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Insect_Lidar_manual_insect_finder_step3.m
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%% Insect_Lidar_manual_insect_finder_step3 | Martin Tauc | 2017-02-02
function []=Insect_lidar_manual_insect_finder_step3()
%set_plot_defaults
start_file='I:\Data_Test\';
date='2016-06-08';
filename=fullfile(start_file,date,'processed_data');
disp(filename)
load(fullfile(filename,'events','manual_insects.mat'))
fols=dir(filename);
fols=fols(~ismember({fols.name},{'.','..','events'}));
try
load(fullfile(filename,'events\manual_final_insect.mat'));
catch
disp('no mfi yet');
end
try
inz=size(manual_final_insect.very_unlikely,2);
catch
inz=0;
end
try
inx=size(manual_final_insect.somewhat_unlikely,2);
catch
inx=0;
end
try
inc=size(manual_final_insect.somewhat_likely,2);
catch
inc=0;
end
try
inv=size(manual_final_insect.very_likely,2);
catch
inv=0;
end
try
inb=size(manual_final_insect.multiple_insects,2);
catch
inb=0;
end
global CB
global tcb
n_start=input('value of n to start? ');
for n=n_start:size(manual_insects,2)
close all
figone=figure(1);
datacursormode on
%% load data and calculate positive data
data=load(fullfile(filename,fols(manual_insects(n).x).name));
fn=fieldnames(data);
%positive_data=abs(data.(fn{:})(manual_insects(n).y).normalized_data(manual_insects(n).z,:)...
% -max(data.(fn{:})(manual_insects(n).y).normalized_data(manual_insects(n).z,:)));
positive_data = data.(fn{:})(manual_insects(n).y).normalized_data(manual_insects(n).z,:);
%% find exact time of insect incident
dateinfo_dir=[start_file,date];
dateinfo=dir(fullfile(dateinfo_dir,'AMK*'));
dateinfo=dateinfo([dateinfo.isdir]);
for k=1:size(dateinfo,1);run_time(k,:)=datenum(dateinfo(k).name(11:end),'HHMMSS');end
mode_run_time=mode(diff(run_time));
exact_dnum=datenum([date,'-',num2str(str2num(data.(fn{:})(manual_insects(n).y).filename(11:16))+...
str2num(datestr(mode_run_time*(str2num(data.(fn{:})(manual_insects(n).y).filename(18:22))/230),'HHMMSS')))],...
'yyyy-mm-dd-HHMMSS');
exact_time=datestr(exact_dnum,'yyyy-mm-dd HH:MM:SS');
%% plot
subplot(2,2,1)
plot(positive_data)
title(sprintf('Insect at AMK Ranch on %s\n at a distance of %2.1f m',...
exact_time, data.(fn{:})(manual_insects(n).y).range(manual_insects(n).z)))
xlabel('pulse number')
ylabel('normalized detected signal (arb)')
%set(figone,'outerposition',[633 213 656 688])
% multiple_insects=input('are there multiple insects (yes (c)/no (v))? ','s');
lower_bound=input('lower bound of insect event ');
upper_bound=input('upper bound of insect event ');
if lower_bound==0
inb=inb+1;
manual_final_insect.multiple_insects(inb).x=manual_insects(n).x;
manual_final_insect.multiple_insects(inb).y=manual_insects(n).y;
manual_final_insect.multiple_insects(inb).z=manual_insects(n).z;
else
subplot(2,2,1)
tcb.plt=plot(data.(fn{:})(manual_insects(n).y).time,positive_data,'b',...
data.(fn{:})(manual_insects(n).y).time,...
ones(size(data.(fn{:})(manual_insects(n).y).time)).*max(positive_data),'k:');
title(sprintf('Insect at AMK Ranch on %s\n at a distance of %2.1f m',...
