code at end of MSPTDfast v2 design (2024-08-02)

peterhcharlton · Aug 2, 2024 · d330da3 · d330da3
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Showing 6 changed files with 881 additions and 4 deletions.
diff --git a/source/align_ppg_ecg_beats.m b/source/align_ppg_ecg_beats.m
@@ -59,7 +59,7 @@
 
 %% calculate the aligned indices of ECG beats
 ecg_beats_a_inds = ecg_beats_inds+lag_ecg_samps;
-ecg_beats_a_inds(ecg_beats_a_inds<0) = []; % some are shifted to before time 0 due to the lag.
+ecg_beats_a_inds(ecg_beats_a_inds<=0) = []; % some are shifted to before time 0 due to the lag.
 
 %% calculate time-shifted ecg exclusion log
 if exist('ecg_exc_log', 'var')

diff --git a/source/assess_multiple_datasets.m b/source/assess_multiple_datasets.m
@@ -621,9 +621,15 @@ function report_best_and_worst_beat_detectors(res, curr_cat, curr_datasets, beat
     up.assessment_datasets = {'mimic_perform_truncated_train_all', 'mimic_perform_truncated_test_all'};
     up.comparison_datasets = {'mimic_perform_truncated_non_af', 'mimic_perform_truncated_af'};
 end
+% (datasets used to design MSPTDfast v2)
+do_msptdfastv2_design = 1;
+if do_msptdfastv2_design
+    up.assessment_datasets = {'capnobase', 'bidmc', 'mimic_train_all', 'ppg_dalia_all_activities'};
+    up.comparison_datasets = {};
+end
 
 % my current datasets
-do_current = 1;
+do_current = 0;
 if do_current
     up.assessment_datasets = {'ppg_dalia_lunch_break'};
     % up.assessment_datasets = {'aurora_sittingarmdown', 'aurora_sittingarmlap', 'aurora_sittingarmup', 'aurora_ambulatory', 'aurora_standingarmup', 'aurora_standingarmdown','aurora_walking', 'aurora_running', 'aurora_supine'};
@@ -1102,10 +1108,15 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
 %options.beat_detectors = {'AMPD', 'MSPTD', 'qppgfast', 'PWD', 'ERMA', 'SPAR', 'ABD', 'HeartPy'};
 options.beat_detectors = {'MSPTD', 'qppgfast'};
 options.beat_detectors = {'SPAR', 'SPAR2', 'MSPTD', 'MSPTDPC', 'PPGPulsesPC', 'qppgfast', 'qppgfastpc', 'qppgfastpcimp', 'qppgfastpcimp2', 'qppgfastpcimp3', 'wepd', 'PDAthree'}; %, 'PDAfour'}; % 'ABDtwo', 
-options.beat_detectors = {'qppgfast', 'MSPTD', 'MSPTDPC1', 'MSPTDPC2', 'MSPTDPC3', 'MSPTDPC4', 'MSPTDPC5', 'MSPTDPC6', 'MSPTDPC7', 'MSPTDPC8', 'MSPTDPC9', 'MSPTDPC10', 'MSPTDPC11', 'MSPTDPC12', 'MSPTDPC13', 'MSPTDPC14', 'MSPTDfastv1'};
+do_msptdfastv2_design = 1;
+if do_msptdfastv2_design
+    options.beat_detectors = {'MSPTDPC1', 'MSPTDPC2', 'MSPTDPC3', 'MSPTDPC4', 'MSPTDPC5', 'MSPTDPC6', 'MSPTDPC7', 'MSPTDPC8', 'MSPTDPC9', 'MSPTDPC10', 'MSPTDPC11', 'MSPTDPC12', 'MSPTDPC14', 'MSPTDPC15', 'MSPTDPC16'};
+end
 
 % specify beat detectors to redo
-options.redo_selected_beat_detectors = {'qppgfast', 'MSPTD', 'MSPTDPC1', 'MSPTDPC2', 'MSPTDPC3', 'MSPTDPC4', 'MSPTDPC5', 'MSPTDPC6', 'MSPTDPC7', 'MSPTDPC8', 'MSPTDPC9', 'MSPTDPC10', 'MSPTDPC11', 'MSPTDPC12', 'MSPTDPC13', 'MSPTDPC14', 'MSPTDfastv1'};
+if do_msptdfastv2_design
+    options.redo_selected_beat_detectors = {'MSPTDPC1', 'MSPTDPC2', 'MSPTDPC3', 'MSPTDPC4', 'MSPTDPC5', 'MSPTDPC6', 'MSPTDPC7', 'MSPTDPC8', 'MSPTDPC9', 'MSPTDPC10', 'MSPTDPC11', 'MSPTDPC12', 'MSPTDPC14', 'MSPTDPC15', 'MSPTDPC16'};
+end
 options.redo_selected_beat_detectors = options.redo_selected_beat_detectors(:);
 
 % Specify the downsampling strategy
@@ -1139,6 +1150,8 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
         dataset_file = '/Users/petercharlton/Documents/Data/ppg_dalia/conv_data/ppg_dalia_table_soccer_data.mat';
     case 'ppg_dalia_cycling'
         dataset_file = '/Users/petercharlton/Documents/Data/ppg_dalia/conv_data/ppg_dalia_cycling_data.mat';
+    case 'ppg_dalia_all_activities'
+        dataset_file = '/Users/petercharlton/Documents/Data/ppg_dalia/conv_data/ppg_dalia_all_activities_data.mat';
     case 'capnobase'
     	dataset_file = '/Users/petercharlton/Documents/Data/capnobase_2021/conv_data/capnobase_data.mat';
 	case 'wesad_amusement'

diff --git a/source/dev/msptdpc15_beat_detector.m b/source/dev/msptdpc15_beat_detector.m
@@ -0,0 +1,10 @@
+function [peaks, onsets] = msptdpc15_beat_detector(sig,fs)
+
+% version: ds to 30 hz
+
+options.do_ds = true;
+options.ds_freq = 40;
+
+[peaks, onsets] = msptdpcref_beat_detector(sig,fs, options);
+
+end
diff --git a/source/dev/msptdpc16_beat_detector.m b/source/dev/msptdpc16_beat_detector.m
@@ -0,0 +1,10 @@
+function [peaks, onsets] = msptdpc16_beat_detector(sig,fs)
+
+% version: ds to 30 hz
+
+options.do_ds = true;
+options.ds_freq = 50;
+
+[peaks, onsets] = msptdpcref_beat_detector(sig,fs, options);
+
+end