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makecookie.m
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function [] = makecookie(POPT)
% makecookie
%
% ***********************************************************************
% *** makecookie [MAKE COOKIE CONFIG] ***********************************
% ***********************************************************************
%
% makecookie(POPT)
% takes 1 argument:
% POPT [STRING] (e.g., 'EXAMPLE_BLANK')
% --> the string for the configuration parameter file
% --> if an empty (i.e., '') value is passed to this parameter
% then the default parameter set is used (makecookie_settings_BLANK)
%
% NOTE: grid/matrix orientations are :: [LAT,LON] (rows x columns)
% (i.e., the orientation as you would view the raw data)
%
% NOTE: for plotting grids (plot_2dgridded)
% arrays need to be flipped up-down
% (to un-do the visually-correct orientation used as standard)
%
% ***********************************************************************
% *** HISTORY ***********************************************************
% ***********************************************************************
%
% 24/10/11: forked from muffingen
% *** v0.9.99 *************************************************
%
% ***********************************************************************
%%
% *********************************************************************** %
% *** INITIALIZE MUFFINGEN ********************************************** %
% *********************************************************************** %
%
% *** initialize cookiegen ********************************************** %
%
disp([' ']);
disp(['>>> INITIALIZING ...']);
% set function name
str_function = 'makecookie';
% set version!
str_cookiegen_ver = 'v0.9.99';
% set date
str_date = [datestr(date,11), datestr(date,5), datestr(date,7)];
% close existing plot windows
close all;
% end any active journaling
ans = get(0,'Diary');
if strcmp(ans,'on'), diary off; end
%
% *** initialize primary paths ****************************************** %
%
% add library path to cookiegen functions
% NOTE: find where cookie lives ...
% remove its name (+ '.m' extension) from the returned path ...
% add relative source path to it
tmp_path = which(str_function);
tmp_path = tmp_path(1:end-length(str_function)-3);
addpath([tmp_path '/' 'source']);
addpath([tmp_path '/' 'DATA']);
addpath([tmp_path '/' 'CONFIGS']);
%
% *** load cookiegen configuration ************************************** %
%
% load configurqation options file
if isempty(POPT)
% WARNING
disp([' ** WARNING: No config file given -- using cookiegen_config_BLANKGRID.']);
disp([' ']);
POPT='cookiegen_config_BLANKGRID';
eval([CONFIGS '/' POPT]);
elseif exist([POPT '.m'],'file')
eval(POPT);
else
% ERROR
disp([' ** ERROR: Cannot find config file: ' POPT '.m']);
disp([' ']);
return;
end
%
% *** cookiegen additional user settings ******************************** %
%
% NOTE: mostly these are parameter previously in the config file
%
% [0-99] # of ocean levels that are 'extra'
if ~exist('par_add_Dk','var'), par_add_Dk=0; end
% surface layer reference thickness (m)
if ~exist('par_sur_D','var'), par_sur_D = 0.0; end
% [0.0-1.0] land fractional area threshold
if ~exist('par_A_frac_threshold','var'), par_A_frac_threshold=0.5; end
% mask mask!
if ~exist('par_mask_name','var'), par_mask_name = ''; end
% [false/true] filter land-sea mask?
if ~exist('opt_filtermask','var'), opt_filtermask=true; end
% [false/true] filter topography?
if ~exist('opt_filtertopo','var'), opt_filtertopo=true; end
% [0-9999] minimum lake size (# cells)
if ~exist('par_min_oceann','var'), par_min_oceann=20; end
% [false/true] edit borders?
if ~exist('opt_user_borders','var'), opt_user_borders=false; end
%
% [0/1/2/3] zonal windstress generation option
% #0 == automatically determine best choice for each hemispheres
% #1 == land world (modern NH / paleo Eocene (both hemispheres))
% #2 == water world (hi lat ocean gateway in both hemispheres))
% #3 == grey world (mean of land-blocked and hi lat ocean gateway)
if ~exist('par_tauopt','var'), par_tauopt=3; end
% [false/true] use random runoff scheme
if ~exist('opt_makerndrunoff','var'), opt_makerndrunoff=false; end
%
% [false/true] create 2x res sediment grid
if ~exist('opt_makehighresseds','var'), opt_makehighresseds=false; end
% minimm (random, option 2) sediment depth
if ~exist('par_sed_Dmin','var'), par_sed_Dmin=1000.0; end
% maximum (random, option 2) sediment depth
if ~exist('par_sed_Dmax','var'), par_sed_Dmax=6000.0; end
%
% [false/true] ask for output directory?
if ~exist('opt_outputdir','var'), opt_outputdir=false; end
% [false/true] debug output?
