more files to update

src/pspm_convert_pixel2unit_core.m

@@ -2,10 +2,10 @@
 % ● Description
 %   pspm_convert_pixel2unit_core converts gaze data from pixel to units.
 % ● Format
-%   [sts, out_data, out_range] = pspm_convert_pixel2unit_core(data, screen_length)
+%   [out_data, out_range] = pspm_convert_pixel2unit_core(data, data_range, screen_length)
 % ● Arguments
 %   *          data: Original data in pixels. No checks are performed.
-%   *         range: Original range in pixels.
+%   *    data_range: Original range in pixels.
 %   * screen_length: Screen width for gaze_x data, or screen height for gaze_y data, in mm
 % ● History
 %   Introduced in PsPM 4.0

src/pspm_eye.m

@@ -2,7 +2,7 @@
 % ● Description
 %   pspm_eye converts legacy use of eye markers into the current version
 % ● Format
-%   Y = pspm_eye(X)
+%   Y = pspm_eye(X,feature)
 % ● Arguments
 %   * X: The input eye marker.
 %   * feature: The feature used for converting eye marker. Accepted values

src/pspm_get_acq_bioread.m

@@ -12,7 +12,9 @@
 % ● Arguments
 %   * datafile : the path of the BIOPAC/AcqKnowledge file to be imported
 %   ┌───import
+%   ├─.channel : channel.
 %   ├──────.sr : sampling rate.
+%   ├────.type : channel type.
 %   ├────.data : The data read from the acq file.
 %   ├───.units : the unit of data.
 %   └──.marker : The type of marker, such as 'continuous'.
@@ -38,8 +40,8 @@
     channel = import{k}.channel;
   else
     channel = pspm_find_channel(channel_labels, import{k}.type);
-    if channel < 1, return; end;
-  end;
+    if channel < 1, return; end
+  end
   if channel > size(channel_labels, 1)
     warning('ID:channel_not_contained_in_file', ...
     'Channel %02.0f not contained in file %s.\n', channel, datafile);
@@ -54,8 +56,8 @@
   import{k}.units = inputdata.channels{channel}.units;
   if strcmpi(settings.channeltypes(import{k}.typeno).data, 'events')
     import{k}.marker = 'continuous';
-  end;
-end;
+  end
+end
 %% Return values
 sts = 1;
 return

src/pspm_get_biograph.m

@@ -41,7 +41,7 @@
     fprintf('\n');
     warning('Please use ''Interval Data Export'' for channels of type ''%s''', ...
       import{1}.type); return
-  end;
+  end
   import{1}.marker = 'timestamps';
   import{1}.sr = 1; % time stamps are in seconds
   import{1}.data = bio.data{1};
@@ -50,7 +50,7 @@
     fprintf('\n');
     warning('Please use ''Export Channel Data'' for channels of type ''%s''', ...
       import{1}.type); return
-  end;
+  end
   import{1}.sr = str2num(cell2mat(regexp(bio.header{1}{1}, '\d', 'match')));
   import{1}.data = bio.data{2};
   % check sample rate --
@@ -70,8 +70,8 @@
   % --> abs(1-diff(timestamps)) < threshold, with threshold = sr * abs(error)
   if any(abs(1-import{1}.sr*diff(bio.data{1})) > threshold)
     warning('Sample rate in header line and timestamps in first column do not match.'); return;
-  end;
-end;
+  end
+end
 %% Return values
 sts = 1;
 return

src/pspm_get_blink_l.m

@@ -7,6 +7,7 @@
 % ● Arguments
 %   ┌──import
 %   ├───.data:  column vector of waveform data
+%   ├──.units:  units of waveform data
 %   └─────.sr:  sample rate
 % ● History
 %   Introduced in PsPM 4.0.2

src/pspm_get_blink_r.m

@@ -7,6 +7,7 @@
 % ● Arguments
 %   ┌────import
 %   ├─────.data : column vector of waveform data
+%   ├────.units : units of waveform data
 %   └───────.sr : sample rate
 % ● History
 %   Introduced in PsPM 4.0.2

src/pspm_get_cnt.m

@@ -37,7 +37,7 @@
   headerformat = 'ns_cnt32';
 else
   headerformat = 'ns_cnt16';
-end;
+end
 
 hdr = ft_read_header(datafile, 'headerformat', headerformat);
 indata = ft_read_data(datafile, 'headerformat', headerformat, 'dataformat', headerformat);
@@ -51,8 +51,8 @@
       channel = import{k}.channel;
     else
       channel = pspm_find_channel(hdr.label, import{k}.type);
-      if channel < 1, return; end;
-    end;
+      if channel < 1, return; end
+    end
 
     sourceinfo.channel{k, 1} = sprintf('Channel %02.0f: %s', channel, hdr.label{channel});
 
