AIM-Harvard · JoostJM · Sep 25, 2019 · Aug 21, 2019 · Sep 2, 2019 · Sep 2, 2019
diff --git a/docker/cli/Dockerfile b/docker/cli/Dockerfile
@@ -2,28 +2,29 @@ FROM centos:6
 MAINTAINER http://github.com/radiomics
 
 RUN yum update -y && \
-  yum groupinstall -y "Development Tools" && \
-  yum install -y curl \
-   curl-devel \
-   coreutils \
-   freetype-devel \
-   gcc \
-   gcc-c++ \
-   gettext \
-   libpng-devel \
-   openssl-devel \
-   perl \
-   perl-CPAN \
-   perl-ExtUtils-MakeMaker \
-   wget \
-   zlib-devel
+    yum groupinstall -y "Development Tools" && \
+    yum install -y bzip2-devel \
+    curl \
+    curl-devel \
+    coreutils \
+    freetype-devel \
+    gcc \
+    gcc-c++ \
+    gettext \
+    libpng-devel \
+    openssl-devel \
+    perl \
+    perl-CPAN \
+    perl-ExtUtils-MakeMaker \
+    wget \
+    zlib-devel
 
 WORKDIR /etc/yum.repos.d
 RUN wget http://people.centos.org/tru/devtools-2/devtools-2.repo
 RUN yum install -y devtoolset-2-gcc \
-  devtoolset-2-binutils \
-  devtoolset-2-gcc-gfortran \
-  devtoolset-2-gcc-c++
+    devtoolset-2-binutils \
+    devtoolset-2-gcc-gfortran \
+    devtoolset-2-gcc-c++
 ENV CC /opt/rh/devtoolset-2/root/usr/bin/gcc
 ENV CXX /opt/rh/devtoolset-2/root/usr/bin/g++
 ENV FC /opt/rh/devtoolset-2/root/usr/bin/gfortran
@@ -42,72 +43,72 @@ ENV FC /opt/rh/devtoolset-2/root/usr/bin/gfortran
 WORKDIR /usr/src
 ENV GIT_VERSION 2.5.0
 RUN wget --no-check-certificate https://www.kernel.org/pub/software/scm/git/git-${GIT_VERSION}.tar.gz && \
-  tar xvzf git-${GIT_VERSION}.tar.gz && \
-  cd git-${GIT_VERSION} && \
-  ./configure --prefix=/usr && \
-  make && \
-  make install && \
-  cd .. && rm -rf git-${GIT_VERSION}*
+    tar xvzf git-${GIT_VERSION}.tar.gz && \
+    cd git-${GIT_VERSION} && \
+    ./configure --prefix=/usr && \
+    make && \
+    make install && \
+    cd .. && rm -rf git-${GIT_VERSION}*
 
 # Build and install CMake from source.
 WORKDIR /usr/src
 RUN git clone git://cmake.org/cmake.git CMake && \
-  cd CMake && \
-  git checkout v3.7.2 && \
-  mkdir /usr/src/CMake-build && \
-  cd /usr/src/CMake-build && \
-  /usr/src/CMake/bootstrap \
-    --parallel=$(grep -c processor /proc/cpuinfo) \
-    --prefix=/usr && \
-  make -j$(grep -c processor /proc/cpuinfo) && \
-  ./bin/cmake \
-    -DCMAKE_BUILD_TYPE:STRING=Release \
-    -DCMAKE_USE_OPENSSL:BOOL=ON . && \
-  make install && \
-  cd .. && rm -rf CMake*
+    cd CMake && \
+    git checkout v3.7.2 && \
+    mkdir /usr/src/CMake-build && \
+    cd /usr/src/CMake-build && \
+    /usr/src/CMake/bootstrap \
+      --parallel=$(grep -c processor /proc/cpuinfo) \
+      --prefix=/usr && \
+    make -j$(grep -c processor /proc/cpuinfo) && \
+    ./bin/cmake \
+      -DCMAKE_BUILD_TYPE:STRING=Release \
+      -DCMAKE_USE_OPENSSL:BOOL=ON . && \
+    make install && \
+    cd .. && rm -rf CMake*
 
 # Build and install Python from source.
 WORKDIR /usr/src
 ENV PYTHON_VERSION 3.6.9
 RUN wget https://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tgz && \
-  tar xvzf Python-${PYTHON_VERSION}.tgz && \
-  cd Python-${PYTHON_VERSION} && \
-  ./configure && \
-  make -j$(grep -c processor /proc/cpuinfo) && \
-  make install && \
-  cd .. && rm -rf Python-${PYTHON_VERSION}*
+    tar xvzf Python-${PYTHON_VERSION}.tgz && \
+    cd Python-${PYTHON_VERSION} && \
+    ./configure && \
+    make -j$(grep -c processor /proc/cpuinfo) && \
+    make install && \
+    cd .. && rm -rf Python-${PYTHON_VERSION}*
 
