Final GUI updates

src/pspm_cfg/pspm_cfg_help_format.m

@@ -4,9 +4,13 @@
 % GUI
 % Format: helptext = pspm_cfg_help_format(funcname, [argname])
 %         helptext = pspm_cfg_help_format('import', helptext)
+%         helptext = pspm_cfg_help_format('pspm_pupil_pp_options', outputname)
 %                funcname: PsPM function name (char)
 %                argname: function argument (potentially a chain of nested
 %                struct fields, e.g. 'options.overwrite')
+%                outputname: output argument (potentially a chain of nested
+%                struct fields)
+
 global settings
 
 if nargin < 2
@@ -35,8 +39,13 @@
     A = strrep(argname, newline, [newline, newline]);
     helptext = splitlines(A);
 else
+    if strcmpi(funcname, 'pspm_pupil_pp_options')
+        fieldtype = 'Outputs';
+    else
+        fieldtype = 'Arguments';
+    end
     % this syntax allows chaining several nested structs into one argname
-    evalc(sprintf('helptext = settings.help.%s.Arguments.%s;', funcname, argname));
+    evalc(sprintf('helptext = settings.help.%s.%s.%s;', funcname, fieldtype, argname));
     % remove entries in square brackets
     [startindx, endindx] = regexp(helptext, '\[\s*([^\[\]]*)\s*\]'); % thanks ChatGPT for finding the regexp
     for k = numel(startindx):-1:1

src/pspm_cfg/pspm_cfg_process_illuminance.m

@@ -25,62 +25,55 @@
 sr.tag          = 'sr';
 sr.strtype      = 'i';
 sr.num          = [1 1];
-sr.help         = {'Specify the sample rate of the illuminance data.'};
+sr.help         = pspm_cfg_help_format('pspm_process_illuminance', 'sr');
 %% Duration
 duration        = cfg_entry;
 duration.name   = 'Duration';
 duration.tag    = 'duration';
 duration.strtype= 'r';
 duration.val    = {20};
 duration.num    = [1 1];
-duration.help   = {['Specify the duration of the basis function ', ...
-                    'in seconds (default: 20s).']};
+duration.help   = pspm_cfg_help_format('pspm_process_illuminance', 'options.bf.duration');
 %% Offset
 offset          = cfg_entry;
 offset.name     = 'Offset';
 offset.tag      = 'offset';
 offset.strtype  = 'r';
 offset.val      = {0.2};
 offset.num      = [1 1];
-offset.help     = {['Specify an offset of the basis function in ', ...
-                    'seconds (default: 0.2s).']};
+offset.help     = pspm_cfg_help_format('pspm_process_illuminance', 'options.bf.offset');
 %% LDRF_GM
 ldrf_gm         = cfg_const;
-ldrf_gm.name    = 'LDRF_GM';
+ldrf_gm.name    = 'pspm_bf_ldrf_gm';
 ldrf_gm.tag     = 'ldrf_gm';
 ldrf_gm.val     = {true};
-ldrf_gm.help    = {['Use gamma probability density function to ', ...
-                    'model the dilation response (default).']};
+ldrf_gm.help    = {'Gamma probability density function.'};
 %% LDRF_GU
 ldrf_gu         = cfg_const;
-ldrf_gu.name    = 'LDRF_GU';
+ldrf_gu.name    = 'pspm_bf_ldrf_gu';
 ldrf_gu.tag     = 'ldrf_gu';
 ldrf_gu.val     = {true};
-ldrf_gu.help    = {['Use a smoothed gaussian function to model ', ...
-                    'the dilation response.']};
+ldrf_gu.help    = {'Smoothed Gaussian.'};
 %% Dilation
 dilation        = cfg_choice;
 dilation.name   = 'Dilation';
 dilation.tag    = 'dilation';
 dilation.values = {ldrf_gm, ldrf_gu};
 dilation.val    = {ldrf_gm};
-dilation.help   = {['Specify the basis function to model the ', ...
-                    'dilation response.']};
+dilation.help   = pspm_cfg_help_format('pspm_process_illuminance', 'options.bf.dilation');
 %% LCRF_GM
 lcrf_gm         = cfg_const;
-lcrf_gm.name    = 'LCRF_GM';
+lcrf_gm.name    = 'pspm_bf_lcrf_gm';
 lcrf_gm.tag     = 'lcrf_gm';
 lcrf_gm.val     = {true};
-lcrf_gm.help    = {['Use gamma probability density function to model ', ...
-                    'the constriction response (default).']};
+lcrf_gm.help    = {};
 %% Constriction
 constrict       = cfg_choice;
 constrict.name  = 'Constriction';
 constrict.tag   = 'constriction';
 constrict.val   = {lcrf_gm};
 constrict.values= {lcrf_gm};
-constrict.help  = {['Specify the basis function to model the ', ...
-                    'constriction response.']};
+constrict.help  = pspm_cfg_help_format('pspm_process_illuminance', 'options.bf.constriction');
 %% Basis function options
 bf              = cfg_branch;
 bf.name         = 'Basis function options';

