From a602e5f6666656594fcd5894a4d668e78133ca3d Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 26 Feb 2019 16:13:30 +0000
Subject: [PATCH 01/16] update to Ubuntu 18.04

---
 docker/Dockerfile            | 2 +-
 docker/docker-compose.yml    | 2 +-
 docker/user_python-ubuntu.sh | 2 +-
 docker/user_sirf-ubuntu.sh   | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 634d64a2..6a20864f 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:16.04 as base
+FROM ubuntu:18.04 as base
 LABEL \
   author.name="Casper da Costa-Luis"          \
   author.email=imaging@caspersci.uk.to        \
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
index a8d689d1..254331f1 100644
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -29,5 +29,5 @@ services:
    context: .
    target: core
    cache_from:
-    - ubuntu:16.04
+    - ubuntu:18.04
     - ccppetmr/sirf:core
diff --git a/docker/user_python-ubuntu.sh b/docker/user_python-ubuntu.sh
index 2dc0a7d5..9cac918d 100755
--- a/docker/user_python-ubuntu.sh
+++ b/docker/user_python-ubuntu.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-set -ev
 [ -f .bashrc ] && . .bashrc
+set -ev
 INSTALL_DIR="${1:-/opt/pyvenv}"
 PYTHON="${2:-miniconda}"
 
diff --git a/docker/user_sirf-ubuntu.sh b/docker/user_sirf-ubuntu.sh
index 0bd65097..d886e961 100755
--- a/docker/user_sirf-ubuntu.sh
+++ b/docker/user_sirf-ubuntu.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
-set -ev
 [ -f .bashrc ] && . .bashrc
+set -ev
 # SIRF
 git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master /opt/SIRF-SuperBuild
 pushd /opt/SIRF-SuperBuild

From 07221726ad83cdc695b4558bcd9a6bc2b12f00be Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 26 Feb 2019 16:38:52 +0000
Subject: [PATCH 02/16] re-enable travis docker, add ITK and ACE

---
 .travis.yml                      | 16 ++++++++--------
 docker/Dockerfile                |  5 +++--
 docker/build_gadgetron-ubuntu.sh |  7 -------
 docker/build_system-ubuntu.sh    | 10 ++++++++++
 4 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index c9b4919f..66459b1a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -65,12 +65,12 @@ matrix:
    # +boost +itk -hdf5 +swig
    env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
  # docker
- #- os: linux
- #  # +armadillo +boost +fftw3 +hdf5 +siemens_to_ismrmrd +swig
- #  env: DOCKER_BUILD=1
- #- os: linux
- #  # +DEVEL +armadillo +boost +fftw3 +hdf5 +siemens_to_ismrmrd +swig
- #  env: DOCKER_BUILD=DEVEL
+ - os: linux
+   # +ace +armadillo +boost +fftw3 +hdf5 +itk +siemens_to_ismrmrd +swig
+   env: DOCKER_BUILD=1
+ - os: linux
+   # +DEVEL +ace +armadillo +boost +fftw3 +hdf5 +itk +siemens_to_ismrmrd +swig
+   env: DOCKER_BUILD=DEVEL
 
