Merge branch 'master' into 'public'

Updates to CI scripts and readme



See merge request !5

.gitlab-ci.yml

@@ -19,3 +19,13 @@ gift-adelie:
  - matlab
  - cuda
 
+gift-skylight:
+ script:
+ - set PATH=%PATH%;C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin
+ - "call .\\ci\\test-win.bat"
+ tags:
+ - gift-skylight
+ - gift-win64
+ - matlab
+ - cuda
+

README.md

@@ -8,13 +8,23 @@ Slic-Seg is a minimally interactive online learning-based segmentation method. A
 Slic-Seg was developed as part of the [GIFT-Surg][giftsurg] project. The algorithm and software were developed by Guotai Wang at the [Translational Imaging Group][tig] in the [Centre for Medical Image Computing][cmic] at [University College London (UCL)][ucl].
 
 Algorithm and code by Guotai Wang.
+
 If you use this software, please cite [this paper][citation]. 
 
 
+How to cite
+----------
+
+If you use this software, please cite [this paper][citation].
+
+ Slic-Seg: A minimally interactive segmentation of the placenta from sparse and motion-corrupted fetal MRI in multiple views
+ Guotai Wang, Maria A. Zuluaga, Rosalind Pratt, Michael Aertsen, Tom Doel, Maria Klusmann, Anna L. David, Jan Deprest, Tom Vercauteren, Sébastien Ourselin
+
+
 Disclaimer
 ----------
 
- * This is PROTOTYPE software and may lead to system instability and crashes which could result in data loss.
+ * This is PROTOTYPE software. Due to the low-level GPU computation there is a risk of system instability and crashes which could result in data loss.
 
 
 Software links
@@ -45,6 +55,34 @@ The current version of Slic-Seg requries:
  * A Matlab-supported C++ compiler installed and configured to work with mex files [see here](http://uk.mathworks.com/help/matlab/matlab_external/what-you-need-to-build-mex-files.html)
  * [The CUDA toolkit](https://developer.nvidia.com/cuda-toolkit) to be installed and configured to work with Matlab
 
+Please note that there are cross-dependencies between Matlab, CUDA, C++ and the OS. Please see below for the platforms and versions we have tested against.
+
+
+Supported Platforms
+-----------------------------
+
+Slic-Seg is a cross-platform Matlab/C++ library. We have tested Slic-Seg on the following platforms:
+
+ - Linux
+ - Ubuntu Desktop 14.04.3 LTS 64-bit
+ - NVIDIA 12GB GTX TITAN X
+ - CUDA 7.5
+ - Matlab R2015b
+
+ - MacOS X
+ - OS X Yosemite 10.10.5
+ - NVIDIA GeForce GT 750M 1024 MB
+ - XCode 7.2.1
+ - CUDA 7.5
+ - Matlab 2015b 64-bit
+
+ - Windows
+ - Windows 10 Professional 64-bit (NOTE: Matlab does not support GPU operations on 32-bit Windows)
+ - 2GB NVIDIA Quadro 4000
+ - Visual Studio 2013 Community Edition (NOTE: CUDA does not support Visual Studio 2015 or gcc)
+ - CUDA 7.5
+ - Matlab 2015b 64-bit
+
 
 How to use
 ------------
@@ -102,25 +140,8 @@ This work was supported through an Innovative Engineering for Health award by th
 
 
 
-Supported Platforms
------------------------------
-
-Slic-Seg is a cross-platform Matlab/C++ library. We have tested Slic-Seg on the following platforms:
 
- - Linux
- - Ubuntu Desktop 14.04.3 LTS 64-bit
- - NVIDIA 12GB GTX TITAN X
- - CUDA 7.5
- - Matlab R2015b
-
- - MacOS X
- - OS X Yosemite 10.10.5
- - NVIDIA GeForce GT 750M 1024 MB
- - XCode 7.2.1
- - CUDA 7.5
-
- - Windows
- - Not yet tested
+
 