if ~exist('opt_debug','var'), opt_debug=false; end
% ['STRING'] templarte base-config name (optional)
if ~exist('par_cfgid','var'), par_cfgid=''; end
%
% *** cookiegen derived user settings *********************************** %
%
par_min_Dk = par_max_k - par_max_k_shallow + 1;
%
% *** check / filter options ******************************************** %
%
% age parameter
if ~exist('par_age','var')
par_age = 0.0;
par_age_emty = true;
else
par_age_emty = false;
end
% process GCM name string
if strcmp(par_gcm,'hadcm3l'), par_gcm = 'hadcm3l'; end
if strcmp(par_gcm,'HadCM3L'), par_gcm = 'hadcm3l'; end
if strcmp(par_gcm,'HADCM3L'), par_gcm = 'hadcm3l'; end
if strcmp(par_gcm,'hadcm3'), par_gcm = 'hadcm3'; end
if strcmp(par_gcm,'HadCM3'), par_gcm = 'hadcm3'; end
if strcmp(par_gcm,'HADCM3'), par_gcm = 'hadcm3'; end
if strcmp(par_gcm,'um'), par_gcm = 'hadcm3'; end
if strcmp(par_gcm,'UM'), par_gcm = 'hadcm3'; end
if strcmp(par_gcm,'FOAM'), par_gcm = 'foam'; end
if strcmp(par_gcm,'CESM'), par_gcm = 'cesm'; end
if strcmp(par_gcm,'ROCKEE'), par_gcm = 'rockee'; end
if strcmp(par_gcm,'K1'), par_gcm = 'k1'; end
if strcmp(par_gcm,'.k1'), par_gcm = 'k1'; end
if strcmp(par_gcm,'.K1'), par_gcm = 'k1'; end
if strcmp(par_gcm,'K2'), par_gcm = 'k2'; end
if strcmp(par_gcm,'MASK'), par_gcm = 'mask'; end
if strcmp(par_gcm,'dat'), par_gcm = 'mask'; end
if strcmp(par_gcm,'.dat'), par_gcm = 'mask'; end
if strcmp(par_gcm,'txt'), par_gcm = 'mask'; end
if strcmp(par_gcm,'.txt'), par_gcm = 'mask'; end
if strcmp(par_gcm,'.mat'), par_gcm = 'mat'; end
if strcmp(par_gcm,'.MAT'), par_gcm = 'mat'; end
if strcmp(par_gcm,''), par_gcm = 'blank'; end
if strcmp(par_gcm,'BLANK'), par_gcm = 'blank'; end
if strcmp(par_gcm,'none'), par_gcm = 'blank'; end
if strcmp(par_gcm,'NONE'), par_gcm = 'blank'; end
%
% rename variables
% NOTE: for some earlier code consistency ... now redundant ...
imax = par_max_i;
jmax = par_max_j;
kmax = par_max_k;
str_nameout = par_wor_name;
% initialize optional netCDF filenames
if ~exist('par_nc_topo_name','var'), par_nc_topo_name = ''; end
if ~exist('par_nc_mask_name','var'), par_nc_mask_name = ''; end
if ~exist('par_nc_axes_name','var'), par_nc_axes_name = ''; end
if ~exist('par_nc_atmos_name','var'), par_nc_atmos_name = ''; end
if ~exist('par_nc_ocean_name','var'), par_nc_ocean_name = ''; end
if ~exist('par_nc_coupl_name','var'), par_nc_coupl_name = ''; end
if ~exist('par_nc_biome_name','var'), par_nc_biome_name = ''; end
if ~exist('par_nc_orog_name','var'), par_nc_orog_name = ''; end
% -> set default variable names
% NOTE: it is not obvious where originally why 'hadcm3','hadcm3l'
% options required: par_expid(1:5)
% (but I have removed it now to enable 6-character UM codes)
switch par_gcm
case {'hadcm3','hadcm3l'}
if isempty(par_nc_topo_name), par_nc_topo_name = [par_expid '.qrparm.omask']; end
if isempty(par_nc_mask_name), par_nc_mask_name = [par_expid '.qrparm.mask']; end
if isempty(par_nc_axes_name), par_nc_axes_name = [par_expid 'a.pdclann']; end
if isempty(par_nc_atmos_name), par_nc_atmos_name = [par_expid '_sed']; end
if isempty(par_nc_ocean_name), par_nc_ocean_name = [par_expid '.qrparm.mask']; end
if isempty(par_nc_coupl_name), par_nc_coupl_name = [par_expid 'a.pdclann']; end
if isempty(par_nc_biome_name), par_nc_biome_name = [par_expid '_inputdata']; end
if isempty(par_nc_orog_name), par_nc_orog_name = [par_expid '.qrparm.orog']; end
case ('foam')
if isempty(par_nc_topo_name), par_nc_topo_name = 'topo'; end
if isempty(par_nc_mask_name), par_nc_mask_name = par_nc_topo_name; end
if isempty(par_nc_axes_name), par_nc_axes_name = par_nc_topo_name; end
if isempty(par_nc_atmos_name), par_nc_atmos_name = 'atmos'; end
if isempty(par_nc_ocean_name), par_nc_ocean_name = ''; end
if isempty(par_nc_coupl_name), par_nc_coupl_name = 'coupl'; end
case {'cesm'}
if isempty(par_nc_topo_name), par_nc_topo_name = 'climo'; end
if isempty(par_nc_mask_name), par_nc_mask_name = par_nc_topo_name; end
if isempty(par_nc_axes_name), par_nc_axes_name = par_nc_topo_name; end
if isempty(par_nc_atmos_name), par_nc_atmos_name = par_nc_topo_name; end
if isempty(par_nc_ocean_name), par_nc_ocean_name = par_nc_topo_name; end
if isempty(par_nc_coupl_name), par_nc_coupl_name = par_nc_topo_name; end
case ('rockee')
if isempty(par_nc_topo_name), par_nc_topo_name = ''; end
