change parsing problems

Author: 4gwe

src/f_SCR.m

@@ -18,14 +18,14 @@
 % ● Format
 %   [fx, dfdx, dfdP] = f_SCR(Xt,Theta,ut,in)
 % ● Arguments
-%   Theta:  4 ER constants (3 ODE params + time)
+% * Theta:  4 ER constants (3 ODE params + time)
 %           3 SF constants (3 ODE params)
 %           3 values per aSCR (invsigma(peaktime), invsigma(std),
 %           log(amplitude))
 %           1 value  per eSCR (log(amplitude))
 %           2 values per SF (invsigma(peaktime), log(amplitude))
 %           2 values per SCL change (invsigma(time), amplitude)
-%      ut:  row 1 - time (after cue onset)
+% *    ut:  row 1 - time (after cue onset)
 %           row 2 - number of aSCR
 %           row 3 - number of eSCR
 %           row 4 - number of SF

src/f_SF.m

@@ -13,10 +13,10 @@
 % ● Format
 %   [fx, dfdx] = f_SF(Xt,Theta,ut,in)
 % ● Arguments
-%   Theta:  3 general constants
-%           2 value  per SF (time, log(amplitude))
-%      ut:  row 1 - time (after cue onset)
-%           row 2 - number of SF
+%   * Theta: 3 general constants
+%            2 value  per SF (time, log(amplitude))
+%   *    ut: row 1 - time (after cue onset)
+%            row 2 - number of SF
 % ● History
 %   Introduced in PsPM 3.0
 %   Written in 2008-2015 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)

src/g_SCR.m

@@ -1,8 +1,10 @@
 function [gx,dgdx,dgdPhi] = g_SCR(Xt,Phi,ut,inG)
-% ● Description 
+% ● Description
 %   This is the SCR observation function required by the VBA toolbox. It 
 %   adds the three generative processes (phasic SCR, SF, SCL) modelled in
 %   f_SCR.
+% ● Format
+%   [gx,dgdx,dgdPhi] = g_SCR(Xt,Phi,ut,inG)
 % ● Arguments
 %     Xt: a 7-element vector
 %    Phi: input required by VBA, ignored

src/pspm_align_channels.m

@@ -9,7 +9,7 @@
 % ● Arguments
 %   *                data : [struct] the input data to be processed, in PsPM data format.
 %   *          induration : [double] the duration of the input data.
-% ● Copyright
+% ● History
 %   Introduced in PsPM 3.1
 %   Written    in 2008-2016 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)
 %   Maintained in 2022      by Teddy

src/pspm_bf_FIR.m

@@ -17,29 +17,29 @@
 %% Check input arguments
 if nargin==0
   errmsg='No sampling interval stated'; warning('ID:invalid_input', errmsg); return;
-end;
+end
 n = 30;
 d = 1;
 td = varargin{1}(1);
 if nargin == 1 && numel(varargin{1}) > 1
   n = varargin{1}(2);
   if numel(varargin{1}) >= 3
     d = varargin{1}(3);
-  end;
+  end
 
 elseif nargin > 1
   if nargin >= 2
     n = varargin{2}(1);
-  end;
+  end
   if nargin >= 3
     d = varargin{3}(1);
-  end;
-end;
+  end
+end
 if td > d
   warning('ID:invalid_input', 'Time resolution is larger than duration of the function.'); return;
 elseif td == 0
   warning('ID:invalid_input', 'Time resolution must be larger than 0.'); return;
-end;
+end
 % initialise FIR
 FIR = [zeros(1, n); zeros(round((d*n/td)), n);];
 % generate timestamps
@@ -50,5 +50,5 @@
   stops=(d*reg)/td;
   FIR(starts:stops, reg)=1;
   starts=stops+1;
-end;
+end
 return

src/pspm_check_model.m

@@ -1,5 +1,5 @@
 function [model, options] = pspm_check_model(model, options, modeltype)
-% ● Definition
+% ● Description
 %   pspm_check_model automatically determine the fields of the struct model
 %   for the corresponding function. It also checks the options structure
 %   and uses it to determine whether overwriting of the model file is

src/pspm_denoise_spike.m

@@ -8,7 +8,7 @@
 %   *    header : header of data
 %   *    kbdata : keyboard channel data
 %   *    cutoff : the cut off value for denoising
-% ● Arguments
+% ● Outputs
 %   *    data: denoised data
 % ● History
 %   Introduced in PsPM 3.0

src/pspm_emg_pp.m

@@ -26,7 +26,7 @@
 %                     be added or the previous outputs of this function should
 %                     be replaced. (Default: 'replace')
 % ● Outputs
-%      channel_index: index of channel containing the processed data
+%   *   channel_index: index of channel containing the processed data
 % ● References
 %   [1] Khemka S, Tzovara A, Gerster S, Quednow BB, Bach DR (2017).
 %       Modelling startle eye blink electromyogram to assess fear learning.