 env:
  global:
@@ -231,7 +231,7 @@ before_install:
  # N.B.: don't put into build matrix to allow caching.
  - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER"
  - cmake --version
- 
+
 install:
  - |
     if [[ -n "$DOCKER_BUILD" ]]; then
@@ -268,7 +268,7 @@ install:
         $PY_EXE -m pip install --user --only-binary=numpy,scipy,matplotlib numpy scipy matplotlib
         cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
         # Job may timeout (>50min) if no ccache, otherwise should be <1min:
-        make 
+        make
         mv INSTALL/share/gadgetron/config/gadgetron.xml.example INSTALL/share/gadgetron/config/gadgetron.xml
       ) || travis_terminate 1
       source $PWD/INSTALL/bin/env_ccppetmr.sh
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 6a20864f..54984076 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -76,9 +76,10 @@ COPY user_sirf-ubuntu.sh .
 COPY devel/.ccache/ /opt/ccache/
 RUN ccache -o cache_dir=/opt/ccache
 ARG BUILD_FLAGS="\
-  -DCMAKE_BUILD_TYPE=Release -DBUILD_STIR_WITH_OPENMP=ON \
+  -DCMAKE_BUILD_TYPE=Release -DBUILD_STIR_WITH_OPENMP=ON -DUSE_SYSTEM_ACE=ON \
   -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON \
-  -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON"
+  -DUSE_SYSTEM_HDF5=ON -DUSE_ITK=ON -DBUILD_siemens_to_ismrmrd=ON \
+  -DUSE_SYSTEM_SWIG=ON"
 ARG EXTRA_BUILD_FLAGS=""
 RUN bash user_sirf-ubuntu.sh
 RUN rm user_sirf-ubuntu.sh
diff --git a/docker/build_gadgetron-ubuntu.sh b/docker/build_gadgetron-ubuntu.sh
index ac9de0a1..c9e46fc7 100755
--- a/docker/build_gadgetron-ubuntu.sh
+++ b/docker/build_gadgetron-ubuntu.sh
@@ -6,11 +6,4 @@ apt-get install -yq --no-install-recommends \
   h5utils              \
   liblapack-dev        \
   libace-dev
-# Not required (yet) by SIRF
-# libxml2-dev
-# libxslt-dev
-# python-h5py
-# python-libxml2
-# python-psutil
-# libplplot-dev
 apt-get clean
diff --git a/docker/build_system-ubuntu.sh b/docker/build_system-ubuntu.sh
index c2c47f53..c9fe45b3 100755
--- a/docker/build_system-ubuntu.sh
+++ b/docker/build_system-ubuntu.sh
@@ -15,3 +15,13 @@ apt-get install -yq --no-install-recommends \
   libxslt-dev          \
   swig
 apt-get clean
+
+# Not required (yet) by SIRF
+# libxml2-dev
+# libxslt-dev
+# python-h5py
+# python-libxml2
+# python-psutil
+# libplplot-dev
+# libopenblas-dev
+# libatlas-base-dev

From 144e5fcec758f602c14e6099e287540b37d54903 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 26 Feb 2019 18:18:39 +0000
Subject: [PATCH 03/16] silly conda fix

https://github.com/conda/conda/issues/6030
---
 docker/user_python-ubuntu.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker/user_python-ubuntu.sh b/docker/user_python-ubuntu.sh
index 9cac918d..88bcfabd 100755
--- a/docker/user_python-ubuntu.sh
+++ b/docker/user_python-ubuntu.sh
@@ -13,8 +13,8 @@ miniconda)
   rm miniconda.sh
   source "$INSTALL_DIR"/bin/activate
   conda config --add channels conda-forge
-  conda update -c conda-forge -y conda
-  conda update -c conda-forge -y --all
+  # https://github.com/conda/conda/issues/6030
+  #conda update -c conda-forge -y conda
   ;;
 *python*)
   # virtualenv

From 02ff0b3b59f2eb2e913ee8001b78ee4bae566563 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 27 Feb 2019 15:54:53 +0000
Subject: [PATCH 04/16] ensure docker uses ccache

https://cmake.org/cmake/help/latest/variable/CMAKE_LANG_COMPILER_LAUNCHER.html
---
 docker/Dockerfile | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 54984076..a2e225ab 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -76,10 +76,12 @@ COPY user_sirf-ubuntu.sh .
 COPY devel/.ccache/ /opt/ccache/
 RUN ccache -o cache_dir=/opt/ccache
 ARG BUILD_FLAGS="\
-  -DCMAKE_BUILD_TYPE=Release -DBUILD_STIR_WITH_OPENMP=ON -DUSE_SYSTEM_ACE=ON \
-  -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON \
-  -DUSE_SYSTEM_HDF5=ON -DUSE_ITK=ON -DBUILD_siemens_to_ismrmrd=ON \
-  -DUSE_SYSTEM_SWIG=ON"
+ -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache\
+ -DCMAKE_BUILD_TYPE=Release\
+ -DBUILD_STIR_WITH_OPENMP=ON -DUSE_SYSTEM_ACE=ON\
+ -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON\
+ -DUSE_SYSTEM_HDF5=ON -DUSE_ITK=ON -DBUILD_siemens_to_ismrmrd=ON\
+ -DUSE_SYSTEM_SWIG=ON"
 ARG EXTRA_BUILD_FLAGS=""
 RUN bash user_sirf-ubuntu.sh
 RUN rm user_sirf-ubuntu.sh

From 0c475a5e1c300f5fcb99d1ce40dd8288dd0b3403 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 27 Feb 2019 16:15:38 +0000
Subject: [PATCH 05/16] update ccache usage assuming cmake>=3.4

