Utility Class

balajisriram · Apr 5, 2016 · 8f34ce6 · 8f34ce6
1 parent bdddeca
commit 8f34ce6
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Showing 41 changed files with 158 additions and 156 deletions.
diff --git a/bootstrap/BCoreServer.m b/bootstrap/BCoreServer.m
@@ -40,7 +40,7 @@
 setupEnvironment;
 addJavaComponents();
 checkForUpdate; % 9/24/08 - check current code version
-dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
+dataPath=fullfile(fileparts(fileparts(BCoreUtil.getBCorePath)),'BCoreData',filesep);
 
 diary off
 warning('off','MATLAB:MKDIR:DirectoryExists')
@@ -310,13 +310,13 @@ function buttonC(source,eventdata)
         closeConn(conn);
         % finished writing stop time of this heat to oracle
         [r, rx, sys]=stopServer(r,rx,servePump,sys,er,subjects);
-        rp=getBCorePath;
+        rp=BCoreUtil.getBCorePath;
         rp=fullfile(rp,'analysis','eflister');
 
         % ==============================================================================================================
         % FIX THIS PART TO ONLY COMPILE SUBJECTS OWNED BY THIS SERVER
         % we need to compile records for every rack used here
-        cmdStr=sprintf('matlab -automation -r "cd(''%s'');setupEnvironment;cd(''%s'');compileDetailedRecords(''%s'');quit" &',fullfile(getBCorePath,'bootstrap'),rp,server_name);
+        cmdStr=sprintf('matlab -automation -r "cd(''%s'');setupEnvironment;cd(''%s'');compileDetailedRecords(''%s'');quit" &',fullfile(BCoreUtil.getBCorePath,'bootstrap'),rp,server_name);
         system(cmdStr); %testing only       
         % END EDITS
         % ==============================================================================================================

diff --git a/bootstrap/bootstrap.m b/bootstrap/bootstrap.m
@@ -3,7 +3,7 @@
 setupEnvironment;
 addJavaComponents();  %might conflict with dbconn
 
-dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
+dataPath=fullfile(fileparts(fileparts(BCoreUtil.getBCorePath)),'BCoreData',filesep);
 
 diary off
 warning('off','MATLAB:MKDIR:DirectoryExists')

diff --git a/bootstrap/getBCorePath.m b/bootstrap/getBCorePath.m
@@ -1,6 +0,0 @@
-% this returns the path to the directory above this directory
-function BCorePath=getBCorePath()
-% DO U SEE ME?
-[pathstr, ~, ~] = fileparts(mfilename('fullpath'));
-    BCorePath = fileparts(pathstr);
-    BCorePath = [BCorePath filesep];

diff --git a/bootstrap/setupEnvironment.m b/bootstrap/setupEnvironment.m
@@ -12,7 +12,7 @@
 lastwarn('')
 
 warning('off','MATLAB:dispatcher:nameConflict')
-addpath((genpath(getBCorePath)));
+addpath((genpath(BCoreUtil.getBCorePath)));
 warning('on','MATLAB:dispatcher:nameConflict')
 
 % intwarning('on');

diff --git a/bootstrap/standAloneRun.m b/bootstrap/standAloneRun.m
@@ -1,4 +1,4 @@
-function standAloneRun(subjectID,BCorePath,setupFile)
+function standAloneRun(subjectID,BCoreServerPath,setupFile)
 %standAloneRun([BCorePath],[setupFile],[subjectID],[recordInOracle],[backupToServer])
 %
 % BCorePath (optional, string path to preexisting BCore 'db.mat' file)
@@ -16,81 +16,43 @@ function standAloneRun(subjectID,BCorePath,setupFile)
 %
 setupEnvironment;
 
