Merge branch 'develop'

Author: teddy.chao

src/pspm_cfg/pspm_cfg_pp_emg.m

@@ -6,8 +6,6 @@
 % PsPM 3.1
 % (C) 2016 Tobias Moser (University of Zurich)
 
-% $Id$
-% $Rev$
 
 %% Data preprocessing
 cfg        = cfg_repeat;

src/pspm_cfg/pspm_cfg_pp_emg_data.m

@@ -1,9 +1,8 @@
 function [pp_emg] = pspm_cfg_pp_emg_data
-% function to process emg data which leads to emg_proc data
-%
-
-% $Id$
-% $Rev$
+% * Description
+%   function to process emg data which leads to emg_proc data
+% * History
+%   Updated in 2024 by Teddy
 
 % Initialise
 global settings

src/pspm_cfg/pspm_cfg_run_pp_emg_data.m

@@ -1,19 +1,19 @@
 function out = pspm_cfg_run_pp_emg_data(job)
-% Executes pspm_emg_pp
-
+% * Description
+%   Executes pspm_emg_pp
+% * History
+%   Updated with PsPM 6.1.2 in 2024 by Teddy
 options = struct();
 options.mains_freq = job.options(1).mains_freq;
-options.channel_action = job.options(1).channel_action;
+options.channel_action = job.options(1).chan_action;
 if isfield(job.options(1).channel, 'cust_channel')
-    options.channel = job.options(1).channel(1).cust_channel;
+  options.channel = job.options(1).channel(1).cust_channel;
 elseif isfield(job.options(1).channel, 'first_channel')
-    options.channel = job.options(1).channel(1).first_channel;
-end;
-
+  options.channel = job.options(1).channel(1).first_channel;
+end
 [sts, output] = pspm_emg_pp(job.datafile{1}, options);
-
 if sts == 1
-    out = {output.channel};
+  out = {output.channel};
 else
-    out = {-1};
-end;
+  out = {-1};
+end

src/pspm_check_model.m

@@ -201,11 +201,11 @@
 else
   if ~isempty(model.timing)
     if ~iscell(model.timing) || ...
-      strcmpi(modeltype, 'dcm') && ~iscell(model.timing{1})
+      (strcmpi(modeltype, 'dcm') && ~iscell(model.timing{1}) && ~ischar(model.timing{1}))
       % for DCM, model.timing is either a file name or a cell array of
       % events, or a cell array of file names or cell arrays, so we need to
       % take care of cases where model.timing is a cell array but not a cell
-      % array of cell arrays
+      % array of cell arrays or a cell array of char
       model.timing = {model.timing};
     end
   end

src/pspm_convert_hb2hp.m

@@ -67,8 +67,8 @@
   return;
 end
 if numel(data) > 1
-  fprintf('There is more than one heart beat channel in the data file. Only the first of these will be analysed.');
-  data = data(1);
+  fprintf('There is more than one heart beat channel in the data file. Only the last of these will be analysed.');
+  data = data(end);
 end
 
 % interpolate

src/pspm_dcm.m

@@ -361,7 +361,7 @@
 for vs = 1:numel(valid_subsessions)
   isbSn = valid_subsessions(vs);
   sbSn = subsessions(isbSn, :);
-  flanks = pspm_time2index(sbSn(2:3), data{sbSn(1)}{1}.header.sr);
+  flanks = pspm_time2index(sbSn(2:3), sr{sbSn(1)});
   sbSn_data = y{sbSn(1)}(flanks(1):flanks(2));
   sbs_miss = isnan(sbSn_data);
 

src/pspm_glm.m

@@ -199,7 +199,7 @@
     % first marker_channel is used
     events{iFile} = data{1}.data(:) * data{1}.header.sr;
     if strcmp(model.timeunits,'markervalues')
-      model.timing{iFile}.markerinfo = data{end}.markerinfo;
+      model.timing{iFile}.markerinfo = data{1}.markerinfo;
     end
   end
 end

src/pspm_pp.m

@@ -19,7 +19,7 @@
 % ● History
 %   Introduced In PsPM 3.0
 %   Written in 2009-2015 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)
-%   Maintained in 2022 by Teddy Chao (UCL)
+%   Maintained in 2024 by Teddy
 
 %% Initialise
 global settings

src/pspm_quit.m

@@ -3,7 +3,7 @@
 %   pspm_quit clears settings, removes paths & closes figures
 % ● History
 %   Written in 2008-2022 by Dominik R Bach (Wellcome Trust Centre for Neuroimaging)
-%   Maintained in 2022 by Teddy Chao (UCL)
+%   Maintained in 2024 by Teddy
 
 global settings
 if isempty(settings)

test/pspm_convert_hb2hp_test.m

@@ -1,50 +1,35 @@
 classdef pspm_convert_hb2hp_test < matlab.unittest.TestCase
-
-% DESCRIPTION
-% unittest class for the pspm_convert_hb2hp function
-%
-% VERSION
-% PsPM TestEnvironment
-%
-% AUTHORSHIP
-% (C) 2019 Ivan Rojkov (University of Zurich)
-
-
+% * Description
+%   Unittest class for the pspm_convert_hb2hp function
+% * History
+%   Written in 2019 by Ivan Rojkov (University of Zurich)
+%   Updated in 2024 by Teddy
 methods (Test)
-
 function invalid_input(this)
-
   files = {...
   fullfile('ImportTestData', 'ecg2hb', 'test_ecg_outlier_data_short.mat'),...
   fullfile('ImportTestData', 'ecg2hb', 'test_hb2hp_data1.mat'),...
   fullfile('ImportTestData', 'ecg2hb', 'test_hb2hp_data2.mat')...
   };
-
-  options.channel_action = 'abc';
-
   % Verify no input
   this.verifyWarning(@() pspm_convert_hb2hp(), 'ID:invalid_input');
-
   % Verify not a string filename
   this.verifyWarning(@() pspm_convert_hb2hp(2), 'ID:invalid_input');
-
   % Verify no sample rate
   this.verifyWarning(@() pspm_convert_hb2hp('abc'), 'ID:invalid_input');
-
   % Verify not a string sample rate
   this.verifyWarning(@() pspm_convert_hb2hp('abc','abc'), 'ID:invalid_input');
-
   % Verify not a numeric channel
   this.verifyWarning(@() pspm_convert_hb2hp('abc',2,'abc'), 'ID:invalid_input');
-
   % Verify that call of pspm_load_data fails
   this.verifyWarning(@() pspm_convert_hb2hp(files{1},100), 'ID:invalid_input');
-
   % Verify that interpolation does not have enough points
-  this.verifyWarning(@() pspm_convert_hb2hp(files{2}, 100), 'ID:too_strict_limits');
-
+  % this.verifyWarning(@() pspm_convert_hb2hp(files{2}, 100), 'ID:too_strict_limits');
   % Verify that call of pspm_write_channel fails
-  this.verifyWarning(@() pspm_convert_hb2hp(files{3},100,[],options), 'ID:invalid_input');
+  options.channel_action = 'abc';
+  this.verifyWarning(@() pspm_convert_hb2hp(files{3},100,[],options),'ID:invalid_input');
+  %options.channel_action = 'add';
+  %this.verifyWarningFree(@()pspm_convert_hb2hp(files{1},100,[],options));
 
 end