if isempty(par_nc_mask_name), par_nc_mask_name = par_nc_topo_name; end
if isempty(par_nc_atmos_name), par_nc_atmos_name = ''; end
if isempty(par_nc_ocean_name), par_nc_ocean_name = ''; end
if isempty(par_nc_axes_name), par_nc_axes_name = par_nc_ocean_name; end
if isempty(par_nc_coupl_name), par_nc_coupl_name = ''; end
end
% set default annual wind averaging to not based on monthly winds
switch par_gcm
case {'hadcm3'}
if ~exist('par_wspeed_avstr','var'), par_wspeed_avstr = 'uvaa'; end
case {'hadcm3l'}
if ~exist('par_wspeed_avstr','var'), par_wspeed_avstr = 'uvaa'; end
case ('foam')
if ~exist('par_wspeed_avstr','var'), par_wspeed_avstr = 'uvaa'; end
case {'cesm'}
if ~exist('par_wspeed_avstr','var'), par_wspeed_avstr = 'wsma'; end
case {'rockee'}
if ~exist('par_wspeed_avstr','var'), par_wspeed_avstr = 'wsaa'; end
otherwise
if ~exist('par_wspeed_avstr','var'), par_wspeed_avstr = ''; end
end
% plot format option
switch par_plotformat
case {'pdf','png','jpg','jpeg','gif','tif','tiff'}
% valid options -- leave alone
otherwise
par_plotformat = '';
end
%
% *** initialize I/O **************************************************** %
%
% set full file name string
if ~isempty(par_gcm)
str_file = [str_function '.' par_gcm '.' str_nameout];
else
str_file = [str_function '.' str_nameout];
end
% set/create output directory
if opt_outputdir
str_dirout = uigetdir(par_pathout);
else
if isempty(par_pathout)
str_dirout = [pwd '/' par_wor_name];
else
if ~(exist(par_pathout,'dir') == 7), mkdir(par_pathout); end
str_dirout = [pwd '/' par_pathout '/' par_wor_name];
end
if ~(exist(str_dirout,'dir') == 7), mkdir(str_dirout); end
end
%
% *** create strings object ********************************************* %
%
str = struct('gcm', {}, 'exp', {}, 'path', {}, 'dir', {}, 'nc', {});
str = setfield(str, {1}, 'gcm', par_gcm);
str = setfield(str, {1}, 'exp', par_expid);
str = setfield(str, {2}, 'exp', str_nameout);
str = setfield(str, {1}, 'path', par_pathin);
str = setfield(str, {2}, 'path', par_pathout);
str = setfield(str, {1}, 'dir', '');
str = setfield(str, {2}, 'dir', str_dirout);
str = setfield(str, {1}, 'nc', par_nc_axes_name);
str = setfield(str, {2}, 'nc', par_nc_topo_name);
str = setfield(str, {3}, 'nc', par_nc_atmos_name);
str = setfield(str, {4}, 'nc', par_nc_mask_name);
str = setfield(str, {5}, 'nc', par_nc_coupl_name);
str = setfield(str, {6}, 'nc', par_nc_ocean_name);
str = setfield(str, {7}, 'nc', par_nc_biome_name);
str = setfield(str, {8}, 'nc', par_nc_orog_name);
str = setfield(str, {1}, 'wspd', par_wspeed_avstr);
str = setfield(str, {1}, 'mask', par_mask_name);
%
% *** initialize reporting ********************************************** %
%
% create copy of .m file options
% NOTE: find where the config file lives ...
% remove its name (+ '.m' extension) from the returned path ...
% add relative source path to it
tmp_path = which([POPT '.m']);
tmp_path = tmp_path(1:end-length(POPT)-3);
copyfile([tmp_path '/' POPT '.m'],[str(2).dir '/' POPT '_' str_date '.m'])
% start logging
% NOTE: delete any existing (current date) log file in the directory first
str_log = [str(2).dir '/' 'log.' str_function '.' str_date '.txt'];
if (exist(str_log,'file') == 2), delete(str_log); end
diary(str_log)
% display warm and comforting welcoming message
disp([' ']);
disp(['------------------------------------------------------------']);
disp([' Hello! Welcome to cookiegen ',str_cookiegen_ver]);
disp([' We are going to make a GREAT model configuration!']);
disp(['------------------------------------------------------------']);
disp([' ']);
% initialize cookiegen step number
n_step = 0;
%
% *********************************************************************** %
% *********************************************************************** %
% *** GET SH*T DONE ***************************************************** %
% *********************************************************************** %
%
% %%% SUMMARY OF STEP SEQUENCE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% NOTE: not all of these steps are carried out, depending on the options
% (initialize)
% CONFIRM OPTIONS
% CREATING GENIE GRID
% READ AXES INFORMATION
% LOAD TOPO & MASK DATA
% RE-GRID MASK
% FILTER MASK
% ADJUST MASK -- USER!
% RE-GRID TOPO
% RE-GRID VERTICALLY
% ADJUST TOPO -- AUTOMATIC BATHYMETRY FILTERING
% ADJUST TOPO -- USER!
