matlab_class/gcmfaces_diags/diags_pre_process.m

function [myswitch]=diags_pre_process(dirModel,dirMat,doInteractive);
%object :      pre-processing for grid, model parameters, budgets,
%              profiles, cost and control, etc if required
%input :       dirModel is the directory containing 'diags/' or 'nctiles/'
%              dirMat is the directory where diagnostics results will be saved
%                     if isempty(dirMat) then [dirModel 'mat/'] is used by default
%(optional)    doInteractive=1 allows users to specify parameters interactively
%                     doInteractive = 0 (default) uses ECCO v4 parameters
%                     and omits budgets and model-data misfits analyses
%output :      myswitch is the set of switches (doBudget, doProfiles, doCost, doCtrl)
%                     that are set here depending on the model output available

gcmfaces_global; global myparms;

dirModel=fullfile(dirModel,filesep);
if isempty(dirMat); dirMat=fullfile(dirModel,'mat',filesep); else; dirMat=fullfile(dirMat,filesep); end;
if isempty(who('doInteractive')); doInteractive=0; end;

%detect which types of files are avaiable
test0=isdir([dirModel 'diags']);
test1=~isempty(dir([dirModel 'nctiles*']));
if test0&test1&doInteractive;
    myenv.nctiles=input('select to use binaries (0) or nctiles (1) files\n');
elseif test1;
    myenv.nctiles=1;
elseif test0;
    myenv.nctiles=0;
else;
    error('no files (diags/ or nctiles/)  were found\n');
end

if doInteractive&~myenv.nctiles;%only works with binaries
    doBudget=~isempty(dir([dirModel 'diags' filesep 'BUDG' filesep]))
    doBudget=doBudget&~myenv.nctiles;
    doCost=~isempty(dir([dirModel 'barfiles' filesep]))
    doCtrl=~isempty(dir([dirModel 'ADXXfiles' filesep]))
else;
    doBudget=0;
    doCost=0;
    doCtrl=0;
end;

doProfiles=~isempty(dir([dirModel 'MITprof' filesep]));
preprocessProfiles=0;
myenv.profiles=fullfile(pwd,filesep,dirModel,'MITprof',filesep);
if ~doProfiles;
    doProfiles=~isempty(dir([dirModel 'profiles' filesep]));
    preprocessProfiles=1;
    myenv.profiles=fullfile(pwd,filesep,dirMat,'profiles',filesep,'output',filesep);
end;

%output switches
myswitch.doBudget=doBudget;
myswitch.doProfiles=doProfiles;
myswitch.doCost=doCost;
myswitch.doCtrl=doCtrl;

%set the list of diags directories and files
if myenv.nctiles;
    if isdir(fullfile(pwd,dirModel,'nctiles',filesep));
        listSubdirs={fullfile(pwd,dirModel,'nctiles',filesep)};
    elseif isdir(fullfile(pwd,dirModel,'nctiles_climatology',filesep));
        listSubdirs={fullfile(pwd,dirModel,'nctiles_climatology',filesep)};
    end;
    
    listFiles=dir(listSubdirs{1}); listFiles={listFiles(:).name};
    %remove irrelevant files/dirs
    test1=ones(size(listFiles));
    for kk=1:length(listFiles);
        tmp1=fullfile(listSubdirs{1},listFiles{kk},[listFiles{kk} '*.nc']);
        test1(kk)=~isempty(dir(tmp1));
    end;
    listFiles={listFiles{find(test1)}};
    %store in myparms for later use
    myenv.nctilesdir=listSubdirs{1};
    myenv.nctileslist=listFiles;
    %
    myenv.diagsdir='';
else;
    myenv.diagsdir=fullfile(pwd,dirModel,['diags' filesep]);
    %
    myenv.nctilesdir='';
    myenv.nctileslist={};
end;
myenv.matdir=fullfile(pwd,dirMat);

%0) create dirMat if needed:
if isempty(dir(dirMat)); mkdir(dirMat); end;

