KerMor.m

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/* (Autoinserted by mtoc++)
 * This source code has been filtered by the mtoc++ executable,
 * which generates code that can be processed by the doxygen documentation tool.
 *
 * On the other hand, it can neither be interpreted by MATLAB, nor can it be compiled with a C++ compiler.
 * Except for the comments, the function bodies of your M-file functions are untouched.
 * Consequently, the FILTER_SOURCE_FILES doxygen switch (default in our Doxyfile.template) will produce
 * attached source files that are highly readable by humans.
 *
 * Additionally, links in the doxygen generated documentation to the source code of functions and class members refer to
 * the correct locations in the source code browser.
 * However, the line numbers most likely do not correspond to the line numbers in the original MATLAB source files.
 */

class KerMor
  :public handle {
    public: /* ( Constant ) */

        static const .char MainVersion = "0";
        static const .char SubVersion = "7";
        static const .char PrefTagPrefix = "KerMor_at_";
    public: /* ( Dependent ) */

        char DataDirectory;
        logical UseDPCM;
        double BlockSize;
        char DesktopLayout = "";
        char rbmatlabDirectory = "";
        char JKerMorSourceDirectory = "";
        integer Verbose = "[]";
        rowvec DefaultFigurePosition = "[]";
        logical UseDiary = "[]";
        char Workspace;
    public:

        HomeDirectory;
    public: /* ( Dependent ) */

        Hasrbmatlab = false;
        char TempDirectory = "";
        /*  Getter & Setter */
    public: /* ( Dependent ) */

        
#if 0 //mtoc++: 'set.DataDirectory'
function  DataDirectory(value) {
            if ~ischar(value)
                error(" DataDirectory must be a char array ");
            elseif ~isempty(value) && ~isdir(value)
                fprintf(" Creating directory %s\n ",value);
                mkdir(value);
            end
            setpref(this.getPrefTag," DATASTORE ",value);
        }

#endif


        
#if 0 //mtoc++: 'set.Workspace'
function  Workspace(value) {
            if ~ischar(value)
                error(" Workspace must be a char array ");
            elseif ~isempty(value) && ~isdir(value)
                fprintf(" Creating directory %s\n ",value);
                mkdir(value);
            end
            setpref(this.getPrefTag," WORKSPACE ",value);
        }

#endif


        
#if 0 //mtoc++: 'set.DesktopLayout'
function  DesktopLayout(value) {
            setpref(this.getPrefTag," DESKLAYOUT ",value);
        }

#endif


        
#if 0 //mtoc++: 'set.rbmatlabDirectory'
function  rbmatlabDirectory(value) {
            if ~isempty(value)
                if ~isdir(value)
                    error(" Invalid directory: %s ",value);
                end
                if ~exist(fullfile(value," startup_rbmatlab.m ")," file ")
                    error(" Invalid rbmatlab directory (no startup script found): %s ",value);
                end
            end
            setpref(this.getPrefTag," RBMATLABDIR ",value);
        }

#endif

#if 0 //mtoc++: 'set.JKerMorSourceDirectory'
function  JKerMorSourceDirectory(value) {
            if ~isempty(value)
                if ~isdir(value)
                    error(" Invalid directory: %s ",value);
                end
                chk = fullfile(value,[" kermor " filesep " ReducedModel.java "]);
                if ~exist(chk," file ")
                    error(" Invalid JKerMor directory (no ReducedModel.java found): %s ",value);
                end
            end
            setpref(this.getPrefTag," JKERMORDIR ",value);
        }

#endif

#if 0 //mtoc++: 'get.HomeDirectory'
function h = HomeDirectory() {
            if isempty(this.HomeDirectory)
                this.HomeDirectory= fileparts(which(" KerMor "));
            end
            h = this.HomeDirectory;
        }

#endif


        
#if 0 //mtoc++: 'get.DataDirectory'
function h = DataDirectory() {
            h = getpref(this.getPrefTag," DATASTORE ",);
        }

#endif


        
#if 0 //mtoc++: 'get.Workspace'
function h = Workspace() {
            h = getpref(this.getPrefTag," WORKSPACE ",);
            /*  If no workspace is set, use the data directory */
            if isempty(h)
                h = this.DataDirectory;
            end
        }

#endif


        
#if 0 //mtoc++: 'get.TempDirectory'
function h = TempDirectory() {
            h = fullfile(this.DataDirectory," tmp ");
            if ~exist(h," file ")
                mkdir(h);
            end
        }

