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rvlmautomationcode_DONOTEDIT.m
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%Light Study Data Automation Tool
%Ethan Baker, eab109(at)pitt.edu
%Yates Lab, University of Pittsburgh
%Last Updated: 11/14/14 @ 9:40AM;
%%%%%%%%%%%%%%%%%%%%%%
%IMPORTANT: This software requires the following dependencies: Signal
%Processing Toolbox, risingEdge.m, risingEdge2.m. M files must be loaded
%into the default MATLAB dir. All SPIKE2 files must be exported as .MAT
%files with the following naming scheme: R(1-6).MAT. HR Channel must be
%generated in SPIKE2 before exporting to MATLAB.
%%%%%%%%%%%%%%%%%%%%%%
%Get files
path = uigetdir('Select directory with .mat files'); %GUI select dir w/ matlab files, can have other files in dir
s=what(path); %Gets info about selected dir
matfiles=s.mat; % gets .MAT file names
cd(path);
for a=1:numel(matfiles); %Load .MAT files
load((char(matfiles(a))));
end
%Run Calculations on R1, if it exists.
if exist('R1_Ch3')==1
%Generate light-time matrix
light_time_start = R1_Ch3.start;
light_time_interval = R1_Ch3.interval;
light_time_length = R1_Ch3.length;
light_values = R1_Ch3.values;
light_end_time = light_time_length/(1/light_time_interval);
light_timematrix = (light_time_start:light_time_interval:light_end_time); %Generates an array with time based on start time, end time, recording interval.
light_timematrix = light_timematrix' ; %Transposes light array.
light_time_data = horzcat(light_timematrix,R1_Ch3.values); %Constructs 2 column array (Time|Value)
%Generate Table-Time matrix
table_time_start = R1_Ch2.start;
table_time_interval = R1_Ch2.interval;
table_time_length = R1_Ch2.length;
table_values = R1_Ch2.values;
table_end_time = table_time_length/(1/table_time_interval);
table_timematrix = (table_time_start:table_time_interval:table_end_time);
table_timematrix = table_timematrix' ;
table_time_data = horzcat(table_timematrix,R1_Ch2.values);
%Generate Carotid-Time Matricies
carotid_time_start = R1_Ch1.start;
carotid_time_interval = R1_Ch1.interval;
carotid_time_length = R1_Ch1.length;
carotid_end_time = carotid_time_length/(1/carotid_time_interval);
carotid_timematrix = (carotid_time_start:carotid_time_interval:carotid_end_time);
carotid_timematrix = carotid_timematrix' ;
carotid_time_data = horzcat(carotid_timematrix,R1_Ch1.values);
%Declare HR times
HR_times = R1_Ch4.times; %Renames time
%Find Peaks in Light Waveform
smoothData = sgolayfilt(light_values,7,21);
invSmoothData = -smoothData;
%%%%%%%
threshold = invSmoothData(57)+ 0.0185 ;
data=invSmoothData;
offsetData = [data(2:end); NaN];
lightpeaks = find(data < threshold & offsetData > threshold);
%lightpeaks = risingEdge2(light_timematrix,invSmoothData);
[m,n] = size(lightpeaks); %Determines number of elements in lightpeaks
%The following if statements create the bounds of regions of interest
%depednent on how many light peaks exist.
if m==10
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1), lightpeaks(7,1), lightpeaks(9,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T4 = lightonsets(4,1);
T4 =light_timematrix(T4,1);
T5 = lightonsets(5,1);
T5 = light_timematrix(T5,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
T3_off = T3+2.03;
T4_off = T4+2.03;
T5_off = T5+2.03;
elseif m==8
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1), lightpeaks(7,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T4 = lightonsets(4,1);
T4 =light_timematrix(T4,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
T3_off = T3+2.03;
T4_off = T4+2.03;
elseif m==6
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
T3_off = T3+2.03;
elseif m==4
lightonsets = [lightpeaks(1,1),lightpeaks(3,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
elseif m==2
lightonsets = [lightpeaks(1,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T1_off = T1+2.03;
end
%Find Table Onset
tilt_starts = risingEdge(table_timematrix,table_values); %Uses the risingEdge function to find table tilt onset.