-if exist('BCorePath','var') && ~isempty(BCorePath)
-    if isdir(BCorePath)
-        rx=BCore(BCorePath,0);
-    else
-        BCorePath
-        error('if BCorePath supplied, it must be a path to a preexisting BCore ''db.mat'' file')
-    end
+% create ratrix if necessary
+if exist('BCorePath','var') && ~isempty(BCoreServerPath)
+    assert(isdir(BCoreServerPath),'standAloneRun:incorrectValue','if BCorePath supplied, it must be a path to a preexisting BCore ''db.mat'' file')
+	rx=BCore(BCoreServerPath,0);
 else
-    dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
-    defaultLoc=fullfile(dataPath, 'ServerData');
-    d=dir(fullfile(defaultLoc, 'db.mat'));
-
-    if length(d)==1
-        rx=BCore(defaultLoc,0);
-        fprintf('loaded BCore from default location\n')
-    else
-        try
-            [success mac]=getMACaddress();
-            if ~success
-                mac='000000000000';
-            end
-        catch
-            mac='000000000000';
-        end
-
-        machines={{'1U',mac,[1 1 1]}};
-        rx=createBCoreWithDefaultStations(machines,dataPath,'localTimed');
-        permStorePath=fullfile(dataPath,'PermanentTrialRecordStore');
-        mkdir(permStorePath);
-        rx.standAlonePath=permStorePath;
-        fprintf('created new BCore\n')
+    d=dir(fullfile(BCoreUtil.getServerDataPath, 'db.mat'));
+    switch length(d)
+        case 0
+            rx = BCoreUtil.createDefaultBCore();
+        case 1
+            rx=BCore(defaultLoc,0);
+        otherwise
+            error('standAloneRun:unknownError','either a single db.mat exists or none exist. We found %d. Clean your database',length(d));
     end
 end
 
-needToAddSubject=false;
-needToCreateSubject=false;
-if ~exist('subjectID','var') || isempty(subjectID)
-    ids=getSubjectIDs(rx);
-    if length(ids)>0
-        subjectID=ids{1};
-    else
-        subjectID='demo1';
-        needToCreateSubject=true;
-        needToAddSubject=true;
-    end
-else
-    subjectID=lower(subjectID);
-    try
-        isSubjectInBCore=getSubjectFromID(rx,subjectID);
-    catch ex
-        if ~isempty(strfind(ex.message,'request for subject id not contained in BCore'))
-
-            needToCreateSubject=true;
-            needToAddSubject=true;
-        else
-            rethrow(ex)
-        end
-    end
-end
 
-if needToCreateSubject
-    warning('creating dummy subject')
-    sub = rat(subjectID, 'male', 'long-evans', datetime(2005,05,10), datetime(2006,05,10), 'unknown', 'wild caught');
-end
-auth='bas';
 
-if needToAddSubject
-    rx=addSubject(rx,sub,auth);
+% should we add the subject to the ratrix?
+if ~exist('subjectID','var') || isempty(subjectID)
+    subjectID='demo1';
+end
+switch rx.subjectIDInRatrix(lower(subjectID))
+    case true
+        sub = rx.getSubjectFromID(subjectID);
+    case false
+        sub = virtual(subjectID, 'unknown');
+        auth = 'bas';
+        rx=rx.addSubject(sub,auth);
 end
 
-if (~exist('setupFile','var') || isempty(setupFile)) && ~isa(getProtocolAndStep(getSubjectFromID(rx,subjectID)),'protocol')
-    setupFile='setProtocolMINBS';
+if ~exist('setupFile','var') || isempty(setupFile)
+    setupFile=@setProtocolMINBS;
+elseif ~isa(setupFile,'function_handle') ||
+    error('standAloneRun:incompatibleInput','you input setupFile thats not a function handle');
 end
 
-if exist('setupFile','var') && ~isempty(setupFile)
     x=what(fileparts(which(setupFile)));
     if isempty(x) || isempty({x.m}) || ~any(ismember(lower({setupFile,[setupFile '.m']}),lower(x.m)))
         setupFile
@@ -99,11 +61,6 @@ function standAloneRun(subjectID,BCorePath,setupFile)
 
     su=str2func(setupFile); %weird, str2func does not check for existence!
     rx=su(rx,{subjectID});
-    %was:  r=feval(setupFile, r,{getID(sub)});
-    %but edf notes: eval is bad style
-    %http://www.mathworks.com/support/tech-notes/1100/1103.html
-    %http://blogs.mathworks.com/loren/2005/12/28/evading-eval/
-end
 