src/pspm_find_eye.m

@@ -1,5 +1,5 @@
 function [sts, eye, new_chantype] = pspm_find_eye(chantype)
-% ● Definition
+% ● Description
 %   pspm_get_eye detects the eye location ('l', 'r', 'c', '') from an
 %   eyetracker channel type
 % ● Format

src/pspm_get_biograph.m

@@ -14,8 +14,8 @@
 %   ├──────.data : The data read from the file.
 %   └────.marker : The type of marker, such as 'continuous'
 % ● Outputs
-%         import : The import struct that saves importing information
-%     sourceinfo : The struct that saves information of original data source
+%   *      import : The import struct that saves importing information
+%   *  sourceinfo : The struct that saves information of original data source
 % ● History
 %   Introduced in PsPM 3.0
 %   Written in 2008-2015 Dominik R Bach (Wellcome Trust Centre for Neuroimaging)

src/pspm_get_biotrace.m

@@ -12,8 +12,8 @@
 %   ├──────.data : The data read from the file.
 %   └────.marker : The type of marker, such as 'continuous'
 % ● Outputs
-%         import : The import struct that saves importing information
-%     sourceinfo : The struct that saves information of original data source
+%   *      import : The import struct that saves importing information
+%   *  sourceinfo : The struct that saves information of original data source
 % ● History
 %   Introduced in PsPM 3.0
 %   Written in 2008-2015 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)

src/pspm_get_markerinfo.m

@@ -7,8 +7,7 @@
 % ● Format
 %   [sts, markerinfo] = pspm_get_markerinfo(filename, options)
 % ● Arguments
-%   *   filename : [char]
-%                  name of PsPM file
+%   *   filename : [char] name of PsPM file
 %                  if empty, you will be prompted for one
 %   ┌────options
 %   ├.marker_chan_num:  [int] marker channel number.
@@ -20,12 +19,11 @@
 %                  Define whether to overwrite existing output files or not.
 %                  Default value: determined by pspm_overwrite.
 % ● Outputs
-%   *        sts : [double]
-%                  default value: -1 if unsuccessful
-%   ┌─markerinfo : [struct]
-%   ├──────.name : [char]
-%   ├─────.value : ...
-%   └───.element : ...
+%   *        sts : [double]  default value: -1 if unsuccessful.
+%   ┌────markerinfo 
+%   ├──────.name : [char]  marker type name, extracted from the data.
+%   ├─────.value : [double]  marker value, representing event codes or timestamps.
+%   └───.element : [array] 
 % ● History
 %   Introduced in PsPM 6.0
 %   Written in 2008-2015 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)

src/pspm_get_smrx.m

@@ -14,9 +14,9 @@
 %   ├────.type : [string]  The type of input channel, such as 'scr'.
 %   └──.typeno : [integer] The number of channel type, please see pspm_init.
 % ● Outputs
-%   sts: the status recording whether the function runs successfully.
-%   import: the struct that stores read information.
-%   sourceinfo: the struct that stores channel titles.
+%   * sts: the status recording whether the function runs successfully.
+%   * import: the struct that stores read information.
+%   * sourceinfo: the struct that stores channel titles.
 % ● Developer
 %   The following fields are read from the datafile and saved in import
 %   * data      | via CEDS64ReadWaveF/CEDS64ReadEvents/CEDS64ReadMarkers

src/pspm_get_timing.m

@@ -11,7 +11,7 @@
 %     [sts, epochs] = pspm_get_timing('missing', epochs, timeunits)
 %   → For recursive calls also:
 %     [sts, epochs] = pspm_get_timing('file', filename)
-% ● Arguments
+% ● Argument(s) // need change
 %   onsets and timeunits are 'seconds', 'samples' or 'markers':
 %      for defining event onsets for multiple conditions (e. g. GLM)
 %      intiming is - a multiple condition file name (single session) OR

