8662f81 100644
--- a/CellBase_R2013a/Functions/database_functions/cells/delcell.m
+++ b/CellBase_R2013a/Functions/database_functions/cells/delcell.m
@@ -7,7 +7,7 @@ function delcell(cellid)
 %
 %   See also ADDCELL, INSERTDATA and DELANALYSIS.
 
-%   Edit log: BH 6/7/12
+%   Edit log: BH 6/7/12, TO 5/2018
 
 % Load CellBase
 load(getpref('cellbase','fname'));
@@ -45,7 +45,7 @@ function delcell(cellid)
 dsr = regexprep(dsr,':','_');
 backup_name = fullfile(pth,[fnm '_' dsr ext]);
 copyfile(cb,backup_name)    % make backup before overwriting
-save(cb,'TheMatrix','ANALYSES','CELLIDLIST');
+save(cb,'TheMatrix','ANALYSES','CELLIDLIST','PREFERENCES');
 
 % Feedback
 if ischar(cellid)
diff --git a/CellBase_R2013a/Functions/database_functions/cells/findallcells.m b/CellBase_R2013a/Functions/database_functions/cells/findallcells.m
index 1781856..2a35594 100644
--- a/CellBase_R2013a/Functions/database_functions/cells/findallcells.m
+++ b/CellBase_R2013a/Functions/database_functions/cells/findallcells.m
@@ -7,7 +7,7 @@
 %
 %   See also FINDCELLPOS.
 
-%   Edit log: AK  3/04; ZFM 7/05; BH 3/21/11, 4/23/13
+%   Edit log: AK  3/04; ZFM 7/05; BH 3/21/11, 4/23/13, TO 05/2018
 
 % Get cellbase preferences
 cellbase_datapath = getpref('cellbase','datapath');
@@ -40,11 +40,11 @@
         
         % Added options for specifying an cut directory below the session
         % directory
-        if ispref('cellbase','group')
-            cell_pattern = getpref('cellbase','cell_pattern');
+        if getcbpref('group')
+            cell_pattern = getcbpref('Spikes_cell_pattern');
             
             % Deal with hierarchy of cut directories
-            cut_dirs = getpref('cellbase','group');
+            cut_dirs = getcbpref('cellbase','group');
             if iscell(cut_dirs)
                 % there is more than one cut directory specified,
                 % return the first existing directory (ie cut directories are in order of
diff --git a/CellBase_R2013a/Functions/database_functions/conversion/cellid2fnames.m b/CellBase_R2013a/Functions/database_functions/conversion/cellid2fnames.m
index 73347c1..7d5b5d2 100644
--- a/CellBase_R2013a/Functions/database_functions/conversion/cellid2fnames.m
+++ b/CellBase_R2013a/Functions/database_functions/conversion/cellid2fnames.m
@@ -29,16 +29,16 @@
 %
 %   See also CELLID2TAGS.
     
-%   Edit log: ZFM 10/7/04, AK 11/06, AK 4/10, SPR 07/2010, BH 6/23/11
+%   Edit log: ZFM 10/7/04, AK 11/06, AK 4/10, SPR 07/2010, BH 6/23/11, TO 5/2018
 
-% Get CellBase preferences
+% get cellbase global preferences
 cellbase_datapath = getpref('cellbase','datapath');
-session_fname = getpref('cellbase','session_filename');
 sep = getpref('cellbase','session_separator');
-if ispref('cellbase','StimEvents_filename')
-	stim_fname = getpref('cellbase','StimEvents_filename');
-end
-cellbase_cell_pattern = getpref('cellbase','cell_pattern');
+
+% get cellbase specific preferences
+TrialEvents_fname = getcbpref('TrialEvents_fname');
+StimEvents_fname = getcbpref('StimEvents_fname');
+cellbase_cell_pattern = getcbpref('Spikes_cell_pattern');
 continuous_channel = 'CSC';
 