src/pspm_cfg/pspm_cfg_pupil_preprocess.m

@@ -32,133 +32,121 @@
 PupilDiameterMin.tag  = 'PupilDiameter_Min';
 PupilDiameterMin.num  = [1 1];
 PupilDiameterMin.val  = {1.5};
-PupilDiameterMin.help = {'Minimum allowed pupil diameter in ',...
-                         'the same unit as the pupil channel.'};
+PupilDiameterMin.help = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.PupilDiameter_Min');
+
 % Pupil diameter maximum
 PupilDiameterMax      = cfg_entry;
 PupilDiameterMax.name = 'Maximum allowed pupil diameter';
 PupilDiameterMax.tag  = 'PupilDiameter_Max';
 PupilDiameterMax.num  = [1 1];
 PupilDiameterMax.val  = {9.0};
-PupilDiameterMax.help = {'Maximum allowed pupil diameter in ',...
-                         'the same unit as the pupil channel.'};
+PupilDiameterMax.help = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.PupilDiameter_Max');
+
 % Island filter separation
 IslandFiltSeparation      = cfg_entry;
 IslandFiltSeparation.name = 'Island separation min distance (ms)';
 IslandFiltSeparation.tag  = 'islandFilter_islandSeparation_ms';
 IslandFiltSeparation.num  = [1 1];
 IslandFiltSeparation.val  = {40};
-IslandFiltSeparation.help = {'Minimum distance used to consider ',...
-                             'samples ''separated'''};
+IslandFiltSeparation.help = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.islandFilter_islandSeperation_ms');
+
 % Minimum valid island width in millisecond
 IslandFiltMinWidth        = cfg_entry;
 IslandFiltMinWidth.name   = 'Min valid island width (ms)';
 IslandFiltMinWidth.tag    = 'islandFilter_minIslandwidth_ms';
 IslandFiltMinWidth.num    = [1 1];
 IslandFiltMinWidth.val    = {50};
-IslandFiltMinWidth.help   = {['Minimum temporal width required to ',...
-                            'still consider a sample island ',...
-                            'valid. If the temporal width of the ',...
-                            'island is less than this value, all the ',...
-                            'samples in the island will be marked ',...
-                            'as invalid.']};
+IslandFiltMinWidth.help   = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.islandFilter_minIslandWidth_ms');
+
 % Dilation speed filter median multiplier
 DilationSpdFiltMedMp      = cfg_entry;
 DilationSpdFiltMedMp.name = 'Number of medians in speed filter';
 DilationSpdFiltMedMp.tag  = 'dilationSpeedFilter_MadMultiplier';
 DilationSpdFiltMedMp.num  = [1 1];
 DilationSpdFiltMedMp.val  = {16};
-DilationSpdFiltMedMp.help = {'Number of median to use as the cutoff ',...
-                            'threshold when applying the speed filter'};
+DilationSpdFiltMedMp.help = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.dilationSpeedFilter_MadMultiplier');
+
 % Dilation speed filter maximum gap in millisecond
 DilationSpdFiltMaxGap       = cfg_entry;
 DilationSpdFiltMaxGap.name  = 'Max gap to compute speed (ms)';
 DilationSpdFiltMaxGap.tag   = 'dilationSpeedFilter_maxGap_ms';
 DilationSpdFiltMaxGap.num   = [1 1];
 DilationSpdFiltMaxGap.val   = {200};
-DilationSpdFiltMaxGap.help  = {'Only calculate the speed when the gap ',...
-                              'between samples is smaller than this value.'};
+DilationSpdFiltMaxGap.help  = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.dilationSpeedFilter_maxGap_ms');
+
 % Gap detect minimum width in millisecond
 GapDetectMinWidth       = cfg_entry;
 GapDetectMinWidth.name  = 'Min missing data width (ms)';
 GapDetectMinWidth.tag   = 'gapDetect_minWidth';
 GapDetectMinWidth.num   = [1 1];
 GapDetectMinWidth.val   = {75};
-GapDetectMinWidth.help  = {'Minimum width of a missing data section ',...
