Merge branch 'develop' into 758-pspm_expand_epochs

src/pspm_cfg/pspm_cfg_help_format.m

@@ -20,7 +20,7 @@
         ['This GUI item calls the function %s. You can also call this function ', ...
          'directly. Type ''help %s'' in the command window for more information.'], funcname, funcname), ...
         '------------------------------------------------------------------------------------------------'};
-    
+
     if isfield(settings.help, funcname)
         if isfield(settings.help.(funcname), 'Description')
             A = settings.help.(funcname).Description;
@@ -56,4 +56,4 @@
         helptext = helptext(2:end);
     end
     helptext = {helptext};
-end
+end

src/pspm_cfg/pspm_cfg_selector_data_design.m

@@ -74,7 +74,7 @@
     end
     % marker channel
     if isfield(job.timeunits, 'markers')
-        options.marker_chan_num = pspm_cfg_channel_selector('run', job.timeunits.markers.chan);
+        options.marker_chan_num = pspm_cfg_selector_channel('run', job.timeunits.markers.chan);
     end
     out1 = model;
     out2 = options;

src/pspm_data_editor.m

@@ -89,9 +89,9 @@ function pspm_data_editor_OpeningFcn(hObject, ~, handles, varargin)
 handles.input_mode = '';
 handles.input_file = '';
 handles.output_file = '';
-set(handles.fgDataEditor, 'WindowButtonDownFcn', @buttonDown_Callback);
-set(handles.fgDataEditor, 'WindowButtonUpFcn', @buttonUp_Callback);
-set(handles.fgDataEditor, 'WindowButtonMotionFcn', @buttonMotion_Callback);
+set(handles.pspm_data_editor, 'WindowButtonDownFcn', @buttonDown_Callback);
+set(handles.pspm_data_editor, 'WindowButtonUpFcn', @buttonUp_Callback);
+set(handles.pspm_data_editor, 'WindowButtonMotionFcn', @buttonMotion_Callback);
 if numel(varargin) > 1 && isstruct(varargin{2}) % load options
   handles.options = varargin{2};
   handles.options = pspm_options(handles.options, 'data_editor');
@@ -139,7 +139,7 @@ function pspm_data_editor_OpeningFcn(hObject, ~, handles, varargin)
     Add_Epochs(hObject, handles)
   end
 end
-uiwait(handles.fgDataEditor);
+uiwait(handles.pspm_data_editor);
 
 function [sts] = CreateOutput(hObject)
 handles = guidata(hObject);
@@ -230,7 +230,7 @@ function loadFromFile(hObject, file)
 [~, infos, data] = pspm_load_data(file); % load file
 channels = cellfun(@(x) {x.header.chantype,x.header.units}, data, 'UniformOutput', 0);
 set(handles.edOpenFilePath, 'String', file);
-corder = get(handles.fgDataEditor, 'defaultAxesColorOrder'); % format channels
+corder = get(handles.pspm_data_editor, 'defaultAxesColorOrder'); % format channels
 cl = length(corder)-2;
 disp_names = cell(numel(channels), 1);
 for i = 1:numel(channels)
@@ -255,6 +255,7 @@ function loadFromFile(hObject, file)
 PlotData(hObject);
 
 function PlotData(hObject)
+global settings
 handles = guidata(hObject);
 channel = {};
 switch handles.input_mode % load data
@@ -286,13 +287,14 @@ function PlotData(hObject)
 end
 
 function AddPlot(hObject, chan_id, action)
+global settings
 handles = guidata(hObject);
 if isempty(action)
   action = 'replace';
 end
 np = get(handles.axData, 'NextPlot');
 set(handles.axData, 'NextPlot', action);
-corder = get(handles.fgDataEditor, 'defaultAxesColorOrder');
+corder = get(handles.pspm_data_editor, 'defaultAxesColorOrder');
 cl = length(corder)-2;
 m = floor((chan_id-0.1)/cl);
 color = corder(chan_id - m*cl, :);
@@ -339,6 +341,7 @@ function AddPlot(hObject, chan_id, action)
 guidata(hObject, handles);
 
 function RemovePlot(hObject, chan_id)
+global settings
 handles = guidata(hObject);
 if numel(handles.plots) >= chan_id
   for i = 1:numel(handles.epochs) % remove response plots
@@ -496,11 +499,11 @@ function lbEpochs_CreateFcn(hObject, ~, ~)
   set(hObject,'BackgroundColor','white');
 end
 
-function fgDataEditor_CreateFcn(~, ~, ~)
+function pspm_data_editor_CreateFcn(~, ~, ~)
 % Feature
 %   Executes during object creation, after setting all properties.
 % Variables
-%   hObject    handle to fgDataEditor (see GCBO)
+%   hObject    handle to pspm_data_editor (see GCBO)
 %   eventdata  reserved - to be defined in a future version of MATLAB
 %   handles    empty - handles not created until after all CreateFcns called
 