exact_time, data.(fn{:})(manual_insects(n).y).range(manual_insects(n).z)))
xlabel('time (s)')
ylabel('normalized detected signal (arb)')
%% do guass
wind=31;
pks=input('number of peaks ');
g=gaussmf(1:length(positive_data),[(upper_bound-lower_bound)/2,mean([upper_bound lower_bound])]);
np=g.*positive_data;
gtmaxv=movmax(np,wind);
gtminv=movmin(np,wind);
sg=unique(sort(gtmaxv));
fsg=sg(end-pks:end);
int=0;
for f=fsg
int=int+1;
loc(int)=find(np==f);
end
pk_f_freq=abs(1/mean(diff(data.(fn{:})(manual_insects(n).y).time(loc))));
%% do fft on positive_data
nop=size(positive_data,2);
delta_t=mean(diff(data.(fn{:})(manual_insects(n).y).time)); %pulse time difference
max_freq=1./(2*delta_t); %max frequency based on avg pulse repetition rate
delta_f=1/data.(fn{:})(manual_insects(n).y).time(end);
fqdata=(-nop/2:nop/2-1).*delta_f;
freq_data=fftshift(fft(positive_data,nop,2),2);
[maxv,maxi]=findpeaks(abs(freq_data(513:end)).^2);
[tminv,mini]=findpeaks(1.01*max(abs(freq_data(513:end)).^2)-abs(freq_data(513:end)).^2);
subplot(2,2,2)
plot(fqdata,(abs(freq_data)).^2,'b',fqdata(512+maxi),maxv,'ro')
xlabel('frequency (Hz)')
ylabel('power (arb)')
title(sprintf('Frequency spectrum using FFT algorithm of\ninsect at AMK Ranch on %s\nat a distance of %2.1f m', exact_time,data.(fn{:})(manual_insects(n).y).range(manual_insects(n).z)))
xlim([0 2200])
ylim([0 max((abs(freq_data(517:end)).^2))+max((abs(freq_data(517:end)).^2))*.05])
%% do fft on gauss_data
sl_coef=.2;
CB.gfreq_data=fftshift(fft(np,nop,2),2);
CB.np=np;
CB.nop=nop;
CB.fqdata=fqdata;
[gmaxv,gmaxi]=findpeaks(abs(CB.gfreq_data(513:end)).^2);
gmovmx=movmax((abs(CB.gfreq_data(513:end))).^2,round(sl_coef*mean(diff(gmaxi(2:end)))));
[umx,igmxnf,igvx]=intersect(gmaxv,gmovmx);
[igmx,indx_igmx]=sort(igmxnf,'ascend');
slmin=.010;
slmax=20;
subplot(2,2,4);
%Triangle Slider
CB.gfax=plot(CB.fqdata,(abs(CB.gfreq_data)).^2,'b',CB.fqdata(512+gmaxi(igmx)),umx(indx_igmx),'m>'); %,CB.fqdata(513:end),gmovmx,'r.'
uicontrol('Style','slider','min',slmin,'Max',slmax,'SliderStep', [.01 .1]./(slmax-slmin),'Value',sl_coef,'Position',[510 10 200 20],'Callback',@SliderCB);
xlabel('frequency (Hz)')
ylabel('power (arb)')
title(sprintf('Windowed - AMK Ranch on %s\nat a distance of %2.1f m', exact_time,data.(fn{:})(manual_insects(n).y).range(manual_insects(n).z)))
xlim([0 2200])
ylim([0 max((abs(CB.gfreq_data(518:end)).^2))+max((abs(CB.gfreq_data(518:end)).^2))*.05])
temp_lf_offset = find(gmaxi<=5);
lf_offset = length(temp_lf_offset)+1;
max_peak=CB.fqdata(512+gmaxi(find(gmaxv==max(gmaxv(lf_offset:end)))));
%% peaks
clear mxval mxtime
wnd_ts_th=.2;
freq_space=1/max_peak;
freq_val=find(data.(fn{:})(manual_insects(n).y).time<=freq_space/2,1,'last');
tcb.freq_val=freq_val;
cur_loc=find(positive_data(1:upper_bound)>=wnd_ts_th*max(positive_data),1,'first');
inu=0;
set(tcb.plt(2),'ydata',ones(size(data.(fn{:})(manual_insects(n).y).time)).*max(positive_data).*wnd_ts_th)
while cur_loc<=upper_bound-freq_val
inu=inu+1;
if cur_loc<=freq_val
mxval(inu)=max(np(cur_loc:cur_loc+freq_val));
else
mxval(inu)=max(np(cur_loc-freq_val:cur_loc+freq_val));
end
cur_loc=cur_loc+freq_val*2+1;
mxtime(inu)=data.(fn{:})(manual_insects(n).y).time(find(np==mxval(inu)));
end
tlmin=.01;
tlmax=1;
tcb.positive_data=positive_data;
tcb.upper_bound=upper_bound;
tcb.lower_bound=lower_bound;
tcb.np=np;
tcb.data=data;
tcb.fn=fn;
tcb.manual_insects=manual_insects;
tcb.n=n;
subplot(2,2,3)
tcb.tax=plot(data.(fn{:})(manual_insects(n).y).time,np,data.(fn{:})(manual_insects(n).y).time,np,'b',...
