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remove_large_output_files
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Mostafa Daoud committed Dec 9, 2024
1 parent 4974da8 commit 33d92a8
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Showing 4 changed files with 44 additions and 23 deletions.
17 changes: 13 additions & 4 deletions src/+io/bin_to_csv.m
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,10 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
Sim_qtot_units = repelem({'cm s-1'}, length(depth));
write_output(Sim_qtot_names, Sim_qtot_units, fnames.Sim_qtot_file, n_col.Sim_qtot, ns, true);

% Comment unnecessary large size files
%{
write_output({'Bottom of canopy irradiance in the shaded fraction, and average BOC irradiance'}, {'First 2162 columns: shaded fraction. Last 2162 columns: average BOC irradiance. Unit: Wm-2 um-1'}, ...
fnames.BOC_irradiance_file, n_col.BOC_irradiance, ns, true);
%% Spectrum (added on 19 September 2008)
spectrum_hemis_optical_names = {'hemispherically integrated radiation spectrum'};
spectrum_hemis_optical_units = {'W m-2 um-1'};
Expand All @@ -112,15 +116,17 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
end
write_output({'irradiance'}, {'W m-2 um-1'}, ...
fnames.irradiance_spectra_file, n_col.irradiance_spectra, ns, true);
%}

write_output({'reflectance'}, {'fraction of radiation in observation direction *pi / irradiance'}, ...
fnames.reflectance_file, n_col.reflectance, ns, true);
%% input and parameter values (added June 2012)
% write_output(fnames.pars_and_input_file, true)
% write_output(fnames.pars_and_input_short_file, true)
%% Optional Output
if options.calc_vert_profiles
write_output({'Fraction leaves in the sun, fraction of observed, fraction of observed&visible per layer'}, {'rows: simulations or time steps, columns: layer numbers'}, ...
fnames.gap_file, n_col.gap, ns, true);
% write_output({'Fraction leaves in the sun, fraction of observed, fraction of observed&visible per layer'}, {'rows: simulations or time steps, columns: layer numbers'}, ...
% fnames.gap_file, n_col.gap, ns, true); % comment unnecessary large size files
write_output({'aPAR per leaf layer'}, {'umol m-2 s-1'}, ...
fnames.layer_aPAR_file, n_col.layer_aPAR, ns, true);
write_output({'aPAR by Cab per leaf layer'}, {'umol m-2 s-1'}, ...
Expand All @@ -145,6 +151,7 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
write_output(fluorescence_names, fluorescence_units, fnames.layer_fluorescence_file, n_col.layer_fluorescence, ns, true);
end
end

if options.calc_fluor
write_output({'fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_file, n_col.fluorescence, ns, true);
Expand All @@ -154,6 +161,9 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
write_output({'fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution, for PSII only'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescencePSII_file, n_col.fluorescencePSII, ns, true);
end

% Comment unnecessary large size files
%{
write_output({'hemispherically integrated fluorescence per simulation for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
fnames.fluorescence_hemis_file, n_col.fluorescence_hemis, ns, true);
write_output({'total emitted fluorescence by all leaves for wavelengths of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1'}, ...
Expand All @@ -166,9 +176,8 @@ function bin_to_csv(fnames, n_col, ns, options, SoilLayer, GroundwaterSettings)
fnames.fluorescence_shaded_file, n_col.fluorescence_shaded, ns, true);
write_output({'TOC fluorescence contribution from from leaves and soil after scattering for wavelenghts of 640 to 850 nm, with 1 nm resolution'}, {'W m-2 um-1 sr-1'}, ...
fnames.fluorescence_scattered_file, n_col.fluorescence_scattered, ns, true);
%}
end
write_output({'Bottom of canopy irradiance in the shaded fraction, and average BOC irradiance'}, {'First 2162 columns: shaded fraction. Last 2162 columns: average BOC irradiance. Unit: Wm-2 um-1'}, ...
fnames.BOC_irradiance_file, n_col.BOC_irradiance, ns, true);

fclose('all');