---
 .travis.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 66459b1a..0e64bb34 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -219,17 +219,11 @@ before_install:
  - $PY_EXE --version
  - $PY_EXE -m pip --version
  - $PY_EXE -m pip freeze
- # ccache compiler override
- - ln -s "$(which ccache)" g++
- - ln -s "$(which ccache)" g++-6
- - ln -s "$(which ccache)" g++-7
- - ln -s "$(which ccache)" gcc
- - ln -s "$(which ccache)" gcc-6
- - ln -s "$(which ccache)" gcc-7
  - export PATH="$PWD:$PATH"
  - popd
  # N.B.: don't put into build matrix to allow caching.
  - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER"
+ - BUILD_FLAGS="$BUILD_FLAGS -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache"
  - cmake --version
 
 install:

From e09ac1688c67b4c1f44ed1413167358a342a8b0b Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 27 Feb 2019 17:44:30 +0000
Subject: [PATCH 06/16] docker: explicitly list build flags

---
 docker/user_sirf-ubuntu.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/user_sirf-ubuntu.sh b/docker/user_sirf-ubuntu.sh
index d886e961..8c43d262 100755
--- a/docker/user_sirf-ubuntu.sh
+++ b/docker/user_sirf-ubuntu.sh
@@ -4,6 +4,7 @@ set -ev
 # SIRF
 git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master /opt/SIRF-SuperBuild
 pushd /opt/SIRF-SuperBuild
+echo $BUILD_FLAGS $EXTRA_BUILD_FLAGS
 cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
 make -j 2
 

From efc2ac8732c2c2b0bb3f09939037c9a2e5025807 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Thu, 28 Feb 2019 17:09:31 +0000
Subject: [PATCH 07/16] for testing. TODO: revert when merging into master

---
 docker/user_sirf-ubuntu.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/user_sirf-ubuntu.sh b/docker/user_sirf-ubuntu.sh
index 8c43d262..3c2fa2ef 100755
--- a/docker/user_sirf-ubuntu.sh
+++ b/docker/user_sirf-ubuntu.sh
@@ -2,7 +2,7 @@
 [ -f .bashrc ] && . .bashrc
 set -ev
 # SIRF
-git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b master /opt/SIRF-SuperBuild
+git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b docker /opt/SIRF-SuperBuild
 pushd /opt/SIRF-SuperBuild
 echo $BUILD_FLAGS $EXTRA_BUILD_FLAGS
 cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .

From acb0088b93d1fea31ff0fff6e8fb122e18a2339e Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Thu, 28 Feb 2019 18:24:10 +0000
Subject: [PATCH 08/16] minor test tidy

---
 docker/devel/test.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docker/devel/test.sh b/docker/devel/test.sh
index 9b081e7e..a227d1d6 100755
--- a/docker/devel/test.sh
+++ b/docker/devel/test.sh
@@ -19,11 +19,12 @@ GCONFIG=./INSTALL/share/gadgetron/config/gadgetron.xml
 [ -f "$GCONFIG" ] || cp "$GCONFIG".example "$GCONFIG"
 ./INSTALL/bin/gadgetron >& gadgetron.log&
 
-# print for debugging
-[ "$DEBUG" != 0 ] && cat builds/SIRF/build/CMakeCache.txt
 ctest -VV
 ret=$?
+kill -n 15 $(pidof gadgetron)
+
 # print for debugging
+[ "$DEBUG" != 0 ] && cat builds/SIRF/build/CMakeCache.txt
 [ "$DEBUG" != 0 ] && cat builds/SIRF/build/Testing/Temporary/LastTest.log
 # may exceed 4MB travis log limit
 [ "$DEBUG" != 0 ] && cat gadgetron.log

From 6563e5ee60963b71370a41210c535ef50fb8fd45 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 01:05:48 +0000
Subject: [PATCH 09/16] fix gadgetron from source