#endif

#if 0 //mtoc++: 'get.DesktopLayout'
function d = DesktopLayout() {
            d = getpref(this.getPrefTag," DESKLAYOUT ",);
        }

#endif


        
#if 0 //mtoc++: 'get.rbmatlabDirectory'
function h = rbmatlabDirectory() {
            h = getpref(this.getPrefTag," RBMATLABDIR ",);
        }

#endif


        
#if 0 //mtoc++: 'get.JKerMorSourceDirectory'
function h = JKerMorSourceDirectory() {
            h = getpref(this.getPrefTag," JKERMORDIR ",);
        }

#endif


        
#if 0 //mtoc++: 'get.Hasrbmatlab'
function flag = Hasrbmatlab() {
            flag = false;
            if ~isempty(this.rbmatlabDirectory)
                flag = ~isempty(which(" rbmatlabhome "));
                if ~flag
                    warning(" KerMor:App ",...
                        [" rbmatlab directory is set, but script "...
                        "   "" rbmatlabhome ""  could not be found in current path.\n "...
                        " Unsure if rbmatlab-dependent models will work, "...
                        "  check if rbmatlab version has changed! "]);
                end
            end
        }

#endif

#if 0 //mtoc++: 'get.DefaultFigurePosition'
function value = DefaultFigurePosition() {
            value = getpref(this.getPrefTag," DefFigPos ",...
                get(0," DefaultFigurePosition "));
        }

#endif


        
#if 0 //mtoc++: 'set.DefaultFigurePosition'
function  DefaultFigurePosition(value) {
            if numel(value) ~= 4
                error(" The figure position must be a four element vector ");
            end
            setpref(this.getPrefTag," DefFigPos ",value);
            set(0," DefaultFigurePosition ",value);
        }

#endif


        
#if 0 //mtoc++: 'get.UseDPCM'
function value = UseDPCM() {
            value = getpref(this.getPrefTag," UseDPCM ", false);
        }

#endif


        
#if 0 //mtoc++: 'set.UseDPCM'
function  UseDPCM(value) {
            if ~islogical(value)
                error(" The UseDPCM flag must be boolean. ");
            end
            setpref(this.getPrefTag," UseDPCM ",value);
        }

#endif


        
#if 0 //mtoc++: 'get.BlockSize'
function value = BlockSize() {
            value = getpref(this.getPrefTag," BlockSize ", data.FileMatrix.BLOCK_SIZE);
        }

#endif


        
#if 0 //mtoc++: 'set.BlockSize'
function  BlockSize(value) {
            if ~isposrealscalar(value)
                error(" The BlockSize property must be a positive real scalar. ");
            end
            setpref(this.getPrefTag," BlockSize ",value);
        }

#endif


        
#if 0 //mtoc++: 'get.UseDiary'
function value = UseDiary() {
            value = getpref(this.getPrefTag," UseDiary ",false);
        }

#endif


        
#if 0 //mtoc++: 'set.UseDiary'
function  UseDiary(value) {
            if ~islogical(value)
                error(" The UseDiary flag must be boolean. ");
            end
            setpref(this.getPrefTag," UseDiary ",value);
        }

#endif


        
#if 0 //mtoc++: 'get.Verbose'
function value = Verbose() {
            value = getpref(this.getPrefTag," Verbose ",1);
        }

#endif


        
#if 0 //mtoc++: 'set.Verbose'
function  Verbose(value) {
            if ~isposintscalar(value)
                error(" The Verbose flag must be a positive integer ");
            end
            setpref(this.getPrefTag," Verbose ",value);
        }

#endif

    
    private: /* ( Dependent ) */


        function  initialize() {

            disp(" <<<<<<<<< Welcome to KerMor! >>>>>>>>>> ");