Expand Down
27 changes: 17 additions & 10 deletions src/+io/create_output_files_binary.m
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,7 @@
fnames.radiation_file = fullfile(Output_dir, 'radiation.bin');
fnames.fluorescence_file = fullfile(Output_dir, 'fluorescence.bin');
fnames.wl_file = fullfile(Output_dir, 'wl.bin'); % wavelength
fnames.irradiance_spectra_file = fullfile(Output_dir, 'irradiance_spectra.bin'); % Fluorescence
fnames.spectrum_hemis_optical_file = fullfile(Output_dir, 'spectrum_hemis.bin');
fnames.spectrum_obsdir_optical_file = fullfile(Output_dir, 'spectrum_obsdir.bin');
fnames.reflectance_file = fullfile(Output_dir, 'reflectance.bin'); % reflectance spectrum
fnames.BOC_irradiance_file = fullfile(Output_dir, 'BOC_irradiance.bin'); % reflectance spectrum
fnames.Sim_Theta_file = fullfile(Output_dir, 'Sim_Theta.bin'); % soil moisture
fnames.Sim_Temp_file = fullfile(Output_dir, 'Sim_Temp.bin'); % soil temperature
fnames.waterStressFactor_file = fullfile(Output_dir, 'waterStressFactor.bin');
Expand All @@ -38,10 +34,23 @@
fnames.Sim_qva_file = fullfile(Output_dir, 'qva.bin'); % vapour flux due to dry air pressure gradient
fnames.Sim_qtot_file = fullfile(Output_dir, 'qtot.bin'); % total flux (liquid + vapour)

% Comment unnecessary large size files
%{
fnames.BOC_irradiance_file = fullfile(Output_dir, 'BOC_irradiance.bin'); % reflectance spectrum
fnames.irradiance_spectra_file = fullfile(Output_dir, 'irradiance_spectra.bin'); % Fluorescence
fnames.spectrum_hemis_optical_file = fullfile(Output_dir, 'spectrum_hemis.bin');
fnames.spectrum_obsdir_optical_file = fullfile(Output_dir, 'spectrum_obsdir.bin');
if options.calc_ebal
fnames.spectrum_obsdir_BlackBody_file = fullfile(Output_dir, 'spectrum_obsdir_BlackBody.bin'); % spectrum observation direction
end
if options.calc_planck && options.calc_ebal
fnames.spectrum_obsdir_thermal_file = fullfile(Output_dir, 'spectrum_obsdir_thermal.bin'); % spectrum observation direction
fnames.spectrum_hemis_thermal_file = fullfile(Output_dir, 'spectrum_hemis_thermal.bin'); % spectrum hemispherically integrated
end
%}

% if ~(options.simulation==1)
fnames.pars_and_input_file = fullfile(Output_dir, 'pars_and_input.bin'); % wavelength

Expand All @@ -60,7 +69,7 @@
%
%% Optional Output
if options.calc_vert_profiles
fnames.gap_file = fullfile(Output_dir, 'gap.bin'); % gap
% fnames.gap_file = fullfile(Output_dir, 'gap.bin'); % gap, comment unnecessary large size files
fnames.leaftemp_file = fullfile(Output_dir, 'leaftemp.bin'); % leaftemp
fnames.layer_H_file = fullfile(Output_dir, 'layer_H.bin'); % vertical profile
fnames.layer_LE_file = fullfile(Output_dir, 'layer_lE.bin'); % latent heat
Expand Down Expand Up @@ -89,12 +98,15 @@
fnames.fluorescencePSI_file = fullfile(Output_dir, 'fluorescencePSI.bin'); % Fluorescence
fnames.fluorescencePSII_file = fullfile(Output_dir, 'fluorescencePSII.bin'); % Fluorescence
end
% Comment unnecessary large size files
%{
fnames.fluorescence_hemis_file = fullfile(Output_dir, 'fluorescence_hemis.bin'); % Fluorescence
fnames.fluorescence_emitted_by_all_leaves_file = fullfile(Output_dir, 'fluorescence_emitted_by_all_leaves.bin');
fnames.fluorescence_emitted_by_all_photosystems_file = fullfile(Output_dir, 'fluorescence_emitted_by_all_photosystems.bin');
fnames.fluorescence_sunlit_file = fullfile(Output_dir, 'fluorescence_sunlit.bin'); % Fluorescence
fnames.fluorescence_shaded_file = fullfile(Output_dir, 'fluorescence_shaded.bin'); % Fluorescence
fnames.fluorescence_scattered_file = fullfile(Output_dir, 'fluorescence_scattered.bin'); % Fluorescence
%}
else
delete([Output_dir, 'fluorescence.bin']);
end
Expand All @@ -103,11 +115,6 @@
delete([Output_dir, 'BRDF/*.bin']);
end

