changes to rename ratrix as BCore

bootstrap/bootstrap.m

@@ -3,7 +3,7 @@
 setupEnvironment;
 addJavaComponents();  %might conflict with dbconn
 
-dataPath=fullfile(fileparts(fileparts(getRatrixPath)),'ratrixData',filesep);
+dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
 
 diary off
 warning('off','MATLAB:MKDIR:DirectoryExists')
@@ -30,7 +30,7 @@
 
     tries=0;
     while true
-        initRatrixPorts;
+        initBCorePorts;
         try
             clearJavaComponents();
             checkForUpdate;
@@ -80,7 +80,7 @@
                 else
                     com=getNextCommand(r);
                     if ~isempty(com)
-                        quit=clientHandleCommand(r,com,constants.statuses.NO_RATRIX);
+                        quit=clientHandleCommand(r,com,constants.statuses.NO_BCORE);
                     else
                         pause(0.1);
                     end

bootstrap/setupEnvironment.m

@@ -12,7 +12,7 @@
 lastwarn('')
 
 warning('off','MATLAB:dispatcher:nameConflict')
-addpath((genpath(getRatrixPath)));
+addpath((genpath(getBCorePath)));
 warning('on','MATLAB:dispatcher:nameConflict')
 
 % intwarning('on');

bootstrap/standAloneRun.m

@@ -1,36 +1,36 @@
-function standAloneRun(subjectID,ratrixPath,setupFile)
-%standAloneRun([ratrixPath],[setupFile],[subjectID],[recordInOracle],[backupToServer])
+function standAloneRun(subjectID,BCorePath,setupFile)
+%standAloneRun([BCorePath],[setupFile],[subjectID],[recordInOracle],[backupToServer])
 %
-% ratrixPath (optional, string path to preexisting ratrix 'db.mat' file)
-% defaults to checking for db.mat in ...\<ratrix install directory>\..\ratrixData\ServerData\
-% if none present, makes new ratrix located there, with a dummy subject
+% BCorePath (optional, string path to preexisting BCore 'db.mat' file)
+% defaults to checking for db.mat in ...\<BCore install directory>\..\BCoreData\ServerData\
+% if none present, makes new BCore located there, with a dummy subject
 %
 % setupFile (optional, name of a setProtocol file on the path, typically in the setup directory)
 % defaults to 'setProtocolDEMO'
-% if subject already exists in ratrix and has a protocol, default is no action
+% if subject already exists in BCore and has a protocol, default is no action
 %
-% subjectID (optional, must be string id of subject -- will add to ratrix if not already present)
-% default is some unspecified subject in ratrix (you can't depend on which
+% subjectID (optional, must be string id of subject -- will add to BCore if not already present)
+% default is some unspecified subject in BCore (you can't depend on which
 % one unless there is only one)
 %
 %
 setupEnvironment;
 
-if exist('ratrixPath','var') && ~isempty(ratrixPath)
-    if isdir(ratrixPath)
-        rx=ratrix(ratrixPath,0);
+if exist('BCorePath','var') && ~isempty(BCorePath)
+    if isdir(BCorePath)
+        rx=BCore(BCorePath,0);
     else
-        ratrixPath
-        error('if ratrixPath supplied, it must be a path to a preexisting ratrix ''db.mat'' file')
+        BCorePath
+        error('if BCorePath supplied, it must be a path to a preexisting BCore ''db.mat'' file')
     end
 else
-    dataPath=fullfile(fileparts(fileparts(getRatrixPath)),'ratrixData',filesep);
+    dataPath=fullfile(fileparts(fileparts(getBCorePath)),'BCoreData',filesep);
     defaultLoc=fullfile(dataPath, 'ServerData');
     d=dir(fullfile(defaultLoc, 'db.mat'));
 
     if length(d)==1
-        rx=ratrix(defaultLoc,0);
-        fprintf('loaded ratrix from default location\n')
+        rx=BCore(defaultLoc,0);
+        fprintf('loaded BCore from default location\n')
     else
         try
             [success mac]=getMACaddress();
@@ -42,11 +42,11 @@ function standAloneRun(subjectID,ratrixPath,setupFile)
         end
 
         machines={{'1U',mac,[1 1 1]}};
-        rx=createRatrixWithDefaultStations(machines,dataPath,'localTimed');
+        rx=createBCoreWithDefaultStations(machines,dataPath,'localTimed');
         permStorePath=fullfile(dataPath,'PermanentTrialRecordStore');
         mkdir(permStorePath);
         rx.standAlonePath=permStorePath;
-        fprintf('created new ratrix\n')
+        fprintf('created new BCore\n')
     end
 end
 