src/pspm_guide.m

@@ -15,7 +15,7 @@
 %       contents{get(hObject,'Value')} returns selected item from the list
 %   * Hint
 %       popupmenu controls usually have a white background on Windows.
-% ● Copyright
+% ● History
 %   Introduced in PsPM 1.0 and terminated in PsPM 6.1.
 %   Written by Dominik R Bach (Wellcome Centre for Human Neuroimaging) in 2008-2021
 %   Lastly updated in PsPM 6.1 by Teddy in 2022

src/pspm_help_init.m

@@ -1,8 +1,10 @@
 function out = pspm_help_init
-% pspm_help_init sets up the help texts for matlabbatch GUI. This is work
-% in progress.
+% ● Description
+%   pspm_help_init sets up the help texts for matlabbatch GUI. 
+% ● Developer
+%   This is work in progress.
 
-% get functions list
+%% get functions list
 [pth, fname, ext] = fileparts(mfilename('fullpath'));
 
 filelist = dir(fullfile(pth, '*.m'));

src/pspm_leaky_integrator.m

@@ -1,6 +1,8 @@
 function filtered_data = pspm_leaky_integrator(data, tau)
 % ● Description
 %   pspm_leaky_integrator applies a leaky integrator filter to the input data
+% ● Format
+%   filtered_data = pspm_leaky_integrator(data, tau)
 % ● Arguments
 %   * data: A numerical vector representing the input signal to be filtered.
 %   * tau: The time constant of the leaky integrator, representing the
@@ -11,7 +13,7 @@
 %   * filtered_data: The filtered signal, of the same size as the input data,
 %                 processed by the leaky integrator.
 
-    % Initialize the filteredData vector with the same size as input data
+%%  Initialize the filteredData vector with the same size as input data
     filtered_data = zeros(size(data));
     % Start with the first value of the input data
     filtered_data(1) = data(1);

src/pspm_load_channel.m

@@ -1,6 +1,6 @@
 function [sts, data_struct, infos, pos_of_channel, chantype_sts] = ...
     pspm_load_channel(fn, channel, channeltype)
-% ● Definition
+% ● Description
 %   pspm_load_channel loads a single data channel and provides integrated
 %   channel checking logic
 % ● Format

src/pspm_logical2epochs.m

@@ -13,7 +13,7 @@
 % ● History
 %   Written in 2024 by Bernhard Agoué von Raußendorf
 
-    
+%%    
 % Compute the differences between consecutive elements in the index array,
 % with padding at the start and end
 diff_index = diff([0; index(:); 0]);

src/pspm_options.m

@@ -1,10 +1,12 @@
 function options = pspm_options(options, FunName)
-% ● Definition
+% ● Description
 %   pspm_options automatically determine the fields of options for the
 %   corresponding function.
 % ● Arguments
-%   options:  a struct to be filled by the function
-%   FunName:  a string, the name of the function where option is used
+%   * options:  a struct to be filled by the function
+%   * FunName:  a string, the name of the function where option is used
+% ● Outputs
+%   * options:   a struct containing the options for the specified function.
 % ● History
 %   Introduced in PsPM 6.1
 %   Written in 2022 by Teddy

src/pspm_pull_zenodo.m

@@ -8,9 +8,7 @@
 %   * datapath: directory where the downloaded files will be stored (string)
 % ● Outputs
 %   * sts: status flag
-% ● Developer
-%   dsgd
-%   edsrgd
+
 fprintf('Pulling data set %i from zenodo.org\n', ID);
 mkdir(datapath);
 

src/pspm_time2index.m

@@ -14,7 +14,7 @@
 %   *      events : vector of timestamps from a marker channel, will be considered if
 %                   given as input.
 % ● Outputs
-%           index : [integer] index or data point.
+%   *       index : [integer] index or data point.
 % ● History
 %   Introduced in PsPM 5.1.2
 %   Written in 2021 by Teddy

src/pspm_ui.m

@@ -1,10 +1,15 @@
 function [hObject, handles] = pspm_ui(hObject,handles,window)
 % ● Description
 %   pspm_ui controls the UI of the referred handle.
+% ● Format
+%   [hObject, handles] = pspm_ui(hObject,handles,window)
 % ● Arguments
 %   * hObject : UI controllor of the specific GUI window.
 %   * handles : UI controllor of the specific GUI window.
 %   *  window : the name of the specific GUI window.
+% ● Outputs
+%   * hObject : The handle of the main UI figure or control element.
+%   * handles : A structure containing handles to all UI components. 
 % ● History
 %   Introduced in PsPM 5.1
 %   Written and maintained in 2021-2022