GUI updates

src/helper/PsPM_installer.m

@@ -0,0 +1,112 @@
+% This is a convenience PsPM installer. As an alternative, download the
+% lastest release from https://github.com/bachlab/PsPM, or clone the
+% develop branch.
+% Uzay Gökay & Dominik Bach, 2024
+
+fprintf('Welcome to the PsPM installer.\n');
+[indx,tf] = listdlg('ListString',{'Latest PsPM release', 'GLM tutorial dataset', 'DCM tutorial dataset'}, ...
+    'PromptString', 'Select items to install.');
+
+if tf == 0
+    fprintf('PsPM installation aborted.\n');
+    return;
+end
+
+fprintf('Please select the parent directory for your PsPM installation.\n');
+destinationFolder = uigetdir('','Select parent directory for your PsPM installation');
+
+% -------------------------------------------------------------------------
+
+if ismember(1, indx)
+
+    % GitHub release URL for PsPM and the desired version
+    githubReleaseURL = 'https://github.com/bachlab/PsPM/releases/download';
+    version = 'v6.1.2';
+    packageName = 'PsPM_v6.1.2';
+
+    % Create the destination folder if it does not exist
+    if ~exist(destinationFolder, 'dir')
+        mkdir(destinationFolder);
+    end
+
+    % Construct the full URL for the specified version and platform (assuming Windows)
+    matlabPackageURL = sprintf('%s/%s/%s.zip', githubReleaseURL, version, packageName);
+
+    % Download the PsPM package
+    disp(['Downloading PsPM version ' version '...']);
+    websave('temp_package.zip', matlabPackageURL);
+
+    % Unzip the contents to the destination folder
+    disp('Unzipping package...');
+    unzip('temp_package.zip', destinationFolder);
+
+    % Clean up: delete the temporary ZIP file
+    delete('temp_package.zip');
+
+    disp(['PsPM package ' version ' download and unzip completed.']);
+
+    %%%%%%%%%%%%%%%%%% add path %%%%%%%%%%%%%%%%%%%%%%%%%%
+    % Add the unzipped PsPM files to the MATLAB search path
+    addpath(fullfile(destinationFolder, packageName));
+
+    disp('PsPM added to MATLAB search path.');
+end
+
+
+%%%%%%%%%%% GLM dataset %%%%%%%%%%%%%%
+if ismember(2, indx)
+    % URL for the PsPM GLM tutorial dataset
+    glmTutorialDatasetURL = 'https://github.com/bachlab/PsPM-tutorial-datasets/releases/download/tutorial-datasets/Tutorial_dataset_GLM.zip';
+    glmTutorialDatasetName = 'Tutorial_dataset_GLM';
+
+    % Destination folder for the tutorial dataset
+    tutorialDestinationFolder = fullfile(destinationFolder, glmTutorialDatasetName);
+
+    % Create the destination folder if it does not exist
+    if ~exist(tutorialDestinationFolder, 'dir')
+        mkdir(tutorialDestinationFolder);
+    end
+
+    % Download the PsPM tutorial dataset
+    disp('Downloading GLM tutorial dataset...');
+    websave('temp_tutorial_dataset.zip', glmTutorialDatasetURL);
+
+    % Unzip the tutorial dataset to the destination folder
+    disp('Unzipping GLM tutorial dataset...');
+    unzip('temp_tutorial_dataset.zip', tutorialDestinationFolder);
+
+    % Clean up: delete the temporary ZIP file
+    delete('temp_tutorial_dataset.zip');
+
+    disp('GLM tutorial dataset download and unzip completed.');
+end
+
+%%%%%%%%%%%%%%% DCM Dataset %%%%%%%%%%%%%%%
+if ismember(3, indx)
+    % URL for the PsPM DCM tutorial dataset
+    dcmTutorialDatasetURL = 'https://github.com/bachlab/PsPM-tutorial-datasets/releases/download/tutorial-datasets/Tutorial_dataset_DCM.zip';
+    dcmTutorialDatasetName = 'Tutorial_dataset_DCM';
+
+    % Destination folder for the DCM tutorial dataset
+    dcmTutorialDestinationFolder = fullfile(destinationFolder, dcmTutorialDatasetName);
+
+    % Create the destination folder if it does not exist
+    if ~exist(dcmTutorialDestinationFolder, 'dir')
+        mkdir(dcmTutorialDestinationFolder);
+    end
+
+    % Download the PsPM DCM tutorial dataset
+    disp('Downloading DCM tutorial dataset...');
+    websave('temp_dcm_tutorial_dataset.zip', dcmTutorialDatasetURL);
+
+    % Unzip the DCM tutorial dataset to the destination folder
+    disp('Unzipping DCM tutorial dataset...');
+    unzip('temp_dcm_tutorial_dataset.zip', dcmTutorialDestinationFolder);
+
+    % Clean up: delete the temporary ZIP file
+    delete('temp_dcm_tutorial_dataset.zip');
+
+    disp('DCM tutorial dataset download and unzip completed.');
+
+end
+

