added git info and stats updates

getGitInfo.m

+function gitInfo=getGitInfo()
+% Get information about the Git repository in the current directory, including: 
+%          - branch name of the current Git Repo 
+%          -Git SHA1 HASH of the most recent commit
+%          -url of corresponding remote repository, if one exists
+%
+% The function first checks to see if a .git/ directory is present. If so it
+% reads the .git/HEAD file to identify the branch name and then it looks up
+% the corresponding commit.
+%
+% It then reads the .git/config file to find out the url of the
+% corresponding remote repository. This is all stored in a gitInfo struct.
+%
+% Note this uses only file information, it makes no external program 
+% calls at all. 
+%
+% This function must be in the base directory of the git repository
+%
+% Released under a BSD open source license. Based on a concept by Marc
+% Gershow.
+%
+% Andrew Leifer
+% Harvard University
+% Program in Biophysics, Center for Brain Science, 
+% and Department of Physics
+% leifer@fas.harvard.edu
+% http://www.andrewleifer.com
+% 12 September 2011
+%
+% 
+%
+
+% Copyright 2011 Andrew Leifer. All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without modification, are
+% permitted provided that the following conditions are met:
+% 
+%    1. Redistributions of source code must retain the above copyright notice, this list of
+%       conditions and the following disclaimer.
+% 
+%    2. Redistributions in binary form must reproduce the above copyright notice, this list
+%       of conditions and the following disclaimer in the documentation and/or other materials
+%       provided with the distribution.
+% 
+% THIS SOFTWARE IS PROVIDED BY <COPYRIGHT HOLDER> ''AS IS'' AND ANY EXPRESS OR IMPLIED
+% WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+% FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> OR
+% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+% SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+% ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+% ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% The views and conclusions contained in the software and documentation are those of the
+% authors and should not be interpreted as representing official policies, either expressed
+% or implied, of <copyright holder>.
+
+ gitInfo=[];
+if ~exist('.git','file') || ~exist('.git/HEAD','file')
+    %Git is not present
+    return
+end
+
+
+
+%Read in the HEAD information, this will tell us the location of the file
+%containing the SHA1
+text=fileread('.git/HEAD');
+parsed=textscan(text,'%s');
+
+if ~strcmp(parsed{1}{1},'ref:') || ~length(parsed{1})>1
+        %the HEAD is not in the expected format.
+        %give up
+        return
+end
+
+path=parsed{1}{2};
+[pathstr, name, ext]=fileparts(path);
+branchName=name;
+
+%save branchname
+gitInfo.branch=branchName;
+
+
+%Read in SHA1
+SHA1text=fileread(fullfile(['.git/' pathstr],[name ext]));
+SHA1=textscan(SHA1text,'%s');
+gitInfo.hash=SHA1{1}{1};
+
+
+%Read in config file
+config=fileread('.git/config');
+%Find everything space delimited
+temp=textscan(config,'%s','delimiter','\n');
+lines=temp{1};
+
+remote='';
+%Lets find the name of the remote corresponding to our branchName
+for k=1:length(lines)
+    
+    %Are we at the section describing our branch?
+    if strcmp(lines{k},['[branch "' branchName '"]'])
+        m=k+1;
+        %While we haven't run out of lines
+        %And while we haven't run into another section (which starts with
+        % an open bracket)
+        while (m<=length(lines) && ~strcmp(lines{m}(1),'[') )
+            temp=textscan(lines{m},'%s');
+            if length(temp{1})>=3
+                if strcmp(temp{1}{1},'remote') && strcmp(temp{1}{2},'=')
+                    %This is the line that tells us the name of the remote 
+                    remote=temp{1}{3};
+                end
+            end
+            
+            m=m+1;
+        end
+        
+        
+    
+    end
+end
+gitInfo.remote=remote;
+
+
+url='';
+%Find the remote's url
+for k=1:length(lines)
+    
+    %Are we at the section describing our branch?
+    if strcmp(lines{k},['[remote "' remote '"]'])
+        m=k+1;
+        %While we haven't run out of lines
+        %And while we haven't run into another section (which starts with
+        % an open bracket)
+        while (m<=length(lines) && ~strcmp(lines{m}(1),'[') )
+            temp=textscan(lines{m},'%s');
+            if length(temp{1})>=3
+                if strcmp(temp{1}{1},'url') && strcmp(temp{1}{2},'=')
+                    %This is the line that tells us the name of the remote 
+                    url=temp{1}{3};
+                end
+            end
+            
+            m=m+1;
+        end
+        
+        
+    
+    end
+end
+
+gitInfo.url=url;
\ No newline at end of file

mergeRoiTool.m

@@ -65,6 +65,7 @@ handles.needsReload = 1;
 handles.roi = struct;
 handles.roiCoords = struct;
 handles.lungGridSize = -1;
+handles.gitInfo = getGitInfo();
 % Update handles structure
 guidata(hObject, handles);
 
@@ -96,6 +97,7 @@ function pushbutton_save_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 lungMatrix = handles.lungMatrix;
+lungStats = handles.lungStats;
 
 savePath = [handles.path '/mergeLungROI'];
 fname = handles.curName;
@@ -730,6 +732,7 @@ lungHypo = size(find(handles.lungMatrix==2),1);
 lungHyper = size(find(handles.lungMatrix==3),1);
 lungBronchodyslasia = size(find(handles.lungMatrix==4),1);
 lungVol = -1;
+
 if strcmp(handles.dcminfo.SOPClassUID,'1.2.840.10008.5.1.4.1.1.4.1')
     %this is an enhanced dicom
     d = handles.dcminfo;
@@ -756,8 +759,20 @@ st = st + sprintf(" Normal Lung Voxels:   %d (%03.2f%%)\n",lungNormal, 100*lungN
 st = st + sprintf(" Hypointense Voxels:   %d (%03.2f%%)\n",lungHypo, 100*lungHypo/lungVoxels);
 st = st + sprintf(" Hyperintense Voxels:   %d (%03.2f%%)\n",lungHyper, 100*lungHyper/lungVoxels);
 st = st + sprintf(" Bronchodyspl Voxels:   %d (%03.2f%%)\n",lungBronchodyslasia, 100*lungBronchodyslasia/lungVoxels);
-st = st + sprintf("\nVolumes:\n");
+
+st = st + sprintf("\n\n\nVolumes:\n\nWarning these may be very wrong\n");
 st = st + sprintf(" Estimated Total Lung Volume:   %06.1f cc", lungVol);
 
 
 set(handles.statsTextbox,'String',st);
+
+lungStats = struct("countLungVoxels", lungVoxels...
+    , "countNormalVoxels", lungNormal...
+    , "countHypointVoxels", lungHypo...
+    , "countHyperintVoxels", lungHyper...
+    , "countBronchodisplasticVoxels", lungBronchodyslasia ...
+    , "estimatedLungVolume", lungVol...
+)
+handles.lungStats = lungStats;
+
+guidata(hObject, handles);
\ No newline at end of file