            /*  Check if preferences are set (i.e. KerMor.setup has been run on this machine) */
            disp(" Checking environment... ")
            pset = ~isempty(getpref(this.getPrefTag," DATASTORE ",[]));
            if ~pset
                if numlabs > 1
                    /*  For parallel computing case, throw an error as KerMor
                     * must be setup on each machine running parallel jobs! */
                    error(" You must run KerMor.setup on each machine you want to run parallel jobs with KerMor! ");
                else
                    fprintf(2," No KerMor preferences on this host found. Searching for settings from other hosts...\n ");
                    phome = getpref;
                    fn = fieldnames(phome);
                    op = strfind(fn,KerMor.PrefTagPrefix);
                    for i=1:numel(op)
                        if op[i] == 1
                            fprintf(" Do you want to copy the following preferences from host '%s'?\n ",fn[i](length(KerMor.PrefTagPrefix)+1:end));
                            disp(phome.(fn[i]));
                            r = lower(input(" (Y)es, (N)o or (C)ancel and start KerMor setup:  "," s "));
                            /*  Yes: copy prefs */
                            if r == " y "
                                /*  Select preferences substruct from host and copy
                                 * NOT using Utils.xx here as this is not yet on
                                 * the PATH! */
                                localp = phome.(fn[i]);
                                pfn = fieldnames(localp);
                                for k = 1:numel(pfn)
                                    setpref(this.getPrefTag,pfn[k],localp.(pfn[k]));
                                end
                                pset = true;
                                break;
                                /*  cancel: start setup */
                            elseif r == " c "
                                break;
                            end
                        end
                    end
                    if ~pset
                        if i == numel(op)
                            fprintf(2," No preferences copied from other hosts. Have to run setup.\n ");
                        end
                        fprintf(2," Entering KerMor setup...\n ");
                        KerMor.setup;
                    end
                end
            else
                fprintf(" KerMor preferences/settings found for tag '%s'...\n ",this.getPrefTag);
            end

            disp(" Initializing environment... ");

            warning off MATLAB:dispatcher:nameConflict;

            /*  Stuff only for single instance mode */
            if exist(" numlabs "," builtin ") == 5 && numlabs == 1
                /*  Preferences & Environment */
                setpref(" Internet "," SMTP_Server "," localhost ");

                /*  Desktop-only stuff */
                if usejava(" desktop ")
                    /*  Figure position settings */
                    if ~isempty(this.DefaultFigurePosition)
                        set(0," DefaultFigurePosition ",this.DefaultFigurePosition);
                    end

                    if ~isempty(this.DesktopLayout)
                        fprintf(" Applying desktop layout %s..\n ",this.DesktopLayout);
                        desktop = com.mathworks.mde.desk.MLDesktop.getInstance;
                        desktop.restoreLayout(this.DesktopLayout);
                    end
                end

                disp(" Calling  "" dbstop if error "" .. ");
                dbstop if error;
            end

            phome = this.HomeDirectory;
            addpath(phome);

            pcore = fullfile(phome," core ");

            /*  Initialize external folders & software */
            initextern(phome, pcore); 

            /*  Setup home directory & paths (AFTER extern, to have the path
             * entries search BEFORE externally created ones) */
            addpath(fullfile(phome," documentation "));
            addpath(fullfile(pcore," visual "));
            addpath(fullfile(pcore," tools "));
            addpath(fullfile(pcore," interfaces "));
            addpath(pcore);
            addpath(phome);

            initParallelization;

            clear(" phome "," pcore ");

            if this.UseDiary
                /*  Fix for non-unix log files */
                if isunix || ~isempty(which(" ppid "))
                    pid = ppid;
                else
                    pid = 0;
                end
                dfile = sprintf(" %s_KerMor%s.%s_pid%d_diary.txt ",datestr(now," yyyy-mm-dd "),...
                    KerMor.MainVersion,KerMor.SubVersion,pid);
                dfile = fullfile(this.TempDirectory,dfile);
                fprintf(" Initializing diary in %s..\n ",dfile);
                diary(dfile);
            end

            /*  Set more narrow format as default */
            format compact;

            warning on MATLAB:dispatcher:nameConflict;

            disp(" <<<<<<<<< Ready to go. >>>>>>>>>> ");

            function initextern(phome, pcore)
                /*  Checks for 3rd party software availability
                 *
                 * @todo include checks for pardiso once pardiso solver is
                 * implemented/wrapped */

                /*  rbmatlab */
                if ~isempty(this.rbmatlabDirectory)
                    disp(" <<<<<<<<< Starting rbmatlab >>>>>>>>>> ");
                    setenv(" RBMATLABTEMP ", this.TempDirectory);
                    setenv(" RBMATLABHOME ", this.rbmatlabDirectory);
                    addpath(this.rbmatlabDirectory);
                    curdir = pwd;
                    evalin(" base "," startup_rbmatlab; ");
                    evalin(" base "," clear all; ");
                    chdir(curdir);
                    disp(" <<<<<<<<< Done Starting rbmatlab >>>>>>>>>> ");
                end

                /*  Add KerMor-included external software paths */
                disp(" Initializing external tools... ")
                addpath(fullfile(pcore," extern "));
                addpath(fullfile(pcore," extern "," export_fig "));
                addpath(fullfile(pcore," extern "," compat "));
                addpath(fullfile(phome," matlabtojarmos "));
                addpath(fullfile(phome," matlabtools "));
                addpath(fullfile(phome," dpcm "));

