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adding MSPTDv2 code (as used for submission on 2024-08-24)
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@peterhcharlton
peterhcharlton committed Aug 23, 2024
1 parent d330da3 commit 3378321
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Showing 8 changed files with 1,035 additions and 42 deletions.
5 changes: 3 additions & 2 deletions source/assess_beat_detectors.m
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,7 @@ function assess_beat_detectors(dataset, options)
assess_ppg_beat_detector_performance(uParams);

%% Calculate stats and create tables
uParams.analysis.redo_analysis = 1;
create_stats_and_tables(uParams);

end
Expand Down Expand Up @@ -399,8 +400,8 @@ function create_stats_and_tables(uParams)
% --- Best strategies with no quality assessment
fprintf('\n - Rankings for strategies with no quality assessment')
rel_strategies = contains(ppg_strategy_perf.stats.strategies, '__none');
score_to_rank = 'mae_ibi'; %'f1_score';
ranking_direction = 'ascend'; %'descend';
score_to_rank = 'f1_score'; % 'mae_ibi'; %
ranking_direction = 'descend'; % 'ascend';
strategy_group_name = 'noQual';
res = create_table_of_top_ranked_strategies(ppg_strategy_perf, rel_strategies, strategy_group_name, score_to_rank, ranking_direction, res);
clear rel_strategies score_to_rank strategy_group_name
Expand Down
131 changes: 100 additions & 31 deletions source/assess_multiple_datasets.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
%% Retrieve results for strategies, and provide latex table of results of selected strategy across all datasets

% strategy for which to output latex table of results
selected_strategy = 'qppgfast__none';
selected_strategy = 'MSPTD__none';
% retrieve results for each strategy
[strategy_res, raw_res] = retrieve_results_for_each_strategy(selected_strategy, up, options);
% remove and rename beat detectors (raw_res)
Expand All @@ -63,7 +63,7 @@
create_comparison_figures(up.datasets, raw_res, res, options, up, curr_strategy_set);

%% Generate results figures
generate_results_figures(res, up);
generate_results_figures(res, options, up);

end

Expand Down Expand Up @@ -113,6 +113,14 @@ function analyse_performance_on_each_dataset(up, options)
res_file = [up.paths.processing_folder, 'ppg_detect_perf.mat'];
load(res_file, 'ppg_strategy_perf'); clear res_file

% check whether the selected strategy exists
if ~sum(strcmp(fieldnames(ppg_strategy_perf.raw), selected_strategy))
temp = fieldnames(ppg_strategy_perf.raw);
new_selected_strategy = temp{1};
fprintf('\n Using %s as selected strategy as the specified %s wasn''t assessed on the %s dataset', new_selected_strategy, selected_strategy, curr_dataset)
selected_strategy = new_selected_strategy;
end

% store total beats and total duration for this dataset
if ~strcmp(curr_dataset, 'mimic_test_n') && ~strcmp(curr_dataset, 'mimic_test_a')
eval(['temp = ppg_strategy_perf.raw.' selected_strategy '.durn_total;']);
Expand Down Expand Up @@ -373,11 +381,11 @@ function report_range_f1_scores(res, all_datasets, all_curr_use_case_datasets, c

end

function generate_results_figures(res, up)
function generate_results_figures(res, options, up)

fprintf('\n\n ~~~ Making performance figures ~~~')
curr_datasets = up.assessment_datasets;
create_perf_box_plots(res, up, curr_datasets);
create_perf_box_plots(res, options, up, curr_datasets);

