Merge branch 'Finalising-version-5.1.0' of https://github.com/bachlab…

…/PsPM into Finalising-version-5.1.0

src/pspm_cfg/pspm_cfg_glm_sps.m

@@ -1,12 +1,17 @@
 function [glm_sps] = pspm_cfg_glm_sps
 % GLM SPS
+% This function applies to the glm model for the modality ScanPath Speed (sps) only
 
-% $Id: pspm_cfg_glm_hp_fc.m 404 2017-01-06 14:02:02Z tmoser $
+% $Id: pspm_cfg_glm_sps.m 404 2017-01-06 14:02:02Z tmoser $
 % $Rev: 404 $
 
+% Updated by Teddy (WCHN)
+
 % Initialise
 global settings
-if isempty(settings), pspm_init; end;
+if isempty(settings)
+    pspm_init; 
+end
 
 % set variables
 
@@ -77,20 +82,20 @@
 chan_def_left         = cfg_const;
 chan_def_left.name    = 'Last left eye';
 chan_def_left.tag     = 'chan_def_left';
-chan_def_left.val     = {'pupil_l'};
-chan_def_left.help    = {'Use last left eye channel.'};
+chan_def_left.val     = {'sps_l'};
+chan_def_left.help    = {'Use the last sps channel from left eye.'};
 
 chan_def_right         = cfg_const;
 chan_def_right.name    = 'Last right eye';
 chan_def_right.tag     = 'chan_def_right';
-chan_def_right.val     = {'pupil_r'};
-chan_def_right.help    = {'Use last right eye channel.'};
+chan_def_right.val     = {'sps_r'};
+chan_def_right.help    = {'Use the last sps channel from right eye.'};
 
 best_eye                = cfg_const;
 best_eye.name           = 'Best eye';
 best_eye.tag            = 'best_eye';
-best_eye.val            = {'pupil'};
-best_eye.help           = {['Use eye with the fewest NaN values.']};
+best_eye.val            = {'sps'};
+best_eye.help           = {'Use the sps data from the eye with fewest NaN values.'};
 
 chan_def                = cfg_choice;
 chan_def.name           = 'Default';

src/pspm_cfg/pspm_cfg_run_glm_sps.m

@@ -1,13 +1,17 @@
 function out = pspm_cfg_run_glm_sps(job)
-% Executes pspm_glm
+% This function executes pspm_glm for the modality ScanPath Speed (sps) only
 
 % $Id: pspm_cfg_run_glm_hp_fc.m 386 2016-11-29 10:30:55Z tmoser $
 % $Rev: 386 $
 
+% Updated 16-06-21 Teddy (WCHN)
+
 global settings
-if isempty(settings), pspm_init; end;
+if isempty(settings)
+	pspm_init;
+end
 
-% set modality
+% set for only the modality sps
 modality = 'sps';
 modelspec = 'sps';
 
@@ -38,11 +42,11 @@
 model.modelspec = modelspec;
 
 if isfield(job.chan.chan_def, 'chan_def_left')
-    model.channel = 'pupil_l';
+    model.channel = 'sps_l';
 elseif isfield(job.chan.chan_def, 'chan_def_right')
-    model.channel = 'pupil_r';
+    model.channel = 'sps_r';
 else
-    model.channel = 'pupil';
+    model.channel = 'sps';
 end
 
 out = pspm_glm(model, options);
@@ -55,4 +59,3 @@
 end;
 
 end
-

src/pspm_glm.m

@@ -25,9 +25,12 @@
 %                   otherwise.
 %
 % optional fields
-% model.modelspec:  'scr' (default); specify the model to be used. See
-%                   pspm_init, defaults.glm() which modelspecs are possible
+% model.modelspec:  'scr' (default); specify the model to be used. 
+%                   See pspm_init, defaults.glm() which modelspecs are possible
 %                   with glm.
+% model.modality:   specify the modality to be processed.
+%                   When model.modality is set to be sps, the model.channel
+%                   should be set among sps_l, sps_r, or defaultly sps.
 % model.bf:         basis function/basis set; modality specific default
 %                   with subfields .fhandle (function handle or string) and
 %                   .args (arguments, first argument sampling interval will
@@ -46,6 +49,8 @@
 %                   precedence order described in its documentation. In a nutshell,
 %                   it prefers preprocessed channels and channels from the best eye
 %                   to other pupil channels.
+%                   SPECIAL: for the modality "sps", the model.channel
+%                   accepts only "sps_l", "sps_r", or "sps".
 %                   DEFAULT: last channel of the specified modality
 %                            (for PSR this is 'pupil')
 % model.norm:       normalise data; default 0

src/pspm_load_data.m

@@ -236,6 +236,8 @@
     if ischar(chan) && ~strcmp(chan, 'none')
         if strcmpi(chan, 'pupil') && isfield(infos.source, 'best_eye')
             flag = get_chans_to_load_for_pupil(data, flag, infos.source.best_eye);
+        elseif strcmpi(chan, 'sps') && isfield(infos.source, 'best_eye')
+            flag = get_chans_to_load_for_sps(data, flag, infos.source.best_eye);
         else
             for k = 1:numel(data)
                 if (any(strcmpi(chan, {'event', 'events'})) && strcmpi(data{k}.header.units, 'events')) || ...
@@ -315,3 +317,58 @@
         flag = besteye_channels;
     end
 end
+
+
+function flag = get_chans_to_load_for_sps(data, flag, best_eye)
+    % 16-06-21 This is a tempory patch for loading sps data, copied from
+    % pupil data
+    % It needs to be updated for testing the compatibility with sps
+    % Set flag variable according to the precedence order:
+    %
+    %   1. Combined channels (by definition also preprocessed)
+    %   2. Preprocessed channels corresponding to best eye
+    %   3. Preprocessed channels
+    %   4. Best eye pupil channels
+    %
+    % The earliest possible option is taken and then the function returns.
+    best_eye = lower(best_eye);
+    chantype_list = cellfun(@(x) x.header.chantype, data, 'uni', false);
+    sps_channels = cell2mat(cellfun(...
+        @(chantype) strncmp(chantype, 'sps',numel('sps')),...
+        chantype_list,...
+        'uni',...
+        false...
+    ));
+    preprocessed_channels = cell2mat(cellfun(...
+        @(chantype) strcmp(chantype(end-2:end), '_pp'),...
+        chantype_list,...
+        'uni',...
+        false...
+    ));
+    combined_channels = cell2mat(cellfun(...
+        @(chantype) contains(chantype, '_lr_') && strcmp(chantype(end-2:end), '_pp'),...
+        chantype_list,...
+        'uni',...
+        false...
+    ));
+    besteye_channels = cell2mat(cellfun(...
+        @(chantype) strcmp(chantype(end-1:end), ['_' best_eye]) || contains(chantype, ['_' best_eye '_']),...
+        chantype_list,...
+        'uni',...
+        false...
+    ));
+    preprocessed_channels = preprocessed_channels & sps_channels;
+    combined_channels = combined_channels & sps_channels;
+    besteye_channels = besteye_channels & sps_channels;
+
+    if any(combined_channels)
+        flag = combined_channels;
+    elseif any(preprocessed_channels)
+        flag = preprocessed_channels & besteye_channels;
+        if ~any(flag)
+            flag = preprocessed_channels;
+        end
+    else
+        flag = besteye_channels;
+    end
+end