 % Get tags
@@ -53,17 +53,17 @@
 % Create names
 if nargin < 2   % if filename was not specified
     fname_spikes = fullfile(cellbase_datapath,ratname,session,tetrodeunit);
-    fname_events = fullfile(cellbase_datapath,ratname,session,session_fname);
+    fname_events = fullfile(cellbase_datapath,ratname,session,TrialEvents_fname);
 else
     % not really spikes, but whatever you specified
     % create unit filename
     if strncmpi(filename,'TrialEvent',10)
-        fname_unit = session_fname;     %'TrialEvents2.mat';
+        fname_unit = TrialEvents_fname;     %'TrialEvents2.mat';
     elseif strncmpi(filename,'StimEvent',9)
-        fname_unit = stim_fname;
+        fname_unit = StimEvents_fname;
     elseif strncmpi(filename,'Session',3)
         fname_unit = '';
-    elseif strncmpi(filename,'Position',3),
+    elseif strncmpi(filename,'Position',3)
         fname_unit='POSITION';
     elseif strncmpi(filename,'Spikes',5)
         fname_unit = sprintf('%s%d_%d.mat',cellbase_cell_pattern,tetrode,unit);
diff --git a/CellBase_R2013a/Functions/database_functions/conversion/fname2cellid.m b/CellBase_R2013a/Functions/database_functions/conversion/fname2cellid.m
index 18ca104..3d94251 100644
--- a/CellBase_R2013a/Functions/database_functions/conversion/fname2cellid.m
+++ b/CellBase_R2013a/Functions/database_functions/conversion/fname2cellid.m
@@ -28,7 +28,7 @@
 cellbase_fname = getpref('cellbase','fname');
 cellbase_path  = getpref('cellbase','datapath');
 if ispref('cellbase','cell_pattern')
-    cell_pattern = getpref('cellbase','cell_pattern');
+    cell_pattern = getcbpref('Spikes_cell_pattern');
 else
     cell_pattern = 'Sc';
 end
diff --git a/CellBase_R2013a/Help/CellBase_functions.html b/CellBase_R2013a/Help/CellBase_functions.html
index 511529c..6e5bd81 100644
--- a/CellBase_R2013a/Help/CellBase_functions.html
+++ b/CellBase_R2013a/Help/CellBase_functions.html
@@ -43,6 +43,10 @@ <h2 align="left"><a name="2">Database functions</a></h2>
 <a href="loadcb.html"><name>loadcb</name></a> - <purpose>Load the CellBase files</purpose><br />
 <a href="checknmcb.html"><name>checknmcb</name></a> - <purpose>Check whether a CellBase name is valid</purpose><br />
 <a href="checkcb.html"><name>checkcb</name></a> - <purpose>Check main CellBase files</purpose><br />
+<a href="getcbpref.html"><name>getcbpref</name></a> - <purpose>Get CellBase-specific preference.</purpose><br />
+<a href="setcbpref.html"><name>setcbpref</name></a> - <purpose>Set CellBase-specific preference.</purpose><br />
+<a href="default_preferences.html"><name>default_preferences</name></a> - <purpose>Get default CellBase-specific preferences.</purpose><br />
+<a href="import_preferences.html"><name>import_preferences</name></a> - <purpose>Import CellBase-specific preferences.</purpose><br />
 <a href="upgradecb.html"><name>upgradecb</name></a> - <purpose>Upgrade CellBase to new version</purpose><br />
 <br>
 
