Fix ecg editor and batch config issues; update pspm_convert_hb2hp and add tests

Author: 4gwe

doc/Tests_Current_Status.docx

@@ -144,15 +144,15 @@
 limit_upper.strtype = 'r';
 limit_upper.num     = [1 1];
 limit_upper.val     = {2};
-limit_upper.help    = pspm_cfg_help_format('pspm_convert_hb2hp', 'options.upper');
+limit_upper.help    = pspm_cfg_help_format('pspm_convert_hb2hp', 'options.limit_upper');
 
 limit_lower         = cfg_entry;
 limit_lower.name    = 'Lower limit';
 limit_lower.tag     = 'lower';
 limit_lower.strtype = 'r';
 limit_lower.num     = [1 1];
 limit_lower.val     = {.2};
-limit_lower.help    = pspm_cfg_help_format('pspm_convert_hb2hp', 'options.lower');
+limit_lower.help    = pspm_cfg_help_format('pspm_convert_hb2hp', 'options.limit_lower');
 
 limit               = cfg_branch;
 limit.name          = 'Limit';

src/pspm_cfg/pspm_cfg_convert_cardiac.m

@@ -48,7 +48,7 @@
 %% Limits
 lim                 = cfg_branch;
 lim.name            = 'Limit';
-lim.tag             = 'limit';
+lim.tag             = 'limits';
 lim.val             = {ulim, llim};
 lim.help            = pspm_cfg_help_format('pspm_ecg_editor', 'options.limits');
 
@@ -58,7 +58,7 @@
 factor.tag          = 'factor';
 factor.strtype      = 'r';
 factor.num          = [1 1];
-factor.val          = {2};
+factor.val          = {1};
 factor.help         = pspm_cfg_help_format('pspm_ecg_editor', 'options.factor');
 
 %% Faulty detection

src/pspm_cfg/pspm_cfg_ecg_editor.m

@@ -34,7 +34,8 @@
         sr = job.pp_type{i}.hb2hp.sr;
         options = struct();
         options.channel = chan;
-        options.limit = job.pp_type{i}.hb2hp.limit;
+        options.limit_lower = job.pp_type{i}.hb2hp.limit.lower; % same convention as in pspm_options
+        options.limit_upper = job.pp_type{i}.hb2hp.limit.upper;
         options = pspm_update_struct(options, job, 'channel_action');
         [sts, outchannel] = pspm_convert_hb2hp(fn, sr, options);
       case 'ecg2hp'

src/pspm_cfg/pspm_cfg_run_convert_cardiac.m

@@ -1,15 +1,22 @@
 function pspm_cfg_run_ecg_editor(job)
 % Updated on 18-12-2023 by Teddy
+% Updated on 12-04-2026 by Bernhard von Raußendorf
+
 options = struct();
 fn = job.datafile{1};
 ecg_chan = pspm_cfg_selector_channel('run', job.ecg_chan);
 options.channel = pspm_cfg_selector_channel('run', job.hb_chan);
 if isfield(job.artefact_epochs, 'artefact_file')
   options.missing = job.artefact_epochs.artefact_file{1};
 else
-  options.missing = 0;
+  options.missing = [];
 end
-options = pspm_update_struct(options, job.faulty_settings, {'factor',...
-                                                            'limit.upper',...
-                                                            'limit.lower'});
+
+% options = pspm_update_struct(options, job.faulty_settings, {'factor',...
+%                                                             'limit.upper',...
+%                                                             'limit.lower'});
+
+options = pspm_update_struct(options, job.faulty_settings, {'factor'});
+options.limits = pspm_update_struct(options, job.faulty_settings.limits, {'upper','lower'}); 
+
 pspm_ecg_editor(fn, ecg_chan, options);

src/pspm_cfg/pspm_cfg_run_ecg_editor.m

@@ -28,10 +28,10 @@
 %   │                 Specifies upper and lower limit for heart
 %   │                 periods. If the limit is exceeded, the values will
 %   │                 be ignored/removed and interpolated.
-%   ├─────────.upper: [numeric]
+%   ├───.limit_upper: [numeric]
 %   │                 Specifies the upper limit of the
 %   │                 heart periods in seconds. Default is 2.
-%   └─────────.lower: [numeric]
+%   └───.limit_lower: [numeric]
 %                     Specifies the lower limit of the
 %                     heart periods in seconds. Default is 0.2.
 % ● Outputs
@@ -70,14 +70,14 @@
 % get data
 % -------------------------------------------------------------------------
 [nsts, data, dinfos] = pspm_load_channel(fn, options.channel, 'hb');
-if nsts == -1, return; end
+if nsts < 1, return; end
 
