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calibrate_thermal.m
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calibrate_thermal.m
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% [cm mm aa stats] = align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/cbt jun 20/thermal/combined/', 20, 1);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/cbt jun 20/temperature_reference_CBT_20_06_2016_Rozi.xlsx', '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/cbt jun 20/thermal/combined/160620_133726-000000-002000-visible.png', 'cbt_2016_06_20_newest.mat');
% [cm mm aa stats]= align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/pfeiler jun 27/thermal/combined/', 10, 1, 0.5, 200);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/pfeiler jun 27/reference_temperature_PFEILER_27_06_2016.xlsx', 800, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/pfeiler jun 27/thermal/thermal_control_160627_173852/160627_173852-000000-000300-visible.png', 'pfeiler_2016_06_27.mat');
% [cm mm aa stats]= align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/painterboy jul 3/thermal/combined/', 2, 1, 0.5, 200);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/painterboy jul 3/PBM 30.06.2016 temperatures.xlsx', -1250, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/painterboy jul 3/thermal/combined/160630_142527-000000-015600-visible.png', 'painterboy_2016_07_03.mat');
% [cm mm aa stats]= align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/almont jul 14/thermal/combined/', 2, 1, 0.5, 200);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/almont jul 14/thermal/Refence Data Sheet almont jul 15.xlsx', 0, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/almont jul 14/thermal/combined/952526-000000-008600-visible.png', 'almont_2016_07_14.mat');
% [cm mm aa stats]= align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/pfeiler july 8/thermal/combined/', 2, 1, 0.5, 200);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/pfeiler july 8/thermal/reference_temperature_PFEILER_08_07_2016.xlsx', 0, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/pfeiler july 8/thermal/combined/104254-000000-000000-visible.png', 'pfeiler_2016_07_08.mat');
% [cm mm aa stats]= align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/road 23 jun/thermal/combined/', 2, 1, 0.5, 200);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/road 23 jun/temperature_reference_ROAD_23_06_2016.xlsx', 1175, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/thermal ecology/thermal data/road 23 jun/thermal/combined/160623_134700-000000-007400-visible.png', 'road_2016_06_23.mat');
% [cm mm aa stats]= align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/combined 1/', 2, 1, 0.5, 200);
% aa_small = aa(:,:,1:2980); % due to high wind & collapse at the end-
% stats_small = stats(1:2980);
% scary frames!
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa_small, stats_small, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/reference_temperature_baldy_28jul.xlsx', 100, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/combined 1/092163-000001-003600-visible.png', 'baldy_partone_2016_07_28.mat');
% [cm mm aa stats]=
% align_thermal('/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/combined 2/', 2, 1, 0.5, 200);`
% take one - with calibration first part of day
% aa_small = aa(:,:,1:2500);
% stats_small = stats(1:2500);
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa_small, stats_small, 263, 343, 1, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/reference_temperature_baldy_28jul.xlsx', 0, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/combined 2/160728_194758-000000-010300-visible.png', 'baldy_parttwo_2016_07_28.mat');
% no ground calibration second time
% [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(aa, stats, 263, 343, 0, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/reference_temperature_baldy_28jul.xlsx', 0, '/Users/benjaminblonder/Documents/rmbl/rmbl 2016/rmbl thermal ecology/thermal data/baldy 28 jul/thermal/combined 2/160728_194758-000000-010300-visible.png', 'baldy_parttwo_2016_07_28.mat');
% assumes that stats (from camera) are in the format of
% [hours, minutes, seconds, temp_black, temp_refl, temp_sky, ...]
