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=[dirModel '/'];
if isempty(dirMat); dirMat=[dirModel 'mat/']; else; dirMat=[dirMat '/']; end;
if isempty(who('doInteractive')); doInteractive=0; end;

%detect which types of files are avaiable
test0=isdir([dirModel 'diags']);
test1=isdir([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;%only works with binaries
    doBudget=~isempty(dir([dirModel 'diags/BUDG/']))
    doBudget=doBudget&~myenv.nctiles;
    doCost=~isempty(dir([dirModel 'barfiles/']))
    doCtrl=~isempty(dir([dirModel 'ADXXfiles/']))
else;
    doBudget=0;
    doCost=0;
    doCtrl=0;
end;

doProfiles=~isempty(dir([dirModel 'MITprof/']));
preprocessProfiles=0;
myenv.profiles=[pwd '/' dirModel 'MITprof/'];
if ~doProfiles;
    doProfiles=~isempty(dir([dirModel 'profiles/']));
    preprocessProfiles=1;
    myenv.profiles=[pwd '/' dirMat 'profiles/output/'];
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;
    listSubdirs={[pwd '/' dirModel 'nctiles/']};
    listFiles=dir(listSubdirs{1}); listFiles={listFiles(:).name};
    %remove irrelevant files/dirs
    test1=ones(size(listFiles));
    for kk=1:length(listFiles);
        tmp1=[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;
end;