 # Build and install ninja from source.
 WORKDIR /usr/src
 RUN git clone https://github.com/martine/ninja.git && \
-  cd ninja && \
-  git checkout v1.6.0 && \
-  ./configure.py --bootstrap && \
-  mv ninja /usr/bin/ && \
-  cd .. && rm -rf ninja
+    cd ninja && \
+    git checkout v1.6.0 && \
+    ./configure.py --bootstrap && \
+    mv ninja /usr/bin/ && \
+    cd .. && rm -rf ninja
 
 # Setup Python package manager (pip)
 WORKDIR /usr/src
 RUN python3 --version && \
-  wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py && \
-  python3 get-pip.py
+    wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py && \
+    python3 get-pip.py && rm get-pip.py
 
 # Setup necessary python packages
-WORKDIR /usr/src
 RUN pip3 install wheel>=0.29.0 && \
-  pip3 install setuptools>=28.0.0 && \
-  pip3 install scipy && \
-  pip3 install trimesh && \
-  pip3 install scikit-image && \
-  pip3 install --trusted-host www.itk.org -f https://itk.org/SimpleITKDoxygen/html/PyDownloadPage.html SimpleITK>=0.9.1 && \
-  python3 -c "import SimpleITK; print('SimpleITK Version:' + SimpleITK.Version_VersionString())"
+    pip3 install setuptools>=28.0.0 && \
+    pip3 install scipy && \
+    pip3 install trimesh && \
+    pip3 install scikit-image && \
+    pip3 install --trusted-host www.itk.org -f https://itk.org/SimpleITKDoxygen/html/PyDownloadPage.html SimpleITK>=0.9.1 && \
+    python3 -c "import SimpleITK; print('SimpleITK Version:' + SimpleITK.Version_VersionString())"
 
-# Install PyRadiomics
+# Install PyRadiomics, then remove the source code to reduce image size
 WORKDIR /usr/src
-RUN git clone https://github.com/radiomics/pyradiomics.git && \
-  cd pyradiomics && \
-  pip3 install -r requirements.txt && \
-  python3 setup.py install
+ADD . /usr/src/pyradiomics
+RUN cd pyradiomics && \
+    pip3 install --no-cache-dir -r requirements.txt && \
+    python3 setup.py install && \
+    cd .. && rm -rf pyradiomics
 
 WORKDIR /usr/src
 ENTRYPOINT ["pyradiomics"]
diff --git a/labs/pyradiomics-dcm/Dockerfile b/labs/pyradiomics-dcm/Dockerfile
@@ -0,0 +1,25 @@
+FROM radiomics/pyradiomics:CLI
+MAINTAINER https://github.com/Radiomics
+
+# Install required dcm2niix converions tools
+WORKDIR /usr/src
+RUN git clone https://github.com/rordenlab/dcm2niix.git && \
+  cd dcm2niix && \
+  mkdir build && cd build && \
+  cmake .. && \
+  make install
+
+# Install additional needed python packages
+# Prevent pandas from installing version 0.25.0, as this version is unable to import
+# module _lzma (in package lmza). See also https://github.com/pandas-dev/pandas/issues/27543
+WORKDIR /usr/src
+RUN pip3 install pandas!=0.25.0 && \
+  pip3 install pydicom
+
+# Copy the required DCMQI tools from the latest DCMQI docker image
+COPY --from=qiicr/dcmqi:latest /usr/bin/tid1500writer /usr/bin/segimage2itkimage /usr/bin/
+# Copy the pyradiomics-dcm.py script to ensure latest changes are included in the image
+COPY ./labs/pyradiomics-dcm/* /usr/src/pyradiomics/labs/pyradiomics-dcm/
+
+WORKDIR /usr/src/pyradiomics/labs/pyradiomics-dcm
+ENTRYPOINT ["python3", "pyradiomics-dcm.py"]
diff --git a/labs/pyradiomics-dcm/pyradiomics-dcm.py b/labs/pyradiomics-dcm/pyradiomics-dcm.py
@@ -20,7 +20,6 @@
 scriptlogger = logging.getLogger('radiomics.dicom')
 scriptlogger.setLevel(logging.DEBUG)
 
-
 def dcmImageToNRRD(inputDICOMImageDir, tempDir):
   scanNRRDFile = os.path.join(tempDir, "image.nrrd")
   if not os.path.isfile(scanNRRDFile):
@@ -35,7 +34,7 @@ def dcmImageToNIfTI(inputDICOMImageDir, tempDir):
   scanJSONFile = os.path.join(inputDICOMImageDir, "volume.json")
   # will save to volume.nii
   if not os.path.isfile(destScanNIfTIFile):
-    cmd = ['dcm2niix', "-m", "y", inputDICOMImageDir]
+    cmd = ['dcm2niix', "-m", "y", "-f", "volume", inputDICOMImageDir]
     call(cmd)
     shutil.move(scanNIfTIFile, destScanNIfTIFile)
     if os.path.isfile(scanJSONFile):