Merge pull request #833 from bachlab/821_helptext_standardization

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.m

@@ -1,7 +1,7 @@
 function pspm(varargin)
 % ● Description
 %   pspm.m handles the main GUI for PsPM
-% ● Developer's notes
+% ● Developer
 %   PsPM will no longer support GUIDE and only use App Designer for UI.
 %   App Designer is available for MATLAB that is later than version R2016a (9.0).
 % ● History

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_bf_hprf_e.m

@@ -8,7 +8,7 @@
 % ● Arguments
 %   *       td : time resolution in second.
 %   *        b : number of basis functions. Default as 1:6.
-% ● Developer's Notes
+% ● Developer
 %   Basis functions will be orthogonalized using spm_orth by default. Onsets
 %   pspm_glm must be shifted by 5 s to account for the pre-event epoch.
 %   Put in values 1:6 for b in order to get following basis functions:

src/pspm_bf_hprf_rew.m

@@ -7,7 +7,7 @@
 %   [bs, x] = pspm_bf_hprf_fc(TD)
 % ● Arguments
 %   *    td : time resolution in second.
-% ● References:
+% ● References
 %   GLM for reward-conditioned bradycardia:
 %   Xia Y, Liu H, Kälin OK, Gerster S, Bach DR (2024). Measuring
 %   human Pavlovian appetitive conditioning and memory retention.

src/pspm_bf_ldrf_gm.m

@@ -14,7 +14,7 @@
 %   *      a : Shape of the function.
 %   *      b : Scale of the function.
 %   *      A : Quantifier or amplitude of the function.
-% ● Reference
+% ● References
 %   Korn, C. W., & Bach, D. R. (2016). A solid frame for the window on
 %   cognition: Modeling event-related pupil responses. Journal of Vision,
 %   16(3), 28. https://doi.org/10.1167/16.3.28

src/pspm_bf_ldrf_gu.m

@@ -16,7 +16,7 @@
 %   *     p2 : Scale for Gaussian response function, or b, default as 2.04.
 %   *     p3 : Parameter for Gaussian response function, or x0, default as 1.48.
 %   *     p4 : Quantifier or amplitude for Gaussian response function, or A, default as 0.004.
-% ● Reference
+% ● References
 %   Korn, C. W., & Bach, D. R. (2016). A solid frame for the window on
 %   cognition: Modeling event-related pupil responses. Journal of Vision,
 %   16(3), 28. https://doi.org/10.1167/16.3.28

src/pspm_bf_psrf_erl.m

@@ -8,7 +8,7 @@
 %   *    td : Time resolution.
 %   *     n : Number of layers / boxes.
 %   *  tmax : t of the maximum amplitude in seconds.
-% ● Reference
+% ● References
 %   Hoeks, B., & Levelt, W.J.M. (1993).
 %   Pupillary Dilation as a Measure of Attention - a Quantitative System-Analysis.
 %   Behavior Research Methods Instruments & Computers, 25, 16-26.

src/pspm_bf_psrf_fc.m

@@ -10,7 +10,7 @@
 %   *  cs_d : Derivative of CS-evoked response in the basis set. Acceptable values are 0 and 1. Default as 0.
 %   *    us : US-evoked response in the basis set. Acceptable values are 0 and 1. Default as 0.
 %   * us_shift : CS-US SOA in seconds. Ignored if us == 0. Default as 3.5.
-% ● Reference
+% ● References
 %   Christoph W. Korn, Matthias Staib, Athina Tzovara, Giuseppe Castegnetti,
 %   and Dominik R. Bach (2017) A pupil size response model to assess fear learning.
 %   Psychophysiology, 54, 330-343, DOI: 10.1111/psyp.12801

src/pspm_bf_rarf_e.m

@@ -8,7 +8,7 @@
 %   *      td:  The time the response function should have.
 %   * bf_type:  Can be either 0 or 1. If 0, returns the response function only.
 %               If 1, (default) returns the response function and the time derivative.
-% ● Reference
+% ● References
 %   Dominik R. Bach, Samuel Gerster, Athina Tzovara, Giuseppe Castegnetti,
 %   A linear model for event-related respiration responses,
 %   Journal of Neuroscience Methods, Volume 270, 1 September 2016, Pages 147-155,

src/pspm_bf_rfrrf_e.m

@@ -9,7 +9,7 @@
 %   * bf_type:  Type of the basis function, can be either 0 or 1. Default as 1.
 %               If 0, returns the response function only.
 %               If 1, returns the response function and the time derivative.
-% ● Reference
+% ● References
 %   Dominik R. Bach, Samuel Gerster, Athina Tzovara, Giuseppe Castegnetti,
 %   A linear model for event-related respiration responses,
 %   Journal of Neuroscience Methods, Volume 270, 1 September 2016, Pages 147-155,

