Merge pull request #40 from SRI-RSST/dev-branch

Updated Dockerfiles and GUI scripts

Dockerfile

@@ -1,7 +1,9 @@
 ARG MIRACL_VERSION=latest
-FROM mgoubran/miracl:base-$MIRACL_VERSION
+#FROM mgoubran/miracl:base-$MIRACL_VERSION
+FROM mgoubran/miracl-modified:latest
 
 ADD . /code
+RUN ls /code
 RUN git clone https://github.com/sergivalverde/nifti_tools && \
     mv nifti_tools /code/depends/NIFTI_TOOLS && \
     pip install -e /code/
@@ -12,7 +14,9 @@ ENV MIRACL_HOME=/code/miracl
 
 WORKDIR /tmp
 RUN mkdir -p "/code/atlases/" && \
-	wget -nH -r --cut-dirs 3 --no-parent -A txt,json,csv,nii.gz -P /code/atlases http://web.stanford.edu/group/zeinehlab/MIRACLextra/
+    wget -nH -r --cut-dirs 3 --no-parent -A txt,json,csv,nii.gz -P /code/atlases http://web.stanford.edu/group/zeinehlab/MIRACLextra/
+
+# RUN conda install -y --no-update-deps pyqt=5
 
 ENV aradir "/code/atlases/ara"
 
@@ -46,4 +50,4 @@ ENV IN_DOCKER_CONTAINER Yes
 
 ################################################################################
 
-ENTRYPOINT ["/opt/miniconda/bin/miracl"]
+ENTRYPOINT ["/bin/bash"]

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 SRI-RSST
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docker/Dockerfile

@@ -5,25 +5,30 @@ ENV DEBIAN_FRONTEND noninteractive
 RUN apt-get update && apt-get install -y git wget build-essential g++ gcc cmake curl clang && \
     apt-get install -y libfreetype6-dev apt-utils pkg-config vim gfortran && \
     apt-get install -y binutils make linux-source unzip && \
+    apt install libxcb-xinerama0 && \
     apt install -y libsm6 libxext6 libfontconfig1 libxrender1 && \
     apt-get install -y itksnap
 
 # Install miniconda
-RUN curl -LO https://repo.anaconda.com/miniconda/Miniconda2-4.6.14-Linux-x86_64.sh && \
-    bash Miniconda2-4.6.14-Linux-x86_64.sh -p /opt/miniconda -b && \
-    rm Miniconda2-4.6.14-Linux-x86_64.sh
+RUN curl -LO https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh && \
+    bash Miniconda3-4.6.14-Linux-x86_64.sh -p /opt/miniconda -b && \
+    rm Miniconda3-4.6.14-Linux-x86_64.sh
 ENV PATH=/opt/miniconda/bin:${PATH}
 
 RUN mkdir -p /code/atlases /data
 WORKDIR /code
 
 RUN apt install -y libhdf5-serial-dev && \
+    apt-get install libatlas-base-dev libblas3 liblapack3 liblapack-dev libblas-dev && \
     pip install --upgrade pip && \
-    pip install matplotlib joblib scipy==1.2.1 && \
-    pip install tifffile && \
-    pip install menpo==0.8.0 opencv-python==4.2.0.32 && \
+    python3 -m pip install numpy && \
+    python3 -m pip install matplotlib joblib && \
+    python3 -m pip install scipy==1.2.1 && \
+    python3 -m pip install tifffile && \
+    conda install -c menpo menpo && \
+    python3 -m pip install opencv-python==4.2.0.32 && \
     apt remove -y cmake && \
-    pip install cmake
+    pip3 install cmake
 
 # Install ANTs
 ###   Install ANTs   ###
@@ -78,12 +83,12 @@ RUN wget https://github.com/ijpb/MorphoLibJ/releases/download/v1.4.0/MorphoLibJ_
 RUN wget https://downloads.sourceforge.net/project/c3d/c3d/Nightly/c3d-nightly-Linux-x86_64.tar.gz && \
     tar -xzvf c3d-nightly-Linux-x86_64.tar.gz && mv c3d-1.1.0-Linux-x86_64 /opt/cd3 && \
     rm c3d-nightly-Linux-x86_64.tar.gz
-ENV PATH /opt/c3d/bin:${PATH}
+ENV PATH /opt/cd3/bin:${PATH}
 
 # Install FSL, cmake
 RUN apt-get update && apt-get install -y fsl && \
     apt remove cmake && \
-    pip install cmake --upgrade
+    pip3 install cmake --upgrade
 
 ENV FSLDIR="/usr/share/fsl/5.0" \
     FSLOUTPUTTYPE="NIFTI_GZ" \
@@ -97,8 +102,12 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
 ENV PATH="/usr/lib/fsl/5.0:${PATH}"
 
 WORKDIR /code
-RUN pip install scikit-image==0.14.2 && \
-    pip install cython h5py && \
-    pip install pandas==0.24.2
+ADD requirements.txt /code
+RUN pip3 install scikit-image==0.14.2 && \
+    pip3 install cython h5py && \
+    pip3 install pandas==0.24.2 && \
+    pip3 install -r requirements.txt
 
-RUN conda install -y --no-update-deps pyqt=4
+#RUN alias python=python3
+
+#RUN conda install -y --no-update-deps pyqt=5

experi/install_c3d.sh

@@ -0,0 +1,9 @@
+c3dpath=$( command -v c3d )
+if [[ -z "${c3dpath}" ]]; then
+	echo "Command c3d was not found. Downloading and installing software to ${SCRIPTPATH}/depends/c3d. Path will be added to PATH environment variable."
+    mkdir -p "${SCRIPTPATH}/depends/c3d/"
+    wget https://downloads.sourceforge.net/project/c3d/c3d/Nightly/c3d-nightly-Linux-x86_64.tar.gz && \
+    tar -xzvf c3d-nightly-Linux-x86_64.tar.gz && mv c3d-1.1.0-Linux-x86_64/* "${SCRIPTPATH}/depends/c3d/" && \
+    rm c3d-nightly-Linux-x86_64.tar.gz
+    export PATH="${SCRIPTPATH}/depends/c3d/c3d-1.1.0-Linux-x86_64/bin/:$PATH"
+fi