% CALCULATE RUNOFF & COMPLETE k1 FILE
% IDENTIFY ISLANDS
% UPDATE ISLANDS AND ISLAND PATHS
% GENERATE ISLAND PATHS
% GENERATE PSI ISLANDS
% GENERATE SEDIMENT GRID
% RE-GRID WIND SPEED/STRESS DATA
% LOAD ALBEDO DATA
% RE-GRID & PROCESS ALBEDO
% LOAD OROGRAPHY AND ICEMASK
% RE-GRID & PROCESS OROGRAPHY AND ICEMASK
% GENERATE CONFIG FILE PARAMETER LINES
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% *** CONFIRM OPTIONS *************************************************** %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. CHECKING PRIMARY OPTIONS ...']);
% check world name
if (length(par_wor_name) ~= 8)
disp([' * ERROR: World name (par_wor_name) must be 8 characters long.']);
disp(['--------------------------------------------------------']);
disp([' ']);
diary off;
return;
end
% check GCM options
switch str(1).gcm
case {'hadcm3','hadcm3l','foam','cesm','rockee'}
disp([' * GCM == ' str(1).gcm ' (OK)']);
case {'mat'}
disp([' * A high resolution topography (only) file: ' str(1).exp]);
case {'k1','mask','k2'}
disp([' * GENIE grid will be loaded directly from k1, mask, or k2 text file: ' str(1).exp]);
case {'blank'}
disp([' * A blank template grid will be generated: ' str(1).exp]);
otherwise
disp([' * ERROR: Unknown GCM name or input format. Maybe it is LOSCAR? Good luck to you! (Bye bye)']);
disp(['--------------------------------------------------------']);
disp([' ']);
diary off;
return;
end
% check compatibility of GCM with cookiegen settings
switch str(1).gcm
case {'cesm','rockee'}
opt_makeents=false;
disp([' * ERROR: ' str(1).gcm ' input is not (yet) supported to generate ENTS fields :(']);
disp([' ----> set opt_makeents=.FALSE. and continue cookiegen']);
disp(['--------------------------------------------------------']);
otherwise
%
end
% adjust options
switch str(1).gcm
case {'hadcm3','hadcm3l','foam'}
%
case {'cesm','rockee'}
%
case {'mat'}
opt_makezonalwind=true;
opt_makezonalalbedo=true;
case {'k1','mask','k2'}
opt_filtermask=false;
opt_makezonalwind=true;
opt_makezonalalbedo=true;
case {'blank'}
opt_makezonalwind=true;
opt_makezonalalbedo=true;
otherwise
%
end
%
% *** SET UP OUTPUT GRID ************************************************ %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. CREATING GENIE GRID ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
% create GENIE grid
[go_lonm,go_lone,go_latm,go_late,go_dm,go_de] = make_genie_grid(imax,jmax,kmax,par_max_D,par_lon_off,opt_equalarea,par_add_Dk);
disp([' - GENIE grid generated.']);
%
% *** LOAD GRID (AXES) DATA ********************************************* %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. READING AXES INFORMATION ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
switch str(1).gcm
case {'hadcm3','hadcm3l','foam','cesm','rockee'}
% read axes
if strcmp(str(1).gcm,'hadcm3')
% NOTE: axes need to be re-generated later (for winds etc.)
[gi_loncm,gi_lonce,gi_latcm,gi_latce] = fun_read_axes_hadcm3(str);
elseif strcmp(str(1).gcm,'hadcm3l')
[gi_loncm,gi_lonce,gi_latcm,gi_latce,gi_lonpm,gi_lonpe,gi_latpm,gi_latpe,gi_lonam,gi_lonae,gi_latam,gi_latae] = fun_read_axes_hadcm3x(str);
elseif strcmp(str(1).gcm,'foam')
[gi_loncm,gi_lonce,gi_latcm,gi_latce,gi_lonpm,gi_lonpe,gi_latpm,gi_latpe,gi_lonam,gi_lonae,gi_latam,gi_latae] = fun_read_axes_foam(str);
elseif strcmp(str(1).gcm,'cesm')
[gi_loncm,gi_lonce,gi_latcm,gi_latce,gi_lonam,gi_lonae,gi_latam,gi_latae] = fun_read_axes_cesm(str);
elseif strcmp(str(1).gcm,'rockee')
[gi_loncm,gi_lonce,gi_latcm,gi_latce,gi_lonam,gi_lonae,gi_latam,gi_latae] = fun_read_axes_rockee(str);
else
disp([' * ERROR: Unknown GCm name.']);
disp([' ']);
diary off;
return;
end
disp([' - Axis info read.']);
case {'mat'}
% NOTE: assume equal Dlon, Dlat grid (non equal area) and 1 degree
% also that the input grid starts at -180E
% >>> EDIT ME >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
gi_lonce = [-180.0:1.0:180.0];
gi_latce = [-90.0:1.0:90.0];
% <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
otherwise
% DO NOTHING
disp([' (Nothing to load.)']);
end
%
% *** LOAD TOPO & MASK DATA ********************************************* %
%
% NOTE: mask is defined with '1' for ocean
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. READING MASK & TOPO GRIDS ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
switch str(1).gcm
case {'hadcm3','hadcm3l','foam','cesm','rockee'}
% read topo
if (strcmp(str(1).gcm,'hadcm3') || strcmp(str(1).gcm,'hadcm3l'))
[gi_mask] = fun_read_omask_hadcm3x(str);
[gi_topo] = fun_read_topo_hadcm3x(str);
elseif strcmp(str(1).gcm,'foam')
[gi_topo,gi_mask] = fun_read_topomask_foam(str);
elseif strcmp(str(1).gcm,'cesm')
[gi_topo,gi_mask] = fun_read_topomask_cesm(str);
elseif strcmp(str(1).gcm,'rockee')
[gi_topo,gi_mask] = fun_read_topomask_rockee(str);
end
disp([' - Mask & topo info read.']);
% plot input mask & topo