%1) pre-processing diags_grid_parms.mat
test0=isempty(dir([dirMat 'diags_grid_parms.mat']));
test1=isempty(dir([dirMat 'lock_mygrid']));

if test0&test1;%this process will do the pre-processing
    fprintf(['pre-processing : started for mygrid, myparms \n']);
    write2file([dirMat 'lock_mygrid'],1);
    %set the list of diags times
    [listTimes]=diags_list_times;
    %set grid and model parameters:
    diags_grid_parms(listTimes,doInteractive);
    %save to disk:
    %if doInteractive;
    eval(['save ' dirMat 'diags_grid_parms.mat mygrid myparms;']);
    %end;
    delete([dirMat 'lock_mygrid']);
    test1=1;
    fprintf(['pre-processing : completed for mygrid, myparms \n\n']);
end;

%here I should test that files are indeed found (may have been moved)

while ~test1;%this process will wait for pre-processing to complete
    fprintf(['waiting 30s for removal of ' dirMat 'lock_mygrid \n']);
    fprintf(['- That should happen automatically after pre-processing is complete \n']);
    fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
    fprintf(['  remove ' dirMat 'lock_grid manually, and start over. \n\n']);
    test1=isempty(dir([dirMat 'lock_mygrid']));
    pause(30);
end;

%here we always reload the grid from dirMat to make sure the same one is used throughout
eval(['load ' dirMat 'diags_grid_parms.mat;']);

%2) pre-processing profiles
test0=isempty(dir([dirMat 'profiles/']));
test1=isempty(dir([dirMat 'lock_profiles']));

if test0&test1&doProfiles&preprocessProfiles;%this process will do the pre-processing
    fprintf(['pre-processing : started for profiles \n']);
    write2file([dirMat 'lock_profiles'],1);
    mkdir([dirMat 'profiles/']);
    % NOTE: if on DOS system change ln to mklink
    system(['ln -s /net/nares/raid11/ecco-shared/ecco-version-4/input/input_insitu ' dirMat 'profiles/input']);
    mkdir([dirMat 'profiles/output/']);
    if dirModel(1)~='/'; dirModelFull=[pwd '/' dirModel]; else; dirModelFull=dirModel; end;
    % NOTE: if on DOS system change ln to mklink
    system(['ln -s ' dirModelFull 'profiles/*equi.data ' dirMat 'profiles/.']);
    listModel={'argo_feb2013_1992_to_2007*','argo_feb2013_2008_to_2010*',...
        'argo_feb2013_2011_to_2012*','ctd_feb2013*','itp_feb2013*',...
        'seals_feb2013*','xbt_feb2013*','climode_feb2013*'};
    MITprof_gcm2nc([dirMat 'profiles/'],listModel);
    delete([dirMat 'lock_profiles']);
    test1=1;
    fprintf(['pre-processing : completed for profiles \n\n']);
end;

while ~test1&doProfiles;%this process will wait for pre-processing to complete
    fprintf(['waiting 30s for removal of ' dirMat 'lock_profiles \n']);
    fprintf(['- That should happen automatically after pre-processing is complete \n']);
    fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
    fprintf(['  remove ' dirMat 'lock_profiles manually, and start over. \n\n']);
    test1=isempty(dir([dirMat 'lock_profiles']));
    pause(30);
end;

%3) budget pre-processing
test0=isempty(dir([dirMat 'BUDG']));
test1=isempty(dir([dirMat 'lock_budg']));%this aims at having only one process do the

if (test0&test1&doBudget);
    fprintf(['pre-processing : started for budget \n']);
    write2file([dirMat 'lock_budg'],1);
    mkdir([dirMat 'BUDG']);
    %compute time derivatives between snwpshots that will be
    %compared in budgets with the time mean flux terms
    tmp1=fullfile(dirModel,'diags',filesep,'BUDG',filesep,'budg2d_snap_set2*meta');
    test3d=isempty(dir(tmp1))
    diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set1');
    if ~test3d;
      diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set2');
    else;
      diags_diff_snapshots(dirModel,dirMat,'budg3d_snap_set1');
    end;
    %diags_diff_snapshots(dirModel,dirMat,'budg3d_snap_set1');
    budget_list=1;
    for kk=1:length(mygrid.RC);
        tmp1=sprintf('%s/diags/BUDG/budg2d_snap_set3_%02i*',dirModel,kk);
        tmp2=~isempty(dir(tmp1));
        if tmp2;
            budget_list=[budget_list kk];
            tmp1=sprintf('budg2d_snap_set3_%02i',kk);
            diags_diff_snapshots(dirModel,dirMat,tmp1);
        end;
    end;
    eval(['save ' dirMat 'diags_select_budget_list.mat budget_list;']);
    delete([dirMat 'lock_budg']);
    test1=1;
    fprintf(['pre-processing : completed for budget \n\n']);
end;