src/pspm_bf_rprf_e.m

@@ -9,7 +9,7 @@
 %   * bf_type:  Type of the basis function, can be either 0 or 1. Default as 0.
 %               If 0, returns the response function only.
 %               If 1, returns the response function and the time derivative.
-% ● Reference
+% ● References
 %   Dominik R. Bach, Samuel Gerster, Athina Tzovara, Giuseppe Castegnetti,
 %   A linear model for event-related respiration responses,
 %   Journal of Neuroscience Methods, Volume 270, 1 September 2016, Pages 147-155,

src/pspm_bf_scrf.m

@@ -8,7 +8,7 @@
 % ● Arguments
 %   *    td : Time resolution in second.
 %   *     d : Number of derivatives. Default as 0.
-% ● Reference
+% ● References
 %   Bach DR, Flandin G, Friston KJ, Dolan RJ (2010). Modelling event-related
 %   skin conductance responses. International Journal of Psychophysiology,
 %   75, 349-356.

src/pspm_bf_scrf_f.m

@@ -8,7 +8,7 @@
 %   *  td : Time resolution in s.
 %   *   p : An array with variables as (1) Time to peak; (2) Variance of rise defining 
 %           gaussian; and (3--4) Decay constants.
-% ● Reference
+% ● References
 %   Bach DR, Flandin G, Friston KJ, Dolan RJ (2010). Modelling event-related skin
 %   conductance responses. International Journal of Psychophysiology, 75, 349-356.
 % ● History

src/pspm_bf_sebrf.m

@@ -9,7 +9,7 @@
 %   *    td : Time resolution in s.
 %   *     d : Whether first derivative should be included (1) or not (0). Default as 0.
 %   *     g : Whether gaussian to model the tail should be included (1) or not (0). Default as 0.
-% ● Reference
+% ● References
 %   Khemka S, Tzovara A, Gerster S, Quednow B and Bach DR (2016)
 %   Modeling Startle Eyeblink Electromyogram to Assess Fear Learning.
 %   Psychophysiology. 2017 Feb; 54(2): 204–214.

src/pspm_bf_spsrf_gamma.m

@@ -9,7 +9,7 @@
 % ● Arguments
 %   *   td : time resolution in second.
 %   *    p : An array of A, x0, a, and b (in order).
-% ● Reference
+% ● 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)

src/pspm_butter.m

@@ -8,7 +8,7 @@
 % ● Arguments
 %   *     order: the order of the Butterworth filter to be designed
 %   * freqratio: the cut-off frequency of the Butterworth filter to be designed
-% ● Output
+% ● Outputs
 %   *       sts: -1 if non-standard filters are requested
 % ● History
 %   Introduced in PsPM 3.0

src/pspm_check_data.m

@@ -6,7 +6,7 @@
 %   conversions.
 % ● Format
 %   [sts, data] = pspm_check_data(data, infos)
-% ● Developer's notes
+% ● Developer
 %   This code is taken from pspm_load_data; it could be improved using cellfun.
 % ● History
 %   Introducted in Version 7.0

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_convert_area2diameter.m

@@ -30,7 +30,7 @@
 %   └.channel_action : ['add'/'replace', default as 'add']
 %                     Defines whether the new channel should be added or the previous
 %                     outputs of this function should be replaced.
-% ● Output
+% ● Outputs
 %   * channel_index : index of channel containing the processed data
 % ● History
 %   Introduced in PsPM 3.1

src/pspm_convert_au2unit.m

@@ -53,7 +53,7 @@
 %   └.channel_action : ['add'/'replace', default as 'add']
 %                     Defines whether the new channel should be added or the previous
 %                     outputs of this function should be replaced.
-% ● Output
+% ● Outputs
 %   * channel_index : Index of channel containing the processed data.
 % ● History
 %   Introduced in PsPM 3.1

src/pspm_convert_ecg2hb.m

@@ -32,10 +32,10 @@
 %                     Defines whether the new channel should be added or
 %                     the previous outputs of this function should be replaced.
 %
-% ● Output
+% ● Outputs
 %   *  channel_index: index of channel containing the processed data
 %   *   quality_info: generated if options.debugmode == 1
-% ● Reference
+% ● References
 %   [1] Adjusted algorithm:
 %       Paulus PC, Castegnetti G, & Bach DR (2016). Modeling event-related
 %       heart period responses. Psychophysiology, 53, 837-846.
@@ -47,7 +47,7 @@
 %   Written in 2013-2015 Philipp C Paulus & Dominik R Bach
 %   (Technische Universitaet Dresden, University of Zurich)
 %   Updated in 2022 Teddy
-% ● Developer's Notes
+% ● Developer
 %   ▶︎ Changes from the original Pan & Tompkins algorithm
 %   filter:       P. & T. intend to achieve a pass band from 5-15 Hz with a
 %                 real-time filter. This function uses an offline second