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(gi_mask),2.0,'',[[str_dirout '/' str_nameout] '.mask_in'],'mask in');
plot_2dgridded(flipud(gi_topo),6000.0,'',[[str_dirout '/' str_nameout] '.topo_in'],'topo in');
else
figure; imagesc(gi_mask); colorbar; title('mask in'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.mask_in'] '.' str_date '.' par_plotformat]);
figure; imagesc(gi_topo); colorbar; title('topo in'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.topo_in'] '.' str_date '.' par_plotformat]);
end
case {'mat'}
% read topo
% NOTE: assume specific (rows==lat, col==lon) orientation
% => flip up/down when loaded
% NOTE: assume topography is positive height (above sealevel)
% >>> EDIT ME >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
if isempty(str(1).path)
loc_str_file = [par_expid '.' par_gcm];
else
loc_str_file = [str(1).path '/' par_expid '.' par_gcm];
end
data = load('-mat',loc_str_file);
vars = fieldnames(data);
gi_topo = data.(vars{1});
gi_topo = flipud(gi_topo);
gi_mask = zeros(size(gi_topo));
gi_mask(find(gi_topo < 0.0)) = 1.0;
% <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
disp([' - Mask & topo info read.']);
% plot input mask & topo
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(gi_mask),2.0,'',[[str_dirout '/' str_nameout] '.mask_in'],'mask in');
plot_2dgridded(flipud(gi_topo),6000.0,'',[[str_dirout '/' str_nameout] '.topo_in'],'topo in');
else
figure; imagesc(gi_mask); colorbar; title('mask in'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.mask_in'] '.' str_date '.' par_plotformat]);
figure; imagesc(gi_topo); colorbar; title('topo in'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.topo_in'] '.' str_date '.' par_plotformat]);
end
case {'k1','k2','mask'}
% load topo directly
[go_k1,go_mask,imax,jmax] = fun_read_k1(str);
disp([' - k1 read.']);
% re-create GENIE grid with derived (/updated?) grid dimensions
% NOTE: the value of kmax is taken from the config file
% (while imax and jmax are deduced from the file)
[go_lonm,go_lone,go_latm,go_late,go_dm,go_de] = make_genie_grid(imax,jmax,kmax,par_max_D,par_lon_off,opt_equalarea,par_sur_D);
disp([' - GENIE grid re-generated.']);
otherwise
% DO NOTHING
disp([' (Nothing to load.)']);
end
%
% *** RE-GRID MASK ****************************************************** %
%
% NOTE: go_fmask == fractional land-sea mask
% used to track whether there is going to be any (GCM) bathymetry
% available (if the original ocean fraction in that cell is not zero)
n_step = n_step+1;
disp(['> ' num2str(n_step) '. RE-GRIDING MASK ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
switch str(1).gcm
case {'hadcm3','hadcm3l','foam','cesm','rockee','mat'}
% initial re-gridding of mask
% NOTE: need to transpose around [gi_mask] to have correct input format
% to make_regrid_2d
% similarly, output needs to be transposed back again
% NOTE: pass edges of c-grid
[go_mask,go_tmp] = make_regrid_2d(gi_lonce,gi_latce,gi_mask',go_lone,go_late,opt_debug);
disp([' - Mask re-gridded.']);
go_mask = go_mask';
go_fmask = go_mask;
% create mask (<>= par_A_frac_threshold fractional area thresold)
% NOTE: 1.0 == 100% ocean
go_mask(find(go_mask>=par_A_frac_threshold)) = 1.0;
go_mask(find(go_mask<par_A_frac_threshold)) = 0.0;
% calculate respective fractional areas
[si_farea,si_farearef] = fun_grid_calc_ftotarea(gi_mask,gi_lonce,gi_latce);
[so_farea,so_farearef] = fun_grid_calc_ftotarea(go_mask,go_lone,go_late);
disp([' * Original land area fraction = ', num2str(1.0-si_farea)]);
disp([' * Re-gridded land area fraction = ', num2str(1.0-so_farea)]);
case {'k1','k2','mask'}
disp([' (Nothing to do ... k1/k2/mask file already loaded.)']);
go_fmask = zeros(jmax,imax) + 1;
otherwise
go_mask = zeros(jmax,imax) + 1;
disp([' - Blank mask created (nothing to re-grid).']);
go_fmask = go_mask;
end
% plot & save initial mask re-grid
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_mask),2.0,'',[[str_dirout '/' str_nameout] '.omask_out.RAW'],'ocean mask out -- RAW re-gridded');
else
figure; imagesc(go_mask); colorbar; title('ocean mask out -- RAW re-gridded'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.omask_out.RAW'] '.' str_date '.' par_plotformat]);
end
%
% *** FILTER MASK ******************************************************* %
%
n_step = n_step+1;
if (opt_debug), input('Press return to CONTINUE ...'); end
% filter mask if requested
% NOTE: when loading in a default 'k1' file, best to skip this step
% set VERSION 0 (raw)
grid_ver = 0;
str_ver = num2str(grid_ver);
%
if (opt_filtermask || (par_min_oceann > 0))
%
disp(['> ' num2str(n_step) '. FILTERING MASK ...']);
%
if opt_filtermask
%
% BASIC MASK FILTERING
%
% filter out single cell embayments iteratively
% initialize
go_mask_fills_cnt = 1;
% LOOP >>>
while (go_mask_fills_cnt > 0)
% increment VERSION
grid_ver = grid_ver + 1;
str_ver = num2str(grid_ver);
% fill in 4-surrounded cells
go_mask_fills = find_grid_4cells(go_mask);