src/pspm_bf_hprf_fc.m

@@ -6,7 +6,7 @@
 %   [bs, x] = pspm_bf_hprf_fc([TD, D, soa])
 % ● Arguments
 %   *    td : time resolution in second.
-%   *     d : number of derivatives. Default as 0.
+%   *     d : number of derivatives. Default is 1.
 % ● History
 %   Introduced in PsPM 3.0
 %   Written in 2015 by Tobias Moser (University of Zurich)
@@ -21,7 +21,7 @@
 end
 td = varargin{1}(1);
 if numel(varargin{1}) == 1 && nargin == 1
-  d = 0;
+  d = 1;
   soa = 3.5;
 else
   if numel(varargin) > 1
@@ -32,7 +32,7 @@
   if numel(va) > 1
     d = va(2);
   else
-    d = 0;
+    d = 1;
   end
   if numel(va) > 2
     soa = va(3);

src/pspm_bf_hprf_rew.m

@@ -1,15 +1,17 @@
 function [bs, x] = pspm_bf_hprf_rew(td)
 % ● Description
 %   This function implements a canonical gamma response function for
-%   reward-conditioned heart period responses.
+%   reward-conditioned heart period responses, based on exps 1-2 in Xia*, 
+%   Liu*, et al. (2024).
 % ● Format
 %   [bs, x] = pspm_bf_hprf_fc(TD)
 % ● Arguments
 %   *    td : time resolution in second.
 % ● References:
 %   GLM for reward-conditioned bradycardia:
-%   Xia Y, Liu H, Kälin OK, Gerster S, Bach DR (under review). Measuring
+%   Xia Y, Liu H, Kälin OK, Gerster S, Bach DR (2024). Measuring
 %   human Pavlovian appetitive conditioning and memory retention.
+%   Pre-print.
 % ● History
 %   Introduced in PsPM 7.0
 %   Written in 2021 by Oliver Keats Kälin and Yanfang Xia (University of Zurich)
@@ -28,7 +30,8 @@
 % default values
 duration = 30;
 % k, theta, c, t0
-p_cs = [1.716239999852250e+02,0.140004209328788,60.095121886556230,-17.607312178043863];
+% p_cs = [1.716239999852250e+02,0.140004209328788,60.095121886556230,-17.607312178043863]; % generated from REW1 data
+p_cs = [73.9977984802746, 0.210014413426350, 71.1984486930105, -9.19655727625912]; % generated from the combined data set of REW1 and REW2
 
 x = (0:td:duration-td)';
 bs = zeros(numel(x), 1);
@@ -51,3 +54,6 @@
 elseif t0 < 0
     bs(1:sto, 1) = g_cs(sta:end);
 end
+
+% normalise
+bs = bs/max(bs);

src/pspm_bf_rarf_fc.m

@@ -7,8 +7,8 @@
 % ● Arguments
 %   *      td:  The time the response function should have.
 %   * bf_type:  Which type of response function should be generated. Can be either 1 or 2.
-%               If 1, first type response function is generated, (default) = gamma_early + gamma_late.
-%               If 2, second type response function is generated, (default) = gamma_early + gamma_early'.
+%               If 1, first type response function is generated (default)                     : gamma_early + gamma_late.
+%               If 2, second type response function is generated (recommended for longer SOAs): gamma_early + gamma_early'.
 % ● History
 %   Introduced in PsPM 3.1
 %   Written in 2016 by G Castegnetti, Tobias Moser (University of Zurich)