@@ -74,10 +74,10 @@
       import{k}.data = [];
       import{k}.markerinfo.value = [];
       import{k}.markerinfo.name = [];
-    end;
-  end;
+    end
+  end
 
-end;
+end
 
 % clear path and return
 % -------------------------------------------------------------------------

src/pspm_get_gaze_x_l.m

@@ -7,7 +7,9 @@
 % ● Arguments
 %   ┌import
 %   ├─.data : column vector of left gaze x data
-%   └───.sr : sample rate
+%   ├─.units: measurement units 
+%   ├───.sr : sample rate
+%   └─.range: range of the gaze data 
 % ● History
 %   Introduced in PsPM 3.1
 %   Written in 2015 by Tobias Moser (University of Zurich)

src/pspm_get_gaze_x_r.m

@@ -7,7 +7,9 @@
 % ● Arguments
 %   ┌import
 %   ├─.data : column vector of right gaze x data
-%   └───.sr : sample rate
+%   ├─.units: measurement units 
+%   ├───.sr : sample rate
+%   └─.range: range of the gaze data 
 % ● History
 %   Introduced in PsPM 3.1
 %   Written in 2015 by Tobias Moser (University of Zurich)

src/pspm_get_gaze_y_l.m

@@ -7,7 +7,9 @@
 % ● Arguments
 %   ┌import
 %   ├─.data : column vector of left gaze y data
-%   └───.sr : sample rate
+%   ├─.units: measurement units 
+%   ├───.sr : sample rate
+%   └─.range: range of the gaze data 
 % ● History
 %   Introduced in PsPM 3.1
 %   Written in 2015 by Tobias Moser (University of Zurich)

src/pspm_get_gaze_y_r.m

@@ -7,7 +7,9 @@
 % ● Arguments
 %   ┌import
 %   ├─.data : column vector of right gaze y data
-%   └───.sr : sample rate
+%   ├─.units: measurement units 
+%   ├───.sr : sample rate
+%   └─.range: range of the gaze data 
 % ● History
 %   Introduced in PsPM 3.1
 %   Written in 2015 by Tobias Moser (University of Zurich)

src/pspm_get_labchart.m

@@ -2,7 +2,7 @@
 % ● Description
 %   pspm_get_labchart imports ADInstruments LabChart *.adicht files. This
 %   function uses an external library that requires Windows as OS. See 
-%   pspm_labchartmat_in and pspm_labchart_mat_ex for import of matlab
+%   pspm_get_labchartmat_in and pspm_get_labchartmat_ext for import of matlab
 %   files that were exported either using the built-in function or the
 %   online conversion tool.
 % ● Format

src/pspm_get_pupil_l.m

@@ -1,4 +1,4 @@
-function [sts, data] = pspm_get_pupil_l(import)
+edit function [sts, data] = pspm_get_pupil_l(import)
 % ● Description
 %   pspm_get_pupil_l is a common function for importing eyelink data
 %   (pupil_l data)

src/pspm_get_rf.m

@@ -35,14 +35,14 @@
   warning('No events specified'); return;
 elseif nargin < 3
   outfile = '';
-end;
+end
 if isempty(outfile) || ~ischar(outfile)
   [pth infn ext] = fileparts(fn);
   outfile = fullfile(pth, ['RF_', infn, ext]);
-end;
+end
 if nargin < 4
   channel = 'scr';
-end;
+end
 
 %% call DCM
 options = pspm_options(options, 'get_rf');
@@ -56,7 +56,7 @@
 else
   % based on aSCR (i. e. updated RF)
   theta = dcm{1}.prior.posterior(3).muTheta(1:7)';
-end;
+end
 