function [Tkelvin_aligned_calibrated, finalstats] = calibrate_thermal(image_array, stats, bound_temp_lo, bound_temp_hi, dogroundcalibration, xlsinputname, time_offset, file_visible_lores, outputname)
if dogroundcalibration==1
xls_raw = xlsread(xlsinputname);
xls_time = (xls_raw(:,1)*60 + xls_raw(:,2)) * 60; % convert to seconds
xls_time_elapsed = xls_time - xls_time(1);
xls_temp_black = xls_raw(:,4) + 273.15;
xls_temp_refl = xls_raw(:,5) + 273.15;
end
num_files = size(image_array,3);
% calculate time deltas
time_raw = nan([length(stats), 6]);
time_elapsed = zeros([length(stats), 1]);
for i=1:length(stats)
%try
%thisdate = stats{i}.gps_utc;
%time_raw(i,:) = datevec(thisdate, 'yyyy-mm-ddTHH:MM:SS.000Z');
%end
try
time_raw(i,:) = datevec(stats{i}.Date,'yymmdd-HHMMSS');
end
end
% convert to elapsed time
for i=1:length(stats)
try
time_elapsed(i) = etime(time_raw(i,:),time_raw(1,:));
end
end
time_elapsed
%return;
image_mean = zeros([size(image_array,1) size(image_array,2)]);
for i=1:num_files
image_mean = image_mean + double(image_array(:,:,i));
fprintf('%d\n',i);
end
image_mean = image_mean / num_files;
% fill in other stats
temp_atm = 293*ones([length(stats), 1]);
temp_reflected = 293*ones([length(stats), 1]);
temp_external_optics = 293*ones([length(stats), 1]);
relative_humidity = 0.5*ones([length(stats), 1]);
emissivity = 0.97*ones([length(stats), 1]);
distance_focal = 2*ones([length(stats), 1]);
light_ir = 0*ones([length(stats), 1]);
light_vis = 0*ones([length(stats), 1]);
light_uv = 0*ones([length(stats), 1]);
pressure = NaN([length(stats), 1]);
temp_sens = 293*ones([length(stats), 1]);
latitude = NaN([length(stats), 1]);
longitude = NaN([length(stats), 1]);
for i=1:length(stats)
try
temp_atm(i) = stats{i}.wx_temp_air_c + 273.15; %in C, convert to K
end
try
temp_reflected(i) = temp_refl(i);
end
try
temp_external_optics(i) = stats{i}.TSens;
end
try
relative_humidity(i) = stats{i}.wx_rel_hum_pct / 100;
end
try
distance_focal(i) = stats{i}.FocusDistance;
if (distance_focal(i) > 2)
distance_focal(i) = 2;
end
end
try
light_ir(i) = stats{i}.wx_ir_lux;
end
try
light_vis(i) = stats{i}.wx_vis_lux;
end
try
light_uv(i) = stats{i}.wx_uv_lux;
end
try
pressure(i) = stats{i}.wx_pressure_hpa;
end
try
temp_sens(i) = stats{i}.TSens;
end
try
latitude(i) = stats{i}.gps_latitude;
end
try
longitude(i) = stats{i}.gps_longitude;
end
end
% convert radiometric counts to temperatures using trefl values
%temp_array = repmat(single(0), size(image_array));
temp_array = repmat(uint16(0), size(image_array));
for i=1:length(stats)
fprintf('*');
ithis = image_array(:,:,i);
%ithis(ithis==0) = NaN; % remove any extraneous values values
temp_this = calibrated_temperature_simple(...
double(image_array(:,:,i)), ...
temp_atm(i), ...
temp_reflected(i), ...
temp_external_optics(i), ...
relative_humidity(i), ...
emissivity(i), ...
distance_focal(i) ...
);
% remove further extraneous values
%temp_this(temp_this < bound_temp_lo) = NaN;
%temp_this(temp_this > bound_temp_hi) = NaN;
temp_this(temp_this < bound_temp_lo) = 0;
temp_this(temp_this > bound_temp_hi) = 0;
%temp_array(:,:,i) = temp_this;
temp_array(:,:,i) = temp_this*100;
end
fprintf('\n');
if (dogroundcalibration==0)
temp_black = NaN([length(time_elapsed) 1]);
end
if (dogroundcalibration==1)
% choose region of interest
f1 = figure('Name','Select ROI for black reference');
imshow(rescale_image_quantile(image_mean,0.05,0.95));
bw = roipoly;
pixels_keep = bw>0;
close(f1)
% calculate stats in this region
temperature_stats = zeros([num_files 5]);
for i=1:num_files
%temp_this = temp_array(:,:,i);
temp_this = double(temp_array(:,:,i)) / 100;
pixels_this = temp_this(pixels_keep);
% keep non-NA pixels
%pixels_this = pixels_this(~isnan(pixels_this));
pixels_this = pixels_this(pixels_this>0);
temperature_stats(i,1) = mean(pixels_this);
temperature_stats(i,2) = std(pixels_this);
temperature_stats(i,3) = quantile(pixels_this,0.05);