@@ -64,9 +64,9 @@ function standAloneRun(subjectID,ratrixPath,setupFile)
 else
     subjectID=lower(subjectID);
     try
-        isSubjectInRatrix=getSubjectFromID(rx,subjectID);
+        isSubjectInBCore=getSubjectFromID(rx,subjectID);
     catch ex
-        if ~isempty(strfind(ex.message,'request for subject id not contained in ratrix'))
+        if ~isempty(strfind(ex.message,'request for subject id not contained in BCore'))
 
             needToCreateSubject=true;
             needToAddSubject=true;
@@ -140,22 +140,6 @@ function standAloneRun(subjectID,ratrixPath,setupFile)
         replicateTrialRecords(replicationPaths,deleteOnSuccess, recordInOracle);
     end
     [rx ids] = emptyAllBoxes(rx,'done running trials in standAloneRun',auth);
-    if ~testMode
-        compilePath=fullfile(fileparts(getStandAlonePath(rx)),'CompiledTrialRecords');
-        mkdir(compilePath);
-        dailyAnalysisPath = fullfile(fileparts(getStandAlonePath(rx)),'DailyAnalysis');
-        mkdir(dailyAnalysisPath);
-        compileDetailedRecords([],{subjectID},[],getStandAlonePath(rx),compilePath);
-
-        selection.type = 'animal status';
-        selection.filter = 'all';
-        selection.filterVal = [];
-        selection.filterParam = [];
-        selection.titles = {sprintf('subject %s',subjectID)};
-        selection.subjects = {subjectID};
-        fs=analysisPlotter(selection,compilePath,true);
-%         subjectAnalysis(compilePath);
-    end
     cleanup;
     % testing
     clear all

bootstrap/startDataListener.m

@@ -1,5 +1,5 @@
 function startDataListener()
-%this opens up the datanet listener so that a ratrix datanet can connect to it;
+%this opens up the datanet listener so that a BCore datanet can connect to it;
 
 setupEnvironment;
 try

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(getRatrixPath,'analysis','bsriram','analysisParameters','getBasicParams.m'); % warning... this is just a record and has no effect
+    p.standardParams = fullfile(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

classes/analysis/cellProperties/@wnAnalysis/getTemporalKernelAtHighPrecision.m

@@ -14,7 +14,7 @@
 channels = {getChannels(s)};
 thrV = [NaN NaN NaN];
 cellBoundary = {'trialRange',trialRange,'trialMask',trialMask};
-standardParams = fullfile(getRatrixPath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
+standardParams = fullfile(getBCorePath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
 analysisMode = 'onlyAnalyze'; % most important
 forceNoInspect = true;
 intelligentUpdate = false;

classes/analysis/cellProperties/@wnAnalysis/reAnalyzeUsingFractionOfSpikes.m

@@ -8,7 +8,7 @@
 channels = {getChannels(s)};
 thrV = [NaN NaN NaN];
 cellBoundary = {'trialRange',trialRange,'trialMask',trialMask};
-standardParams = fullfile(getRatrixPath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
+standardParams = fullfile(getBCorePath,'analysis','bsriram','analysisParameters','params_01_06_2011.m');
 analysisMode = 'onlyAnalyze'; % most important
 forceNoInspect = true;
 intelligentUpdate = false;

classes/analysis/glmTool.m

@@ -406,7 +406,7 @@ function tutorial(g) %basic demo
                     load('physAnalysis_485-20100604T200707')
                     %how to get or make this data:
                     %   source: datanetOutput\231\analysis\475-485\485-20100604T200707\
-                    %   make:  spikeSortFiddler in RatrixTrunk@svnRev.2954
+                    %   make:  spikeSortFiddler in BCoreTrunk@svnRev.2954
                     %   subjectID = '231';
                     %   path='\\132.239.158.179\datanetOutput'  %on the G drive remote
                     %   channels={1};

classes/core/boxes/box.m

@@ -48,14 +48,14 @@ function clearSubjectDataDir(b)
         end
 
         function subPath=getBoxPathForSubjectID(b,sID,r)
-            if isa(r,'ratrix')
+            if isa(r,'BCore')
                 if getBoxIDForSubjectID(r,sID)==b.id
                     subPath=fullfile(getSubjectDataDir(b),sID);  %[b.path 'subjectData' filesep sID filesep];
                 else
                     error('subject not in this box')
                 end
             else
-                error('ratrix does not contain subject')
+                error('BCore does not contain subject')
             end
         end
 