 %% write response function to file
 if ~isempty(outfile)
@@ -85,6 +85,6 @@
   job = strvcat(job');
   outfile = fullfile(pth, [fn, '.m']);
   dlmwrite(outfile, job, 'delimiter', '');
-end;
+end
 sts = 1;
 return

src/pspm_get_saccade_l.m

@@ -7,8 +7,8 @@
 % ● Arguments
 %   ┌import
 %   ├─.data : column vector of left saccade data
-%   ├───.sr : sample rate
-%   └.units : unit of left saccade data
+%   ├.units : unit of left saccade data
+%   └───.sr : sample rate
 % ● History
 %   Introduced in PsPM 4.0.2
 %   Written in 2018 by Laure Ciernik

src/pspm_get_smr.m

@@ -5,15 +5,14 @@
 % ● Format
 %   [sts, import, sourceinfo] = pspm_get_smr(datafile, import);
 % ● Arguments
-%     datafile
+%   *  datafile : the data file to be imported. 
 %   ┌───import
-%   └───denoise: for marker channels in CED spike format (recorded as 'level'),
-%                only retains markers with duration longer than the value given here (in ms).
+%   ├───channel : X
+%   └───denoise : for marker channels in CED spike format (recorded as 'level'),
+%                 only retains markers with duration longer than the value given here (in ms).
 % ● Outputs
-%     import
-%   ┌──sourceinfo
-%   └───channel:
-%     sts
+%   *   import  : the import struct with added information.
+%   * sourceinfo: the struct that includes source information.
 % ● History
 %   Introduced in PsPM 3.0
 %   Written    in 2008-2015 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)

src/pspm_get_smrx.m

@@ -1,9 +1,9 @@
 function [sts, import, sourceinfo] = pspm_get_smrx(datafile, import)
 % ● Description
-%   pspm_get_smr imports *.smrx files generated by Cambridge Electronics
+%   pspm_get_smrx imports *.smrx files generated by Cambridge Electronics
 %   Design (CED) Spike software.
 % ● Format
-%   [sts, import, sourceinfo] = pspm_get_smr(datafile, import);
+%   [sts, import, sourceinfo] = pspm_get_smrx(datafile, import);
 % ● Arguments
 %   * datafile : path to the smrx file
 %   ┌───import

src/pspm_get_sound.m

@@ -6,6 +6,7 @@
 % ● Arguments
 %   ┌─import
 %   ├──.data : column vector of waveform data.
+%   ├─.units : units of data.
 %   └────.sr : sample rate.
 % ● History
 %   Introduced in PsPM 3.0

src/pspm_glm_recon.m

@@ -4,11 +4,11 @@
 %   Reconstructed responses are written into the field glm.resp, and
 %   reconstructed response peaks into the field glm.recon in original GLM file.
 % ● Format
-%   glm = pspm_glm_recon(glmfile) or [sts, glm] = pspm_glm_recon(glmfile)
+%   glm = pspm_glm_recon(modelfile) or [sts, glm] = pspm_glm_recon(modelfile)
 % ● Arguments
-%   * glmfile : the GLM file
+%   * modelfile : the GLM file
 % ● Outputs
-%   *     glm : calculated GLM struct
+%   *       glm : calculated GLM struct
 % ● History
 %   Introduced in PsPM 3.0
 %   Written    in 2008-2018 Dominik R Bach (Wellcome Trust Centre for Neuroimaging)

src/pspm_load1.m

@@ -33,6 +33,7 @@
 %                        'stats', 'recon', 'cond')
 %                        - con structure (for 'con')
 %                        - full first level structure (for 'all')
+%  *  mdltype : model type e.g. 'glm', 'sf', 'dcm', 'tam'
 % ● Developer's Notes
 %   General structure of PsPM 1st level model files
 %   Each file contains one struct variable with the model