temperature_stats(i,4) = quantile(pixels_this,0.5);
temperature_stats(i,5) = quantile(pixels_this,0.95);
fprintf('.');
end
fprintf('\n')
regressionfitagain = true;
while (regressionfitagain==true)
inputans = inputdlg({'Start time (s)','Stop time (s)','Delta (s)'},'Select index range', 1, {'0','45000',sprintf('%d', time_offset)});
start_time = str2num(inputans{1});
stop_time = str2num(inputans{2});
time_offset = str2num(inputans{3});
index_start = find(time_elapsed >= (start_time),1,'first');
index_stop = find(time_elapsed < (stop_time),1,'last');
% get values of the xls temperatures at these times
if dogroundcalibration==1
temp_black = interp1(xls_time_elapsed - time_offset, xls_temp_black, time_elapsed,'spline',NaN);
end
% show plots
f2 = figure('Name','Black ref (black) uncalibrated (green) xlstime (blue) recalibrated (red)');
plot(time_elapsed, temp_black,'-k'); hold on;
plot(time_elapsed, temperature_stats(:,4),'-g');
ts = temperature_stats(index_start:index_stop,4);
[b,~,~,~,~] = regress(temp_black(index_start:index_stop), [ones(size(ts)) ts ts.^2 ]);
plot(xls_time_elapsed - time_offset, xls_temp_black,'-b'); hold on;
plot(time_elapsed(index_start:index_stop), b(1) + b(2) * ts + b(3) * ts.^2, '-r');
drawnow;
regressionfitagain = ~strcmp(questdlg('Done?','Fit','Yes','No','Yes'),'Yes');
close(f2);
end
Tkelvin_aligned_calibrated = uint16(temp_array);
for i=1:num_files
temp_this = double(temp_array(:,:,i))/100;
Tkelvin_aligned_calibrated(:,:,i) = uint16(100*( b(1) + b(2) * temp_this + b(3) * temp_this.^2 ) );
fprintf('|');
end
fprintf('\n');
%Tkelvin_aligned_calibrated = b(1) + (b(2)*100)*temp_array + (b(3)*100^2)*temp_array.^2;
%Tkelvin_aligned_calibrated = temp_array;
temp_new = zeros([num_files 1]);
for i=1:num_files
temp_this = double(Tkelvin_aligned_calibrated(:,:,i))/100;
pixels_this = temp_this(pixels_keep);
pixels_this = pixels_this(pixels_this>0);
temp_new(i) = quantile(pixels_this,0.5);
fprintf('/');
end
fprintf('\n');
plot(time_elapsed, temp_new,'-r')
else
Tkelvin_aligned_calibrated = temp_array;
end
% mediantemp = zeros([size(Tkelvin_aligned_calibrated,3) 1]);
% mediantime = zeros([size(Tkelvin_aligned_calibrated,3) 1]);
% for i=1:size(Tkelvin_aligned_calibrated,3)
% pixels_all = double(Tkelvin_aligned_calibrated(:,:,i))/100;
% %pixels_all = pixels_all(~isnan(pixels_all));
% pixels_all = pixels_all(pixels_all>0);
%
% mediantemp(i) = median(pixels_all);
% mediantime(i) = time_elapsed(i);
% fprintf('-');
% end
% fprintf('\n');
%f4 = figure('Name','Image median (magenta)');
%plot(time_elapsed, mediantemp,'-m');
finalstats = table(time_elapsed, temp_black, temp_atm, temp_reflected, temp_external_optics, relative_humidity, emissivity, distance_focal, light_vis, light_ir, light_uv, pressure, temp_sens, latitude, longitude, time_raw);
% do visible alignment
image_visible_lores = imread(file_visible_lores);
points_thermal_lores = [];
points_visible_lores = [];
whichim = floor(size(Tkelvin_aligned_calibrated,3)/2);
image_thermal_representative = double(Tkelvin_aligned_calibrated(:,:,whichim))/100;
image_thermal_representative = imresize(image_thermal_representative, 2);
image_thermal_representative = rescale_image_quantile(image_thermal_representative, 0.01, 0.99);
image_thermal_representative = imsharpen(image_thermal_representative,'Radius',2,'Amount',1.5);
image_thermal_representative = ind2rgb(floor(255*image_thermal_representative),hot(255));
[image_fused_lores, image_visible_lores_registered, points_thermal_lores, points_visible_lores] = image_align(image_thermal_representative, image_visible_lores, points_thermal_lores, points_visible_lores);
dosave = questdlg('Save matrix of output','Do save?','yes','no','yes');
if (strcmp(dosave,'yes'))
if dogroundcalibration==0
b = NaN; % this allows for partial loading
end
save(outputname, 'Tkelvin_aligned_calibrated', 'finalstats','image_visible_lores_registered','b','time_offset', '-v7.3'); % this allows for partial loading
end
end