tilt_starts = tilt_starts/(1/table_time_interval); %Converts to time in s
[m,n] = size(tilt_starts); %Finds size of tilt_starts array
%Create regions dependent on the number of tilt onsets in the file
if m==1
tilt_onset_1 =tilt_starts(1,1); %Gets 1st table tilt onset time and stores as tilt_onset_1
elseif m==2
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
elseif m==3
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
tilt_onset_3 = tilt_starts(3,1);
elseif m==4
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
tilt_onset_3 = tilt_starts(3,1);
tilt_onset_4 = tilt_starts(4,1);
elseif m==5
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
tilt_onset_3 = tilt_starts(3,1);
tilt_onset_4 = tilt_starts(4,1);
tilt_onset_5 = tilt_starts(5,1);
end
%Calculate Regions of Interest
%Segment 1 - 5 seconds before Light Onset
seg1_start = T1 - 5;
seg1_end = T1;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T1_off;
seg2a_end = T1_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_1 - 5;
seg2_end = tilt_onset_1;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_1;
seg3_end = tilt_onset_1 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_1 + 5;
seg4_end = tilt_onset_1 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R1_Output1 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R1_1_table = array2table(R1_Output1,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
%Calculate Regions of Interest for second trial, if it exists.
a = exist('T2'); %Check if a second tilt exists in the file
b = exist('tilt_onset_2'); %Check if a onset exists for the second tilt
if a+b==2 %If both exist do the following:
%Segment 1 - 5 seconds before Light Onset
seg1_start = T2 - 5;
seg1_end = T2;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T2_off;
seg2a_end = T2_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_2 - 5;
seg2_end = tilt_onset_2;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_2;
seg3_end = tilt_onset_2 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_2 + 5;
seg4_end = tilt_onset_2 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R1_Output2 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R1_2_table = array2table(R1_Output2,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
%Calculate Regions of Interest for third trial, if it exists.
a = exist('T3'); %Check if 3rd tilt exists
b = exist('tilt_onset_3'); %Check if 3rd onset time exists
if a+b==2 %If both exist, do the calculations:
%Segment 1 - 5 seconds before Light Onset
seg1_start = T3 - 5;
seg1_end = T3;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T3_off;
seg2a_end = T3_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_3 - 5;
seg2_end = tilt_onset_3;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_3;
seg3_end = tilt_onset_3 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_3 + 5;
seg4_end = tilt_onset_3 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R1_Output3 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R1_3_table = array2table(R1_Output3,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
%Calculate Regions of Interest for 4th trial, if it exists.
a = exist('T4'); %Check if 4th tilt exists
b = exist('tilt_onset_4');
if a+b==2 %If tilt exists & onset time exists, do the calculations:
%Segment 1 - 5 seconds before Light Onset
seg1_start = T4 - 5;
seg1_end = T4;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T4_off;
seg2a_end = T4_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_4 - 5;
seg2_end = tilt_onset_4;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_4;
seg3_end = tilt_onset_4 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_4 + 5;
seg4_end = tilt_onset_4 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R1_Output4 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R1_4_table = array2table(R1_Output4,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
%Calculate Regions of Interest for 5th trial, if it exists.
a = exist('T5');
b = exist('tilt_onset_5');
if a+b==2
%Segment 1 - 5 seconds before Light Onset
seg1_start = T5 - 5;
seg1_end = T5;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T5_off;
seg2a_end = T5_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_5 - 5;
seg2_end = tilt_onset_5;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_5;
seg3_end = tilt_onset_5 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_5 + 5;
seg4_end = tilt_onset_5 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R1_Output5 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R1_5_table = array2table(R1_Output5,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
end
%Run Calculations on R2, if it exists.