diff --git a/CellBase_R2013a/Help/MakeTrialEvents2_gonogo.html b/CellBase_R2013a/Help/MakeTrialEvents2_gonogo.html
index f985857..64f8723 100644
--- a/CellBase_R2013a/Help/MakeTrialEvents2_gonogo.html
+++ b/CellBase_R2013a/Help/MakeTrialEvents2_gonogo.html
@@ -44,7 +44,7 @@ <h2>Description</h2>
  	trial events structure is saved under the name 'TrialEvents.mat'. This
  	file becomes the primary store of behavioral data for a particular
  	session; it is retrieved by <tt>loadcb</tt> via <tt>cellid2fnames.</tt> This default
- 	file name is one of the preference settings of CellBase - type<br /> <tt>getpref('cellbase','session_filename')</tt>;</p>
+ 	file name is one of the preference settings of CellBase - type<br /> <tt>getcbpref('cellbase','TrialEvents_filename')</tt>;</p>
 <p>
 <tt>MakeTrialEvents2_gonogo(sessionpath,'StimNttl',TTL)</tt> specifies the TTL channel which serves as the basis for synchronization.</p>
 <h2>See Also</h2>
diff --git a/CellBase_R2013a/Help/default_preferences.html b/CellBase_R2013a/Help/default_preferences.html
new file mode 100644
index 0000000..55c4e27
--- /dev/null
+++ b/CellBase_R2013a/Help/default_preferences.html
@@ -0,0 +1,49 @@
+<html>
+<head>
+<title>default_preferences</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<style>
+body {
+  background-color: white;
+  margin:1px;
+}
+h1 {
+  color: #990000; 
+  font-size: 30;
+  font-weight: normal;
+  margin-top: 12px;
+  margin-bottom: 0px;
+}
+h2 {
+  color: #990000;
+  font-size: 20;
+  margin-top: 24px;
+  margin-bottom: 0px;
+}
+pre.codeinput {
+  margin-left: 30px;
+}
+bld {
+  font-weight: bold;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000001">
+<h1 align="left">default_preferences</h1>
+<align="left">Get default CellBase-specific parameters.
+<h2>Syntax</h2>
+<p>
+<tt>PREFERENCES = default_preferences()</tt></blockquote>
+</p>
+<h2>Description</h2>
+<p><tt>default_preferences</tt> returns CellBase-specific default parameters in struct <tt>PREFERENCES</tt>.
+Note that <tt>default_preferences</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>setpref/getpref('cellbase',...)</tt>. </p>
+
+<h2>See Also</h2>
+<p>
+ <a href="import_preferences.html"><tt>import_preferences</tt></a>, <a href="setcbpref.html"><tt>setcbpref</tt></a>,<a href="getcbpref.html"><tt>getcbpref</tt></a>
+</p>
+
+</body>
+</html>
diff --git a/CellBase_R2013a/Help/getcbpref.html b/CellBase_R2013a/Help/getcbpref.html
new file mode 100644
index 0000000..7b6ecae
--- /dev/null
+++ b/CellBase_R2013a/Help/getcbpref.html
@@ -0,0 +1,49 @@
+<html>
+<head>
+<title>getcbpref</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<style>
+body {
+  background-color: white;
+  margin:1px;
+}
+h1 {
+  color: #990000; 
+  font-size: 30;
+  font-weight: normal;
+  margin-top: 12px;
+  margin-bottom: 0px;
+}
+h2 {
+  color: #990000;
+  font-size: 20;
+  margin-top: 24px;
+  margin-bottom: 0px;
+}
+pre.codeinput {
+  margin-left: 30px;
+}
+bld {
+  font-weight: bold;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000001">
+<h1 align="left">getcbpref</h1>
+<align="left">Get CellBase-specific parameter.
+<h2>Syntax</h2>
+<p>
+<tt>val = getcbpref(name)</tt></blockquote>
+</p>
+<h2>Description</h2>
+<p><tt>getcbpref</tt> gets CellBase-specific parameter with name <tt> name</tt> and returns the parameters value in <tt>val</tt>.
+Note that <tt>getcbpref</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>getpref('cellbase',name)</tt>. </p>
+
+<h2>See Also</h2>
+<p>
+<a href="setcbpref.html"><tt>setcbpref</tt></a>, <a href="default_preferences.html"><tt>default_preferences</tt></a>,<a href="initcb.html"><tt>initcb</tt></a>
+</p>
+
+</body>
+</html>
diff --git a/CellBase_R2013a/Help/import_preferences.html b/CellBase_R2013a/Help/import_preferences.html
new file mode 100644
index 0000000..9a3c6a9
--- /dev/null
+++ b/CellBase_R2013a/Help/import_preferences.html
@@ -0,0 +1,52 @@
+<html>
+<head>
+<title>import_preferences</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<style>
+body {
+  background-color: white;
+  margin:1px;
+}
+h1 {
+  color: #990000; 
+  font-size: 30;
+  font-weight: normal;
+  margin-top: 12px;
+  margin-bottom: 0px;
+}
+h2 {
+  color: #990000;
+  font-size: 20;
+  margin-top: 24px;
+  margin-bottom: 0px;
+}
+pre.codeinput {
+  margin-left: 30px;
+}
+bld {
+  font-weight: bold;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000001">
+<h1 align="left">import_preferences</h1>
+<align="left">Create CellBase-specific default parameters or import old parameters.
+<h2>Syntax</h2>
+<p>
+<tt>import_preferences()</tt></blockquote>
+</p>
+<h2>Description</h2>
+<p><tt>import_preferences</tt> creates a struct PREFERENCES containing default parameters
+or loads preferences from <tt>getpref('cellbase')</tt>. This is a
+convenience function to maintain backwards compatibility to cellbase
+<tt>5fbf007</tt> (12 Sep 2017) and prior.
+Note that <tt>import_preferences</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>setpref/getpref('cellbase',...)</tt>. </p>
+
+<h2>See Also</h2>
+<p>
+ <a href="default_preferences.html"><tt>default_preferences</tt></a>, <a href="setcbpref.html"><tt>setcbpref</tt></a>,<a href="getcbpref.html"><tt>getcbpref</tt></a>
+</p>
+
+</body>
+</html>
diff --git a/CellBase_R2013a/Help/setcbpref.html b/CellBase_R2013a/Help/setcbpref.html
new file mode 100644
index 0000000..77538dd
--- /dev/null
+++ b/CellBase_R2013a/Help/setcbpref.html
@@ -0,0 +1,49 @@
+<html>
+<head>
+<title>setcbpref</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<style>
+body {
+  background-color: white;
+  margin:1px;
+}
+h1 {
+  color: #990000; 
+  font-size: 30;
+  font-weight: normal;
+  margin-top: 12px;
+  margin-bottom: 0px;
+}
+h2 {
+  color: #990000;
+  font-size: 20;
+  margin-top: 24px;
+  margin-bottom: 0px;
+}
+pre.codeinput {
+  margin-left: 30px;
+}
+bld {
+  font-weight: bold;
+}
+</style>
+</head>
+
+<body bgcolor="#FFFFFF" text="#000001">
+<h1 align="left">setcbpref</h1>
+<align="left">Set CellBase-specific parameter.
+<h2>Syntax</h2>
+<p>
+<tt>setpref(name, value)</tt></blockquote>
+</p>
+<h2>Description</h2>
+<p><tt>setcbpref</tt> sets CellBase-specific parameter with name <tt> name</tt> to value <tt>value</tt>.
+Note that <tt>setcbpref</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>setpref('cellbase',...)</tt>. </p>
+
+<h2>See Also</h2>
+<p>
+<a href="getcbpref.html"><tt>getcbpref</tt></a>, <a href="default_preferences.html"><tt>default_preferences</tt></a>,<a href="initcb.html"><tt>initcb</tt></a>
+</p>
+
+</body>
+</html>