% fill in 3-surrounded cells (excepting open ocean bordering ones)
go_mask_fills = go_mask_fills + find_grid_3cells(go_mask);
% update mask
go_mask = go_mask - go_mask_fills;
% count number of cell changes
go_mask_fills_cnt = sum(sum(go_mask_fills));
end
% <<< LOOP
fprintf(' - Single cell embayments filtered out.\n')
% plot mask
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_mask),2.0,'',[[str_dirout '/' str_nameout] '.omask_out.v' str_ver],['ocean mask out -- version ' str_ver]);
else
figure; imagesc(go_mask); colorbar; title(['ocean mask out -- version ' str_ver]); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.omask_out.v' str_ver] '.' str_date '.' par_plotformat]);
end
%
end
%
if opt_filtermask
%
% ADJUST MASK -- CLEAN UP POLAR CONNECTIONS
%
% increment VERSION
grid_ver = grid_ver + 1;
str_ver = num2str(grid_ver);
% open up narrow polar connections
go_mask_fills = find_grid_poleopen(go_mask);
% update mask
go_mask = go_mask + go_mask_fills;
%
fprintf(' - Polar connections cleaned up.\n')
% plot mask
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_mask),2.0,'',[[str_dirout '/' str_nameout] '.omask_out.v' str_ver],['ocean mask out -- version ' str_ver]);
else
figure; imagesc(go_mask); colorbar; title(['ocean mask out -- version ' str_ver]); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.omask_out.v' str_ver] '.' str_date '.' par_plotformat]);
end
%
end
%
if (par_min_oceann > 0)
%
% SMALL WATER BODY FILTERING MASK FILTERING
%
[go_oceans,n_oceans,i_oceans] = find_grid_oceans(go_mask);
% plot oceans!
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf')),
plot_2dgridded(flipud(go_oceans),999,'',[[str_dirout '/' str_nameout] '.ocean_out.INIT'],'oceans out -- INITIAL');
else
figure; imagesc(go_mask); colorbar; title('oceans out -- INITIAL'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.ocean_out.INIT'] '.' str_date '.' par_plotformat]);
end
% increment VERSION
grid_ver = grid_ver + 1;
str_ver = num2str(grid_ver);
% clean up small water bodies
[go_mask,go_oceans,n_oceans] = find_grid_oceans_update(go_mask,go_oceans,n_oceans,par_min_oceann);
fprintf(' - Small water bodies cleaned up.\n')
% plot mask
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_mask),2.0,'',[[str_dirout '/' str_nameout] '.omask_out.v' str_ver],['ocean mask out -- version ' str_ver]);
else
figure; imagesc(go_mask); colorbar; title(['ocean mask out -- version ' str_ver]); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.omask_out.v' str_ver] '.' str_date '.' par_plotformat]);
end
%
end
%
% calculate new fractional area
[so_farea,so_farearef] = fun_grid_calc_ftotarea(go_mask,go_lone,go_late);
disp([' * Revised land area fraction = ', num2str(1.0-so_farea)]);
%
end
%
% *** ADJUST MASK -- APPLY OPTIONAL PRESCRIBED MASK CHANGES ************* %
%
% load and apply mask to the ocean mask!
if ~isempty(str(1).mask)
n_step = n_step+1;
if (opt_debug), input('Press return to CONTINUE ...'); end
disp(['> ' num2str(n_step) '. APPLYING LAND-SEA MASK ADJUSTMENTS FROM FILE: ' [str(1).mask '.txt']]);
% read in mask file ... exit if it cannot be found ...
loc_mask = fun_read_mask(str);
% for a '1' in the mask => force to ocean
% for a '-1' in the mask => force to land
go_mask(find(loc_mask == 1)) = 1;
go_mask(find(loc_mask == -1)) = 0;
end
%
% *** ADJUST MASK -- USER! ********************************************** %
%
n_step = n_step+1;
if (opt_debug), input('Press return to CONTINUE ...'); end
%
if opt_user
%
disp(['> ' num2str(n_step) '. USER EDITING OF MASK ...']);
%
[go_mask] = fun_grid_edit_mask(go_mask,go_fmask);
% increment VERSION
grid_ver = grid_ver + 1;
str_ver = num2str(grid_ver);
% plot mask
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_mask),2,'',[[str_dirout '/' str_nameout] '.omask_out.v' str_ver],['ocean mask out -- version ' str_ver]);
else
figure; imagesc(go_mask); colorbar; title(['ocean mask out -- version ' str_ver]); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.omask_out.v' str_ver] '.' str_date '.' par_plotformat]);
end
% calculate new fractional area
[so_farea,so_farearef] = fun_grid_calc_ftotarea(go_mask,go_lone,go_late);
disp([' * Revised land area fraction = ', num2str(1.0-so_farea)]);
%
fprintf(' - User-editing complete.\n')
%
end
%
% *** CREATE FINAL MASK ************************************************* %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. CREATE FINAL MASK ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
% create GENIE NaN masks
go_masknan = go_mask;
go_masknan(find(go_mask == 0)) = NaN;
go_masknotnan = go_mask;
go_masknotnan(find(go_mask ~= 0)) = NaN;
go_masknotnan(find(go_masknotnan == 0)) = 1;
%
% plot final mask
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_mask),99999.0,'',[[str_dirout '/' str_nameout] '.omask_out.FINAL'],'ocean mask out -- FINAL version');
else