@@ -917,7 +920,7 @@ function pbApply_Callback(hObject, ~, handles)
 %   eventdata  reserved - to be defined in a future version of MATLAB
 %   handles    structure with handles and user data (see GUIDATA)
 if CreateOutput(hObject) == 1
-  uiresume(handles.fgDataEditor);
+  uiresume(handles.pspm_data_editor);
 end
 
 function pbCancel_Callback(hObject, ~, handles)
@@ -929,8 +932,8 @@ function pbCancel_Callback(hObject, ~, handles)
 %   handles    structure with handles and user data (see GUIDATA)
 handles.output = {};
 guidata(hObject, handles);
-if isfield(handles, 'fgDataEditor')
-  uiresume(handles.fgDataEditor);
+if isfield(handles, 'pspm_data_editor')
+  uiresume(handles.pspm_data_editor);
 end
 
 function cbInterpolate_Callback(hObject, ~, ~)
@@ -958,18 +961,18 @@ function ppOutput_CreateFcn(hObject, ~, ~)
   set(hObject,'BackgroundColor','white');
 end
 
-function fgDataEditor_CloseRequestFcn(hObject, ~, handles)
+function pspm_data_editor_CloseRequestFcn(hObject, ~, handles)
 % Feature
-%   Executes when user attempts to close fgDataEditor.
+%   Executes when user attempts to close pspm_data_editor.
 % Variables
-%   hObject    handle to fgDataEditor (see GCBO)
+%   hObject    handle to pspm_data_editor (see GCBO)
 %   eventdata  reserved - to be defined in a future version of MATLAB
 %   handles    structure with handles and user data (see GUIDATA)
 % Hint
 %   delete(hObject) closes the figure
 handles.output = {};
-if isfield(handles, 'fgDataEditor')
-  uiresume(handles.fgDataEditor);
+if isfield(handles, 'pspm_data_editor')
+  uiresume(handles.pspm_data_editor);
 end
 delete(hObject);
 
@@ -1039,7 +1042,7 @@ function rbInterpolate_Callback(hObject, eventdata, handles)
 % selection changed callback
 bgOutputFormat_SelectionChangedFcn(hObject, eventdata, handles);
 
-function pbOpenInputFile_Callback(hObject, ~, handles)
+function pbOpenInputFile_Callback(hObject, ~, handles, varargin)
 % Feature
 %   Executes on button press in pbOpenInputFile.
 % Variables

src/pspm_display.m

@@ -71,7 +71,6 @@ function pspm_display_OpeningFcn(hObject, ~, handles, varargin)
 if isempty(settings)
   pspm_init;
 end
-
 % load channeltypes from settings variable
 
 j = 1 ; l = 1;
@@ -156,8 +155,11 @@ function pspm_display_OpeningFcn(hObject, ~, handles, varargin)
 % Update handles structure
 guidata(hObject, handles);
 
+handles.pspm_display.HandleVisibility = settings.handle;
+
 % UIWAIT makes pspm_display wait for user response (see UIRESUME)
-% uiwait(handles.figure1);
+%uiwait(handles.pspm_display);
+
 end
 
 
@@ -523,7 +525,7 @@ function saveas_Callback(~, ~, handles)
 close(q)
 end
 % --------------------------------------------------------------------
-function exit_Callback(~, ~, ~)
+function exit_Callback(~, ~, handles)
 % hObject    handle to exit (see GCBO)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
@@ -693,14 +695,8 @@ function edit_y_max_CreateFcn(hObject, ~, ~)
 %% pp_plot
 
 function pp_plot(handles)
-
-global settings;
-if isempty(settings)
-  pspm_init;
-end
-
 % ---header----------------------------------------------------------------
-
+global settings
 %      handles.name ... filename
 %      prop... struct with fields
 %              .wave (channel number)