From 6f05f26f8dde993680838467f7b1b908104b2d4c Mon Sep 17 00:00:00 2001
From: "TORBEN-XPS\\torben" <torben.cshl@gmail.com>
Date: Wed, 2 May 2018 11:11:53 -0400
Subject: [PATCH 2/2] minor improvements.

---
 .../database_functions/cellbase/getcbpref.m   | 67 ++++++++++++-------
 .../cellbase/import_preferences.m             |  2 +-
 .../database_functions/cellbase/setcbpref.m   |  6 +-
 CellBase_R2013a/Help/default_preferences.html |  6 +-
 CellBase_R2013a/Help/getcbpref.html           |  7 +-
 CellBase_R2013a/Help/import_preferences.html  |  6 +-
 CellBase_R2013a/Help/setcbpref.html           |  6 +-
 7 files changed, 58 insertions(+), 42 deletions(-)

diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m b/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m
index a89f887..f698c24 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/getcbpref.m
@@ -1,40 +1,55 @@
-function val = getcbpref(name)
-% GETCBPREF() returns current cellbase's preference value for preference name STR.
+function val = getcbpref(varargin)
+% GETCBPREF returns current cellbase's preference value(s).
 % Cellbase-specific preferences are stored in cellbase file
-% (getpref('cellbase','fname')). Note than cellbase-general preferences
+% (getpref('cellbase','fname')). Note that cellbase-general preferences
 % (cellbase name, data folder, cellbase file) are manipulated with
 % getpref('cellbase')/setpref('cellbase',...).
 %
-% Returns VAL, the value of preference NAME. Returns FALSE if n preference
-% with NAME exists.
+% Usage
+%
+% val = getcbpref() - returns all cellbase preferences in struct VAL (including global preferenes).
+% val = getcbpref(name) - returns cellbase preference with name NAME in VAL.
+%
+% Example
+%
+% val = getcppref('TrialEvents_fname')
 %
 % See also: setcbpref(name,value), default_preferences()
 %
 % TO 05/2018
 