 
 % interpolate
 % -------------------------------------------------------------------------
 hb  = data.data;
 ibi = diff(hb);
-idx = find(ibi > options.limit.lower & ibi < options.limit.upper);
+idx = find(ibi > options.limit_lower & ibi < options.limit_upper);
 hp = 1000 * ibi; % in ms
 newt = (1/sr):(1/sr):dinfos.duration;
 try
@@ -103,7 +103,7 @@
 o.msg.prefix = 'Heart beat converted to heart period and';
 try
   [nsts,winfos] = pspm_write_channel(fn, newdata, options.channel_action, o);
-  if nsts == -1, return;
+  if nsts < 1, return;
   end
 catch
   warning('ID:invalid_input', 'call of pspm_write_channel failed');

src/pspm_convert_hb2hp.m

@@ -4,13 +4,33 @@
 % * History
 %   Written in 2019 by Ivan Rojkov (University of Zurich)
 %   Updated in 2024 by Teddy
+%   Updated in 2026 by Bernhard von Raußendorf
+
+properties (Constant)
+    input_filename = fullfile(fileparts(mfilename('fullpath')), 'ImportTestData', 'ecg2hb', 'test_ecg_outlier_data_short_hb.mat');
+    backup_filename = fullfile(fileparts(mfilename('fullpath')),'ImportTestData', 'ecg2hb', 'test_backup.mat');
+end
+
+methods (TestClassSetup)
+ function backup(this)
+    this.assertTrue(isfile(this.input_filename), ...
+        sprintf('Input file not found: %s', this.input_filename));
+
+    [sts, msg] = copyfile(this.input_filename, this.backup_filename);
+    this.assertTrue(sts, msg);
+ end
+end
+
+methods (TestMethodSetup)
+ function reset_input_file(this)
+    [sts, msg] = copyfile(this.backup_filename, this.input_filename);
+    this.assertTrue(sts, msg);
+ end
+end
+
+% Tests
 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')...
-  };
   % Verify no input
   this.verifyWarning(@() pspm_convert_hb2hp(), 'ID:invalid_input');
   % Verify not a string filename
@@ -21,18 +41,74 @@ function invalid_input(this)
   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:nonexistent_file');
-  % Verify that interpolation does not have enough points
-  % this.verifyWarning(@() pspm_convert_hb2hp(files{2}, 100), 'ID:too_strict_limits');
-  % Verify that call of pspm_write_channel fails
-  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));
+
+  % 
+  % % Verify that call of pspm_load_data fails
+  % this.verifyWarning(@() pspm_convert_hb2hp(files{1},100), 'ID:nonexistent_file');
+  % % Verify that interpolation does not have enough points
+  % % this.verifyWarning(@() pspm_convert_hb2hp(files{2}, 100), 'ID:too_strict_limits');
+  % % Verify that call of pspm_write_channel fails
+  % 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
+
+function basic_conversion(this)
+    sr = 1000;
+
+    % this.verifyWarningFree(@() pspm_convert_hb2hp(this.input_filename, sr));
+
+    [sts, outchannel] = pspm_convert_hb2hp(this.input_filename, sr);
+
+    this.verifyEqual(sts, 1);
+    this.verifyTrue(isnumeric(outchannel));
+    this.verifyGreaterThan(outchannel, 0);
+end
+
+function too_strict_limits(this)
+    % fn = fullfile('ImportTestData', 'ecg2hb', 'test_hb2hp_data2.mat');
+    sr = 100;
+    options = struct();
+    options = struct('limit_lower', 10, 'limit_upper', 11);
+
+    this.verifyWarning(@() pspm_convert_hb2hp(this.input_filename, sr, options), 'ID:too_strict_limits');
+
+    [sts, outchannel] = pspm_convert_hb2hp(this.input_filename, sr, options);
+    this.verifyEqual(sts, 1);
+    this.verifyTrue(isnumeric(outchannel));
+    this.verifyGreaterThan(outchannel, 0);
+end
+
+function add_channel_action(this)
+    fn = fullfile('ImportTestData', 'ecg2hb', 'test_ecg_outlier_data_short_hb.mat');
+    sr = 100;
+    options = struct();
+    options.channel_action = 'add';
+
+    this.verifyWarningFree(@() pspm_convert_hb2hp(fn, sr, options));
+
+    [sts, outchannel] = pspm_convert_hb2hp(fn, sr, options);
+
+    this.verifyEqual(sts, 1);
+    this.verifyTrue(isnumeric(outchannel));
+    this.verifyGreaterThan(outchannel, 0);
+end
+
+
+
 
 end
 
+methods (TestClassTeardown)
+ function restore(this)
+    if isfile(this.backup_filename)
+        [sts, msg] = copyfile(this.backup_filename, this.input_filename);
+        this.assertTrue(sts, msg);
+        delete(this.backup_filename);
+    end
+ end
 end
 
 end