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 ~myenv.nctiles;%only works with binaries
    dirSnap=fullfile(dirModel,'diags',filesep);
    doBudget=~isempty(dir([dirSnap 'budg2d_snap_set1*']));
    if ~doBudget;
      dirSnap=fullfile(dirModel,'diags',filesep,'BUDG',filesep);
      doBudget=~isempty(dir([dirSnap 'budg2d_snap_set1*']));
    end;

    doCost=~isempty(dir([dirModel 'barfiles' filesep 'm_eta_day.*.data']));
    doCost=doCost|~isempty(dir([dirModel 'm_eta_day.*.data']));

    doCtrl=~isempty(dir([dirModel 'ADXXfiles' filesep 'xx*.effective.*']));
    doCtrl=doCtrl|~isempty(dir([dirModel 'xx*.effective.*']));
else;
    dirSnap=fullfile(dirModel,'diags',filesep);
    doBudget=0;
    doCost=0;
    doCtrl=0;
end;

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

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

disp(myswitch);
if doInteractive;
  test0=input('edit switches (1) or proceed (0)?\n');
  while test0;
    test0=input('type modification (e.g. as ''myswitch.doBudget=1;'') or hit return to stop editing.\n');
    if ~isempty(test0); eval(test0); disp(myswitch); end;
  end;
end;


%set the list of diags directories and files
if myenv.nctiles;
    if isdir(fullfile(dirModel,'nctiles',filesep));
        listSubdirs={fullfile(dirModel,'nctiles',filesep)};
    elseif isdir(fullfile(dirModel,'nctiles_climatology',filesep));
        listSubdirs={fullfile(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(dirModel,['diags' filesep]);
    %
    myenv.nctilesdir='';
    myenv.nctileslist={};
end;
myenv.matdir=fullfile(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_mygrid 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/']);
    mkdir([dirMat 'profiles/input/']);
    mkdir([dirMat 'profiles/output/']);
    % NOTE: if on DOS system change ln to mklink

    %system(['ln -s /nobackupp7/gforget2/ecco_v4/input_v4r5/input_insitu/*.nc ' dirMat 'profiles/input/.']);
    system(['cp -av ' dirModel '*.nc ' dirMat 'profiles/input/.']);

