Merge branch 'master' of https://github.com/uncbiag/PStrip

.dockerignore

@@ -0,0 +1,7 @@
+dockerfolder
+func_code
+.git
+.gitignore
+main_code
+README.md
+tmp_res

.gitignore

@@ -1,2 +1,3 @@
 *.pyc
 func_code/*.pyc
+dockerfolder

Dockerfile

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+FROM nvidia/cuda:9.0-devel-ubuntu16.04
+
+MAINTAINER Xu Han [email protected]
+
+RUN apt-get update; \ 
+    apt-get -y upgrade; \
+    apt-get install -y \
+    python-pip \
+    git \
+    wget \
+    g++ \
+    cmake \
+    doxygen \
+    vim
+
+RUN python -m pip install --upgrade pip
+RUN pip install numpy scipy
+RUN python -m pip install scikit-build
+RUN python -m pip install SimpleITK
+
+RUN apt-get install -y \
+    zlib1g-dev \
+    libpng-dev
+
+RUN git clone https://git.code.sf.net/p/niftyreg/git niftyreg-git; \
+    cd niftyreg-git; \
+    mkdir build; \
+    mkdir install; \
+    cd build; \
+    cmake -D CMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=/niftyreg-git/install ../; \
+    make; \
+    make install
+
+ENV NIFTYREG_INSTALL /niftyreg-git/install
+ENV PATH $PATH:$NIFTYREG_INSTALL/bin
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:$NIFTYREG_INSTALL/lib
+
+RUN apt-get -y update; \
+    apt-get install -y \
+    libboost-all-dev \
+    build-essential \
+    python-dev \
+    python-setuptools \
+    libboost-python-dev \
+    libboost-thread-dev
+
+
+
+RUN wget https://pypi.python.org/packages/b3/30/9e1c0a4c10e90b4c59ca7aa3c518e96f37aabcac73ffe6b5d9658f6ef843/pycuda-2017.1.1.tar.gz; \
+    tar xfz pycuda-2017.1.1.tar.gz; \
+    cd pycuda-2017.1.1; \
+    python configure.py \
+    --cuda-root=/usr/local/cuda \
+    --cudadrv-lib-dir=/usr/lib/x86_64-linux-gnu \
+    --boost-inc-dir=/usr/include \
+    --boost-lib-dir=/usr/lib \
+    --boost-python-libname=boost_python \
+    --boost-thread-libname=boost_thread \
+    --no-use-shipped-boost; \
+    make install; \
+    rm -rf pycuda-2017.1.1.tar.gz
+
+RUN git clone https://github.com/lebedov/scikit-cuda.git; \
+    cd scikit-cuda; \
+    python setup.py install
+
+RUN git clone https://github.com/uncbiag/PStrip.git
+
+COPY data/atlas/ /PStrip/data/atlas/
+COPY data/pca/pca_100/ /PStrip/data/pca/pca_100/
+

func_code/niftyreg.conf

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+nifty_bin = '/niftyreg-git/install/bin'

func_code/niftyreg.py

@@ -1,4 +1,12 @@
-nifty_bin = '/playpen/xhs400/Research/niftyreg-git/niftyreg_install/bin'
+import os
+import imp
+import sys
+
+f = open(os.path.join(sys.path[0], '..', 'func_code', 'niftyreg.conf'))
+config = imp.load_source('config', '', f)
+f.close()
+
+nifty_bin = config.nifty_bin
 
 def nifty_reg_bspline(ref, flo, res = False, cpp = False, rmask = False, fmask = False, levels = False ):
     executable = nifty_bin + '/reg_f3d'