src/pspm_bf_spsrf_box.m

@@ -1,18 +1,17 @@
 function [bs, x] = pspm_bf_spsrf_box(varargin)
 % ● Description
 %   pspm_bf_spsrf_box constructs a boxcar function to produce the averaged
-%   scanpath speed over a 2-s time window in the end of SOA, which equals
-%   to scanpath length over a 2-s time window divided by 2/s
+%   scanpath speed over a 2-s time window in the end of SOA. This equals
+%   to scanpath length over a 2-s time window divided by 2.
 % ● Format
 %   [bs, x] = pspm_bf_spsrf_box(td, soa)
 %   [bs, x] = pspm_bf_spsrf_box([td, soa])
 % ● Arguments
 %   *    td : time resolution in second.
 % ● References
-%   Xia Y, Melinscak F, Bach DR (2020)
-%   Saccadic Scanpath Length: An Index for Human Threat Conditioning
-%   Behavioral Research Methods 53, pages 1426–1439 (2021)
-%   doi: 10.3758/s13428-020-01490-5
+%   Xia Y, Melinščak F, Bach DR (2020). Saccadic scanpath length: an
+%   index for human threat conditioning. Behavior Research Methods, 53,
+%   1426-1439.
 % ● History
 %   Introduced in PsPM 4.0
 

src/pspm_cfg/pspm_cfg_combine_markerchannels.m

@@ -12,9 +12,7 @@
 channel_action   = pspm_cfg_selector_channel_action;
 
 %% Specific items
-marker_chan.help    = {['Choose any number of marker channel numbers ',...
-                           'to combine. If 0, all marker ',...
-                           'channels in the file are combined.']};
+marker_chan.help    = pspm_cfg_help_format('pspm_combine_markerchannels', 'options.marker_chan_num');
 
 %% Executable branch
 combine_markerchannels        = cfg_exbranch;

src/pspm_cfg/pspm_cfg_data_preprocessing.m

@@ -11,9 +11,11 @@
 cfg.name   = 'Data Preprocessing';
 cfg.tag    = 'data_preprocessing';
 cfg.values = {pspm_cfg_scr_pp,...
-    pspm_cfg_pp_cardiac, ...
-    pspm_cfg_resp_pp, ...
     pspm_cfg_pp_pupil, ...
-    pspm_cfg_pp_emg};
+    pspm_cfg_pp_cardiac, ...
+    pspm_cfg_resp_pp, ...    
+    pspm_cfg_pp_emg, ...
+    pspm_cfg_combine_markerchannels, ...
+    pspm_cfg_pp_general};
 cfg.forcestruct = true;
 cfg.help   = {'Help: Data preprocessing'};

src/pspm_cfg/pspm_cfg_dcm.m

@@ -16,7 +16,7 @@
 timingfile.tag     = 'timingfile';
 timingfile.num     = [1 1];
 timingfile.filter  = '.*\.(mat|MAT)$';
-timingfile.help    = {'See general help for this item for more information on how to specify timings'};
+timingfile.help    = {'See general DCM help for more information on how to specify timings'};
 
 
 name         = cfg_entry;
@@ -44,7 +44,7 @@
 timing_man_rep.tag    = 'timing_man_rep';
 timing_man_rep.values = {timing_man};
 timing_man_rep.num   = [1 Inf];
-timing_man_rep.help   = {'See general help for this item for more information on how to specify timings'};
+timing_man_rep.help   = {'See general DCM help for more information on how to specify timings'};
 
 
 timing        = cfg_choice;

src/pspm_cfg/pspm_cfg_find_valid_fixations.m

@@ -12,12 +12,12 @@
 ChanAct          = pspm_cfg_selector_channel_action;
 
 %% Visual angle
-box_degree              = cfg_entry;
-box_degree.name         = 'Visual angle';
-box_degree.tag          = 'box_degree';
-box_degree.strtype      = 'i';
-box_degree.num          = [1 1];
-box_degree.help         = pspm_cfg_help_format('pspm_find_valid_fixations', 'circle_degree');
+circle_degree              = cfg_entry;
+circle_degree.name         = 'Visual angle';
+circle_degree.tag          = 'circle_degree';
+circle_degree.strtype      = 'i';
+circle_degree.num          = [1 1];
+circle_degree.help         = pspm_cfg_help_format('pspm_find_valid_fixations', 'circle_degree');
 