data.(fn{:})(manual_insects(n).y).time,np,data.(fn{:})(manual_insects(n).y).time,np,'r.',...
mxtime,mxval,'ko');
title(sprintf('Windowed - AMK Ranch on %s\n at a distance of %2.1f m',...
exact_time, data.(fn{:})(manual_insects(n).y).range(manual_insects(n).z)))
xlim([data.(fn{:})(manual_insects(n).y).time(lower_bound)...
data.(fn{:})(manual_insects(n).y).time(upper_bound)])
xlabel('time (s)')
ylabel('normalized detected signal (arb)')
%Circle Slider
uicontrol('Style','slider','min',tlmin,'Max',tlmax,'SliderStep', [.001 .01]./(slmax-slmin),'Value',wnd_ts_th,'Position',[96 8 188 19],'Callback',@SliderTCB);
% set(figone,'outerposition',[1043 515 1696 1026])
peak=input('which peaks should be isolated? ');
pk_freq=1/mean(diff(tcb.mxtime));
mean_pksnz=mean(diff([CB.fqdata(512+CB.gmaxi(CB.igmx(1:peak)))]));
std_pksnz=std(diff([CB.fqdata(512+CB.gmaxi(CB.igmx(1:peak)))]));
mean_peaks=mean(diff([0 CB.fqdata(512+CB.gmaxi(CB.igmx(1:peak)))]));
std_peaks=std(diff([0 CB.fqdata(512+CB.gmaxi(CB.igmx(1:peak)))]));
sprintf('mean nonz frequency peaks: %4.2f Hz\nstd no ze frequency peaks: %4.2f Hz\nmean btwn frequency peaks: %4.2f Hz\nstd betwn frequency peaks: %4.2f Hz\nmaximum frequency peak is: %4.2f Hz\nmean freq some time peaks: %4.2f Hz\nmean freq from time peaks: %4.2f Hz\n%s at a distance of %2.1f m',...
mean_pksnz,std_pksnz,mean_peaks,std_peaks,max_peak,pk_freq,pk_f_freq,exact_time,data.(fn{:})(manual_insects(n).y).range(manual_insects(n).z))
%% rateing
rate=input('rate from not likly to likely (z->x->c->v)','s');
if strcmp(rate,'z')==1
inz=inz+1;
manual_final_insect.very_unlikely(inz).x=manual_insects(n).x;
manual_final_insect.very_unlikely(inz).y=manual_insects(n).y;
manual_final_insect.very_unlikely(inz).z=manual_insects(n).z;
manual_final_insect.very_unlikely(inz).f_d_mean_pks=mean_peaks;
manual_final_insect.very_unlikely(inz).f_d_std_pks=std_peaks;
manual_final_insect.very_unlikely(inz).f_max_pk=max_peak;
manual_final_insect.very_unlikely(inz).t_s_pks=pk_freq;
manual_final_insect.very_unlikely(inz).t_all_pks=pk_f_freq;
elseif strcmp(rate,'x')==1
inx=inx+1;
manual_final_insect.somewhat_unlikely(inx).x=manual_insects(n).x;
manual_final_insect.somewhat_unlikely(inx).y=manual_insects(n).y;
manual_final_insect.somewhat_unlikely(inx).z=manual_insects(n).z;
manual_final_insect.somewhat_unlikely(inx).f_d_mean_pks=mean_peaks;
manual_final_insect.somewhat_unlikely(inx).f_d_std_pks=std_peaks;
manual_final_insect.somewhat_unlikely(inx).f_max_pk=max_peak;
manual_final_insect.somewhat_unlikely(inx).t_s_pks=pk_freq;
manual_final_insect.somewhat_unlikely(inx).t_all_pks=pk_f_freq;
elseif strcmp(rate,'c')==1
inc=inc+1;
manual_final_insect.somewhat_likely(inc).x=manual_insects(n).x;