src/pspm_doc.m

@@ -24,31 +24,33 @@
 % 3.1 Add title
 Title       = pspm_doc_get_title(func_name);
 M = [M, '# ', Title, newline];
+M = [M, '[Back to index](/PsPM/ref/)', newline];
 % 3.2 Add description
 if isfield(S, 'Description')
   Description = pspm_doc_get_description(S.Description);
-  M = [M, '## ', 'Description',  newline, Description, newline];
+  M = [M, newline, '## ', 'Description',  newline, newline, Description, newline, newline];
 end
 % 3.3 Add format
 if isfield(S, 'Format')
   Format      = pspm_doc_get_format(S.Format);
-  M = [M, '## ', 'Format',       newline, Format,      newline];
+  M = [M, '## ', 'Format',       newline, newline, Format,      newline, newline];
 end
 % 3.4 Add arguments
 if isfield(S, 'Arguments')
   Arguments   = pspm_doc_get_struct_fields(S.Arguments);
-  M = [M, '## ', 'Arguments',    newline, Arguments,   newline];
+  M = [M, '## ', 'Arguments',    newline, newline, Arguments,   newline, newline];
 end
 % 3.5 Add outputs
 if isfield(S, 'Outputs')
   Outputs   = pspm_doc_get_struct_fields(S.Outputs);
-  M = [M, '## ', 'Outputs',    newline, Outputs,   newline];
+  M = [M, '## ', 'Outputs',      newline, newline, Outputs,     newline, newline];
 end
 % 3.6 Add references
 if isfield(S, 'References')
   References  = pspm_doc_get_references(S.References);
-  M = [M, '## ', 'References',   newline, References,  newline];
+  M = [M, '## ', 'References',   newline, newline, References,  newline, newline];
 end
+M = [M, '[Back to index](/PsPM/ref/)', newline];
 %% 4 Write to file
 if isfield(options, 'path')
   writelines(M, [options.path, '/', Title,'.md']);
@@ -85,7 +87,6 @@
 end
 Y(LocRm) = [];
 Y = [Y, newline];
-
 end
 function Y = pspm_doc_get_description(X)
 X = insertAfter(X, newline, newline);
@@ -99,7 +100,7 @@
     case 'char'
       Y = [Y, '| ', list_arg{i_arg}, ' | ', X.(list_arg{i_arg}), ' |', newline];
     case 'struct'
-      Y = [Y, '| ', list_arg{i_arg}, ' | ', 'See following fields.'                , ' |', newline];
+      Y = [Y, '| ', list_arg{i_arg}, ' | ', 'See following fields.', ' |', newline];
       list_arg2 = fieldnames(X.(list_arg{i_arg}));
       for i_arg2 = 1:length(list_arg2)
         switch class(X.(list_arg{i_arg}).(list_arg2{i_arg2}))
@@ -112,12 +113,17 @@
             for i_arg3 = 1:length(list_arg3)
               Y = [Y, '| ', list_arg{i_arg}, '.', list_arg2{i_arg2}, '.', list_arg3{i_arg3}, ' | ', ...
                 X.(list_arg{i_arg}).(list_arg2{i_arg2}).(list_arg3{i_arg3}), ' |'];
-              Y = [Y, newline];
+              if i_arg3 < length(list_arg3)
+                Y = [Y, newline];
+              end
             end
         end
         if i_arg2 < length(list_arg2)
           Y = [Y, newline];
         end
+        if i_arg2 == length(list_arg2) && isstruct(X.(list_arg{i_arg}).(list_arg2{i_arg2}))
+          Y = [Y, newline];
+        end
       end
   end
 end

src/pspm_doc_gen.m

@@ -0,0 +1,80 @@
+function sts = pspm_doc_gen(varargin)
+% ● Description
+%   pspm_doc_gen generates the documents of help text 
+%   in pspm functions into markdown files.
+% ● Format
+%   sts = pspm_doc_gen()
+%   sts = pspm_doc_gen({'pspm_dcm'})
+%   sts = pspm_doc_gen('/Users/pspm/')
+%   sts = pspm_doc_gen({'pspm_dcm'}, '/Users/pspm/')
+% ● History
+%   Introduced in PsPM 7.0
+%   Written in 2024 by Teddy
+
+global settings
+if isempty(settings)
+  pspm_init;
+end
+sts = 1;
+switch nargin
+  case 0
+    savepath = [settings.path, '/ref'];
+    mkdir(savepath);
+  case 1
+    switch class(varargin{1})
+      case 'char'
+        savepath = varargin{1};
+      case 'cell'
+        savepath = [settings.path, '/ref'];
+        mkdir(savepath);
+        list_func = varargin{1};
+    end
+  case 2
+    list_func = varargin{1};
+    savepath = varargin{2};
+end
+if ~exist('list_func', 'var')
+ list_func = { ...
+     'pspm_trim', ... 
+     'pspm_split_sessions', ... 
+     'pspm_merge', ... 
+     'pspm_rename', ... 
+     'pspm_combine_markerchannels', ... 
+     'pspm_convert_area2diameter', ... 
+     'pspm_convert_au2unit', ... 
+     'pspm_convert_ecg2hb', ... 
+     'pspm_convert_ecg2hb_amri', ... 
+     'pspm_convert_gaze', ... 
+     'pspm_convert_hb2hp', ... 
+     'pspm_convert_ppg2hb', ... 
+     'pspm_emg_pp', ... 
+     'pspm_find_sounds', ... 
+     'pspm_find_valid_fixations', ... 
+     'pspm_gaze_pp', ... 
+     'pspm_interpolate', ... 
+     'pspm_pp', ... 
+     'pspm_pupil_correct_eyelink', ... 
+     'pspm_pupil_pp', ... 
+     'pspm_remove_epochs', ... 
+     'pspm_resp_pp', ... 
+     'pspm_scr_pp', ... 
+     'pspm_dcm', ... 
+     'pspm_glm', ... 
+     'pspm_process_illuminance', ... 
+     'pspm_sf', ... 
+     'pspm_tam', ... 
+     'pspm_export', ... 
+     'pspm_extract_segments', ...
+     'pspm_get_markerinfo' ...
+     };
+end
+for i_func = 1:length(list_func)
+  options = struct();
+  options.path = savepath;
+  disp(list_func{i_func});
+  sts_temp = pspm_doc(list_func{i_func}, options);
+  if sts_temp == -1
+    sts = -1;
+  end
+end
+end