while ~test1&doBudget;%this process will wait for pre-processing to complete
    fprintf(['waiting 30s more for removal of ' dirMat 'lock_budg \n']);
    fprintf(['- That should happen automatically after pre-processing is complete \n']);
    fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
    fprintf(['  remove ' dirMat 'lock_budg manually, and start over. \n\n']);
    test1=isempty(dir([dirMat 'lock_budg']));
    pause(30);
end;

%set budget list
myparms.budgetList=1;
if ~isempty(dir([dirMat 'diags_select_budget_list.mat']));
    eval(['load ' dirMat 'diags_select_budget_list.mat;']);
    myparms.budgetList=budget_list;
end;
1	gforget	1.8	function [myswitch]=diags_pre_process(dirModel,dirMat,doInteractive);
2	gforget	1.10	%object : pre-processing for grid, model parameters, budgets,
3	gforget	1.8	% profiles, cost and control, etc if required
4			%input : dirModel is the directory containing 'diags/' or 'nctiles/'
5			% dirMat is the directory where diagnostics results will be saved
6			% if isempty(dirMat) then [dirModel 'mat/'] is used by default
7			%(optional) doInteractive=1 allows users to specify parameters interactively
8			% doInteractive = 0 (default) uses ECCO v4 parameters
9			% and omits budgets and model-data misfits analyses
10			%output : myswitch is the set of switches (doBudget, doProfiles, doCost, doCtrl)
11			% that are set here depending on the model output available
12	gforget	1.1
13			gcmfaces_global; global myparms;
14
15	gforget	1.12	dirModel=fullfile(dirModel,filesep);
16			if isempty(dirMat); dirMat=fullfile(dirModel,'mat',filesep); else; dirMat=fullfile(dirMat,filesep); end;
17	gforget	1.8	if isempty(who('doInteractive')); doInteractive=0; end;
18	gforget	1.1
19	gforget	1.6	%detect which types of files are avaiable
20			test0=isdir([dirModel 'diags']);
21	gforget	1.11	test1=~isempty(dir([dirModel 'nctiles*']));
22	gforget	1.10	if test0&test1&doInteractive;
23			myenv.nctiles=input('select to use binaries (0) or nctiles (1) files\n');
24	gforget	1.8	elseif test1;
25	gforget	1.10	myenv.nctiles=1;
26	gforget	1.6	elseif test0;
27	gforget	1.10	myenv.nctiles=0;
28	gforget	1.6	else;
29	gforget	1.10	error('no files (diags/ or nctiles/) were found\n');
30	gforget	1.6	end
31
32	gforget	1.12	if doInteractive&~myenv.nctiles;%only works with binaries
33			doBudget=~isempty(dir([dirModel 'diags' filesep 'BUDG' filesep]))
34	gforget	1.10	doBudget=doBudget&~myenv.nctiles;
35	gforget	1.12	doCost=~isempty(dir([dirModel 'barfiles' filesep]))
36			doCtrl=~isempty(dir([dirModel 'ADXXfiles' filesep]))
37	gforget	1.8	else;
38	gforget	1.10	doBudget=0;
39			doCost=0;
40			doCtrl=0;
41	gforget	1.8	end;
42
43	gforget	1.12	doProfiles=~isempty(dir([dirModel 'MITprof' filesep]));
44	gforget	1.8	preprocessProfiles=0;
45	gforget	1.12	myenv.profiles=fullfile(pwd,filesep,dirModel,'MITprof',filesep);
46	gforget	1.8	if ~doProfiles;
47	gforget	1.12	doProfiles=~isempty(dir([dirModel 'profiles' filesep]));
48	gforget	1.10	preprocessProfiles=1;
49	gforget	1.12	myenv.profiles=fullfile(pwd,filesep,dirMat,'profiles',filesep,'output',filesep);
50	gforget	1.8	end;
51	gforget	1.1
52			%output switches
53			myswitch.doBudget=doBudget;
54			myswitch.doProfiles=doProfiles;
55			myswitch.doCost=doCost;
56			myswitch.doCtrl=doCtrl;
57
58	gforget	1.6	%set the list of diags directories and files
59			if myenv.nctiles;