end

Expand Down Expand Up @@ -622,18 +630,20 @@ function report_best_and_worst_beat_detectors(res, curr_cat, curr_datasets, beat
up.comparison_datasets = {'mimic_perform_truncated_non_af', 'mimic_perform_truncated_af'};
end
% (datasets used to design MSPTDfast v2)
do_msptdfastv2_design = 1;
do_msptdfastv2_design = 0;
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 = 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'};
up.comparison_datasets = {}; %{'mimic_non_af', 'mimic_af'};
do_msptdfastv2_internal_validation = 0;
if do_msptdfastv2_internal_validation
up.assessment_datasets = {'capnobase', 'bidmc', 'mimic_train_all', 'ppg_dalia_all_activities'};
up.comparison_datasets = {};
end
do_msptdfastv2_benchmarking = 1;
if do_msptdfastv2_benchmarking
up.assessment_datasets = {'mimic_test_all', 'wesad_all_activities'};
up.comparison_datasets = {'mimic_B', 'mimic_W', 'mimic_test_a', 'mimic_test_n', 'mimic_non_af', 'mimic_af'};
end

% (all datasets)
Expand All @@ -648,6 +658,9 @@ function report_best_and_worst_beat_detectors(res, curr_cat, curr_datasets, beat
up.settings.comparisons(comparison_no, 1:2) = up.comparison_datasets(comparison_no*2-1:comparison_no*2);
end

% Plot settings
up.do_dataset_specific_ylims = true;

%% Display startup message
display_startup_message;

Expand All @@ -673,8 +686,13 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
ftsize = 22;
all_datasets = fieldnames(raw_res); all_datasets = all_datasets(~strcmp(all_datasets, 'rel_strategies'));

primary_dataset = find_primary_dataset(datasets);
eval(['beat_detector_names = res.' primary_dataset '.noQual.num.strategy;']);
if isempty(options.specified_plotting_order)
primary_dataset = find_primary_dataset(datasets);
eval(['beat_detector_names = res.' primary_dataset '.noQual.num.strategy;']);
else
beat_detector_names = options.specified_plotting_order;
beat_detector_names = correct_beat_detector_names(beat_detector_names);
end

% cycle through each comparison (i.e. pair of datasets)
no_comparisons = size(uParams.settings.comparisons,1);
Expand Down Expand Up @@ -767,6 +785,7 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
else
ylim(ylims);
end

ylabel(ylab_txt, 'FontSize', ftsize)

% adjust whiskers to be 10th and 90th percentiles, inspired by: https://www.mathworks.com/matlabcentral/fileexchange/22526-box-plot-with-whiskers-plotted-at-fixed-percentiles
Expand Down Expand Up @@ -813,6 +832,8 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
leg_labels = {'Black', 'White'};
elseif isequal(uParams.settings.comparisons(comparison_no,:), {'mimic_test_a','mimic_test_n'})
leg_labels = {'Adults', 'Neonates'};
elseif isequal(uParams.settings.comparisons(comparison_no,:), {'mimic_a','mimic_n'})
leg_labels = {'Adults', 'Neonates'};
elseif isequal(uParams.settings.comparisons(comparison_no,:), {'mimic_non_af','mimic_af'})
leg_labels = {'Non-AF', 'AF'};
elseif isequal(uParams.settings.comparisons(comparison_no,:), {'mimic_perform_truncated_non_af', 'mimic_perform_truncated_af'})
Expand All @@ -823,19 +844,20 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
% add significant differences
pos = get(gca, 'Position');
xlims = get(gca, 'XLim');
holm_sidak_alpha = 0.0019;
holm_sidak_alpha = 0.0034;
no_sig = 0;
y_coord_offset = .42; %.28;
for strategy_no = 1 :size(temp_p,2)
if strcmp(vars{var_no}, 'f1_score') && temp_p(comparison_no,strategy_no,var_no) < holm_sidak_alpha
pos_x_coord = -0.01 + pos(1) + 0.975*pos(3)*((beat_detector_xticks(strategy_no)-xlims(1))/(xlims(2)-xlims(1)));
y_coord = .28-0.05*rem(no_sig,2);
y_coord = y_coord_offset-0.05*rem(no_sig,2);
dim = [pos_x_coord-0.05 y_coord .1 .1];
str = 'p<0.002';
str = sprintf('p<%.3f', holm_sidak_alpha);
annotation('textbox',dim,'String',str,'FitBoxToText','on','HorizontalAlignment','center','VerticalAlignment','bottom','FontSize', ftsize-8, 'LineStyle', 'none');
no_sig = no_sig + 1;
elseif temp_p(comparison_no,strategy_no,var_no) < 0.05
pos_x_coord = -0.01 + pos(1) + 0.975*pos(3)*((beat_detector_xticks(strategy_no)-xlims(1))/(xlims(2)-xlims(1)));
y_coord = .28-0.05*rem(no_sig,2);
y_coord = y_coord_offset-0.05*rem(no_sig,2);
dim = [pos_x_coord-0.05 y_coord .1 .1];
str = 'p<0.05';
annotation('textbox',dim,'String',str,'FitBoxToText','on','HorizontalAlignment','center','VerticalAlignment','bottom','FontSize', ftsize-8, 'LineStyle', 'none');
Expand All @@ -856,6 +878,7 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
save_figure(gcf, fig_name, uParams);