 %[isExperimentSubject, xtraExptBackupPath, experiment] = identifySpecificExperiment(subjectID);
 

diff --git a/classes/analysis/@neuronDB/process.m b/classes/analysis/@neuronDB/process.m
@@ -49,7 +49,7 @@
     %start building a parameters of the calls to runAnalysis
     p.channels={db.data{neurons(i)}.channels};  % all singleUnits have only a single set of channels
     p.analysisMode=mode;
-    p.standardParams = fullfile(getBCorePath,'analysis','bsriram','analysisParameters','getBasicParams.m'); % warning... this is just a record and has no effect
+    p.standardParams = fullfile(BCoreUtil.getBCorePath,'analysis','bsriram','analysisParameters','getBasicParams.m'); % warning... this is just a record and has no effect
     p.cellBoundary={'trialRange',minmax(trials),'trialMask',mask};
 
     %default parameters are faster and no inspect for pre-processing

diff --git a/classes/analysis/cellProperties/@wnAnalysis/getTemporalKernelAtHighPrecision.m b/classes/analysis/cellProperties/@wnAnalysis/getTemporalKernelAtHighPrecision.m
@@ -14,7 +14,7 @@
 channels = {getChannels(s)};
 thrV = [NaN NaN NaN];
 cellBoundary = {'trialRange',trialRange,'trialMask',trialMask};
-standardParams = fullfile(getBCorePath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
+standardParams = fullfile(BCoreUtil.getBCorePath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
 analysisMode = 'onlyAnalyze'; % most important
 forceNoInspect = true;
 intelligentUpdate = false;

diff --git a/classes/analysis/cellProperties/@wnAnalysis/reAnalyzeUsingFractionOfSpikes.m b/classes/analysis/cellProperties/@wnAnalysis/reAnalyzeUsingFractionOfSpikes.m
@@ -8,7 +8,7 @@
 channels = {getChannels(s)};
 thrV = [NaN NaN NaN];
 cellBoundary = {'trialRange',trialRange,'trialMask',trialMask};
-standardParams = fullfile(getBCorePath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
+standardParams = fullfile(BCoreUtil.getBCorePath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
 analysisMode = 'onlyAnalyze'; % most important
 forceNoInspect = true;
 intelligentUpdate = false;

diff --git a/classes/core/BCoreUtil.m b/classes/core/BCoreUtil.m
@@ -0,0 +1,68 @@
+classdef BCoreUtil
+    properties
+    end
+
+    methods (Static)
+
+        function BCorePath=getBCorePath()
+            [pathstr, ~, ~] = fileparts(mfilename('fullpath'));
+            [pathstr, ~, ~] = fileparts(pathstr);
+            BCorePath = fileparts(pathstr);
+            BCorePath = [BCorePath filesep];
+        end
+
+        function BasePath = getBasePath()
+            p = BCoreUtil.getBCorePath();
+            [BasePath, ~, ~] = fileparts(p);
+        end
+
+        function ServerDataPath = getServerDataPath()
+            p = BCoreUtil.getBasePath();
+            p = fullfile(p,'BCoreData');
+            ServerDataPath = fullfile(p,'ServerData');
+        end
+
+        function rx = createDefaultBCore()
+            try
+                [success, mac]=getMACaddress();
+                if ~success
+                    mac='000000000000';
+                end
+            catch
+                mac='000000000000';
+            end
+
+            machines={{'1U',mac,[1 1 1]}};
+            rx=createBCoreWithDefaultStations(machines,dataPath,'localTimed');
+            permStorePath=fullfile(dataPath,'PermanentTrialRecordStore');
+            mkdir(permStorePath);
+            rx.standAlonePath=permStorePath;
+            fprintf('created new BCore\n')
+        end
+
+        function [success, mac]=getMACaddress()
+            success=false;
+            switch computer
+                case {'PCWIN64','PCWIN32'}
+                    macidcom = fullfile(PsychtoolboxRoot,'PsychContributed','macid');
+                    [rc, mac] = system(macidcom);
+                    mac=mac(~isstrprop(mac,'wspace'));
+                    if rc==0 && isMACaddress(mac)
+                        success=true;
+                    end
+                case {'GLNXA64','MACI64'}
+                    error('BCoreUtil:getMACAddress:unsupportedSystem','This system: %s is not supported', computer);
+                    compinfo = Screen('Computer');
+                    if isfield(compinfo, 'MACAddress')
+                        mac = compinfo.MACAddress;
+                        % Remove the : that are a part of the string
+                        mac = mac(mac~=':');
+                        if isMACaddress(mac)
+                            success = true;
+                        end
+                    end
+                otherwise
+                    error('BCoreUtil:getMACAddress:unsupportedSystem','In getMACaddress() unknown OS');
+            end
+    end
+end
diff --git a/classes/core/protocols/stimManagers/afcCoherentDots.m b/classes/core/protocols/stimManagers/afcCoherentDots.m
@@ -815,7 +815,7 @@
 