 %% Distance
 distance                = cfg_entry;
@@ -41,7 +41,7 @@
 Resol.tag               = 'resolution';
 Resol.strtype           = 'i';
 Resol.num               = [1 2];
-Resol.val               = {[1280 1024]};
+Resol.val               = {[1 1]};
 Resol.help              = pspm_cfg_help_format('pspm_find_valid_fixations', 'options.resolution');
 %% Fixation point default
 FixPtDefault            = cfg_const;
@@ -55,18 +55,16 @@
 FixPtFile.name          = 'File';
 FixPtFile.tag           = 'fixpoint_file';
 FixPtFile.num           = [1 1];
-FixPtFile.help          = {['.mat file containing a variable F with an ', ...
-                            'n x 2 matrix. N should have the length of ', ...
-                            'the recorded data and each row should ', ...
-                            'define the fixation point for the ', ...
-                            'respective recorded data row.']};
+temphelp                = pspm_cfg_help_format('pspm_find_valid_fixations', 'options.fixation_point');
+FixPtFile.help          = {['Specify a .mat file containing a variable ''F'': ', ...
+                           temphelp{1}]};
 %% Fixation point value
 FixPtVal                = cfg_entry;
 FixPtVal.name           = 'Point';
 FixPtVal.tag            = 'fixpoint';
 FixPtVal.strtype        = 'r';
 FixPtVal.num            = [1 2];
-FixPtVal.help           = {['x/y coordinates of constant fixation point.']};
+FixPtVal.help           = {'x/y coordinates of constant fixation point.'};
 
 %% Fixation point
 FixPt                   = cfg_choice;
@@ -79,15 +77,17 @@
 ValidSet                = cfg_branch;
 ValidSet.name           = 'Fixation point';
 ValidSet.tag            = 'validation_settings';
-ValidSet.val            = {box_degree, distance, unit, Resol, FixPt};
+ValidSet.val            = {circle_degree, distance, unit, Resol, FixPt};
 ValidSet.help           = {};
 
 %% Validate on bitmap
 bitmap                  = cfg_files;
 bitmap.name             = 'Bitmap file';
 bitmap.tag              = 'bitmap_file';
 bitmap.num              = [1 1];
-bitmap.help             = pspm_cfg_help_format('pspm_find_valid_fixations', 'bitmap');
+temphelp                = pspm_cfg_help_format('pspm_find_valid_fixations', 'bitmap');
+bitmap.help          = {['Specify a .mat file containing a variable ''bitmap'': ', ...
+                           temphelp{1}]};
 %% Validation method
 val_method              = cfg_choice;
 val_method.name         = 'Validation method';
@@ -96,8 +96,8 @@
 val_method.help         = {};
 %% Missing
 missing                 = cfg_menu;
-missing.name            = 'Add channel with information invalid data points';
-missing.tag             = 'missing';
+missing.name            = 'Add channel with information on invalid data points';
+missing.tag             = 'add_invalid';
 missing.labels          = {'Yes', 'No'};
 missing.values          = {1, 0};
 missing.val             = {0};

src/pspm_cfg/pspm_cfg_first_level.m

@@ -8,10 +8,11 @@
 cfg        = cfg_repeat;
 cfg.name   = 'First Level';
 cfg.tag    = 'first_level';
-cfg.values = {pspm_cfg_first_level_scr, pspm_cfg_first_level_hp, ...
-    pspm_cfg_first_level_resp, ...
+cfg.values = {pspm_cfg_first_level_scr, ...
     pspm_cfg_first_level_ps, ...
     pspm_cfg_first_level_sebr, ...
+    pspm_cfg_first_level_hp, ...
+    pspm_cfg_first_level_resp, ...
     pspm_cfg_first_level_sps, ...
     pspm_cfg_review1, ...
     pspm_cfg_export}; % Values in a cfg_repeat can be any cfg_item objects