-                          'that causes it to be classified as a gap.'};
+GapDetectMinWidth.help  = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.gapDetect_minWidth');
+
 % Gap detect maximum width in millisecond
 GapDetectMaxWidth       = cfg_entry;
 GapDetectMaxWidth.name  = 'Max missing data width (ms)';
 GapDetectMaxWidth.tag   = 'gapDetect_maxWidth';
 GapDetectMaxWidth.num   = [1 1];
 GapDetectMaxWidth.val   = {2000};
-GapDetectMaxWidth.help  = {'Maximum width of a missing data section ',...
-                          'that causes it to be classified as a gap.'};
+GapDetectMaxWidth.help  = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.gapDetect_maxWidth');
+
 % Gap padding backword
 GapPaddingBwd           = cfg_entry;
 GapPaddingBwd.name      = 'Reject before missing data (ms)';
 GapPaddingBwd.tag       = 'gapPadding_backward';
 GapPaddingBwd.num       = [1 1];
 GapPaddingBwd.val       = {50};
-GapPaddingBwd.help      = {'The section right before the start of a ',...
-                           'gap within which samples are to be rejected.'};
+GapPaddingBwd.help      = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.gapPadding_backward');
+
 % Gap padding forward
 GapPaddingFwd           = cfg_entry;
 GapPaddingFwd.name      = 'Reject after missing data (ms)';
 GapPaddingFwd.tag       = 'gapPadding_forward';
 GapPaddingFwd.num       = [1 1];
 GapPaddingFwd.val       = {50};
-GapPaddingFwd.help      = {'The section right after the end of a gap ',...
-                            'within which samples are to be rejected.'};
+GapPaddingFwd.help      = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.gapPadding_forward');
+
 % Residual filter passes
 ResdFiltPass            = cfg_entry;
 ResdFiltPass.name       = 'Deviation filter passes';
 ResdFiltPass.tag        = 'residualsFilter_passes';
 ResdFiltPass.num        = [1 1];
 ResdFiltPass.val        = {4};
-ResdFiltPass.help       = {'Number of passes deviation filter makes'};
+ResdFiltPass.help       = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.residualsFilter_passes');
+
 % Residual filter median multiplier
 ResdFiltMedMp           = cfg_entry;
 ResdFiltMedMp.name      = 'Number of medians in deviation filter';
 ResdFiltMedMp.tag       = 'residualsFilter_MadMultiplier';
 ResdFiltMedMp.num       = [1 1];
 ResdFiltMedMp.val       = {16};
-ResdFiltMedMp.help      = {['The multiplier used when defining the ',...
-                            'threshold. Threshold equals this ',...
-                            'multiplier times the median. After ',...
-                            'each pass, all the input samples that ',...
-                            'are outside the threshold are removed. ',...
-                            'Please note that all samples (even the ',...
-                            'ones which may have been rejected by ',...
-                            'the previous devation filter pass) are ',...
-                            'considered.']};
+ResdFiltMedMp.help      = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.residualsFilter_MadMultiplier');
+
 % Residual filter interpolation sampling frequency
 ResdFiltInterpFs        = cfg_entry;
 ResdFiltInterpFs.name   = 'Butterworth sampling frequency (Hz)';
 ResdFiltInterpFs.tag    = 'residualsFilter_interpFs';
 ResdFiltInterpFs.num    = [1 1];
 ResdFiltInterpFs.val    = {100};
-ResdFiltInterpFs.help   = {'Sampling frequency for first order ',...
-                           'Butterworth filter.'};
+ResdFiltInterpFs.help   = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.residualsFilter_interpFs');
+
 % Residual filter for lowpass cut-off