if exist('R2_Ch3')==1
%Generate light-time matrix
light_time_start = R2_Ch3.start;
light_time_interval = R2_Ch3.interval;
light_time_length = R2_Ch3.length;
light_values = R2_Ch3.values;
light_end_time = light_time_length/(1/light_time_interval);
light_timematrix = (light_time_start:light_time_interval:light_end_time); %Generates an array with time based on start time, end time, recording interval.
light_timematrix = light_timematrix' ; %Transposes light array.
light_time_data = horzcat(light_timematrix,R2_Ch3.values); %Constructs 2 column array (Time|Value)
%Generate Table-Time matrix
table_time_start = R2_Ch2.start;
table_time_interval = R2_Ch2.interval;
table_time_length = R2_Ch2.length;
table_values = R2_Ch2.values;
table_end_time = table_time_length/(1/table_time_interval);
table_timematrix = (table_time_start:table_time_interval:table_end_time);
table_timematrix = table_timematrix' ;
table_time_data = horzcat(table_timematrix,R2_Ch2.values);
%Generate Carotid-Time Matricies
carotid_time_start = R2_Ch2.start;
carotid_time_interval = R2_Ch2.interval;
carotid_time_length = R2_Ch2.length;
carotid_end_time = carotid_time_length/(1/carotid_time_interval);
carotid_timematrix = (carotid_time_start:carotid_time_interval:carotid_end_time);
carotid_timematrix = carotid_timematrix' ;
carotid_time_data = horzcat(carotid_timematrix,R2_Ch1.values);
%Declare HR times
HR_times = R2_Ch4.times; %Renames time
%Find Peaks in Light Waveform
smoothData = sgolayfilt(light_values,7,21);
invSmoothData = -smoothData;
%%%%%%%
threshold = invSmoothData(57)+ 0.0185 ;
data=invSmoothData;
offsetData = [data(2:end); NaN];
lightpeaks = find(data < threshold & offsetData > threshold);
%lightpeaks = risingEdge2(light_timematrix,invSmoothData);
[m,n] = size(lightpeaks);
if m==10
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1), lightpeaks(7,1), lightpeaks(9,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T4 = lightonsets(4,1);
T4 =light_timematrix(T4,1);
T5 = lightonsets(5,1);
T5 = light_timematrix(T5,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
T3_off = T3+2.03;
T4_off = T4+2.03;
T5_off = T5+2.03;
elseif m==8
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1), lightpeaks(7,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T4 = lightonsets(4,1);
T4 =light_timematrix(T4,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
T3_off = T3+2.03;
T4_off = T4+2.03;
elseif m==6
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
T3_off = T3+2.03;
elseif m==4
lightonsets = [lightpeaks(1,1),lightpeaks(3,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T1_off = T1+2.03;
T2_off = T2+2.03;
elseif m==2
lightonsets = [lightpeaks(1,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T1_off = T1+2.03;
end
%Find Table Onset
tilt_starts = risingEdge(table_timematrix,table_values); %Uses the risingEdge function to find table tilt onset.
tilt_starts = tilt_starts/(1/table_time_interval); %Converts to time in s
[m,n] = size(tilt_starts);
if m==1
tilt_onset_1 =tilt_starts(1,1); %Gets 1st table tilt onset time and stores as tilt_onset_1
elseif m==2
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
elseif m==3
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
tilt_onset_3 = tilt_starts(3,1);
elseif m==4
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
tilt_onset_3 = tilt_starts(3,1);
tilt_onset_4 = tilt_starts(4,1);
elseif m==5
tilt_onset_1 =tilt_starts(1,1);
tilt_onset_2 = tilt_starts(2,1);
tilt_onset_3 = tilt_starts(3,1);
tilt_onset_4 = tilt_starts(4,1);
tilt_onset_5 = tilt_starts(5,1);
end
%Calculate Regions of Interest
%Segment 1 - 5 seconds before Light Onset
seg1_start = T1 - 5;
seg1_end = T1;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T1_off;
seg2a_end = T1_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_1 - 5;
seg2_end = tilt_onset_1;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_1;
seg3_end = tilt_onset_1 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_1 + 5;
seg4_end = tilt_onset_1 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R2_Output1 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R2_1_table = array2table(R2_Output1,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
%Calculate Regions of Interest for second trial, if it exists.
