Merge pull request automaticanalysis#213 from tiborauer/master

aacache, toolboxes

README.md

@@ -25,7 +25,7 @@ More information can be found on the [wiki](https://github.com/automaticanalysis
  - System: Linux or MacOX (Windows is not supported. Sorry!)
  - Softwares: 
    - **MATLAB** - It has been tested with version r2013a and later
-   - **SPM** - It has been tested with versions SPM12 and later (SPM12 r7487 is recommended!)
+   - **SPM** - It has been tested with versions SPM12 and later (SPM12 r7487 or later **required**!)
  - Recommended software for features:
    - For MEG (maxfilter): Neuromag (Elekta Instrument AB Stockholm, Stockholm, Sweden)
    - For visual representation of the pipeline: [GraphViz](http://www.graphviz.org)
@@ -58,7 +58,7 @@ Some parameters (path settings, format settings) stored in **_<aarootdir>/aa_par
  - *directory_conventions/seriesoutputformat*: `sprintf` formatting string to get series directory as stored in subject directory
  - *directory_conventions/protocol_structural*: Name of the structural/anatomical protocol as stored in the DICOM header
  - *directory_conventions/dicomfilter*: Directory listing filter to find DICOM data
- - *directory_conventions/spmdir*: Path to SPM. **N.B.: You should not modify SPM version in your user script but rather in your local parameter file.**
+ - *directory_conventions/toolboxes/spm*: Settings for SPM. **N.B.: You should not modify SPM version in your user script but rather in your local parameter file.**
 Optional:
  - For distortion correction using fieldmap:
    - *directory_conventions/protocol_fieldmap*: Name of the fieldmap protocol as stored in the DICOM header
@@ -84,10 +84,10 @@ Optional:
      - *directory_conventions/freesurfershell*: Shell used to run FreeSurfer. It should be in accordance with *directory_conventions/freesurfersetup* and *directory_conventions/freesurferenvironment*
      - *directory_conventions/freesurferenvironment*: Path to FreeSurfer environmental setup script, executing before any FreeSurfer command
 
-   - *directory_conventions/eeglabdir*: Path to EEGLab
+   - *directory_conventions/toolboxes/eeglab*: Settings for EEGLab
    - *directory_conventions/GIFTdir*: Path to GIFT
    - *directory_conventions/ANTSdir*: Path to ANTS
-   - *directory_conventions/fieldtripdir*: Path to FieldTrip
+   - *directory_conventions/toolboxes/fieldtrip*: Settings for FieldTrip
    - *directory_conventions/BrainWaveletdir*: Path to BrainWavelet
    - *directory_conventions/spmtoolsdir*: Path to external/custom SPM toolboxes
 

aaClass.m

@@ -63,7 +63,7 @@
                 fprintf(' <a href = "%s">%s</a>\n',obj.ManuscriptURL,d{2});
                 fprintf(' <a href = "%s">%s</a>\n',obj.ManuscriptURL,d{3});
                 fprintf('\nPlease visit <a href = "%s">The aa website</a> for more information!\n',obj.aaURL);
-                fprintf('\nHere you can find example <a href = "matlab: cd %s">tasklists</a> and <a href = "matlab: cd %s">scripts</a>.\n',...
+                fprintf('\nHere you can find example <a href = "matlab: cd %s">parameter sets</a> and <a href = "matlab: cd %s">examples</a>.\n',...
                     fullfile(obj.Path,'aa_parametersets'),fullfile(obj.Path,'examples'));
                 fprintf('Ready.\n');
             end

aa_engine/aa_close.m

@@ -12,21 +12,20 @@ function aa_close(varargin)
         tasks = varargin(2:end);
 end
 
-global aacache;
-
 if cell_index(tasks,'restorepath') && ...
         (~isstruct(aap) || ~isfield(aap.options,'restorepath') ||... % not specified
         aap.options.restorepath) % specified and enabled
-    if isstruct(aacache) && isfield(aacache,'path')
-        if isfield(aacache.path,'bcp_path'), path(aacache.path.bcp_path); end
-        if isfield(aacache.path,'bcp_shellpath'), setenv('PATH', aacache.path.bcp_shellpath); end
-    end
+    [s,p] = aas_cache_get(aap,'bcp_path','system'); if s, path(p); end
+    [s,p] = aas_cache_get(aap,'bcp_shellpath','system'); if s, setenv('PATH', p); end
 end
 