60	gforget	1.12	if isdir(fullfile(pwd,dirModel,'nctiles',filesep));
61			listSubdirs={fullfile(pwd,dirModel,'nctiles',filesep)};
62			elseif isdir(fullfile(pwd,dirModel,'nctiles_climatology',filesep));
63			listSubdirs={fullfile(pwd,dirModel,'nctiles_climatology',filesep)};
64	gforget	1.11	end;
65
66	gforget	1.6	listFiles=dir(listSubdirs{1}); listFiles={listFiles(:).name};
67			%remove irrelevant files/dirs
68			test1=ones(size(listFiles));
69			for kk=1:length(listFiles);
70	gforget	1.12	tmp1=fullfile(listSubdirs{1},listFiles{kk},[listFiles{kk} '*.nc']);
71	gforget	1.10	test1(kk)=~isempty(dir(tmp1));
72	gforget	1.6	end;
73			listFiles={listFiles{find(test1)}};
74			%store in myparms for later use
75			myenv.nctilesdir=listSubdirs{1};
76			myenv.nctileslist=listFiles;
77	gforget	1.12	%
78			myenv.diagsdir='';
79			else;
80			myenv.diagsdir=fullfile(pwd,dirModel,['diags' filesep]);
81			%
82			myenv.nctilesdir='';
83			myenv.nctileslist={};
84	gforget	1.6	end;
85	gforget	1.12	myenv.matdir=fullfile(pwd,dirMat);
86	gforget	1.6
87	gforget	1.1	%0) create dirMat if needed:
88	gforget	1.7	if isempty(dir(dirMat)); mkdir(dirMat); end;
89	gforget	1.1
90			%1) pre-processing diags_grid_parms.mat
91			test0=isempty(dir([dirMat 'diags_grid_parms.mat']));
92			test1=isempty(dir([dirMat 'lock_mygrid']));
93
94			if test0&test1;%this process will do the pre-processing
95	gforget	1.8	fprintf(['pre-processing : started for mygrid, myparms \n']);
96	gforget	1.1	write2file([dirMat 'lock_mygrid'],1);
97			%set the list of diags times
98	gforget	1.10	[listTimes]=diags_list_times;
99	gforget	1.1	%set grid and model parameters:
100	gforget	1.8	diags_grid_parms(listTimes,doInteractive);
101	gforget	1.1	%save to disk:
102	gforget	1.10	%if doInteractive;
103			eval(['save ' dirMat 'diags_grid_parms.mat mygrid myparms;']);
104			%end;
105	gforget	1.7	delete([dirMat 'lock_mygrid']);
106	gforget	1.1	test1=1;
107	gforget	1.8	fprintf(['pre-processing : completed for mygrid, myparms \n\n']);
108	gforget	1.1	end;
109
110	gforget	1.6	%here I should test that files are indeed found (may have been moved)
111
112	gforget	1.1	while ~test1;%this process will wait for pre-processing to complete
113			fprintf(['waiting 30s for removal of ' dirMat 'lock_mygrid \n']);
114	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
115			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
116			fprintf([' remove ' dirMat 'lock_grid manually, and start over. \n\n']);
117	gforget	1.1	test1=isempty(dir([dirMat 'lock_mygrid']));
118			pause(30);
119			end;
120
121			%here we always reload the grid from dirMat to make sure the same one is used throughout
122	gforget	1.10	eval(['load ' dirMat 'diags_grid_parms.mat;']);
123	gforget	1.1
124			%2) pre-processing profiles
125			test0=isempty(dir([dirMat 'profiles/']));
126			test1=isempty(dir([dirMat 'lock_profiles']));
127
128	gforget	1.8	if test0&test1&doProfiles&preprocessProfiles;%this process will do the pre-processing
129	gforget	1.1	fprintf(['pre-processing : started for profiles \n']);
130			write2file([dirMat 'lock_profiles'],1);
131	gforget	1.7	mkdir([dirMat 'profiles/']);
132	gforget	1.10	% NOTE: if on DOS system change ln to mklink
133	gforget	1.7	system(['ln -s /net/nares/raid11/ecco-shared/ecco-version-4/input/input_insitu ' dirMat 'profiles/input']);
134			mkdir([dirMat 'profiles/output/']);