a = exist('T2');
b = exist('tilt_onset_2');
if a+b==2
%Segment 1 - 5 seconds before Light Onset
seg1_start = T2 - 5;
seg1_end = T2;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T2_off;
seg2a_end = T2_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_2 - 5;
seg2_end = tilt_onset_2;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_2;
seg3_end = tilt_onset_2 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_2 + 5;
seg4_end = tilt_onset_2 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R2_Output2 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R2_2_table = array2table(R2_Output2,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
%Calculate Regions of Interest for third trial, if it exists.
a = exist('T3');
b = exist('tilt_onset_3');
if a+b==2
%Segment 1 - 5 seconds before Light Onset
seg1_start = T3 - 5;
seg1_end = T3;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T3_off;
seg2a_end = T3_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_3 - 5;
seg2_end = tilt_onset_3;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_3;
seg3_end = tilt_onset_3 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_3 + 5;
seg4_end = tilt_onset_3 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R2_Output3 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R2_3_table = array2table(R2_Output3,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
%Calculate Regions of Interest for 4th trial, if it exists.
a = exist('T4');
b = exist('tilt_onset_4');
if a+b==2
%Segment 1 - 5 seconds before Light Onset
seg1_start = T4 - 5;
seg1_end = T4;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T4_off;
seg2a_end = T4_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_4 - 5;
seg2_end = tilt_onset_4;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_4;
seg3_end = tilt_onset_4 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_4 + 5;
seg4_end = tilt_onset_4 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R2_Output4 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R2_4_table = array2table(R2_Output4,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
%Calculate Regions of Interest for 5th trial, if it exists.
a = exist('T5');
b = exist('tilt_onset_5');
if a+b==2
%Segment 1 - 5 seconds before Light Onset
seg1_start = T5 - 5;
seg1_end = T5;
x = find((carotid_time_data(:,1)>=seg1_start) & (carotid_time_data(:,1)<=seg1_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg1_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg1_start) & (HR_times(:,1)<=seg1_end));
beat_num = numel(z);
HR_interval= seg1_end - seg1_start;
seg1_avgHR = beat_num/HR_interval;
%Segment 2a - 5 Seconds After Light Offset
seg2a_start = T5_off;
seg2a_end = T5_off + 5;
x = find((carotid_time_data(:,1)>=seg2a_start) & (carotid_time_data(:,1)<=seg2a_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2a_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2a_start) & (HR_times(:,1)<=seg2a_end));
beat_num = numel(z);
HR_interval = seg2a_end - seg2a_start;
seg2a_avgHR = beat_num/HR_interval;
%Segment 2 - 5seconds before tilt onset
seg2_start = tilt_onset_5 - 5;
seg2_end = tilt_onset_5;
x = find((carotid_time_data(:,1)>=seg2_start) & (carotid_time_data(:,1)<=seg2_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg2_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg2_start) & (HR_times(:,1)<=seg2_end));
beat_num = numel(z);
HR_interval = seg2_end - seg2_start;
seg2_avgHR = beat_num/HR_interval;