%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
    diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set1');
    diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set2');
    diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set3');
    %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			dirModel=[dirModel '/'];
16			if isempty(dirMat); dirMat=[dirModel 'mat/']; else; dirMat=[dirMat '/']; 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			test1=isdir([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	1.10	if doInteractive;%only works with binaries
33			doBudget=~isempty(dir([dirModel 'diags/BUDG/']))
34			doBudget=doBudget&~myenv.nctiles;
35			doCost=~isempty(dir([dirModel 'barfiles/']))
36			doCtrl=~isempty(dir([dirModel 'ADXXfiles/']))
37	gforget	1.8	else;
38	gforget	1.10	doBudget=0;
39			doCost=0;
40			doCtrl=0;
41	gforget	1.8	end;
42
43			doProfiles=~isempty(dir([dirModel 'MITprof/']));
44			preprocessProfiles=0;
45			myenv.profiles=[pwd '/' dirModel 'MITprof/'];
46			if ~doProfiles;
47	gforget	1.10	doProfiles=~isempty(dir([dirModel 'profiles/']));
48			preprocessProfiles=1;
49			myenv.profiles=[pwd '/' dirMat 'profiles/output/'];
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			listSubdirs={[pwd '/' dirModel 'nctiles/']};
61			listFiles=dir(listSubdirs{1}); listFiles={listFiles(:).name};
62			%remove irrelevant files/dirs
63			test1=ones(size(listFiles));
64			for kk=1:length(listFiles);
65	gforget	1.10	tmp1=[listSubdirs{1} listFiles{kk} '/' listFiles{kk} '*.nc'];
66			test1(kk)=~isempty(dir(tmp1));
67	gforget	1.6	end;
68			listFiles={listFiles{find(test1)}};
69			%store in myparms for later use
70			myenv.nctilesdir=listSubdirs{1};
71			myenv.nctileslist=listFiles;
72			end;
73
74	gforget	1.1	%0) create dirMat if needed:
75	gforget	1.7	if isempty(dir(dirMat)); mkdir(dirMat); end;
76	gforget	1.1
77			%1) pre-processing diags_grid_parms.mat
78			test0=isempty(dir([dirMat 'diags_grid_parms.mat']));
79			test1=isempty(dir([dirMat 'lock_mygrid']));
80
81			if test0&test1;%this process will do the pre-processing
82	gforget	1.8	fprintf(['pre-processing : started for mygrid, myparms \n']);
83	gforget	1.1	write2file([dirMat 'lock_mygrid'],1);
84			%set the list of diags times
85	gforget	1.10	[listTimes]=diags_list_times;
86	gforget	1.1	%set grid and model parameters:
87	gforget	1.8	diags_grid_parms(listTimes,doInteractive);
88	gforget	1.1	%save to disk:
89	gforget	1.10	%if doInteractive;
90			eval(['save ' dirMat 'diags_grid_parms.mat mygrid myparms;']);
91			%end;
92	gforget	1.7	delete([dirMat 'lock_mygrid']);
93	gforget	1.1	test1=1;
94	gforget	1.8	fprintf(['pre-processing : completed for mygrid, myparms \n\n']);
95	gforget	1.1	end;
96
97	gforget	1.6	%here I should test that files are indeed found (may have been moved)
98
99	gforget	1.1	while ~test1;%this process will wait for pre-processing to complete
100			fprintf(['waiting 30s for removal of ' dirMat 'lock_mygrid \n']);
101	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
102			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
103			fprintf([' remove ' dirMat 'lock_grid manually, and start over. \n\n']);
104	gforget	1.1	test1=isempty(dir([dirMat 'lock_mygrid']));
105			pause(30);
106			end;
107
108			%here we always reload the grid from dirMat to make sure the same one is used throughout
109	gforget	1.10	eval(['load ' dirMat 'diags_grid_parms.mat;']);
110	gforget	1.1
111			%2) pre-processing profiles
112			test0=isempty(dir([dirMat 'profiles/']));
113			test1=isempty(dir([dirMat 'lock_profiles']));
114
115	gforget	1.8	if test0&test1&doProfiles&preprocessProfiles;%this process will do the pre-processing
116	gforget	1.1	fprintf(['pre-processing : started for profiles \n']);
117			write2file([dirMat 'lock_profiles'],1);
118	gforget	1.7	mkdir([dirMat 'profiles/']);
119	gforget	1.10	% NOTE: if on DOS system change ln to mklink
120	gforget	1.7	system(['ln -s /net/nares/raid11/ecco-shared/ecco-version-4/input/input_insitu ' dirMat 'profiles/input']);
121			mkdir([dirMat 'profiles/output/']);
122	gforget	1.1	if dirModel(1)~='/'; dirModelFull=[pwd '/' dirModel]; else; dirModelFull=dirModel; end;
123	gforget	1.10	% NOTE: if on DOS system change ln to mklink
124	gforget	1.7	system(['ln -s ' dirModelFull 'profiles/*equi.data ' dirMat 'profiles/.']);
125	gforget	1.4	listModel={'argo_feb2013_1992_to_2007','argo_feb2013_2008_to_2010',...
126	gforget	1.3	'argo_feb2013_2011_to_2012','ctd_feb2013','itp_feb2013*',...
127			'seals_feb2013','xbt_feb2013','climode_feb2013*'};
128	gforget	1.1	MITprof_gcm2nc([dirMat 'profiles/'],listModel);
129	gforget	1.7	delete([dirMat 'lock_profiles']);
130	gforget	1.1	test1=1;
131			fprintf(['pre-processing : completed for profiles \n\n']);
132			end;
133
134			while ~test1&doProfiles;%this process will wait for pre-processing to complete
135			fprintf(['waiting 30s for removal of ' dirMat 'lock_profiles \n']);
136	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
137			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
138			fprintf([' remove ' dirMat 'lock_profiles manually, and start over. \n\n']);
139	gforget	1.1	test1=isempty(dir([dirMat 'lock_profiles']));
140			pause(30);
141			end;
142
143			%3) budget pre-processing
144			test0=isempty(dir([dirMat 'BUDG/']));
145			test1=isempty(dir([dirMat 'lock_budg']));%this aims at having only one process do the
146
147			if (test0&test1&doBudget);
148			fprintf(['pre-processing : started for budget \n']);
149			write2file([dirMat 'lock_budg'],1);
150	gforget	1.7	mkdir([dirMat 'BUDG/']);
151	gforget	1.1	%compute time derivatives between snwpshots that will be
152			%compared in budgets with the time mean flux terms
153	gforget	1.5	diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set1');
154			diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set2');
155			diags_diff_snapshots(dirModel,dirMat,'budg2d_snap_set3');
156			%diags_diff_snapshots(dirModel,dirMat,'budg3d_snap_set1');
157	gforget	1.1	budget_list=1;
158			for kk=1:length(mygrid.RC);
159			tmp1=sprintf('%s/diags/BUDG/budg2d_snap_set3_%02i*',dirModel,kk);
160			tmp2=~isempty(dir(tmp1));
161			if tmp2;
162			budget_list=[budget_list kk];
163			tmp1=sprintf('budg2d_snap_set3_%02i',kk);
164	gforget	1.5	diags_diff_snapshots(dirModel,dirMat,tmp1);
165	gforget	1.1	end;
166			end;
167			eval(['save ' dirMat 'diags_select_budget_list.mat budget_list;']);
168	gforget	1.7	delete([dirMat 'lock_budg']);
169	gforget	1.1	test1=1;
170			fprintf(['pre-processing : completed for budget \n\n']);
171			end;
172
173			while ~test1&doBudget;%this process will wait for pre-processing to complete
174			fprintf(['waiting 30s more for removal of ' dirMat 'lock_budg \n']);
175	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
176			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
177			fprintf([' remove ' dirMat 'lock_budg manually, and start over. \n\n']);
178	gforget	1.1	test1=isempty(dir([dirMat 'lock_budg']));
179			pause(30);
180			end;
181
182	gforget	1.10	%set budget list
183			myparms.budgetList=1;
184			if ~isempty(dir([dirMat 'diags_select_budget_list.mat']));
185			eval(['load ' dirMat 'diags_select_budget_list.mat;']);
186			myparms.budgetList=budget_list;
187			end;