src/pspm_convert_gaze.m

@@ -30,7 +30,7 @@
 %   │                 Default is 'gaze'.
 %   └.channel_action: Channel action for sps data, add / replace existing sps
 %                     data (default: add)
-% ● Output
+% ● Outputs
 %   *  channel_index: index of channel containing the processed data
 % ● History
 %   Introduced in PsPM 4.3.1

src/pspm_convert_hb2hp.m

@@ -34,9 +34,9 @@
 %   └─────────.lower: [numeric]
 %                     Specifies the lower limit of the
 %                     heart periods in seconds. Default is 0.2.
-% ● Output
+% ● Outputs
 %   *  channel_index: index of channel containing the processed data
-% ● Reference
+% ● References
 %   [1] Paulus PC, Castegnetti G, & Bach DR (2016). Modeling event-related
 %       heart period responses. Psychophysiology, 53, 837-846.
 % ● History

src/pspm_convert_ppg2hb.m

@@ -42,7 +42,7 @@
 %   └───.python_path: [char] for method 'heartpy'
 %                     The path where python can be found. Mandatory if
 %                     python environment is not yet set up
-% ● Output
+% ● Outputs
 %   *  channel_index: index of channel containing the processed data
 % ● References
 %   [1] van Gent, P, Farah, H, van Nes, N, & van Arem, B. (2019) Heartpy: 

src/pspm_convert_visual_angle_core.m

@@ -12,7 +12,7 @@
 %   *     width: screen width in same units as data
 %   *    height: screen height in same units as data
 %   *  distance: screen distance in same units as data
-% ● Output
+% ● Outputs
 %   *       lat: the latitude in degrees (x-direction)
 %   *       lon: the longitude in degrees (y-direction)
 %   * lat_range: the latitude range

src/pspm_dcm.m

@@ -130,13 +130,13 @@
 %   └.eventnames: Cell array of names for individual events,
 %                 in the order they are specified in the model.timing array -
 %                 to be used for display and export only
-% ● Output
+% ● Outputs
 %   * fn        : Name of the model file.
 %   * dcm       : Model struct. Output units: all timeunits are in seconds;
 %                 eSCR and aSCR amplitude are in SN units such that an
 %                 eSCR SN pulse with 1 unit amplitude causes an eSCR with
 %                 1 mcS amplitude.
-% ● Developer's Notes
+% ● Developer
 %   1. pspm_dcm can handle NaN values in data channels. Either by specifying
 %   missing epochs manually using model.missing, or by detecting NaN epochs
 %   in the data. Missing epochs shorter than model.substhresh will be ignored

src/pspm_dcm_inv.m

@@ -64,7 +64,7 @@
 %                     and aSCR amplitude are in SN units such that an
 %                     eSCR SN pulse with 1 unit amplitude causes an eSCR
 %                     with 1 mcS amplitude (unless model.norm = 1).
-% ● Developer Notes
+% ● Developer
 %   There are two event types: flexible and fixed. The terminology is to call
 %   flexible responses aSCR (anticipatory) and fixed responses eSCR (evoked
 %   SCR).

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_downsample.m

@@ -11,7 +11,7 @@
 %   *        sr:      original sampling rate of the input data.
 %   *        sr_down: targeted downsampling rate.
 %
-% ● Output
+% ● Outputs
 %   *       sts: -1 if the frequency ratio is not an integer
 % ● History
 %   Introduced in PsPM 3.0

src/pspm_emg_pp.m

@@ -25,8 +25,8 @@
 %   └.channel_action: ['add'/'replace'] Defines whether the new channel should
 %                     be added or the previous outputs of this function should
 %                     be replaced. (Default: 'replace')
-% ● Output
-%      channel_index: index of channel containing the processed data
+% ● Outputs
+%   *   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_epochs2logical.m

@@ -12,7 +12,7 @@
 %   *   datalength : length of the resulting logical index
 %   *           sr : if epochs are specified in seconds: sample rate
 %                    if epochs are specified in terms of data samples: 1
-% ● Output
+% ● Outputs
 %   *        index : [logical] index
 % ● History
 %   Introduced in PsPM 6.1.2

src/pspm_expand_epochs.m

@@ -21,7 +21,7 @@
 %   │                     is epochs file.)
 %   └────.channel_action: Channel action, add / replace existing data
 %                         data (default: add)
-% ● Output
+% ● Outputs
 %   *  channel_index: index of channel containing the processed data
 % ● History
 %   Introduced in PsPM 7.0