---
 docker/build_gadgetron-ubuntu.sh | 20 +++++++++++++++++---
 docker/build_system-ubuntu.sh    | 14 --------------
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/docker/build_gadgetron-ubuntu.sh b/docker/build_gadgetron-ubuntu.sh
index c9e46fc7..a57281d5 100755
--- a/docker/build_gadgetron-ubuntu.sh
+++ b/docker/build_gadgetron-ubuntu.sh
@@ -1,9 +1,23 @@
 #!/usr/bin/env bash
 set -ev
 # Gadgetron
+# from https://github.com/gadgetron/gadgetron/blob/master/docker/base/ubuntu_1804/Dockerfile#L8
 apt-get update -qq
 apt-get install -yq --no-install-recommends \
-  h5utils              \
-  liblapack-dev        \
-  libace-dev
+  libhdf5-serial-dev     \
+  libboost-all-dev       \
+  libfftw3-dev           \
+  h5utils                \
+  jq                     \
+  hdf5-tools             \
+  libatlas-base-dev      \
+  libxml2-dev            \
+  libfreetype6-dev       \
+  libxslt-dev            \
+  libarmadillo-dev       \
+  libace-dev             \
+  liblapack-dev          \
+  liblapacke-dev         \
+  libplplot-dev          \
+  libdcmtk-dev
 apt-get clean
diff --git a/docker/build_system-ubuntu.sh b/docker/build_system-ubuntu.sh
index c9fe45b3..0bb70995 100755
--- a/docker/build_system-ubuntu.sh
+++ b/docker/build_system-ubuntu.sh
@@ -3,25 +3,11 @@ set -ev
 # SIRF external dependencies
 apt-get update -qq
 apt-get install -yq --no-install-recommends \
-  hdf5-tools           \
   hdfview              \
-  libarmadillo-dev     \
   libboost-all-dev     \
-  libfftw3-dev         \
   libgtest-dev         \
-  libhdf5-serial-dev   \
-  libplplot-dev        \
-  libxml2-dev          \
-  libxslt-dev          \
   swig
 apt-get clean
 
 # Not required (yet) by SIRF
-# libxml2-dev
-# libxslt-dev
-# python-h5py
-# python-libxml2
-# python-psutil
-# libplplot-dev
 # libopenblas-dev
-# libatlas-base-dev

From 12262d9be9969dcc98944396e489ee835c7c1bb2 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 12:42:41 +0000
Subject: [PATCH 10/16] Revert "update ccache usage assuming cmake>=3.4"

This reverts commit 0c475a5e1c300f5fcb99d1ce40dd8288dd0b3403.
---
 .travis.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 0e64bb34..66459b1a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -219,11 +219,17 @@ before_install:
  - $PY_EXE --version
  - $PY_EXE -m pip --version
  - $PY_EXE -m pip freeze
+ # ccache compiler override
+ - ln -s "$(which ccache)" g++
+ - ln -s "$(which ccache)" g++-6
+ - ln -s "$(which ccache)" g++-7
+ - ln -s "$(which ccache)" gcc
+ - ln -s "$(which ccache)" gcc-6
+ - ln -s "$(which ccache)" gcc-7
  - export PATH="$PWD:$PATH"
  - popd
  # N.B.: don't put into build matrix to allow caching.
  - BUILD_FLAGS="$BUILD_FLAGS -DPYVER=$PYMVER"
- - BUILD_FLAGS="$BUILD_FLAGS -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache"
  - cmake --version
 
 install:

From f2141dd15a303ece4aea4e4755fc0d38041785ad Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 12:59:29 +0000
Subject: [PATCH 11/16] update cmake patch v3.13.1 -> v3.13.4, use ccache in
 docker

---
 .travis.yml                      |  9 ++++-----
 docker/Dockerfile                |  1 -
 docker/build_essential-ubuntu.sh | 26 +++++++++++++++++++++-----
 3 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 66459b1a..acf2766e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -184,7 +184,7 @@ before_install:
         brew install curl
         #brew install cmake # already present
         # alternative: get our own
-        #curl -L -O https://cmake.org/files/v3.8/cmake-3.8.0-Darwin-x86_64.tar.gz
+        #curl -L -O https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Darwin-x86_64.tar.gz
         #tar xzf cmake-*.tar.gz
         #mv cmake-*/CMake.app/Contents/* cmake
         #export PATH="$PWD/cmake/bin:$PATH"
@@ -192,10 +192,9 @@ before_install:
     elif [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
       PY_EXE=python$PYMVER
       if [[ -z "$DOCKER_BUILD" ]]; then
-        curl -L -O https://github.com/Kitware/CMake/releases/download/v3.13.1/cmake-3.13.1-Linux-x86_64.tar.gz
-        ls -l cmake-*
-        tar xzf cmake-*.tar.gz
-        mv cmake-*x86_64 cmake
+        curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Linux-x86_64.tar.gz
+        tar xzf cmake.tgz && rm cmake.tgz
+        ln -s cmake-*x86_64 cmake
         export PATH="$PWD/cmake/bin:$PATH"
       fi
     fi
diff --git a/docker/Dockerfile b/docker/Dockerfile
index a2e225ab..47679f55 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -76,7 +76,6 @@ COPY user_sirf-ubuntu.sh .
 COPY devel/.ccache/ /opt/ccache/
 RUN ccache -o cache_dir=/opt/ccache
 ARG BUILD_FLAGS="\
- -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache\
  -DCMAKE_BUILD_TYPE=Release\
  -DBUILD_STIR_WITH_OPENMP=ON -DUSE_SYSTEM_ACE=ON\
  -DUSE_SYSTEM_Armadillo=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON\
diff --git a/docker/build_essential-ubuntu.sh b/docker/build_essential-ubuntu.sh
index 6dd4dc41..6b068b3a 100755
--- a/docker/build_essential-ubuntu.sh
+++ b/docker/build_essential-ubuntu.sh
@@ -14,9 +14,25 @@ apt-get install -yq --no-install-recommends \
   sudo
 apt-get clean
 