135	gforget	1.1	if dirModel(1)~='/'; dirModelFull=[pwd '/' dirModel]; else; dirModelFull=dirModel; end;
136	gforget	1.10	% NOTE: if on DOS system change ln to mklink
137	gforget	1.7	system(['ln -s ' dirModelFull 'profiles/*equi.data ' dirMat 'profiles/.']);
138	gforget	1.4	listModel={'argo_feb2013_1992_to_2007','argo_feb2013_2008_to_2010',...
139	gforget	1.3	'argo_feb2013_2011_to_2012','ctd_feb2013','itp_feb2013*',...
140			'seals_feb2013','xbt_feb2013','climode_feb2013*'};
141	gforget	1.1	MITprof_gcm2nc([dirMat 'profiles/'],listModel);
142	gforget	1.7	delete([dirMat 'lock_profiles']);
143	gforget	1.1	test1=1;
144			fprintf(['pre-processing : completed for profiles \n\n']);
145			end;
146
147			while ~test1&doProfiles;%this process will wait for pre-processing to complete
148			fprintf(['waiting 30s for removal of ' dirMat 'lock_profiles \n']);
149	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
150			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
151			fprintf([' remove ' dirMat 'lock_profiles manually, and start over. \n\n']);
152	gforget	1.1	test1=isempty(dir([dirMat 'lock_profiles']));
153			pause(30);
154			end;
155
156			%3) budget pre-processing
157	gforget	1.12	test0=isempty(dir([dirMat 'BUDG']));
158	gforget	1.1	test1=isempty(dir([dirMat 'lock_budg']));%this aims at having only one process do the
159
160			if (test0&test1&doBudget);
161			fprintf(['pre-processing : started for budget \n']);
162			write2file([dirMat 'lock_budg'],1);
163	gforget	1.12	mkdir([dirMat 'BUDG']);
164	gforget	1.1	%compute time derivatives between snwpshots that will be
165			%compared in budgets with the time mean flux terms
166	gforget	1.13	tmp1=fullfile(dirModel,'diags',filesep,'BUDG',filesep,'budg2d_snap_set2*meta');
167			test3d=isempty(dir(tmp1))
168	gforget	1.5	diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set1');
169	gforget	1.13	if ~test3d;
170			diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set2');
171			else;
172			diags_diff_snapshots(dirModel,dirMat,'budg3d_snap_set1');
173			end;
174	gforget	1.5	%diags_diff_snapshots(dirModel,dirMat,'budg3d_snap_set1');
175	gforget	1.1	budget_list=1;
176			for kk=1:length(mygrid.RC);
177			tmp1=sprintf('%s/diags/BUDG/budg2d_snap_set3_%02i*',dirModel,kk);
178			tmp2=~isempty(dir(tmp1));
179			if tmp2;
180			budget_list=[budget_list kk];
181			tmp1=sprintf('budg2d_snap_set3_%02i',kk);
182	gforget	1.5	diags_diff_snapshots(dirModel,dirMat,tmp1);
183	gforget	1.1	end;
184			end;
185			eval(['save ' dirMat 'diags_select_budget_list.mat budget_list;']);
186	gforget	1.7	delete([dirMat 'lock_budg']);
187	gforget	1.1	test1=1;
188			fprintf(['pre-processing : completed for budget \n\n']);
189			end;
190
191			while ~test1&doBudget;%this process will wait for pre-processing to complete
192			fprintf(['waiting 30s more for removal of ' dirMat 'lock_budg \n']);
193	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
194			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
195			fprintf([' remove ' dirMat 'lock_budg manually, and start over. \n\n']);
196	gforget	1.1	test1=isempty(dir([dirMat 'lock_budg']));
197			pause(30);
198			end;
199
200	gforget	1.10	%set budget list
201			myparms.budgetList=1;
202			if ~isempty(dir([dirMat 'diags_select_budget_list.mat']));
203			eval(['load ' dirMat 'diags_select_budget_list.mat;']);
204			myparms.budgetList=budget_list;
205			end;