close all;
clear leg_labels

end
clear var_no curr_var
Expand Down Expand Up @@ -1108,20 +1131,42 @@ 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',
do_msptdfastv2_design = 1;
options.redo_selected_beat_detectors = options.beat_detectors;
do_msptdfastv2_design = 0;
if do_msptdfastv2_design
options.beat_detectors = {'MSPTDPC1', 'MSPTDPC2', 'MSPTDPC3', 'MSPTDPC4', 'MSPTDPC5', 'MSPTDPC6', 'MSPTDPC7', 'MSPTDPC8', 'MSPTDPC9', 'MSPTDPC10', 'MSPTDPC11', 'MSPTDPC12', 'MSPTDPC14', 'MSPTDPC15', 'MSPTDPC16'};
options.redo_selected_beat_detectors = options.beat_detectors;
options.do_downsample = 0;
end
do_msptdfastv2_internal_validation = 0;
if do_msptdfastv2_internal_validation
options.beat_detectors = {'MSPTD', 'MSPTDfastv2'}; % {'MSPTD', 'MSPTDfastv1', 'MSPTDfastv2', 'MSPTDfastv2b'};
options.redo_selected_beat_detectors = options.beat_detectors;
options.do_downsample = 0;
end
do_msptdfastv2_benchmarking = 1;
if do_msptdfastv2_benchmarking
options.beat_detectors = {'MSPTDfastv2', 'MSPTD', 'MSPTDfastv1', 'AMPD', 'qppgfast', 'ABD', 'MMPDv2', 'WEPD'};
options.redo_selected_beat_detectors = options.beat_detectors;
options.specified_plotting_order = options.beat_detectors;
options.do_downsample = 0;
end

% specify beat detectors to redo
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
options.do_downsample = 1; % downsample PPG signals
options.downsample_freq = 100; % frequency in Hz
if ~sum(strcmp(fieldnames(options), 'do_downsample'))
options.do_downsample = 1; % downsample PPG signals
options.downsample_freq = 100; % frequency in Hz
end

% whether or not to specify the plotting order for beat detector algorithms
if ~sum(strcmp(fieldnames(options), 'specified_plotting_order'))
options.specified_plotting_order = {};
else
options.specified_plotting_order = options.specified_plotting_order(:);
end

close all
end
Expand Down Expand Up @@ -1154,6 +1199,8 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur
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_all_activities'
dataset_file = '/Users/petercharlton/Documents/Data/WESAD/conv_data/wesad_all_activities_data.mat';
case 'wesad_amusement'
dataset_file = '/Users/petercharlton/Documents/Data/WESAD/conv_data/wesad_amusement_data.mat';
case 'wesad_baseline'
Expand Down Expand Up @@ -1214,7 +1261,9 @@ function create_comparison_figures(datasets, raw_res, res, options, uParams, cur

end

function create_perf_box_plots(res, uParams, curr_datasets)
function create_perf_box_plots(res, options, uParams, curr_datasets)

uParams.specified_plotting_order = options.specified_plotting_order;

