classdef ECGtask_QRS_detections_post_process < ECGtask
% ECGtask for ECGwrapper (for Matlab)
% ---------------------------------
%
% Description:
%
% Abstract class for defining ECGtask interface
%
% Adding user-defined QRS detectors:
% A QRS detector that has the following interface can be added to the task:
%
% [positions_single_lead, position_multilead] = your_ECG_delineator( ECG_matrix, ECG_header, progress_handle, payload_in);
%
% where the arguments are:
% + ECG_matrix, is a matrix size [ECG_header.nsamp ECG_header.nsig]
% + ECG_header, is a struct with info about the ECG signal, such as:
% .freq, the sampling frequency
% .desc, description about the signals.
% + progress_handle, is a handle to a waitbar object, that can be used
% to track the progress within your function. See the
% documentation about this class in this kit.
% + payload_in, is a user data variable allowed to be sent each call to
% your function. It is sent, via the payload property of this
% class, for example:
%
% this_ECG_wrappers.ECGtaskHandle.payload = your_variable;
% this_ECG_wrappers.ECGtaskHandle.payload = {your_var1 your_var2};
% this_ECG_wrappers.ECGtaskHandle.payload = load(cached_filenames);
%
% In the context of delineation, it is thought to be a user
% corrected, or "gold quality" QRS location, in order to
% improve the wave delineation quality. If "payload_in" is a
% struct, this function will automatically filter and time-shift
% all QRS detection fields started with the string "corrected_".
% For this purpose, QRScorrector task, automatically appends this
% string to eachm anually reviewed QRS location series.
%
% the output of your function must be:
% + positions_single_lead, a cell array size ECG_header.nsig with the
% QRS sample locations found in each lead.
% + position_multilead, a numeric vector with the QRS locations
% calculated using multilead rules.
%
%
% Author: Mariano Llamedo Soria (llamedom at {electron.frba.utn.edu.ar; unizar.es}
% Version: 0.1 beta
% Birthdate : 18/2/2013
% Last update: 18/2/2013
properties(GetAccess = public, Constant)
name = 'QRS_detections_post_process';
target_units = 'ADCu';
doPayload = true;
end
properties( GetAccess = public, SetAccess = private)
% if user = memory;
% memory_constant is the fraction respect to user.MaxPossibleArrayBytes
% which determines the maximum input data size.
memory_constant = 0.3;
started = false;
end
properties( Access = private, Constant)
end
properties( Access = private )
tmp_path_local
end
properties
post_proc_func
progress_handle
payload
tmp_path
CalculatePerformance = false;
end
methods
function obj = ECGtask_QRS_detections_post_process (obj)
end
function Start(obj, ECG_header, ECG_annotations)
obj.started = true;
end
function payload_out = Process(obj, ECG, ECG_start_offset, ECG_sample_start_end_idx, ECG_header, ECG_annotations, ECG_annotations_start_end_idx )
payload_out = [];
if( ~obj.started )
obj.Start(ECG_header);
if( ~obj.started )
cprintf('*[1,0.5,0]', 'Task %s unable to be started for %s.\n', obj.name, ECG_header.recname);
return
end
end
% payload property is used in this task to input an external QRS
% detector, or manually corrected detections.
if( isstruct(obj.payload) )
AnnNames = obj.payload.series_quality.AnnNames(:,1);
aux_struct = obj.payload;
for fn = rowvec(AnnNames)
aux_val = obj.payload.(fn{1}).time - ECG_start_offset + 1;
aux_val = aux_val( aux_val >= ECG_sample_start_end_idx(1) & aux_val < ECG_sample_start_end_idx(2) );
aux_struct.(fn{1}).time = aux_val;
end
else
return
end
for this_func = rowvec(obj.post_proc_func)
try
obj.progress_handle.checkpoint([ 'User defined function: ' this_func{1}])
% this_func_ptr = eval(['@' this_func]);
this_func_ptr = str2func(this_func{1});
this_payload = this_func_ptr( aux_struct, ECG_header, ECG_sample_start_end_idx );
for fn = rowvec(fieldnames(this_payload))
payload_out.(fn{1}) = this_payload.(fn{1});
end
catch aux_ME
disp_string_framed(2, sprintf('User-function "%s" failed in recording %s', this_func{1}, ECG_header.recname ) );
report = getReport(aux_ME);
fprintf(2, 'Error report:\n%s', report);
end
end
obj.progress_handle.checkpoint('Adding quality metrics')
% Add QRS detections quality metrics, Names, etc.
payload_out = calculateSeriesQuality(payload_out, ECG_header, ECG_sample_start_end_idx );
% offset in time
AnnNames = payload_out.series_quality.AnnNames(:,1);
for fn = rowvec(AnnNames)
aux_val = payload_out.(fn{1}).time + ECG_start_offset - 1;
payload_out.(fn{1}).time = aux_val;
end
% calculate performance
if( obj.CalculatePerformance )
AnnNames = payload_out.series_quality.AnnNames(:,1);
cant_lead_name = size(AnnNames,1);
payload_out.series_performance.conf_mat = zeros(2,2,cant_lead_name);
if(isempty(ECG_annotations))
disp_string_framed(2, sprintf('Trusted references not found for %s', ECG_header.recname) );
else
% offset refs, produced anns were already shifted
ECG_annotations.time = ECG_annotations.time + ECG_start_offset - 1;
for kk = 1:cant_lead_name
payload_out.series_performance.conf_mat(:,:,kk) = bxb(ECG_annotations, payload_out.(AnnNames{kk}).time, ECG_header );
end
end
end
obj.progress_handle.checkpoint('Done')
end
function payload = Finish(obj, payload, ECG_header)
if( isfield(payload, 'series_quality') && isfield(payload.series_quality, 'ratios') )
payload.series_quality.ratios = mean(payload.series_quality.ratios, 2);
end
end
function payload = Concatenate(obj, plA, plB)
payload = ConcatenateQRSdetectionPayloads(obj, plA, plB);
end
%% property restriction functions
function set.post_proc_func(obj, x)
if( ischar(x) )
if( exist(x) == 2 )
obj.post_proc_func = cellstr(x);
else
disp_string_framed(2, sprintf('Function "%s" is not reachable in path.', x));
fprintf(1, 'Make sure that exist(%s) == 2\n',x);
end
elseif( iscellstr(x) )
if( any( cellfun( @(a)(exist(a)), x) == 2) )
obj.post_proc_func = x;
else
disp_string_framed(2, sprintf('Function "%s" is not reachable in path.', x));
fprintf(1, 'Make sure that exist(%s) == 2\n',x);
end
else
warning('ECGtask_QRS_detections_post_process:BadArg', 'post_proc_func must be a string.');
end
end
function set.tmp_path_local(obj,x)
if( ischar(x) )
if(exist(x, 'dir'))
obj.tmp_path_local = x;
else
if(mkdir(x))
obj.tmp_path_local = x;
else
warning('ECGtask_QRS_detections_post_process:BadArg', ['Could not create ' x ]);
end
end
else
warning('ECGtask_QRS_detections_post_process:BadArg', 'tmp_path_local must be a string.');
end
end
function set.tmp_path(obj,x)
if( ischar(x) )
if(exist(x, 'dir'))
obj.tmp_path = x;
else
if(mkdir(x))
obj.tmp_path = x;
else
warning('ECGtask_QRS_detections_post_process:BadArg', ['Could not create ' x ]);
end
end
else
warning('ECGtask_QRS_detections_post_process:BadArg', 'tmp_path_local must be a string.');
end
end
end
methods ( Access = private )
end
end