Som clean merge

.deploy/DeploymentREADME

@@ -5,13 +5,36 @@ degree of localization, as they usually don't know where they've been cloned to.
 you'll find some scripts and hooks in this directory. Follow the following instructions to enable
 this support.
 
-1. Copy post-checkout to .git/hooks
-2. If this clone is an active deployment (i.e. you expect users to copy templates out of this
-directory before doing work on them, and it's very unlikely that commits will ever occur from this
-clone), then touch a regular file named .local/deployment. This will influence the behavior of
-deploy.sh which is called from the post-checkout hook.
+If this is a development repository, consider running
+setup_developer.sh. At present, this will just copy the hook from
+.deploy/src/post-checkout to .git/hooks/. 
 
-That's it!
+If this is a deployment repository, run setup_deployment.sh
+
+This will
+1. Add a remote called github/universe to point to the
+UMPsychMethodsCore/MethodsCore repo on github
+2. Copy the post-checkout hook up to where it will be active
+3. Make a .local directory in your repo (this is ignored by a
+.gitignore file)
+4. Create a file called deployment in .local (this affects behavior of
+the hook)
+5. Generate a keypair for you in .local called deploy and deploy.pub
+6. Create a file in .local called branch, and echo "public" into it
+
+After you run this, you need to 
+
+1. Grab the content of .local/deploy.pub and add it as a deployment
+key at Github.
+2. Edit .local/branch to contain the content of the branch that you
+want this repository to automatically update to
+3. Run at regular intervals, or schedule with cron, the process
+.deploy/src/self_update.sh which will automatically pull the latest
+version of the file specified in .local/branch from universe, update
+your working tree, and then run the hook to clean paths up for users.
+
+
+###Here is what the hook does###
 
 Once you've done this, you'll get the following behavior everytime you perform a checkout.
 
@@ -36,4 +59,4 @@ string "*_mc_template*". It will the loop over these files and do the following
 
 This tool might get fancier in the future (e.g. strip off any leading comment characters in lines
 that contain the search string described in 2 or 3 to give you more flexibility in your use of
-wildcards, but for now this is all that is supported.
+wildcards, but for now this is all that is supported.

.deploy/setup_deployment.sh

@@ -0,0 +1,23 @@
+#!/bin/sh
+
+thisdir=`dirname $0`
+
+
+# Add universe remote
+git remote add github/universe git@github.com:UMPsychMethodsCore/MethodsCore
+
+# Copy hooks
+cp $thisdir/src/post-checkout $thisdir/../.git/hooks
+
+
+#Make .local directory if it doesn't exist, and add deployment
+mkdir -p ${thisdir}/../.local
+
+#Mark this as a deployment
+touch $thisdir/../.local/deployment
+
+#Add file to indicate which branch should be updated by self-checkout
+echo public > $thisdir/../.local/branch
+
+#Make keyfiles
+ssh-keygen -f $thisdir/../.local/deploy -N ""

.deploy/setup_developer.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+
+thisdir=`dirname $0`
+
+#Copy hooks
+cp $thisdir/src/post-checkout $thisdir/../.git/hooks

.deploy/deploy.sh → .deploy/src/checkout.sh

@@ -3,7 +3,6 @@
 #Grab Current Root
 mcRoot=`pwd`
 
-#Make sure .local directory exists
 mkdir -p .local
 
 #Identify Current Version

.deploy/src/git_ssh.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+thisdir=`dirname $0`
+
+idfile=$thisdir/../../.local/deploy
+
+ssh -i ${idfile} $@

.deploy/src/post-checkout

@@ -0,0 +1,7 @@
+#!/bin/sh
+#
+
+#Run your checkout script
+if [ -f .deploy/src/checkout.sh ]; then
+.deploy/src/checkout.sh
+fi

.deploy/src/self_update.sh

@@ -0,0 +1,21 @@
+#!/bin/sh
+
+
+
+thisdir=`dirname $0`
+
+origdir=`pwd`
+cd $thisdir
+harddir=`pwd`
+cd $origdir
+
+export GIT_SSH=${harddir}/git_ssh.sh
+
+branch=`cat $thisdir/../../.local/branch`
+
+git reset HEAD --hard
+
+git pull github/universe $branch:$branch
+
+git checkout $branch
+

FirstLevel/PreprocessFirstLevel_central.m

@@ -535,7 +535,7 @@
 			    end
 			    normsource = ['mean' b c];
 
-                ImageDirCheck = struct('Template',ImageTmeplate,...
+                ImageDirCheck = struct('Template',ImageTemplate,...
                                        'mode','check');
 			    ImageDir=mc_GenPath(ImageDirCheck);
 
@@ -559,7 +559,7 @@
 
 		    	    %job{6}.spm.util.defs.comp{1}.def = {fullfile(subjdir,anatdir,['y_r' hires '.' imagetype])};
 