    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 snapshots that will be
    %compared in budgets with the time mean flux terms
    tmp1=fullfile(dirSnap,'budg3d_snap_set1*meta');
    test3d=~isempty(dir(tmp1));
    tmp1=fullfile(dirSnap,'budg3d_snap_set1*meta');
    test3d=test3d|~isempty(dir(tmp1));
    diags_diff_snapshots(dirSnap,dirMat,'budg2d_snap_set1');
    if ~test3d;
      diags_diff_snapshots(dirSnap,dirMat,'budg2d_snap_set2');
    else;
      diags_diff_snapshots(dirSnap,dirMat,'budg3d_snap_set1');
    end;
    budget_list=1;
    for kk=1:length(mygrid.RC);
        tmp1=sprintf('%s/budg2d_snap_set3_%02i*',dirSnap,kk);
        tmp2=~isempty(dir(tmp1));
        if tmp2;
            budget_list=[budget_list kk];
            tmp1=sprintf('budg2d_snap_set3_%02i',kk);
            diags_diff_snapshots(dirSnap,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	1.15	if ~myenv.nctiles;%only works with binaries
33			dirSnap=fullfile(dirModel,'diags',filesep);
34			doBudget=~isempty(dir([dirSnap 'budg2d_snap_set1*']));
35			if ~doBudget;
36			dirSnap=fullfile(dirModel,'diags',filesep,'BUDG',filesep);
37			doBudget=~isempty(dir([dirSnap 'budg2d_snap_set1*']));
38			end;
39
40			doCost=~isempty(dir([dirModel 'barfiles' filesep 'm_eta_day.*.data']));
41			doCost=doCost\|~isempty(dir([dirModel 'm_eta_day.*.data']));
42
43			doCtrl=~isempty(dir([dirModel 'ADXXfiles' filesep 'xx.effective.']));
44			doCtrl=doCtrl\|~isempty(dir([dirModel 'xx.effective.']));
45	gforget	1.8	else;
46	gforget	1.15	dirSnap=fullfile(dirModel,'diags',filesep);
47	gforget	1.10	doBudget=0;
48			doCost=0;
49			doCtrl=0;
50	gforget	1.8	end;
51
52	gforget	1.12	doProfiles=~isempty(dir([dirModel 'MITprof' filesep]));
53	gforget	1.8	preprocessProfiles=0;
54	gforget	1.14	myenv.profiles=fullfile(dirModel,'MITprof',filesep);
55	gforget	1.8	if ~doProfiles;
56	gforget	1.12	doProfiles=~isempty(dir([dirModel 'profiles' filesep]));
57	gforget	1.10	preprocessProfiles=1;
58	gforget	1.14	myenv.profiles=fullfile(dirMat,'profiles',filesep,'output',filesep);
59	gforget	1.8	end;
60	gforget	1.1
61			%output switches
62			myswitch.doBudget=doBudget;
63			myswitch.doProfiles=doProfiles;
64			myswitch.doCost=doCost;
65			myswitch.doCtrl=doCtrl;
66
67	gforget	1.15	disp(myswitch);
68			if doInteractive;
69			test0=input('edit switches (1) or proceed (0)?\n');
70			while test0;
71			test0=input('type modification (e.g. as ''myswitch.doBudget=1;'') or hit return to stop editing.\n');
72			if ~isempty(test0); eval(test0); disp(myswitch); end;
73			end;
74			end;
75
76
77	gforget	1.6	%set the list of diags directories and files
78			if myenv.nctiles;
79	gforget	1.14	if isdir(fullfile(dirModel,'nctiles',filesep));
80			listSubdirs={fullfile(dirModel,'nctiles',filesep)};
81			elseif isdir(fullfile(dirModel,'nctiles_climatology',filesep));
82			listSubdirs={fullfile(dirModel,'nctiles_climatology',filesep)};
83	gforget	1.11	end;
84
85	gforget	1.6	listFiles=dir(listSubdirs{1}); listFiles={listFiles(:).name};
86			%remove irrelevant files/dirs
87			test1=ones(size(listFiles));
88			for kk=1:length(listFiles);
89	gforget	1.12	tmp1=fullfile(listSubdirs{1},listFiles{kk},[listFiles{kk} '*.nc']);
90	gforget	1.10	test1(kk)=~isempty(dir(tmp1));
91	gforget	1.6	end;
92			listFiles={listFiles{find(test1)}};
93			%store in myparms for later use
94			myenv.nctilesdir=listSubdirs{1};
95			myenv.nctileslist=listFiles;
96	gforget	1.12	%
97			myenv.diagsdir='';
98			else;
99	gforget	1.14	myenv.diagsdir=fullfile(dirModel,['diags' filesep]);
100	gforget	1.12	%
101			myenv.nctilesdir='';
102			myenv.nctileslist={};
103	gforget	1.6	end;
104	gforget	1.14	myenv.matdir=fullfile(dirMat);
105	gforget	1.6
106	gforget	1.1	%0) create dirMat if needed:
107	gforget	1.7	if isempty(dir(dirMat)); mkdir(dirMat); end;
108	gforget	1.1
109			%1) pre-processing diags_grid_parms.mat
110			test0=isempty(dir([dirMat 'diags_grid_parms.mat']));
111			test1=isempty(dir([dirMat 'lock_mygrid']));
112
113			if test0&test1;%this process will do the pre-processing
114	gforget	1.8	fprintf(['pre-processing : started for mygrid, myparms \n']);
115	gforget	1.1	write2file([dirMat 'lock_mygrid'],1);
116			%set the list of diags times
117	gforget	1.10	[listTimes]=diags_list_times;
118	gforget	1.1	%set grid and model parameters:
119	gforget	1.8	diags_grid_parms(listTimes,doInteractive);
120	gforget	1.1	%save to disk:
121	gforget	1.10	%if doInteractive;
122			eval(['save ' dirMat 'diags_grid_parms.mat mygrid myparms;']);
123			%end;
124	gforget	1.7	delete([dirMat 'lock_mygrid']);
125	gforget	1.1	test1=1;
126	gforget	1.8	fprintf(['pre-processing : completed for mygrid, myparms \n\n']);
127	gforget	1.1	end;
128
129	gforget	1.6	%here I should test that files are indeed found (may have been moved)
130
131	gforget	1.1	while ~test1;%this process will wait for pre-processing to complete