+pushd /opt
+
 # CMake
-mkdir /opt/cmake
-curl https://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.sh > cmake.sh
-echo y | bash cmake.sh --prefix=/opt/cmake --exclude-subdir
-export PATH="/opt/cmake/bin:$PATH"
-rm cmake.sh
+curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Linux-x86_64.tar.gz
+tar xzf cmake.tgz && rm cmake.tgz
+ln -s cmake-*x86_64 cmake
+export PATH="$PWD/cmake/bin:$PATH"
+
+# ccache
+mkdir -p bin
+pushd bin
+# ccache compiler override
+ln -s "$(which ccache)" g++
+ln -s "$(which ccache)" g++-6
+ln -s "$(which ccache)" g++-7
+ln -s "$(which ccache)" gcc
+ln -s "$(which ccache)" gcc-6
+ln -s "$(which ccache)" gcc-7
+export PATH="$PWD:$PATH"
+popd
+
+popd

From 3fff29474f05338e7b265e947363ceebe6da0e6d Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 13:01:08 +0000
Subject: [PATCH 12/16] prepare for possibly external gadgetron

---
 docker/devel/test.sh       | 6 +++---
 docker/docker-compose.yml  | 9 +++++++++
 docker/user_sirf-ubuntu.sh | 3 +++
 3 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/docker/devel/test.sh b/docker/devel/test.sh
index a227d1d6..33c783da 100755
--- a/docker/devel/test.sh
+++ b/docker/devel/test.sh
@@ -17,17 +17,17 @@ pushd $SIRF_PATH/../..
 # start gadgetron
 GCONFIG=./INSTALL/share/gadgetron/config/gadgetron.xml
 [ -f "$GCONFIG" ] || cp "$GCONFIG".example "$GCONFIG"
-./INSTALL/bin/gadgetron >& gadgetron.log&
+[ -f ./INSTALL/bin/gadgetron ] && ./INSTALL/bin/gadgetron >& gadgetron.log&
 
 ctest -VV
 ret=$?
-kill -n 15 $(pidof gadgetron)
+[ -n "$(pidof gadgetron)" ] && kill -n 15 $(pidof gadgetron)
 
 # print for debugging
 [ "$DEBUG" != 0 ] && cat builds/SIRF/build/CMakeCache.txt
 [ "$DEBUG" != 0 ] && cat builds/SIRF/build/Testing/Temporary/LastTest.log
 # may exceed 4MB travis log limit
-[ "$DEBUG" != 0 ] && cat gadgetron.log
+[ "$DEBUG" != 0 ] && [ -f gadgetron.log ] && cat gadgetron.log
 
 popd
 
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
index 254331f1..f310e6b1 100644
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -31,3 +31,12 @@ services:
    cache_from:
     - ubuntu:18.04
     - ccppetmr/sirf:core
+ gadgetron:
+  container_name: gadgetron
+  image: gadgetron/ubuntu_1804_no_cuda:latest
+  environment:
+   GADGETRON_RELAY_HOST: sirf
+  ports:
+   - "9002:9002"  # supervisord web interface
+   - "9080:9080"  # ReST API
+   - "8002:8002"  # CloudBus relay
diff --git a/docker/user_sirf-ubuntu.sh b/docker/user_sirf-ubuntu.sh
index 3c2fa2ef..927b4a86 100755
--- a/docker/user_sirf-ubuntu.sh
+++ b/docker/user_sirf-ubuntu.sh
@@ -4,11 +4,14 @@ set -ev
 # SIRF
 git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b docker /opt/SIRF-SuperBuild
 pushd /opt/SIRF-SuperBuild
+
 echo $BUILD_FLAGS $EXTRA_BUILD_FLAGS
 cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .
 make -j 2
 