-                    [HiResPath HiResName]=fileparts(HiResTemplate);
+                    [HiResPath HiResName]=fileparts(HiresTemplate);
 
 		    	    job{6}.spm.util.defs.comp{1}.def = {fullfile(HiResPath,['y_r' HiResName '.nii'])}; %%%Mike needs to check this
 		    	    job{6}.spm.util.defs.fnames = wscan;

matlabScripts/mc_Error.m

@@ -0,0 +1,45 @@
+function mc_Error(errorString,varargin)
+% A utility function to make error handling and logging more compact
+% A single call to mc_Error will log the error to the global mc_LogName, 
+% bring up an error dialog box with your error message, and actually throw
+% an exception with the Matlab error function.
+%
+% FORMAT mc_Error(errorString,other variable arguments)
+%
+% errorString             This is a string message that will be displayed
+%                         to the user.  This can either be a simple string,
+%                         or it can take the format of an sprintf
+%                         formatting string using % format specifiers (see
+%                         sprintf documentation for more information about
+%                         these format strings).  
+%
+% other variables         If you are using the sprintf format string, you
+%                         need to pass in the other variables that need to
+%                         appear in the formatted string.
+%
+% EXAMPLES
+%    mc_Error('File does not exist.');
+%    mc_Error('File %s does not exist.',filename);
+%    mc_Error('File %s does not exist at path %s.',filename, folder);
+%    mc_Error('You specified %d images but I found %d.\nPlease double 
+%              check subject %s folder %s for images.',NumScan(iRun),
+%              size(P,1),subjDir,RunDir{iRun});
+
+    if (~isempty(varargin))
+        formatcount = size(strfind(errorString,'%'),2);
+        if (formatcount == size(varargin,2))
+            errormsg = sprintf(errorString,varargin{:});
+        else
+            mc_Error('Found %d format specifiers but %d other variables were provided.\n\nError String: %s\n',formatcount,size(varargin,2),errorString);
+
+        end
+    else
+        errormsg = errorString;
+    end
+
+    %add future code to call mc_Logger with loglevel Error
+
+    errordlg(errormsg);
+    error(errormsg);
+
+

matlabScripts/mc_GetBoundingBox.m

@@ -0,0 +1,21 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function bb = mc_GetBoundingBox(V)
+%  world-bb -- get bounding box in world (mm) coordinates
+
+d = V.dim(1:3);
+% corners in voxel-space
+c = [ 1    1    1    1
+    1    1    d(3) 1
+    1    d(2) 1    1
+    1    d(2) d(3) 1
+    d(1) 1    1    1
+    d(1) 1    d(3) 1
+    d(1) d(2) 1    1
+    d(1) d(2) d(3) 1 ]';
+% corners in world-space
+tc = V.mat(1:3,1:4)*c;
+
+% bounding box (world) min and max
+mn = min(tc,[],2)';
+mx = max(tc,[],2)';
+bb = [mn; mx];

som/SOM_CalculateCorrelationImages.m

@@ -33,7 +33,7 @@
 results = [];
 
 rMap    = zeros(size(D0,1),1);
-rMapVol = zeros(parameters.maskHdr.dim(1:3));
+rMapVol = zeros(parameters.maskHdr.dim(1:3)); %this fails if user specified no masking %% This should now be fixed with change in SOM_PreProcessData - 2012-03-29 - RCWelsh
 
 for iROI = 1 : parameters.rois.nroisRequested
 
@@ -63,7 +63,7 @@
 
         clear rMapHdr;
 
-        rMapHdr.fname = fullfile(parameters.Output.directory,sprintf('rmap_%s_%03d.nii',parameters.Output.name,iROI));
+        rMapHdr.fname = fullfile(parameters.Output.directory,sprintf('rmap_%s_%04d.nii',parameters.Output.name,iROI));
         rMapHdr.mat   = parameters.maskHdr.mat;
 
         % Make sure we write out float32.....
@@ -75,7 +75,7 @@
 	% Now the probability map.
 
         pMapHdr       = rMapHdr;
-	pMapHdr.fname = fullfile(parameters.Output.directory,sprintf('pmap_%s_%03d.nii',parameters.Output.name,iROI));
+	pMapHdr.fname = fullfile(parameters.Output.directory,sprintf('pmap_%s_%04d.nii',parameters.Output.name,iROI));
 
         spm_write_vol(rMapHdr,rMapVol);
         spm_write_vol(pMapHdr,pMapVol);
@@ -85,7 +85,7 @@
         if exist(rMapHdr.fname) == 2
             clear Vo
             Vi         = spm_vol(rMapHdr.fname);
-            Vo.fname   = sprintf('zmap_%s_%03d.nii',parameters.Output.name,iROI);
+            Vo.fname   = fullfile(parameters.Output.directory,sprintf('zmap_%s_%04d.nii',parameters.Output.name,iROI));
             Vo.mat     = Vi.mat;
             Vo.dim     = Vi.dim;
             Vo.dt      = [16 0];