                /*  md5 */
                d = fullfile(pcore," extern "," calcmd5 ");
                addpath(d);
                if ~exist(fullfile(d,[" CalcMD5. " mexext])," file ")
                    warning(" KerMor:init "," No compiled CalcMD5 mex file found. Did you run KerMor.setup completely?\nKerMor might not run properly. ");
                end

                /*  md5 */
                d = fullfile(pcore," extern "," typecastx ");
                addpath(d);
                if ~exist(fullfile(d,[" typecastx. " mexext])," file ")
                    warning(" KerMor:init "," No compiled typecastx mex file found. Did you run KerMor.setup completely?\nKerMor might not run properly. ");
                end
            end   

            function initParallelization
                /*  Initializes variables for parallel computation
                 *
                 * @todo wrap with try-catch and set flag in KerMor.App
                 * class!
                 *
                 * @note The 'feature' command is undocumented, see
                 * http://www.mathworks.com/matlabcentral/newsreader/view_thread/154551
                 * for more information. */

                /*  Sets the maximum number of threads to create by OpenMP
                 * binaries according to the number of cores available on
                 * the machine. */
                setenv(" OMP_NUM_THREADS ",num2str(feature(" numCores ")));
            end
        }
        function  shutdown() {

            if this.UseDiary
                disp(" Disabling diary.. ");
                diary off;
            end

            dbclear if error;
        }
    public: /* ( Static ) */ /* ( Dependent ) */

        static function KerMortheinstance = App() {
            persistent instance;
            if isempty(instance)
                instance = KerMor;
            end
            theinstance = instance;
        }
        static function  setup() {
            disp(" <<<<<<<<<< Welcome to the KerMor setup script. >>>>>>>>>> ");

            a = KerMor.App;
            addpath(a.HomeDirectory);
            addpath(genpath(fullfile(a.HomeDirectory," documentation ")));

            /* % KerMor directories
             * Setup the data storage directory */
            ds = a.DataDirectory;
            word = " keep ";
            if isempty(ds)
                ds = fullfile(a.HomeDirectory," data ");
                word = " set ";
            end
            str = sprintf(" Do you want to %s %s as your KerMor data file directory? Choosing 'No' opens a directory selection dialog.\n(Y)es/(N)o?:  ",word,strrep(ds," \ "," \\ "));
            if isequal(lower(input(str," s "))," n ")
                d = uigetdir(ds," Please specify the KerMor data file directory ");
                if d == 0
                    error(" No KerMor data file directory specified. Aborting setup. ");
                end
                ds = d;
            end
            a.DataDirectory= ds;

            /* % Setup KerMor development */
            if isempty(getpref(" KERMOR_DEVEL "," author ",))
                str = sprintf(" Do you want to develop KerMor on this machine?\n(Y)es/(N)o:  ");
                ds = lower(input(str," s "));
                if isequal(ds," y ")
                    addpath(fullfile(a.HomeDirectory," core "," tools "));
                    Devel.setup;

                    /* % Call setup for documentation creation */
                    addpath(fullfile(a.HomeDirectory," core "," extern "));
                    MatlabDocMaker.setup;
                end
            end

            /* % 3rd party programs */
            KerMor.setupextern;