manual_final_insect.somewhat_likely(inc).y=manual_insects(n).y;
manual_final_insect.somewhat_likely(inc).z=manual_insects(n).z;
manual_final_insect.somewhat_likely(inc).f_d_mean_pks=mean_peaks;
manual_final_insect.somewhat_likely(inc).f_d_std_pks=std_peaks;
manual_final_insect.somewhat_likely(inc).f_max_pk=max_peak;
manual_final_insect.somewhat_likely(inc).t_s_pks=pk_freq;
manual_final_insect.somewhat_likely(inc).t_all_pks=pk_f_freq;
elseif strcmp(rate,'v')==1
inv=inv+1;
manual_final_insect.very_likely(inv).x=manual_insects(n).x;
manual_final_insect.very_likely(inv).y=manual_insects(n).y;
manual_final_insect.very_likely(inv).z=manual_insects(n).z;
manual_final_insect.very_likely(inv).f_d_mean_pks=mean_peaks;
manual_final_insect.very_likely(inv).f_d_std_pks=std_peaks;
manual_final_insect.very_likely(inv).f_max_pk=max_peak;
manual_final_insect.very_likely(inv).t_s_pks=pk_freq;
manual_final_insect.very_likely(inv).t_all_pks=pk_f_freq;
else
inb=inb+1;
manual_final_insect.multiple_insects(inb).x=manual_insects(n).x;
manual_final_insect.multiple_insects(inb).y=manual_insects(n).y;
manual_final_insect.multiple_insects(inb).z=manual_insects(n).z;
end
end
close all
disp(manual_final_insect)
save(fullfile(filename,'events','manual_final_insect.mat'),'manual_final_insect','-v7.3')
disp(n)
end
function []=SliderCB(source,event)
global CB
sl_coef=source.Value;
CB.gfreq_data=fftshift(fft(CB.np,CB.nop,2),2);
[gmaxv,gmaxi]=findpeaks(abs(CB.gfreq_data(513:end)).^2);
rndval=round(sl_coef*mean(diff(gmaxi(2:end))));
gmovmx=movmax((abs(CB.gfreq_data(513:end))).^2,rndval);
[umx,igmxnf,igvx]=intersect(gmaxv,gmovmx);
[igmx,indx_igmx]=sort(igmxnf,'ascend');
set(CB.gfax(2),'ydata',umx(indx_igmx))
set(CB.gfax(2),'xdata',CB.fqdata(512+gmaxi(igmx)))
CB.gmaxv=gmaxv;
CB.gmaxi=gmaxi;
CB.igmx=igmx;
function []=SliderTCB(source,event)
global tcb
wnd_ts_th=source.Value;
cur_loc=find(tcb.positive_data(1:tcb.upper_bound)>=wnd_ts_th*max(tcb.positive_data),1,'first');
inu=0;
while cur_loc<=tcb.upper_bound-tcb.freq_val
if cur_loc<=tcb.freq_val
inu=inu+1;
mxval(inu)=max(tcb.np(cur_loc:cur_loc+tcb.freq_val));
elseif cur_loc==tcb.upper_bound
inu=inu+1;
mxva(inu)=max(tcb.np(cur_loc-tcb.freq_val));
else
inu=inu+1;
mxval(inu)=max(tcb.np(cur_loc-tcb.freq_val:cur_loc+tcb.freq_val));
end
cur_loc=cur_loc+tcb.freq_val*2+1;
if exist('mxval','var')
mxtime(inu)=tcb.data.(tcb.fn{:})(tcb.manual_insects(tcb.n).y).time(find(tcb.np==mxval(inu)));
end
end
try
set(tcb.tax(5),'ydata',mxval)
set(tcb.tax(5),'xdata',mxtime)
set(tcb.plt(2),'ydata',ones(size(tcb.data.(tcb.fn{:})(tcb.manual_insects(tcb.n).y).time)).*max(tcb.positive_data).*wnd_ts_th)
tcb.mxtime=mxtime;
tcb.mxval=mxval;
tcb.wnd_ts_th=wnd_ts_th;
catch
disp('impossible value')
end