@@ -66,11 +66,11 @@ function clearSubjectDataDir(b)
         function trialRecords=getTrialRecordsForSubjectID(b,sID,r)
             disp(sprintf('loading records for %s (from box)',sID))
             startTime=GetSecs();
-            if isa(r,'ratrix')
+            if isa(r,'BCore')
                 subPath=getBoxPathForSubjectID(b,sID,r);
                 trialRecords=loadMakeOrSaveTrialRecords(subPath);
             else
-                error('need ratrix object')
+                error('need BCore object')
             end
             disp(sprintf('done loading records for %s: %g s elapsed',sID,GetSecs()-startTime))
         end
@@ -97,11 +97,11 @@ function clearSubjectDataDir(b)
         function updateTrialRecordsForSubjectID(b,sID,trialRecords,r)
             disp(sprintf('saving records for %s (from box)',sID))
             startTime=GetSecs();
-            if isa(r,'ratrix')
+            if isa(r,'BCore')
                 subPath=getBoxPathForSubjectID(b,sID,r);
                 loadMakeOrSaveTrialRecords(subPath,trialRecords);
             else
-                error('need ratrix object')
+                error('need BCore object')
             end
             disp(sprintf('done saving records for %s: %g s elapsed',sID,GetSecs()-startTime))
         end

classes/core/datanets/datanet.m

@@ -144,13 +144,13 @@
 
         function [datanet, quit, retval] = handleCommands(datanet,params)
             % This function gets called by the client's bootstrap function, and also at the doTrial/runRealTimeLoop level to handle any available
-            % server commands. also gets called during physiologyServer's doServerIteration (to handle any commands sent from ratrix side)
+            % server commands. also gets called during physiologyServer's doServerIteration (to handle any commands sent from BCore side)
             % INPUTS:
             %	datanet - a datanet object (either stim or data)
             %   params - a struct containing additional information that may be needed to process commands
             %       for now, this is a timestamp that was taken during 'trial start' and passed to 'trial end' for serverHandleCommand
             % OUTPUTS:
-            %	quit - a quit flag (not sure if this will be doTrial's stopEarly or realtimeloop's quit), but something to tell ratrix to stop running trials!
+            %	quit - a quit flag (not sure if this will be doTrial's stopEarly or realtimeloop's quit), but something to tell BCore to stop running trials!
             %	retval - some return value (in the case of doServerIteration, should be an event to add to events_data), may be other stuff....
 
             quit = false;
@@ -250,7 +250,7 @@
             % (this may be useful for waiting for the omni-message END_OF_DOTRIALS)
 
 
-            % 4/3 to do - remove trialData? - for now, just handle simple acks. this function should work from both the ratrix and data sides...
+            % 4/3 to do - remove trialData? - for now, just handle simple acks. this function should work from both the BCore and data sides...
             MAXSIZE = 1024*1024;
             CMDSIZE = 1;
             trialData = [];
@@ -434,7 +434,7 @@
                         retval(end).stimManagerClass=cparams.stimManagerClass;
                         retval(end).stepName=cparams.stepName;
                         retval(end).stepNumber=cparams.stepNumber;
-                        fprintf('got trial start command from ratrix\n')
+                        fprintf('got trial start command from BCore\n')
                     case constants.stimToDataCommands.S_TRIAL_END_EVENT_CMD
                         % mark end of trial - how do we add an event to events_data, which is all the way out in physiologyServer?
                         response=constants.dataToStimResponses.D_TRIAL_END_EVENT_ACK;
@@ -468,7 +468,7 @@
                         retval(end).datablock = params.datablock;
                         retval(end).ai = params.ai;
 
-                        fprintf('got trial end command from ratrix\n')
+                        fprintf('got trial end command from BCore\n')
                     case constants.stimToDataCommands.S_ERROR_RECOVERY_METHOD
                         % whether client pressed 'Restart' or 'Quit'
                         response=constants.dataToStimResponses.D_ERROR_METHOD_RECEIVED;
@@ -566,7 +566,7 @@
             % INPUTS:
             %	datanet - the server-side datanet object; should have a valid pnet connection with parameters (timeout) already set
             %	subjectID - the ID string of the subject to start
-            %		(pass to station.doTrials or whoever sets quit on ratrix side - just to make sure this is the correct subject to stop)
+            %		(pass to station.doTrials or whoever sets quit on BCore side - just to make sure this is the correct subject to stop)
             %   params - the struct of params that includes the ai object so we can get the last trial's data
             % OUTPUTS:
             %	gotAck - true if we get an ack from the client