figure; imagesc(go_mask); colorbar; title('ocean mask out -- FINAL version'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.omask_out.FINAL'] '.' str_date '.' par_plotformat]);
end
%
% calculate new fractional area
[so_farea,so_farearef] = fun_grid_calc_ftotarea(go_mask,go_lone,go_late);
disp([' * Final land area fraction = ', num2str(1.0-so_farea)]);
%
% save mask for reference (not used as an input)
% NOTE: pass mask in as 2nd parameter to force difference in land vs. ocean number format
fprint_2DM(go_mask(:,:),go_mask(:,:),[[str_dirout '/' str_nameout] '.mask.txt'],'%4.1f','%4.0f',true,false);
fprintf(' - .mask.txt saved\n')
% save in an alternative format with all zeros
fprint_2DM(0.0*go_mask(:,:),go_mask(:,:),[[str_dirout '/' str_nameout] '.maskzeros.txt'],'%4.1f','%4.0f',true,false);
fprintf(' - .maskzeros.txt saved\n')
%
% *** RE-GRID TOPO ****************************************************** %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. RE-GRIDING TOPOGRAPHY ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
switch str(1).gcm
case {'hadcm3','hadcm3l','foam','cesm','rockee','mat'}
% initial re-gridding of topo
% NOTE: need to transpose around [gi_topo] to have correct input format
% to make_regrid_2d
% similarly, output needs to be transposed back again
% NOTE: pass edges of c-grid
[go_topo,go_ftopo] = make_regrid_2d(gi_lonce,gi_latce,gi_topo',go_lone,go_late,opt_debug);
disp([' - Topography re-gridded.']);
go_topo = go_topo';
go_ftopo = go_ftopo';
case {'k1','k2'}
% ensure that any new 'land' is assigned '90' in the k1
loc_dry = intersect(find(go_mask == 0),find(go_k1 <= par_max_k));
if ~isempty(loc_dry)
go_k1(loc_dry) = 90;
end
% convert k1 to depth
[go_topo] = fun_conv_k1(go_de,go_k1);
disp([' (Nothing to re-grid -- convert k1 file data.)']);
otherwise
% create a k1 first and convert to depth
% (even though later this is converted back again ...)
% NOTE: scale depth cannot be used because it is not necessary
% the final maximum ocean depth
% filter mask value 0 (land) to a k1 value 'land' (90)
%%%go_topo = par_max_D*go_mask;
go_k1 = par_min_k*go_mask;
go_k1(find(go_k1==0))=90;
[go_topo] = fun_conv_k1(go_de,go_k1);
disp([' (Nothing to re-grid -- set uniform ocean depth.)']);
end
% plot & save initial topo re-grid
if ( ~strcmp(str(1).gcm,'k1') || ~strcmp(str(1).gcm,'k2') )
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_topo),99999.0,'',[[str_dirout '/' str_nameout] '.topo_out.RAW'],'topo out -- RAW');
else
figure; imagesc(go_topo); colorbar; title('topo out -- RAW'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.topo_out.RAW'] '.' str_date '.' par_plotformat]);
end
end
%
% *** RE-GRID VERTICALLY ************************************************ %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. RE-GRIDING OCEAN BATHYMETRY ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
switch str(1).gcm
case {'k1','k2'}
disp([' (Nothing to re-grid as k1 file already loaded.)']);
otherwise
% convert depth into k levels (and create k1 grid)
[go_k1] = find_grid_k(par_min_Dk,go_dm,go_de,go_mask,go_topo);
fprintf(' - Bathymetry re-gridding complete.\n')
end
% filter min k value
go_k1(find(go_k1 < par_min_k)) = par_min_k;
% plot initial k1 re-grid
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_k1),89.0,'',[[str_dirout '/' str_nameout] '.k1_out.RAW'],'k1 out -- RAW re-gridded');
else
figure; imagesc(go_k1); colorbar; title('k1 out -- RAW re-gridded'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.k1_out.RAW'] '.' str_date '.' par_plotformat]);
end
%
% *** ADJUST TOPO -- AUTOMATIC BATHYMETRY FILTERING ********************* %
%
n_step = n_step+1;
if (opt_debug), input('Press return to CONTINUE ...'); end
%
% carry out basic automatic topo filtering
if (opt_filtertopo)
%
disp(['> ' num2str(n_step) '. FILTERING BATHYMETRY ...']);
%
[go_k1] = fun_grid_topo_filter(go_k1);
fprintf(' - Topography filtered.\n')
% plot adjusted k1 re-grid
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_k1),89.0,'',[[str_dirout '/' str_nameout] '.k1_out.FILTERED'],'k1 out -- auto filtered');
else
figure; imagesc(go_k1); colorbar; title('k1 out -- auto filtered'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.k1_out.FILTERED'] '.' str_date '.' par_plotformat]);
end
end
%
% *** ADJUST TOPO -- USER! ********************************************** %
%
if (opt_user)
n_step = n_step+1;
disp(['> ' num2str(n_step) '. USER EDITING OF TOPO ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
% filter for ocean but not depth info (k > kmax)
% search for ocean in the mask that has a 'land' value ...
% set to the shallowest k1 level and a nominal middepth of that level
% NOTE: shallowest *allowed* k1 level (by par_min_Dk)
loc_dry = intersect(find(go_mask == 1),find(go_k1 > par_max_k));
if ~isempty(loc_dry)
go_k1(loc_dry) = (par_max_k-(par_min_Dk-1));
go_topo(loc_dry) = -go_dm(par_max_k);
end
% user-editing! what can go wrong?