 % restore warnings
-if cell_index(tasks,'restorewarnings') && isstruct(aacache) && isfield(aacache,'warnings')
-    for w = aacache.warnings
-        warning(w);
+if cell_index(tasks,'restorewarnings')
+    [s,ws] = aas_cache_get(aap,'warnings','system');
+    if s
+       for w = ws
+           warning(w);
+       end
     end
 end
 

aa_engine/aa_doprocessing_onetask.m

@@ -1,9 +1,13 @@
 function aap=aa_doprocessing_onetask(aap,task,modulenum,indices,gaaworker)
 
 global aaworker
+global aacache
 if nargin == 5 % aaworker passed
     aaworker = gaaworker;
 end
+if isfield(aaworker,'aacache')
+   aacache = aaworker.aacache; 
+end
 
 aaworker.modulestarttime=now;
 

aa_engine/aa_init.m

@@ -1,5 +1,4 @@
 % Automatic analysis - initialise paths from recipe
-
 function [aap]=aa_init(aap)
 
 global aa
@@ -31,47 +30,70 @@
     end
 end
 
-global aacache
 % Set UTC time function
 if exist('utc_time','file')
-    aacache.utc_time = @utc_time;
+    utime = @utc_time;
 else
     aas_log(aap,false,'INFO: utc_time is not found. java function will be used\n')
-    aacache.utc_time = @java.lang.System.currentTimeMillis;
+    utime = @java.lang.System.currentTimeMillis;
 end
+aas_cache_put(aap,'utc_time',utime,'utils');
 
 %% Set Paths
-aacache.path.bcp_path = path;
-aacache.path.bcp_shellpath = getenv('PATH');
+aas_cache_put(aap,'bcp_path',path,'system');
+aas_cache_put(aap,'bcp_shellpath',getenv('PATH'),'system');
+
 % Path for SPM
-if ~isempty(aap.directory_conventions.spmdir)
-    % by setting this environment variable it becomes possible to define other
-    % paths relative to $SPMDIR in defaults files and task lists
-    setenv('SPMDIR',aap.directory_conventions.spmdir);
+SPMDIR = '';
+doKeepInPath = true;
+% backward compatibility
+if isfield(aap.directory_conventions,'spmdir') && ~isempty(aap.directory_conventions.spmdir)
+    SPMDIR = aap.directory_conventions.spmdir;
 end
-
+% toolboxes
+if isfield(aap.directory_conventions,'toolbox')
+    tbxInd = strcmp({aap.directory_conventions.toolbox.name},'spm');
+    if any(tbxInd)
+        SPMDIR = aap.directory_conventions.toolbox(tbxInd).dir;
+        doKeepInPath = aap.directory_conventions.toolbox(tbxInd).extraparameters.doKeepInPath;
+    end
+end
+% path
+if isempty(SPMDIR)
+    if isempty(which('spm'))
+        aas_log(aap,true,'You''re going to need SPM, add it to your paths manually or set in aap.directory_conventions.toolbox');
+    else
+        SPMDIR = spm('Dir');
+        doKeepInPath = true;
+    end
+end
+% deployed
 if isdeployed
-    aap.directory_conventions.spmdir = spm('Dir');
-    setenv('SPMDIR',aap.directory_conventions.spmdir);
+    SPMDIR = spm('Dir');
+    doKeepInPath = true;
+end
+% reset
+if isfield(aap.directory_conventions,'spmdir'), aap.directory_conventions.spmdir = SPMDIR; end
+if isfield(aap.directory_conventions,'toolbox') && any(tbxInd)
+    aap.directory_conventions.toolbox(tbxInd).name = 'spm';
+    aap.directory_conventions.toolbox(tbxInd).dir = SPMDIR; 
+    aap.directory_conventions.toolbox(tbxInd).extraparameters.doKeepInPath = 1;
 end
 
+% by setting this environment variable it becomes possible to define other
+% paths relative to $SPMDIR in defaults files and task lists
+setenv('SPMDIR',SPMDIR);
+
 % expand shell paths (before SPM so SPM can be in e.g. home directory)
 aap = aas_expandpathbyvars(aap, aap.options.verbose>2);
 
-if isempty(aap.directory_conventions.spmdir)
-    if isempty(which('spm'))
-        aas_log(aap,true,'You''re going to need SPM, add it to your paths manually or set aap.directory_conventions.spmdir');
-    else
-        aap.directory_conventions.spmdir=spm('Dir');
-    end;
-end;
-
 if isfield(aap, 'spm') && isfield(aap.spm, 'defaults')
     oldspmdefaults = aap.spm.defaults;
 end
 