                 case 'localCalibStore'
                     try
-                        temp = load(fullfile(getBCorePath,'monitorCalibration','tempCLUT.mat'));
+                        temp = load(fullfile(BCoreUtil.getBCorePath,'monitorCalibration','tempCLUT.mat'));
                         uncorrected = temp.linearizedCLUT;
                         useUncorrected=1;
                     catch ex

diff --git a/classes/core/protocols/stimManagers/afcGratings.m b/classes/core/protocols/stimManagers/afcGratings.m
@@ -859,7 +859,7 @@
 
                 case 'localCalibStore'
                     try
-                        temp = load(fullfile(getBCorePath,'monitorCalibration','tempCLUT.mat'));
+                        temp = load(fullfile(BCoreUtil.getBCorePath,'monitorCalibration','tempCLUT.mat'));
                         uncorrected = temp.linearizedCLUT;
                         useUncorrected=1;
                     catch ex

diff --git a/classes/core/protocols/stimManagers/afcGratingsPDPhases.m b/classes/core/protocols/stimManagers/afcGratingsPDPhases.m
@@ -876,7 +876,7 @@
 
                 case 'localCalibStore'
                     try
-                        temp = load(fullfile(getBCorePath,'monitorCalibration','tempCLUT.mat'));
+                        temp = load(fullfile(BCoreUtil.getBCorePath,'monitorCalibration','tempCLUT.mat'));
                         uncorrected = temp.linearizedCLUT;
                         useUncorrected=1;
                     catch ex

diff --git a/classes/core/protocols/stimManagers/afcGratingsWithOrientedSurround.m b/classes/core/protocols/stimManagers/afcGratingsWithOrientedSurround.m
@@ -943,7 +943,7 @@
 
                 case 'localCalibStore'
                     try
-                        temp = load(fullfile(getBCorePath,'monitorCalibration','tempCLUT.mat'));
+                        temp = load(fullfile(BCoreUtil.getBCorePath,'monitorCalibration','tempCLUT.mat'));
                         uncorrected = temp.linearizedCLUT;
                         useUncorrected=1;
                     catch ex

diff --git a/classes/core/protocols/stimManagers/afcObjects.m b/classes/core/protocols/stimManagers/afcObjects.m
@@ -606,7 +606,7 @@
 
                 case 'localCalibStore'
                     try
-                        temp = load(fullfile(getBCorePath,'monitorCalibration','tempCLUT.mat'));
+                        temp = load(fullfile(BCoreUtil.getBCorePath,'monitorCalibration','tempCLUT.mat'));
                         uncorrected = temp.linearizedCLUT;
                         useUncorrected=1;
                     catch ex

diff --git a/classes/core/ratrices/BCore.m b/classes/core/ratrices/BCore.m
@@ -31,6 +31,12 @@
             end
         end
 