-if any(strcmp({'datapath','name','fname','filesep','cellbases'},name)) %global settings
-    warning('Please use getpref to get global cellbase settings.');
-    val = getpref('cellbase',name);
-else %correct use for cellbase-specific parameters
-    if exist(fullfile(getpref('cellbase','fname')),'file')==2
-        P = load(fullfile(getpref('cellbase','fname')),'PREFERENCES');
-        fields = fieldnames(P);
-        if ~isempty(fields)
-            P=P.PREFERENCES;
-            if isfield(P,name)
-                val=P.(name);
-            else %no parameter in PREFERENCES with that name
-                val = false;
-                warning('getcbpref: no parameter with the specified name found. Try setcbpref() first.');
+if nargin<2
+    if nargin==1 && any(strcmp({'datapath','name','fname','filesep','cellbases'},varargin{1})) %global preferencces
+        warning('Please use getpref to get global cellbase settings.');
+        val = getpref('cellbase',varargin{1});     
+    else %correct use for cellbase-specific preferences
+        if exist(fullfile(getpref('cellbase','fname')),'file')==2
+            P = load(fullfile(getpref('cellbase','fname')),'PREFERENCES');
+            fields = fieldnames(P);
+            if ~isempty(fields)
+                P=P.PREFERENCES;
+                if isempty(varargin) %get all
+                    val = P;
+                    val.datapath = getpref('cellbase','datapath');
+                    val.name = getpref('cellbase','name');
+                    val.fname = getpref('cellbase','fname');
+                else
+                    if isfield(P,varargin{1})
+                        val=P.(varargin{1});
+                    else %no parameter in PREFERENCES with that name
+                        error('getcbpref: no parameter with the specified name found. Try setcbpref() first.');
+                    end
+                end
+            else %no preference file
+                import_preferences();
+                val = getcbpref(varargin);
             end
-        else %no preference file
-            import_preferences();
-            val=getcbpref(name);
+            
+        else %no cellbase
+            error('getcbpref: No Cellbase database found. Check cellbase filename.');
         end
-        
-    else %no cellbase
-        error('getcbpref: No Cellbase database found. Check cellbase filename.');
     end
+else
+    error('getcbpref: Too many input arguments.')
 end
 
-end
\ No newline at end of file
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m b/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m
index 2f08abc..cdd1866 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/import_preferences.m
@@ -9,7 +9,7 @@ function import_preferences()
 % TO 05/2018
 
 str = 'No PREFERENCE variable found. Likely due to use of older cellbase version. Please choose if you want to use default parameters or import from getpref("cellbase"). ';
-str=strcat(str,'Preferences can be manipulated using getpref and setpref and are stored in your cellbase file.');
+str=strcat(str,'Preferences can be manipulated using getcbpref and setcbpref and are stored in your cellbase file.');
 
 A = questdlg(str,'convert_preferences','Default','Import','Default');
 
diff --git a/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m b/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m
index ad4f47e..3eecc28 100644
--- a/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m
+++ b/CellBase_R2013a/Functions/database_functions/cellbase/setcbpref.m
@@ -2,7 +2,7 @@ function setcbpref(name,val)
 % SETCBPREF() sets current cellbase's preference value for preference NAME
 % to VAL.
 % Cellbase-specific preferences are stored in cellbase file
-% (getpref('cellbase','fname')). Note than cellbase-general preferences
+% (getpref('cellbase','fname')). Note that cellbase-general preferences
 % (cellbase name, data folder, cellbase file) are manipulated with
 % getpref('cellbase')/setpref('cellbase',...).
 %
@@ -10,10 +10,10 @@ function setcbpref(name,val)
 %
 % TO 05/2018
 
-if any(strcmp({'datapath','name','fname','filesep','cellbases'},name)) %global settings
+if any(strcmp({'datapath','name','fname','filesep','cellbases'},name)) %global preferences
     warning('Please use setpref to set global cellbase settings.');
     setpref('cellbase',name,val);
-else %correct use for cellbase-specific parameters
+else %correct use for cellbase-specific preferences
     if exist(fullfile(getpref('cellbase','fname')),'file')==2
         CB = load(fullfile(getpref('cellbase','fname')));
         fields = fieldnames(CB);
diff --git a/CellBase_R2013a/Help/default_preferences.html b/CellBase_R2013a/Help/default_preferences.html
index 55c4e27..d3978c2 100644
--- a/CellBase_R2013a/Help/default_preferences.html
+++ b/CellBase_R2013a/Help/default_preferences.html
@@ -31,14 +31,14 @@
 
 <body bgcolor="#FFFFFF" text="#000001">
 <h1 align="left">default_preferences</h1>
-<align="left">Get default CellBase-specific parameters.
+<align="left">Get default CellBase-specific preferences.
 <h2>Syntax</h2>
 <p>
 <tt>PREFERENCES = default_preferences()</tt></blockquote>
 </p>
 <h2>Description</h2>
-<p><tt>default_preferences</tt> returns CellBase-specific default parameters in struct <tt>PREFERENCES</tt>.
-Note that <tt>default_preferences</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>setpref/getpref('cellbase',...)</tt>. </p>
+<p><tt>default_preferences</tt> returns CellBase-specific default preferences in struct <tt>PREFERENCES</tt>.
+Note that <tt>default_preferences</tt> is used for CellBase-specific preferences only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase preferences use MATLAB function <tt>setpref/getpref('cellbase',...)</tt>. </p>
 