do_no_qual = 1;
if do_no_qual
Expand Down Expand Up @@ -1446,7 +1495,11 @@ function make_boxplot_figure(res, primary_dataset, curr_datasets, curr_beat_dete

fprintf('\n - Making boxplot figure for: %s', rel_metric);

eval(['beat_detectors = res.' primary_dataset '.noQual.num.strategy;']);
if isempty(uParams.specified_plotting_order)
eval(['beat_detectors = res.' primary_dataset '.noQual.num.strategy;']);
else
beat_detectors = uParams.specified_plotting_order;
end
beat_detectors = curr_beat_detectors;
beat_detector_names = correct_beat_detector_names(beat_detectors);

Expand All @@ -1456,6 +1509,10 @@ function make_boxplot_figure(res, primary_dataset, curr_datasets, curr_beat_dete
[ylims, ylab_txt] = get_ylabel_settings(rel_metric);
ftsize = 12;

if strcmp(rel_metric, 'perc_time')
uParams.do_dataset_specific_ylims = false;
end

for dataset_no = 1 : length(datasets)

curr_dataset = datasets{dataset_no};
Expand Down Expand Up @@ -1488,7 +1545,9 @@ function make_boxplot_figure(res, primary_dataset, curr_datasets, curr_beat_dete
%end
curr_x = rem(temp_dataset_no-1, no_x)+1;
curr_y = no_y-floor((temp_dataset_no-1)/no_x);
if no_y ~= 4
if no_y == 1
subplot('Position', [0.05+(0.95*(curr_x-1)/no_x), 0.08+((curr_y-1)/no_y), 0.85/no_x, 0.8/no_y])
elseif no_y ~= 4
subplot('Position', [0.05+(0.95*(curr_x-1)/no_x), 0.08+((curr_y-1)/no_y), 0.85/no_x, 0.6/no_y])
else
subplot('Position', [0.05+(0.97*(curr_x-1)/no_x), 0.08+(0.96*(curr_y-1)/no_y), 0.87/no_x, 0.6/no_y])
Expand All @@ -1500,11 +1559,17 @@ function make_boxplot_figure(res, primary_dataset, curr_datasets, curr_beat_dete
end
boxplot(data', beat_detector_names, 'Widths',0.8, 'MedianStyle', 'target', 'Symbol', 'r')
set(gca, 'XTickLabelRotation', 90, 'FontSize', ftsize-2)
ylim(ylims)

if ~uParams.do_dataset_specific_ylims
ylim(ylims)
end

if curr_x == 1
ylabel(ylab_txt, 'FontSize', ftsize)
else
set(gca, 'YTickLabel', [])
if ~uParams.do_dataset_specific_ylims
set(gca, 'YTickLabel', [])
end
end
set(gca,'XGrid', 'on', 'YGrid', 'on')
box off
Expand Down Expand Up @@ -1839,8 +1904,8 @@ function make_boxplot_figure_multiple_approaches(res, primary_dataset, curr_data
ylims = [40,100];
ylab_txt = 'F_1 score (%)';
elseif strcmp(rel_metric, 'perc_time')
ylims = [0,0.2];
ylab_txt = 'Percentage time to run (%)';
ylims = [0,0.071];
ylab_txt = 'Execution time (%)';
elseif strcmp(rel_metric, 'ppv')
ylims = [60,100];
ylab_txt = 'Positive predictive value (%)';
Expand Down Expand Up @@ -1876,8 +1941,12 @@ function make_boxplot_figure_multiple_approaches(res, primary_dataset, curr_data
switch curr_dataset
case 'capnobase'
title_txt = 'CapnoBase';
case 'ppg_dalia_all_activities'
title_txt = 'PPG-DaLiA (all activities)';
case 'ppg_dalia_sitting'
title_txt = 'PPG-DaLiA (sitting)';
case 'wesad_all_activities'
title_txt = 'WESAD (all activities)';
case 'wesad_baseline'
title_txt = 'WESAD (baseline)';
case 'wesad_stress'
Expand Down
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