 ResdFiltLPCF            = cfg_entry;
 ResdFiltLPCF.name       = 'Butterworth cutoff frequency (Hz)';
 ResdFiltLPCF.tag        = 'residualsFilter_interpFs';
 ResdFiltLPCF.num        = [1 1];
 ResdFiltLPCF.val        = {100};
-ResdFiltLPCF.help       = {'Cutoff frequency for first order ',...
-                            'Butterworth filter.'};
+ResdFiltLPCF.help       = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.residualsFilter_lowpassCF');
+
 % Keep filter data
 KeepFiltData            = cfg_menu;
 KeepFiltData.name       = 'Store intermediate steps';
 KeepFiltData.tag        = 'keepFilterData';
 KeepFiltData.values     = {true, false};
 KeepFiltData.labels     = {'True', 'False'};
 KeepFiltData.val        = {false};
-KeepFiltData.help       = {['If true, intermediate filter data will ',...
-                            'be stored for plotting. ',...
-                            'Set to false to save memory and improve ',...
-                            'plotting performance.']};
+KeepFiltData.help       = pspm_cfg_help_format('pspm_pupil_pp_options', 'raw.keepFilterData');
+
 % Raw custom setting
 RawCustomSet            = cfg_branch;
 RawCustomSet.name       = 'Settings for raw data preprocessing';
@@ -185,35 +173,33 @@
 InterpUpSampFreq.tag    = 'interp_upsamplingFreq';
 InterpUpSampFreq.num    = [1 1];
 InterpUpSampFreq.val    = {1000};
-InterpUpSampFreq.help   = {'The upsampling frequency used to generate ',...
-                           'the smooth signal. (Hz)'};
+InterpUpSampFreq.help   = pspm_cfg_help_format('pspm_pupil_pp_options', 'valid.interp_maxGap');
+
 % Low pass filter cutoff frequency in Hz
 LPFiltCutoffFreq        = cfg_entry;
 LPFiltCutoffFreq.name   = 'Lowpass filter cutoff frequency (Hz)';
 LPFiltCutoffFreq.tag    = 'LpFilt_cutoffFreq';
 LPFiltCutoffFreq.num    = [1 1];
 LPFiltCutoffFreq.val    = {4};
-LPFiltCutoffFreq.help   = {'Cutoff frequency of the lowpass filter ',...
-                           'used during final smoothing. (Hz)'};
+LPFiltCutoffFreq.help   = pspm_cfg_help_format('pspm_pupil_pp_options', 'valid.interp_maxGap');
+
 % Low pass filter order
 LPFiltOrder             = cfg_entry;
 LPFiltOrder.name        = 'Lowpass filter order';
 LPFiltOrder.tag         = 'LpFilt_order';
 LPFiltOrder.num         = [1 1];
 LPFiltOrder.val         = {4};
-LPFiltOrder.help        = {'Filter order of the lowpass filter used ',...
-                           'during final smoothing.'};
+LPFiltOrder.help        = pspm_cfg_help_format('pspm_pupil_pp_options', 'valid.interp_maxGap');
+
+
 % Interpolation maximum gap in millisecond
 InterpMaxGap            = cfg_entry;
 InterpMaxGap.name       = 'Interpolation max gap (ms)';
 InterpMaxGap.tag        = 'interp_maxGap';
 InterpMaxGap.num        = [1 1];
 InterpMaxGap.val        = {250};
-InterpMaxGap.help       = {['Maximum gap in the used (valid) raw ',...
-                            'samples to interpolate over. ',...
-                            'Sections that were interpolated over ',...
-                            'distances larger than this value will ',...
-                            'be set to NaN. (ms)']};
+InterpMaxGap.help       = pspm_cfg_help_format('pspm_pupil_pp_options', 'valid.interp_maxGap');
+
 %% Settings
 % Settings for valid data preprocessing
 ValidCustomSet          = cfg_branch;
@@ -233,7 +219,7 @@
 DefaultSet              = cfg_const;
 DefaultSet.name         = 'Default settings';
 DefaultSet.tag          = 'default_settings';
-DefaultSet.val          = {};
+DefaultSet.val          = {struct()};
 % Settings
 Set                     = cfg_choice;
 Set.name                = 'Settings';