-addpath(aap.directory_conventions.spmdir);
-spm_jobman('initcfg');
+SPM = spmClass(SPMDIR,'doAddToPath',true,'doKeepInPath',doKeepInPath);
+SPM.load;
+aas_cache_put(aap,'spm',SPM);
 
 try
     aap.spm.defaults=spm_get_defaults;
@@ -92,8 +114,7 @@
 
 % Path for SPM MEG/EEG
 addpath(fullfile(spm('Dir'),'external','fieldtrip'));
-clear ft_defaults
-clear global ft_default
+global ft_default; ft_default = [];
 ft_defaults;
 global ft_default
 ft_default.trackcallinfo = 'no';
@@ -109,35 +130,35 @@
     fullfile(spm('Dir'),'toolbox', 'Neural_Models'),...
     fullfile(spm('Dir'),'toolbox', 'MEEGtools'));
 
-% Path fore spmtools
-if isfield(aap.directory_conventions,'spmtoolsdir') && ~isempty(aap.directory_conventions.spmtoolsdir)
-    SPMTools = textscan(aap.directory_conventions.spmtoolsdir,'%s','delimiter', ':'); SPMTools = SPMTools{1};
-    for pp = SPMTools'
-        addpath(genpath(pp{1}));
-    end
+% Path fore matlabtools
+if isfield(aap.directory_conventions,'matlabtoolsdir') && ~isempty(aap.directory_conventions.matlabtoolsdir)
+    addpath(strrep(aap.directory_conventions.matlabtoolsdir,':',pathsep))
 end
 
-% Path for EEGLAB, if specified
-if ~isempty(aap.directory_conventions.eeglabdir)
-    addpath(...
-        fullfile(aap.directory_conventions.eeglabdir,'functions'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'adminfunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'sigprocfunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'guifunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'studyfunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'popfunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'statistics'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'timefreqfunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'miscfunc'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'resources'),...
-        fullfile(aap.directory_conventions.eeglabdir,'functions', 'javachatfunc')...
-        );
-else
-    % Check whether already in path, give warning if not
-    if isempty(which('eeglab'))
-       aas_log(aap,false,sprintf('EEG lab not found, if you need this you should add it to the matlab path manually, or set aap.directory_conventions.eeglabdir'));
-    end;
-end;
+
+% Toolboxes
+if isfield(aap.directory_conventions,'toolbox') && isstruct(aap.directory_conventions.toolbox)
+    for TBX = aap.directory_conventions.toolbox
+        if strcmp(TBX.name,'spm'), continue; end
+        if ~exist([TBX.name 'Class'],'class')
+            aas_log(aap,false,sprintf('No interfaces for %s in extrafunctions/toolboxes',TBX.name));
+        else
+            constr = str2func([TBX.name 'Class']);
+            params = {};
+            if isfield(TBX,'extraparameters')
+                for p = fieldnames(TBX.extraparameters)
+                    val = TBX.extraparameters.(p{1});
+                    if isempty(val), continue; end
+                    if ischar(val) && contains(val,':'), val = strsplit(val,':'); end
+                    params{end+1} = p{1};
+                    params{end+1} = val;
+                end
+            end
+            T = constr(TBX.dir,params{:});
+            aas_cache_put(aap,TBX.name,T);
+        end
+    end
+end
 
 % Path to GIFT
 if ~isempty(aap.directory_conventions.GIFTdir)
@@ -146,8 +167,8 @@
     % Check whether already in path, give warning if not
     if isempty(which('icatb_runAnalysis'))
        aas_log(aap,false,sprintf('GIFT not found, if you need this you should add it to the matlab path manually, or set aap.directory_conventions.GIFTdir'));
-    end;
-end;
+    end
+end
 
 % Path to BrainWavelet
 if ~isempty(aap.directory_conventions.BrainWaveletdir)
@@ -160,7 +181,7 @@
     % Check whether already in path, give warning if not
     if isempty(which('WaveletDespike'))
        aas_log(aap,false,sprintf('BrainWavelet not found, if you need this you should add it to the matlab path manually, or set aap.directory_conventions.BrainWaveletdir'));
-    end;
+    end
 end
 
 % Path to FaceMasking
@@ -170,8 +191,8 @@
     % Check whether already in path, give warning if not
     if isempty(which('mask_surf_auto'))
        aas_log(aap,false,sprintf('FaceMasking not found, if you need this you should add it to the matlab path manually, or set aap.directory_conventions.FaceMaskingdir'));
-    end;
-end;
+    end
+end
 
 % Path to LI toolbox
 if isfield(aap.directory_conventions,'LIdir') && ~isempty(aap.directory_conventions.LIdir)
@@ -180,13 +201,14 @@
     % Check whether already in path, give warning if not
     if isempty(which('LI'))
        aas_log(aap,false,sprintf('LI toolbox not found, if you need this you should add it to the matlab path manually, or set aap.directory_conventions.LIdir'));
-    end;
-end;
+    end
+end
 