src/pspm_load_data.m

@@ -1,9 +1,10 @@
 function [sts, infos, data, filestruct] = pspm_load_data(fn, channel)
 % ● Description
-%   pspm_load_data checks and returns the structure of PsPM 3-5.x and
+%   pspm_load_data checks and returns the structure of PsPM 3-7.x and
 %   SCRalyze 2.x data files - SCRalyze 1.x is not supported
 % ● Format
 %   [sts, infos, data, filestruct] = pspm_load_data(fn, channel)
+%   [sts, infos, data, filestruct] = pspm_load_data(fn)
 % ● Arguments
 %        * fn: [char] filename / [struct] with fields
 %   ┌──────fn
@@ -25,7 +26,7 @@
 %                           returns the respective channels (see settings for
 %                           permissible channel types)
 %                'none'    just checks the file
-%              ▶ struct  check and save file
+%              ▶ struct  check and save file 
 %   ┌────channel
 %   ├───.infos: (mandatory)
 %   ├────.data: (mandatory)

src/pspm_multi_channel.m

@@ -5,7 +5,7 @@
 %   function multiple times and so does accelerate processing time. It
 %   creates the required loop and handles any processing errors.
 % ● Format
-%   [sts, channel_index] = pspm_multi_channel(function, channels, argument1, argument2, ..., options)
+%   [sts, channel_index] = pspm_multi_channel(fhandle, channels, argument1, argument2, ..., options)
 % ● Arguments
 %   *       fhandle : [char or function handle] Preprocessing function
 %   *      channels : [char, vector, cell array] Channel specifications:

src/pspm_sf_mp.m

@@ -4,11 +4,12 @@
 %   matching pursuit algorithm, and f_SF for the forward model the input data is assumed
 %   to be in mcS, and sampling rate in Hz.
 % ● Format
-%   [sts, mp] = pspm_sf_mp(model, options)
+%   [sts, out] = pspm_sf_mp(model, options)
 % ● Arguments
-%   *     scr : skin conductance epoch (maximum size depends on computing power, a
-%               sensible size is 60 s at 10 Hz)
-%   *      sr : sampling rate in Hz
+%   ┌─model
+%   ├─────scr : skin conductance epoch (maximum size depends on computing power, a
+%   │           sensible size is 60 s at 10 Hz)
+%   └──────sr : sampling rate in Hz
 %   ┌─options
 %   ├─.threshold: threshold for SN detection (default 0.1 mcS)
 %   ├──.theta : a (1 x 5) vector of theta values for f_SF (default: read from pspm_sf_theta)
@@ -23,15 +24,19 @@
 %   ├──────.n : number of responses above threshold
 %   ├──────.f : frequency of responses above threshold in Hz
 %   ├─────.ma : mean amplitude of responses above threshold
-%   ├──────.t : timing of responses
-%   ├──────.a : amplitude of responses (re-estimated)
-%   ├───.rawa : amplitude of responses (initial estimate)
+%   ├──────.t : timing of responses (adjusted for conduction delay)
+%   ├──────.a : amplitude of responses (re-estimated via ML)
+%   ├───.rawa : amplitude of responses (initial greedy estimate)
 %   ├──.theta : parameters used for f_SF
-%   ├─.threshold : threshold
-%   ├───.yhat : fitted time series (reestimated amplitudes)
-%   ├.yhatraw : fitted time series (original amplitudes)
-%   ├──────.S : inversion settings
-%   └──────.D : inversion dictionary
+%   ├─.threshold : threshold applied for response detection
+%   ├───.yhat : fitted time series (using reestimated amplitudes)
+%   ├.yhatraw : fitted time series (using initial amplitudes)
+%   ├──────.ind : indices of selected dictionary atoms in D.D
+%   ├──.sortind : sorted indices of selected atoms (after pruning)
+%   ├───────.y : preprocessed input data (baseline-centered scr)
+%   ├───.time : total execution time in seconds
+%   ├──────.S : inversion settings (struct with algorithm parameters)
+%   └──────.D : inversion dictionary (struct with atoms and metadata)
 % ● References
 %   [1] Bach DR, Staib M (2015). A matching pursuit algorithm for inferring tonic
 %       sympathetic arousal from spontaneous skin conductance fluctuations.

src/pspm_sf_scl.m

@@ -2,7 +2,7 @@
 % ● Description
 %   pspm_sf_scl returns the mean skin conductance level for an epoch
 % ● Format
-%   [sts, scl] = pspm_sf_scl(scr, sr)
+%   [sts, scl] = pspm_sf_scl(model, options)
 % ● Arguments
 %   ┌────────model
 %   ├─────────.scr : skin conductance epoch (maximum size depends on computing power,