if options.calc_planck && options.calc_ebal
fnames.spectrum_obsdir_thermal_file = fullfile(Output_dir, 'spectrum_obsdir_thermal.bin'); % spectrum observation direction
fnames.spectrum_hemis_thermal_file = fullfile(Output_dir, 'spectrum_hemis_thermal.bin'); % spectrum hemispherically integrated
end

% Create empty files for appending
structfun(@(x) fopen(x, 'w'), fnames, 'UniformOutput', false);
fclose("all");
Expand Down
21 changes: 13 additions & 8 deletions src/+io/output_data_binary.m
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,8 @@
n_col.Sim_qtot = length(Sim_qtot_out);
fwrite(f.Sim_qtot_file, Sim_qtot_out, 'double');

% Comment unnecessary large size files
%{
%% Spectrum (added on 19 September 2008)
spectrum_hemis_optical_out = rad.Eout_;
n_col.spectrum_hemis_optical = length(spectrum_hemis_optical_out);
Expand Down Expand Up @@ -115,6 +117,11 @@
n_col.irradiance_spectra = length(irradiance_spectra_out);
fwrite(f.irradiance_spectra_file, irradiance_spectra_out, 'double');
BOC_irradiance_out = [rad.Emin_(canopy.nlayers + 1, :), rad.Emin_(canopy.nlayers + 1, :) + (rad.Esun_ * gap.Ps(canopy.nlayers + 1)')'];
n_col.BOC_irradiance = length(BOC_irradiance_out);
fwrite(f.BOC_irradiance_file, BOC_irradiance_out, 'double');
%}

reflectance = pi * rad.Lo_ ./ (rad.Esun_ + rad.Esky_);
reflectance(spectral.wlS > 3000) = NaN;
reflectance_out = [reflectance'];
Expand All @@ -140,9 +147,9 @@
if options.calc_vert_profiles

% gap
gap_out = [gap.Ps gap.Po gap.Pso];
n_col.gap = numel(gap_out(:));
fwrite(f.gap_file, gap_out, 'double');
% gap_out = [gap.Ps gap.Po gap.Pso];
% n_col.gap = numel(gap_out(:));
% fwrite(f.gap_file, gap_out, 'double'); % comment unnecessary large size files

layer_aPAR_out = [1E6 * profiles.Pn1d' 0];
n_col.layer_aPAR = length(layer_aPAR_out);
Expand Down Expand Up @@ -202,7 +209,8 @@
n_col.fluorescencePSII = length(fluorescencePSII_out);
fwrite(f.fluorescencePSII_file, fluorescencePSII_out, 'double');
end

% Comment unnecessary large size files
%{
fluorescence_hemis_out = [rad.Fhem_];
n_col.fluorescence_hemis = length(fluorescence_hemis_out);
fwrite(f.fluorescence_hemis_file, fluorescence_hemis_out, 'double');
Expand All @@ -226,12 +234,9 @@
fluorescence_scattered_out = [sum(rad.LoF_scattered, 2) + sum(rad.LoF_soil, 2)];
n_col.fluorescence_scattered = length(fluorescence_scattered_out);
fwrite(f.fluorescence_scattered_file, fluorescence_scattered_out, 'double');

%}
end
end
BOC_irradiance_out = [rad.Emin_(canopy.nlayers + 1, :), rad.Emin_(canopy.nlayers + 1, :) + (rad.Esun_ * gap.Ps(canopy.nlayers + 1)')'];
n_col.BOC_irradiance = length(BOC_irradiance_out);
fwrite(f.BOC_irradiance_file, BOC_irradiance_out, 'double');

%%
if options.calc_directional && options.calc_ebal
Expand Down
2 changes: 1 addition & 1 deletion src/STEMMUS_SCOPE.m
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@

% set CFG to a path if it is not defined
if exist('CFG', 'var') == 0
CFG = '../config_file_crib.txt';
% CFG = '../config_file_crib.txt';
end

% set runMode to "full" if it is not defined
Expand Down

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