 
 % Path to DCMTK
 if isfield(aap.directory_conventions,'DCMTKdir') && ~isempty(aap.directory_conventions.DCMTKdir)
-    setenv('PATH',[aacache.path.bcp_shellpath ':' fullfile(aap.directory_conventions.DCMTKdir,'bin')]);
+    [s,p] = aas_cache_get(aap,'bcp_shellpath','system');
+    setenv('PATH',[p ':' fullfile(aap.directory_conventions.DCMTKdir,'bin')]);
 end
 
 
@@ -201,17 +223,24 @@
 p = textscan(path,'%s','delimiter',':'); p = p{1};
 
 % spm
-p_ind = cell_index(p,aap.directory_conventions.spmdir); % SPM-related dir
+p_ind = cell_index(p,SPMDIR); % SPM-related dir
 for ip = p_ind
     reqpath{end+1} = p{ip};
 end
-% spmtools
-if isfield(aap.directory_conventions,'spmtoolsdir') && ~isempty(aap.directory_conventions.spmtoolsdir)
-    SPMTools = textscan(aap.directory_conventions.spmtoolsdir,'%s','delimiter', ':'); SPMTools = SPMTools{1};
-    for pp = SPMTools'
-        if exist(pp{1},'dir')
-            pdir = textscan(genpath(pp{1}),'%s','delimiter', ':'); pdir = pdir{1};
-            reqpath = [reqpath; pdir];
+
+% matlabtoolsdir
+if isfield(aap.directory_conventions,'matlabtoolsdir') && ~isempty(aap.directory_conventions.matlabtoolsdir)
+    matlabtools = textscan(aap.directory_conventions.matlabtoolsdir,'%s','delimiter', ':'); matlabtools = matlabtools{1};
+    for pp = matlabtools'
+        if exist(pp{1},'dir'), reqpath = [reqpath; pp{1}]; end
+    end
+end
+
+% Toolboxes
+if isfield(aap.directory_conventions,'toolbox') && isstruct(aap.directory_conventions.toolbox)
+    for TBX = aap.directory_conventions.toolbox
+        if isfield(TBX,'extraparameters') && isfield(TBX.extraparameters,'doAddToPath') && TBX.extraparameters.doAddToPath
+            reqpath{end+1} = TBX.dir;
         end
     end
 end
@@ -224,14 +253,6 @@
     end
 end
 
-% EEGLAB
-if ~isempty(aap.directory_conventions.eeglabdir)
-    p_ind = cell_index(p,aap.directory_conventions.eeglabdir);
-    for ip = p_ind
-        reqpath{end+1} = p{ip};
-    end
-end;
-
 % GIFT
 if ~isempty(aap.directory_conventions.GIFTdir)
     p_ind = cell_index(p,aap.directory_conventions.GIFTdir);
@@ -265,12 +286,12 @@
 end
 
 % clean
-reqpath=reqpath(strcmp('',reqpath)==0);
+reqpath = reqpath(strcmp('',reqpath)==0);
 exc = cell_index(reqpath,'.git');
 if exc, reqpath(exc) = []; end
 
-aacache.path.reqpath = reqpath;
+aas_cache_put(aap,'reqpath',reqpath,'system');
 % switch off warnings
-aacache.warnings(1) = warning('off','MATLAB:Completion:CorrespondingMCodeIsEmpty');
-aacache.warnings(2) = warning('off','MATLAB:getframe:RequestedRectangleExceedsFigureBounds');
-
+warnings(1) = warning('off','MATLAB:Completion:CorrespondingMCodeIsEmpty');
+warnings(2) = warning('off','MATLAB:getframe:RequestedRectangleExceedsFigureBounds');
+aas_cache_put(aap,'warnings',warnings,'system');

aa_engine/aaq/aaq_qsub.m

@@ -439,6 +439,8 @@ function close(obj)
         function [obj]=qsub_q_job(obj,job)
             global aaworker
             global aacache
+            aaworker.aacache = aacache;
+            [s, reqpath] = aas_cache_get(obj.aap,'reqpath','system');
             % Let's store all our qsub thingies in one particular directory
             qsubpath=fullfile(aaworker.parmpath,'qsub');
             aas_makedir(obj.aap,qsubpath);
@@ -468,9 +470,9 @@ function close(obj)
                 % them the aa paths. Users don't need to remember to update
                 % their own default paths (e.g. for a new aa version)
                 if isprop(J,'AdditionalPaths')
-                    J.AdditionalPaths = aacache.path.reqpath;
+                    J.AdditionalPaths = reqpath;
                 elseif isprop(J,'PathDependencies')
-                    J.PathDependencies = aacache.path.reqpath;
+                    J.PathDependencies = reqpath;
                 end
                 createTask(J,cj,nrtn,inparg,'CaptureDiary',true);
                 success = false;