[go_k1] = fun_grid_edit_k1(go_k1,kmax);
% plot mask
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_k1),89.0,'',[str_dirout '/' str_nameout '.k1_out.USEREDITED'],'k1 out -- user edited version');
else
figure; imagesc(go_k1); colorbar; title('k1 out -- user edited version'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.k1_out.USEREDITED'] '.' str_date '.' par_plotformat]);
end
% convert k-levels back to depth
[go_topo] = fun_conv_k1(go_de,go_k1);
%
fprintf(' - User-editing complete.\n')
%
end
%
% *** REPORT FINAL TOPO ************************************************* %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. FINAL TOPO ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
% plot final topo
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_masknan.*go_topo),99999.0,'',[[str_dirout '/' str_nameout] '.topo_out.FINAL'],'topo out -- FINAL version');
else
figure; imagesc(go_masknan.*go_topo); colorbar; title('topo out -- FINAL version'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.topo_out.FINAL'] '.' str_date '.' par_plotformat]);
end
%
% *** REPORT FINAL K1 *************************************************** %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. FINAL K1 ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
% plot final k1
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_masknan.*go_k1),89.0,'',[str_dirout '/' str_nameout '.k1_out.ocean.FINAL'],'k1 out -- FINAL ocean version');
else
figure; imagesc(go_masknan.*go_k1); colorbar; title('k1 out -- FINAL ocean version'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.k1_out.ocean.FINAL'] '.' str_date '.' par_plotformat]);
end
% save topo for reference (not used as an input)
fprint_2DM(go_k1,[],[[str_dirout '/' str_nameout] '.topo.txt'],'%4.0f','%4.0f',true,false);
fprintf(' - .grid.txt saved\n')
%
% *** CALCULATE RUNOFF & COMPLETE k1 FILE ******************************* %
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. CALCULATING RUN-OFF AND GENERATE .k1 FILE ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
%
% NOTE: ordering is a little illogical becasue
% make_grid_runoff_rnd requires the extended grid, while
% make_grid_runoff_roof is easier done without ...
%
% (A) create roofing runoff scheme
% NOTE: existing runoff information will be retained ...
% values of '90' will indicate run-off needs to be re-generated
if ( ~opt_makerndrunoff && (max(go_k1,[],"all") >= 90) )
[go_k1] = make_grid_runoff_roof(go_mask,go_k1,str);
% create simplified k1 grid value scale for plotting
loc_k1 = go_k1;
loc_k1(find(loc_k1 < 91)) = 95;
end
% extend k1 grid
% NOTE: mark first row: maxk+1, last as maxk+2
% (so, slightly different from standard/original GENIE format)
goex_k1 = go_k1;
goex_k1 = [goex_k1(1,:); goex_k1; goex_k1(end,:)];
goex_k1(1,:) = kmax+1;
goex_k1(end,:) = kmax+2;
% add buffer columns for E-W wall
goex_k1 = [goex_k1(:,end) goex_k1 goex_k1(:,1)];
%
% (B) create random runoff grid (if selected)
if ( opt_makerndrunoff && (max(go_k1,[],"all") >= 90) )
[goex_k1] = make_grid_runoff_rnd(goex_k1,str,opt_debug);
% create simplified k1 grid value scale for plotting
loc_k1 = goex_k1(2:end-1,2:end-1);
loc_k1(find(loc_k1 < 91)) = 95;
end
%
% PLOT & SAVE
% plot runoff
if (max(go_k1,[],"all") >= 90)
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(loc_k1),95.0,'',[str_dirout '/' str_nameout '.k1_out.RUNOFF'],'k1 out -- RUNOFF');
else
figure; imagesc(loc_k1); colorbar; title('k1 out -- RUNOFF'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.k1_out.RUNOFF'] '.' str_date '.' par_plotformat]);
end
end
% save final land k1
fprint_2DM(goex_k1(:,:),[],[[str_dirout '/' str_nameout] '.k1'],'%3i','%3i',true,false);
fprintf(' - .k1 file saved\n')
% plot final land k1
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_masknotnan.*go_k1),95.0,'',[str_dirout '/' str_nameout '.k1_out.land.FINAL'],'k1 out -- FINAL land version');
else
figure; imagesc(go_masknotnan.*go_k1); colorbar; title('k1 out -- FINAL land version'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.k1_out.land.FINAL'] '.' str_date '.' par_plotformat]);
end
%
% *** IDENTIFY ISLANDS ************************************************** %
%
if opt_makegold
%
n_step = n_step+1;
disp(['> ' num2str(n_step) '. IDENTIFY ISLANDS ...']);
if (opt_debug), input('Press return to CONTINUE ...'); end
% initial islands count
[go_islands,n_islands,i_islands] = find_grid_islands(go_mask);
% plot islands
if (isempty(par_plotformat))
%
elseif (strcmp(par_plotformat,'pdf'))
plot_2dgridded(flipud(go_islands),999,'',[[str_dirout '/' str_nameout] '.islnd_out.INIT'],'island out -- INITIAL');
else
figure; imagesc(go_islands); colorbar; title('island out -- INITIAL'); exportgraphics(gcf,[[[str_dirout '/' str_nameout] '.islnd_out.INIT'] '.' str_date '.' par_plotformat]);
end
%
end
%
% *** UPDATE ISLANDS AND ISLAND PATHS *********************************** %
%
if opt_makegold
%