 
 Please note that NVIDA CUDA drivers and Matlab have specific compatibility requirements regarding C++ compilers

ci/test-win.bat

@@ -1,5 +1,5 @@
-echo Running Windows build and testscript %~dp0%\matlab\CIBuildAndTest.m
-call "C:\Program Files\MATLAB\R2015b\bin\matlab.exe" -wait -nodisplay -nosplash -nodesktop -r "try, run('%~dp0%\matlab\CIBuildAndTest.m'), catch ex, disp(['Exception during CIBuildAndTest.m: ' ex.message]), exit(1), end, exit(0);"
+echo Running Windows build and testscript %~dp0..\matlab\CIBuildAndTest.m
+call "C:\Program Files\MATLAB\R2015b\bin\matlab.exe" -wait -nodisplay -nosplash -nodesktop -r "try, run('%~dp0..\matlab\CIBuildAndTest.m'), catch ex, disp(['Exception during CIBuildAndTest.m: ' ex.message]), exit(1), end, exit(0);"
 
 if not "%ERRORLEVEL%" == "0" (
  echo Exit Code = %ERRORLEVEL%

matlab/library/OnlineRandomForest/ORForest.cpp

@@ -81,17 +81,21 @@ void ORForest::Train(const double *i_trainData, int i_Ns,int i_Nfp1)
  }
 }
 
-void ORForest::Predict(const double *i_testData, int i_Ns, int i_Nf, double *o_predict)
+void ORForest::Predict(const double *i_testData, const int i_Ns, const int i_Nf, double *o_predict)
 {
- double tempPredict[i_Ns];
- for(int i=0;i<treeNumber;i++)
+ double *tempPredict;
+ tempPredict = new double[i_Ns];
+
+ for(int i=0;i<treeNumber;i++)
  {
  tree[i].Predict(i_testData, i_Ns, i_Nf,tempPredict);
  for(int i=0;i<i_Ns;i++)
  {
  o_predict[i]+=tempPredict[i];
  }
  }
+ delete [] tempPredict; 
+
  for(int i=0;i<i_Ns;i++)
  {
  o_predict[i]=o_predict[i]/treeNumber;

matlab/library/OnlineRandomForest/ORForest.h

@@ -22,7 +22,7 @@ class ORForest
  ~ ORForest();
  void Init(int Ntree, int treeDepth, int leastNsampleForSplit);
  void Train(const double *i_trainData, int i_Ns,int i_Nfp1);
- void Predict(const double *i_testData, int i_Ns, int i_Nf, double *o_predict);
+ void Predict(const double *i_testData, const int i_Ns, const int i_Nf, double *o_predict);
  void ConvertTreeToList(int * io_left, int * io_right, 
  int *io_splitFeature, double *io_splitValue, 
  int maxNodeNumber);

matlab/library/coremat/MexCompile/CoreCompileMexFiles.m

@@ -271,6 +271,7 @@ function CheckMexFiles(mex_files_to_compile, cached_mex_file_info, output_direct
  cuda_compiler = TryToFindCudaCompilerPc(fullfile(getenv('ProgramFiles(x86)'), 'NVIDIA GPU Computing Toolkit', 'CUDA'));
  end
  end
+ cuda_compiler = CoreTextUtilities.RemoveNonprintableCharacters(cuda_compiler);
  else
  [status, cuda_compiler] = system('which nvcc');
 

matlab/library/coremat/MexCompile/CoreCudaCompile.m

@@ -12,7 +12,7 @@
 
  methods (Static)
  function mex_result = Compile(compiler, mex_file, src_fullfile, output_directory)
- compile_arguments = [compiler ' -ptx --output-directory ' output_directory ' ' src_fullfile, ' ' mex_file.OtherCompilerFiles];
+ compile_arguments = ['"' compiler '" -ptx --output-directory ' output_directory ' ' src_fullfile, ' ' mex_file.OtherCompilerFiles];
  mex_result = system(compile_arguments);
  end
  end