%Segment 3 - 0-5s after tilt onset
seg3_start = tilt_onset_5;
seg3_end = tilt_onset_5 + 5;
x = find((carotid_time_data(:,1)>=seg3_start) & (carotid_time_data(:,1)<=seg3_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg3_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg3_start) & (HR_times(:,1)<=seg3_end));
beat_num = numel(z);
HR_interval = seg3_end - seg3_start;
seg3_avgHR = beat_num/HR_interval;
%Segment 4 - 5-10s after tilt onset
seg4_start = tilt_onset_5 + 5;
seg4_end = tilt_onset_5 + 10;
x = find((carotid_time_data(:,1)>=seg4_start) & (carotid_time_data(:,1)<=seg4_end)); %Returns index values of desired blood flow points
y = carotid_time_data(x,2); %Returns the 2nd column in datatable corresponding to indicies(x)
seg4_mean_flow = mean(y);
z = find((HR_times(:,1)>=seg4_start) & (HR_times(:,1)<=seg4_end));
beat_num = numel(z);
HR_interval = seg4_end - seg4_start;
seg4_avgHR = beat_num/HR_interval;
%Generate Output Matrix
R2_Output5 = [seg1_avgHR,seg2a_avgHR,seg2_avgHR,seg3_avgHR,seg4_avgHR;seg1_mean_flow,seg2a_mean_flow,seg2_mean_flow,seg3_mean_flow,seg4_mean_flow];
R2_5_table = array2table(R2_Output5,'VariableNames',{'Seg1' 'Seg2a' 'Seg2' 'Seg3' 'Seg4'}, 'RowNames',{'HR' 'Flow'})
end
end
%Run Calculations on R3, if it exists.
if exist('R3_Ch3')==1
%Generate light-time matrix
light_time_start = R3_Ch3.start;
light_time_interval = R3_Ch3.interval;
light_time_length = R3_Ch3.length;
light_values = R3_Ch3.values;
light_end_time = light_time_length/(1/light_time_interval);
light_timematrix = (light_time_start:light_time_interval:light_end_time); %Generates an array with time based on start time, end time, recording interval.
light_timematrix = light_timematrix' ; %Transposes light array.
light_time_data = horzcat(light_timematrix,R3_Ch3.values); %Constructs 2 column array (Time|Value)
%Generate Table-Time matrix
table_time_start = R3_Ch2.start;
table_time_interval = R3_Ch2.interval;
table_time_length = R3_Ch2.length;
table_values = R3_Ch2.values;
table_end_time = table_time_length/(1/table_time_interval);
table_timematrix = (table_time_start:table_time_interval:table_end_time);
table_timematrix = table_timematrix' ;
table_time_data = horzcat(table_timematrix,R3_Ch2.values);
%Generate Carotid-Time Matricies
carotid_time_start = R3_Ch1.start;
carotid_time_interval = R3_Ch1.interval;
carotid_time_length = R3_Ch1.length;
carotid_end_time = carotid_time_length/(1/carotid_time_interval);
carotid_timematrix = (carotid_time_start:carotid_time_interval:carotid_end_time);
carotid_timematrix = carotid_timematrix' ;
carotid_time_data = horzcat(carotid_timematrix,R3_Ch1.values);
%Declare HR times
HR_times = R3_Ch4.times; %Renames time
%Find Peaks in Light Waveform
smoothData = sgolayfilt(light_values,7,21);
invSmoothData = -smoothData;
%%%%%%%
threshold = invSmoothData(57)+ 0.0185 ;
data=invSmoothData;
offsetData = [data(2:end); NaN];
lightpeaks = find(data < threshold & offsetData > threshold);
%lightpeaks = risingEdge2(light_timematrix,invSmoothData);
[m,n] = size(lightpeaks);
if m==10
lightonsets = [lightpeaks(1,1),lightpeaks(3,1),lightpeaks(5,1), lightpeaks(7,1), lightpeaks(9,1)];
lightonsets = lightonsets';
T1 = lightonsets(1,1);
T1 = light_timematrix(T1,1);
T2 = lightonsets(2,1);
T2 = light_timematrix(T2,1);
T3 = lightonsets(3,1);
T3 = light_timematrix(T3,1);
T4 = lightonsets(4,1);
T4 =light_timematrix(T4,1);
T5 = lightonsets(5,1);
T5 = light_timematrix(T5,1);
T1_off = T1+2.03;
T2_off = T2+2.03;