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fish_speed.m
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fish_speed.m
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% 2018 01 17 Calculate expansion and shrinking speed of fish
% aggregation
clear
addpath('~/code_matlab_dn/saveSameSize');
addpath(['~/code_git/trex_fish/Triplet_processing_toolbox'])
base_save_path = '~/internal_2tb/trex/figs_results/';
base_data_path = '~/internal_2tb/trex/figs_results/';
% Set up various paths
data_path = 'subset_beamform_cardioid_coherent_run131';
ss = strsplit(data_path,'_');
run_num = str2double(ss{end}(4:end));
[~,script_name,~] = fileparts(mfilename('fullpath'));
save_path = fullfile(base_save_path,sprintf('%s_run%03d',script_name,run_num));
if ~exist(save_path,'dir')
mkdir(save_path);
end
% Ping range
ping_all = 1:2:1000; % use LF waveform
% Set params
cmap = 'jet';
sm_len = 1;
axis_lim = [-5 -1 -5 -1];
color_axis = [180 210];
S.param.ping_all = ping_all;
S.param.cmap = cmap;
S.param.sm_len = sm_len;
S.param.axis_lim = axis_lim;
S.param.color_axis = color_axis;
% Load 1 file to calculate location params
scat_fname = sprintf('%s_ping%04d.mat',data_path,100);
A = load(fullfile(base_data_path,data_path,scat_fname));
angle_all = -90:30:90;
for iA=1:length(angle_all)
% Marks and directions for fish expansion and contraction
wr_ctr = [-2.749, -2.948]; % center of wreck
dl.a = angle_all(iA); % [deg] degree from +x-axis
dl.r_total = 1.6; % [km] range from center of wreck
dl.r_diff_div = 4;
dl.unit_vec = [cos(dl.a/180*pi),sin(dl.a/180*pi)];
dl.end = wr_ctr + dl.r_total*[cos(dl.a/180*pi),sin(dl.a/180*pi)];
dl.r_vec = 0:mean(diff(A.data.range_beam))/dl.r_diff_div:dl.r_total;
dl.xy_vec = repmat(wr_ctr,length(dl.r_vec),1) +...
dl.r_vec'*[cos(dl.a/180*pi),sin(dl.a/180*pi)];
[I,xy_loc,r_proj] = get_xyloc_along_line(A,sm_len,wr_ctr,dl);
A.wr_ctr = wr_ctr;
S.directional_line = dl;
S.index_selected = I;
S.xy_loc_selected = xy_loc;
S.projected_range_from_wreck = r_proj;
% Plot echogram overlaid with specified direction
figure
plot_small_echogram(gca,A,100,color_axis,axis_lim);
hold on
plot([wr_ctr(1) dl.end(1)],[wr_ctr(2) dl.end(2)],'m:','linewidth',2);
colorbar('location','southoutside')
set(gca,'fontsize',12,'xtick',-4.3:1:-1.3,'ytick',-4.5:1:-1.5);
axis([-4.3 -1.3 -4.5 -1.5]);
xlabel('Distance (km)','fontsize',16)
ylabel('Distance (km)','fontsize',16)
set(gca,'layer','top')
save_fname = sprintf('%s_run%03d_angle%04d_echogram',script_name,run_num,dl.a);
epswrite(fullfile(save_path,[save_fname,'.eps']))
saveas(gcf,fullfile(save_path,[save_fname,'.fig']),'fig');
saveSameSize_150(gcf,'file',fullfile(save_path,[save_fname,'.png']),...
'format','png');
for iP=1:length(ping_all)
% Load file and set filename
ping_num = ping_all(iP);
scat_fname = sprintf('%s_ping%04d.mat',data_path,ping_num);
save_fname = sprintf('%s_run%03d_ping%04d',script_name,run_num,ping_num);
disp(['Processing ',scat_fname])
A = load(fullfile(base_data_path,data_path,scat_fname));
% Calculate echo level by 1D interpolation along the specified
% direction. Range from xy_loc to wr_ctr calculated by projection.
echo_level(iP,:) = get_echo_level_along_line(A,sm_len,I,r_proj,dl);
% Get time stamps in mins
if A.data.time_hh_local<15
hh = A.data.time_hh_local+24;
else
hh = A.data.time_hh_local;
end
time_hh(iP) = hh+A.data.time_mm_local/60+A.data.time_ss_local/3600;
end
S.echo_level = echo_level;
S.time_hh = time_hh;
% Save results
save_fname = sprintf('%s_run%03d_angle%04d_div%d_results',...
script_name,run_num,dl.a,dl.r_diff_div);
save(fullfile(save_path,[save_fname,'.mat']),'-struct','S');
% Plotting
medfilt_sz = [3,3; 5,3; 11,3; 15,3; 21,3];
% -- raw echo level --
figure
imagesc(r_proj,time_hh,echo_level);
xlabel('Range from center of wreck (km)');
ylabel('Local time (hour)');
title('Raw echo level');
caxis([180 210])
colorbar
set(gca,'ytick',16:2:32,'yticklabel',num2str([16:2:22,0:2:8]'));
save_fname = sprintf('%s_run%03d_angle%04d_div%d_raw', ...
script_name,run_num,dl.a,dl.r_diff_div);
epswrite(fullfile(save_path,[save_fname,'.eps']))
saveas(gcf,fullfile(save_path,[save_fname,'.fig']),'fig');
saveSameSize_150(gcf,'file',fullfile(save_path,[save_fname,'.png']),...
'format','png');
% -- median filtered echo level --
for iM=1:size(medfilt_sz)
figure
imagesc(r_proj,time_hh,medfilt2(echo_level,medfilt_sz(iM,:)));
xlabel('Range from center of wreck (km)');
ylabel('Local time (hour)');
title(sprintf('Echo level, medfilt [%d,%d]',medfilt_sz(iM,1),medfilt_sz(iM,2)));
caxis([180 210])
colorbar
set(gca,'ytick',16:2:32,'yticklabel',num2str([16:2:22,0:2:8]'));
save_fname = sprintf('%s_run%03d_angle%04d_div%d_medfilt%d-%d',...
script_name,run_num,dl.a,dl.r_diff_div, ...
medfilt_sz(iM,1),medfilt_sz(iM,2));
epswrite(fullfile(save_path,[save_fname,'.eps']))
saveas(gcf,fullfile(save_path,[save_fname,'.fig']),'fig');
saveSameSize_150(gcf,'file',fullfile(save_path,[save_fname,'.png']),...
'format','png');
end
close all
end