            disp(" <<<<<<<<<< Setup complete. You can now start KerMor by running 'KerMor.start;'. >>>>>>>>>> ");
        }
        static function KerMorapp = start() {
            app = KerMor.App;
            app.initialize;
        }
        static function  stop() {
            KerMor.App.shutdown;
        }
        static function host = getHost() {
            try
                host = char(getHostName(java.net.InetAddress.getLocalHost));
            catch ME
/*                  warning('KerMor:hostdetection','Your Host could not be identified. Using "unknown"'); */
                host = " unknown ";
            end
            host = regexprep(strtrim(host)," [^\d\w] ",);
        }
        static function b = getGitBranch(dir) {
            if nargin < 1
                dir = KerMor.App.HomeDirectory;
            end
            olddir = pwd;
            cd(dir);
            /* [s, m] = system(sprintf('export TERM=%s; git log -n 1 --pretty=format:"%%H: %%s%%+ai by %%an<%%ae>"',getenv('TERM'))); */
            [s, msg] = system(" git log -n 1 --pretty=format:'%H: %s%+ai by %an<%ae>' > .gitbranch ");
            if s == 0
                b = fileread(" .gitbranch ");
                delete .gitbranch;
            else
                fprintf(2," KerMor.getGitBranch: %s\n ",strrep(msg,char(10),));
                b = [];
            end            
            cd(olddir);
        }
        static function chard = DocumentationLocation() {
            d = MatlabDocMaker.getOutputDirectory;
            if isempty(d) || ~exist(fullfile(d," index.html ")," file ")
                d = " http://www.morepas.org/software/kermor/index.html ";
            end
        }
        static function  createLogo() {
            h = figure;
            [X,Y] = meshgrid(-10:.5:10);
            Z = exp(-(X.^2+Y.^2-2*X" *Y)/20);% + .5*exp(-(X2.^2+Y2.^2-2*X2 "*Y2)/5);
            surfl(X,Y,Z," Parent ",h);
            lighting gouraud;
            colormap autumn;
            grid on;
        }
        static function tag = getPrefTag() {
            tag = [KerMor.PrefTagPrefix KerMor.getHost];
        }
        static function d = getDir() {
            t = KerMor.getPrefTag;
            path = getpref(t," LASTPATH ",KerMor.App.HomeDirectory);
            if exist(path," dir ") ~= 7
                path = fileparts(path);
                if exist(path," dir ") ~= 7
                    path = pwd;
                end
            end
            d = uigetdir(path," Select directory ");
            if ~isequal(d, 0) && exist(d," dir ") == 7
                setpref(t," LASTPATH ",d);
            else
                d = false;
            end
        }
    private: /* ( Static ) */ /* ( Dependent ) */


        static function  setupextern() {
            a = KerMor.App;

            /* % Optional: rbmatlab */
            rbmat = a.rbmatlabDirectory;
            if ~isempty(rbmat)
                str = sprintf(" Do you want to keep the local rbmatlab version at %s with KerMor?\n(Y)es/(N)o:  ",strrep(rbmat," \ "," \\ "));
                resp = " n ";
            else
                str = sprintf(" Do you want to register a local rbmatlab version with KerMor?\n(Y)es/(N)o:  ");
                resp = " y ";
            end
            ds = lower(input(str," s "));
            if isequal(ds,resp)
                rbmat = uigetdir(pwd," Please select the rbmatlab source root folder. ");
                if rbmat == 0
                    warning(" KerMor:setup ",[" No rbmatlab directory specified. Continuing witout using rbmatlab.\n "...
                        " You can still register a local version of rbmatlab by setting the KerMor.App.rbmatlabDirectory manually. "]);
                else
                    a.rbmatlabDirectory= rbmat;
                end
            end

            /* % Optional: JKerMor */
            jk = a.JKerMorSourceDirectory;
            if ~isempty(jk)
                str = sprintf(" Do you want to keep the local JKerMor version at %s with KerMor?\n(Y)es/(N)o:  ",strrep(jk," \ "," \\ "));
                resp = " n ";
            else
                str = sprintf(" Do you want to register a local JKerMor version with KerMor?\n(Y)es/(N)o:  ");
                resp = " y ";
            end
            ds = lower(input(str," s "));
            if isequal(ds,resp)
                jk = uigetdir(pwd," Please select the JKerMor source root folder. ");
                if jk == 0
                    warning(" KerMor:setup ",[" No JKerMor directory specified. Continuing witout using JKerMor.\n "...
                        " You can still register a local version of JKerMor by setting the KerMor.App.JKerMorSourceDirectory manually. "]);
                else
                    a.JKerMorSourceDirectory= jk;
                end
            end

            /* % Compile MEX files */
            warning off MATLAB:dispatcher:nameConflict
            olddir = pwd;
            /*  CalcMD5 */
            disp(" Compliling CalcMD5.. ");
            cd(fullfile(a.HomeDirectory," core "," extern "," calcmd5 "));
            mex CFLAGS="\$CFLAGS -std=c99" CalcMD5.c

            /*  typecast/x */
            disp(" Compliling typecast/x.. ");
            cd(fullfile(a.HomeDirectory," core "," extern "," typecastx "));
            mex typecast.c
            mex typecastx.c

            if isunix
                disp(" Compliling ppid.. ");
                cd(fullfile(a.HomeDirectory," core "," extern "));
                mex ppid.c
            else
                warning(" KerMor:setup "," No ppid function available (win32 platform) ");
            end

            warning on MATLAB:dispatcher:nameConflict
            cd(olddir);
        }


        static function app = loadobj(unused1) {
            app = KerMor.App;
        }
    private: /* ( Dependent ) */

        KerMor() {
        }
        function obj = saveobj() {
            obj = [];
        }
};