132			fprintf(['waiting 30s for removal of ' dirMat 'lock_mygrid \n']);
133	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
134			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
135	gforget	1.14	fprintf([' remove ' dirMat 'lock_mygrid manually, and start over. \n\n']);
136	gforget	1.1	test1=isempty(dir([dirMat 'lock_mygrid']));
137			pause(30);
138			end;
139
140			%here we always reload the grid from dirMat to make sure the same one is used throughout
141	gforget	1.10	eval(['load ' dirMat 'diags_grid_parms.mat;']);
142	gforget	1.1
143			%2) pre-processing profiles
144			test0=isempty(dir([dirMat 'profiles/']));
145			test1=isempty(dir([dirMat 'lock_profiles']));
146
147	gforget	1.8	if test0&test1&doProfiles&preprocessProfiles;%this process will do the pre-processing
148	gforget	1.1	fprintf(['pre-processing : started for profiles \n']);
149			write2file([dirMat 'lock_profiles'],1);
150	gforget	1.7	mkdir([dirMat 'profiles/']);
151	gforget	1.14	mkdir([dirMat 'profiles/input/']);
152			mkdir([dirMat 'profiles/output/']);
153	gforget	1.10	% NOTE: if on DOS system change ln to mklink
154	gforget	1.15
155			%system(['ln -s /nobackupp7/gforget2/ecco_v4/input_v4r5/input_insitu/*.nc ' dirMat 'profiles/input/.']);
156			system(['cp -av ' dirModel '*.nc ' dirMat 'profiles/input/.']);
157
158	gforget	1.1	if dirModel(1)~='/'; dirModelFull=[pwd '/' dirModel]; else; dirModelFull=dirModel; end;
159	gforget	1.10	% NOTE: if on DOS system change ln to mklink
160	gforget	1.7	system(['ln -s ' dirModelFull 'profiles/*equi.data ' dirMat 'profiles/.']);
161	gforget	1.4	listModel={'argo_feb2013_1992_to_2007','argo_feb2013_2008_to_2010',...
162	gforget	1.3	'argo_feb2013_2011_to_2012','ctd_feb2013','itp_feb2013*',...
163			'seals_feb2013','xbt_feb2013','climode_feb2013*'};
164	gforget	1.1	MITprof_gcm2nc([dirMat 'profiles/'],listModel);
165	gforget	1.7	delete([dirMat 'lock_profiles']);
166	gforget	1.1	test1=1;
167			fprintf(['pre-processing : completed for profiles \n\n']);
168			end;
169
170			while ~test1&doProfiles;%this process will wait for pre-processing to complete
171			fprintf(['waiting 30s for removal of ' dirMat 'lock_profiles \n']);
172	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
173			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
174			fprintf([' remove ' dirMat 'lock_profiles manually, and start over. \n\n']);
175	gforget	1.1	test1=isempty(dir([dirMat 'lock_profiles']));
176			pause(30);
177			end;
178
179			%3) budget pre-processing
180	gforget	1.12	test0=isempty(dir([dirMat 'BUDG']));
181	gforget	1.1	test1=isempty(dir([dirMat 'lock_budg']));%this aims at having only one process do the
182
183			if (test0&test1&doBudget);
184			fprintf(['pre-processing : started for budget \n']);
185			write2file([dirMat 'lock_budg'],1);
186	gforget	1.12	mkdir([dirMat 'BUDG']);
187	gforget	1.15	%compute time derivatives between snapshots that will be
188	gforget	1.1	%compared in budgets with the time mean flux terms
189	gforget	1.15	tmp1=fullfile(dirSnap,'budg3d_snap_set1*meta');
190			test3d=~isempty(dir(tmp1));
191			tmp1=fullfile(dirSnap,'budg3d_snap_set1*meta');
192			test3d=test3d\|~isempty(dir(tmp1));
193			diags_diff_snapshots(dirSnap,dirMat,'budg2d_snap_set1');
194	gforget	1.13	if ~test3d;
195	gforget	1.15	diags_diff_snapshots(dirSnap,dirMat,'budg2d_snap_set2');
196	gforget	1.13	else;
197	gforget	1.15	diags_diff_snapshots(dirSnap,dirMat,'budg3d_snap_set1');
198	gforget	1.13	end;
199	gforget	1.1	budget_list=1;
200			for kk=1:length(mygrid.RC);
201	gforget	1.15	tmp1=sprintf('%s/budg2d_snap_set3_%02i*',dirSnap,kk);
202	gforget	1.1	tmp2=~isempty(dir(tmp1));
203			if tmp2;
204			budget_list=[budget_list kk];
205			tmp1=sprintf('budg2d_snap_set3_%02i',kk);
206	gforget	1.15	diags_diff_snapshots(dirSnap,dirMat,tmp1);
207	gforget	1.1	end;
208			end;
209			eval(['save ' dirMat 'diags_select_budget_list.mat budget_list;']);
210	gforget	1.7	delete([dirMat 'lock_budg']);
211	gforget	1.1	test1=1;
212			fprintf(['pre-processing : completed for budget \n\n']);
213			end;
214
215			while ~test1&doBudget;%this process will wait for pre-processing to complete
216			fprintf(['waiting 30s more for removal of ' dirMat 'lock_budg \n']);
217	gforget	1.2	fprintf(['- That should happen automatically after pre-processing is complete \n']);
218			fprintf(['- But if a previous session was interupted, you may need to stop this one, \n ']);
219			fprintf([' remove ' dirMat 'lock_budg manually, and start over. \n\n']);
220	gforget	1.1	test1=isempty(dir([dirMat 'lock_budg']));
221			pause(30);
222			end;
223
224	gforget	1.10	%set budget list
225			myparms.budgetList=1;
226			if ~isempty(dir([dirMat 'diags_select_budget_list.mat']));
227			eval(['load ' dirMat 'diags_select_budget_list.mat;']);
228			myparms.budgetList=budget_list;
229			end;