 <h2>See Also</h2>
 <p>
diff --git a/CellBase_R2013a/Help/getcbpref.html b/CellBase_R2013a/Help/getcbpref.html
index 7b6ecae..0dbfb39 100644
--- a/CellBase_R2013a/Help/getcbpref.html
+++ b/CellBase_R2013a/Help/getcbpref.html
@@ -31,14 +31,15 @@
 
 <body bgcolor="#FFFFFF" text="#000001">
 <h1 align="left">getcbpref</h1>
-<align="left">Get CellBase-specific parameter.
+<align="left">Get CellBase-specific preference(s).
 <h2>Syntax</h2>
 <p>
+<tt>val = getcbpref()</tt></br>
 <tt>val = getcbpref(name)</tt></blockquote>
 </p>
 <h2>Description</h2>
-<p><tt>getcbpref</tt> gets CellBase-specific parameter with name <tt> name</tt> and returns the parameters value in <tt>val</tt>.
-Note that <tt>getcbpref</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>getpref('cellbase',name)</tt>. </p>
+<p><tt>getcbpref</tt> returns all CellBase-specific preferences in struct <tt> val</tt> or value of preference with name <tt> name</tt> in <tt>val</tt>.
+Note that <tt>getcbpref</tt> is used for CellBase-specific preferences only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase preferences use MATLAB function <tt>getpref('cellbase',name)</tt>. </p>
 
 <h2>See Also</h2>
 <p>
diff --git a/CellBase_R2013a/Help/import_preferences.html b/CellBase_R2013a/Help/import_preferences.html
index 9a3c6a9..15eb386 100644
--- a/CellBase_R2013a/Help/import_preferences.html
+++ b/CellBase_R2013a/Help/import_preferences.html
@@ -31,17 +31,17 @@
 
 <body bgcolor="#FFFFFF" text="#000001">
 <h1 align="left">import_preferences</h1>
-<align="left">Create CellBase-specific default parameters or import old parameters.
+<align="left">Create CellBase-specific default preferences or import old preferences.
 <h2>Syntax</h2>
 <p>
 <tt>import_preferences()</tt></blockquote>
 </p>
 <h2>Description</h2>
-<p><tt>import_preferences</tt> creates a struct PREFERENCES containing default parameters
+<p><tt>import_preferences</tt> creates a struct PREFERENCES containing default preferences
 or loads preferences from <tt>getpref('cellbase')</tt>. This is a
 convenience function to maintain backwards compatibility to cellbase
 <tt>5fbf007</tt> (12 Sep 2017) and prior.
-Note that <tt>import_preferences</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>setpref/getpref('cellbase',...)</tt>. </p>
+Note that <tt>import_preferences</tt> is used for CellBase-specific preferences only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase preferences use MATLAB function <tt>setpref/getpref('cellbase',...)</tt>. </p>
 
 <h2>See Also</h2>
 <p>
diff --git a/CellBase_R2013a/Help/setcbpref.html b/CellBase_R2013a/Help/setcbpref.html
index 77538dd..b5314c8 100644
--- a/CellBase_R2013a/Help/setcbpref.html
+++ b/CellBase_R2013a/Help/setcbpref.html
@@ -31,14 +31,14 @@
 
 <body bgcolor="#FFFFFF" text="#000001">
 <h1 align="left">setcbpref</h1>
-<align="left">Set CellBase-specific parameter.
+<align="left">Set CellBase-specific preference.
 <h2>Syntax</h2>
 <p>
 <tt>setpref(name, value)</tt></blockquote>
 </p>
 <h2>Description</h2>
-<p><tt>setcbpref</tt> sets CellBase-specific parameter with name <tt> name</tt> to value <tt>value</tt>.
-Note that <tt>setcbpref</tt> is used for CellBase-specific parameters only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase parameters use MATLAB function <tt>setpref('cellbase',...)</tt>. </p>
+<p><tt>setcbpref</tt> sets CellBase-specific preference with name <tt> name</tt> to value <tt>value</tt>.
+Note that <tt>setcbpref</tt> is used for CellBase-specific preferences only, which are stored in your CellBase mat-file in the variable <tt>PREFERENCES</tt>. For global CellBase preferences use MATLAB function <tt>setpref('cellbase',...)</tt>. </p>
 
 <h2>See Also</h2>
 <p>