+        function out = subjectIDInBCore(r,id)
+            assert(ischar(id),'BCore:subjectIDInBCore:incorrectValue','''id'' needs to be a char. instead is of class:%s',class(id));
+            ids = r.getSubjectIDs();
+            out = any(ismember(id,ids));
+        end
+
         function r = set.standAlonePath(r,path)
             assert(isdir(path),'BCore:set.standAlonePath:incorrectValue','Argument to permanentStorePath (%s) is not a directory',path)
             r.standAlonePath = path;
@@ -1351,7 +1357,7 @@ function recordInLog(r,s,str,author)
             end
         end
 
-        function out = testBoxSubjectDirs(r,b)
+        function out =testBoxSubjectDirs(r,b)
             validateattributes(b,{'box'},{'nonempty'})
             subIDs=getSubjectIDsForBoxID(r,b.id);
             success=1;
@@ -1510,6 +1516,5 @@ function recordInLog(r,s,str,author)
                 error('not a station object')
             end
         end
-
     end
 end
diff --git a/classes/core/rnet/rnet.m b/classes/core/rnet/rnet.m
@@ -455,7 +455,7 @@ function clearTemporaryFiles(r)
             quit=false;
             constants = getConstants(r);
 
-            BCoreDataPath=fullfile(fileparts(fileparts(getBCorePath)),'testdata',filesep);
+            BCoreDataPath=fullfile(fileparts(fileparts(BCoreUtil.getBCorePath)),'testdata',filesep);
             %BCoreDataPath='C:\Documents and Settings\rlab\Desktop\testdata\'; 
             %figure out where to store this
             %actually, this is an ok place -- there's nothing persistent
@@ -1654,7 +1654,7 @@ function removeAllDisconnectedClients(r)
             svnPath = GetSubversionPath;
 
             % Construct svn update command
-            info.updateCommand=[svnPath 'svn update '  targetRevision getBCorePath ];
+            info.updateCommand=[svnPath 'svn update '  targetRevision BCoreUtil.getBCorePath ];
             save('info.mat','info');
 
             % Clear java classes

diff --git a/util/calibration/linearization/calibrateMonitor.m b/util/calibration/linearization/calibrateMonitor.m
@@ -250,7 +250,7 @@
         CLUT=fread(fid,'*uint8');
         fclose(fid);
         timestamp=datestr(now,'mm-dd-yyyy HH:MM');
-        svnRev=getSVNRevisionFromXML(getBCorePath);
+        svnRev=getSVNRevisionFromXML(BCoreUtil.getBCorePath);
         addCalibrationData(CLUT,mac,timestamp,svnRev,comment,calibrationString)
         closeConn(conn);
     catch ex
@@ -263,7 +263,7 @@
     % data is always stored on the local BCore folder currently overwrites
     % old calibration data.
     disp('saving calibration to local store...')
-    BCoreFolder = getBCorePath;
+    BCoreFolder = BCoreUtil.getBCorePath;
     if ~exist(fullfile(BCoreFolder,'monitorCalibration'),'dir')
         mkdir(fullfile(BCoreFolder,'monitorCalibration'));
     end

diff --git a/util/infrastructure/calibrateLocal.m b/util/infrastructure/calibrateLocal.m
@@ -3,7 +3,7 @@ function calibrateLocal( numReps, amts, timeBtw, requiredAccuracy )
 
 clc
 
-dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
+dataPath=fullfile(fileparts(fileparts(BCoreUtil.getBCorePath)),'BCoreData',filesep);
 
 rewardMethod = 'localTimed';
-Original file line number
+Diff line change
@@ Expand Up @@
     clc
-    dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
+    dataPath=fullfile(fileparts(fileparts(BCoreUtil.getBCorePath)),'BCoreData',filesep);
     rewardMethod = 'localTimed';
@@ Expand Down @@