src/pspm_cfg/pspm_cfg_selector_overwrite.m

@@ -4,7 +4,7 @@
 overwrite         = cfg_menu;
 overwrite.name    = 'Overwrite Existing File';
 overwrite.tag     = 'overwrite';
-overwrite.val     = {0};
-overwrite.labels  = {'No', 'Yes'};
-overwrite.values  = {0, 1};
+overwrite.val     = {2};
+overwrite.labels  = {'Discard data if file exists', 'Always overwrite', 'Ask user every time a file exists'};
+overwrite.values  = {0, 1, 2};
 overwrite.help    = {'Specify whether you want to overwrite an existing file with the same name.'};

src/pspm_process_illuminance.m

@@ -17,7 +17,7 @@
 %   [sts, out] = pspm_process_illuminance(ldata, sr, options)
 % ● Arguments
 %   *          ldata: Illuminance data as (cell of) 1x1 double or filename.
-%   *             sr: Sample rate in Hz of the input data.
+%   *             sr: Sample rate in Hz of the input illuminance data.
 %   ┌────────options
 %   ├────────────.fn: [filename] Ff specified ldata{i,j} will be saved to a file
 %   │                 with filename options.fn{i,j} into the variable 'R'.
@@ -27,14 +27,14 @@
 %   ├──────.transfer: Params for the transfer function
 %   └────────────.bf: Settings for the basis functions, described as following.
 %   ┌─────options.bf 
-%   ├──.constriction: Options to the constriction response function. It has a field
-%   │                 ".fhandle" that handles to the constriction response function, 
-%   │                 and its allowed values are @pspm_bf_lcrf_gm.
-%   ├──────.dilation: Options for the dilation basis function. It has a field ".fhandle" 
-%   │                 that handle to the dilation response function, and its allowed 
+%   ├──.constriction: [struct with field .fhandle] Options for the 
+%   │                 constriction response function. Currently
+%   │                 allowed values are @pspm_bf_lcrf_gm.
+%   ├──────.dilation: [struct with field .fhandle] Options for the 
+%   │                 dilation response function. Currently allowed 
 %   │                 values are @pspm_bf_ldrf_gm and @pspm_bf_ldrf_gu.
-%   ├──────.duration: Duration of the basis functions in second.
-%   └────────.offset: Offset in second.
+%   ├──────.duration: Duration of the basis functions in seconds.
+%   └────────.offset: Offset in seconds.
 % ● Outputs
 %   *            sts: status
 %   *            out: has same size as ldata and contains either the