 [ -f INSTALL/share/gadgetron/config/gadgetron.xml ] || \
+[ -f INSTALL/share/gadgetron/config/gadgetron.xml.example ] && \
   mv INSTALL/share/gadgetron/config/gadgetron.xml.example \
      INSTALL/share/gadgetron/config/gadgetron.xml
+
 popd

From 5dd4b9334f10ed8f6299e9ab2187468513835337 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 17:15:28 +0000
Subject: [PATCH 13/16] minor external gadgetron tweaks

required for #206
---
 docker/docker-compose.yml | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
index f310e6b1..131229c9 100644
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -18,9 +18,12 @@ services:
     - ccppetmr/sirf:latest
   stdin_open: true
   tty: true
-  cap_add:
-   - NET_ADMIN
-  network_mode: "bridge"
+  # cap_add:
+  #  - NET_ADMIN
+  #TODO: uncomment for external gadgetron
+  # network_mode: "host"  # host only works on linux: https://docs.docker.com/network/host/
+  # depends_on:
+  #  - gadgetron
   volumes:
    - ./devel:/devel
  core:
@@ -34,9 +37,15 @@ services:
  gadgetron:
   container_name: gadgetron
   image: gadgetron/ubuntu_1804_no_cuda:latest
+  restart: unless-stopped
   environment:
-   GADGETRON_RELAY_HOST: sirf
+   GADGETRON_RELAY_HOST: 0.0.0.0
   ports:
-   - "9002:9002"  # supervisord web interface
+   - "9002:9002"  # gadgetron
    - "9080:9080"  # ReST API
    - "8002:8002"  # CloudBus relay
+   - "9888:8888"  # ? https://github.com/gadgetron/gadgetron/wiki/How-to-set-up-Gadgetron-cloud-in-the-LAN-environment
+   - "18002:18002"  # ReST API
+   - "9001:9001"  # supervisord web interface
+  volumes:
+   - ./devel/gadgetron_data:/tmp/gadgetron_data

From e6863633c747b6b77a54d2b03e534e13f0ffca48 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 23:40:22 +0000
Subject: [PATCH 14/16] re-add SIRF essentials

---
 docker/build_system-ubuntu.sh | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/docker/build_system-ubuntu.sh b/docker/build_system-ubuntu.sh
index 0bb70995..9a36fa24 100755
--- a/docker/build_system-ubuntu.sh
+++ b/docker/build_system-ubuntu.sh
@@ -3,11 +3,8 @@ set -ev
 # SIRF external dependencies
 apt-get update -qq
 apt-get install -yq --no-install-recommends \
-  hdfview              \
   libboost-all-dev     \
-  libgtest-dev         \
+  libfftw3-dev         \
+  libhdf5-serial-dev   \
   swig
 apt-get clean
-
-# Not required (yet) by SIRF
-# libopenblas-dev

From c357d17414c7d84a69306d4a7b6e803cb1974fd9 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 1 Mar 2019 23:47:24 +0000
Subject: [PATCH 15/16] expose install directory in bash helpers

---
 docker/build_essential-ubuntu.sh | 3 ++-
 docker/user_sirf-ubuntu.sh       | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/docker/build_essential-ubuntu.sh b/docker/build_essential-ubuntu.sh
index 6b068b3a..49724544 100755
--- a/docker/build_essential-ubuntu.sh
+++ b/docker/build_essential-ubuntu.sh
@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
 set -ev
+INSTALL_DIR="${1:-/opt}"
 # Essential
 apt-get update -qq
 apt-get install -yq curl
@@ -14,7 +15,7 @@ apt-get install -yq --no-install-recommends \
   sudo
 apt-get clean
 
-pushd /opt
+pushd $INSTALL_DIR
 
 # CMake
 curl -o cmake.tgz -L https://github.com/Kitware/CMake/releases/download/v3.13.4/cmake-3.13.4-Linux-x86_64.tar.gz
diff --git a/docker/user_sirf-ubuntu.sh b/docker/user_sirf-ubuntu.sh
index 927b4a86..8f7957f5 100755
--- a/docker/user_sirf-ubuntu.sh
+++ b/docker/user_sirf-ubuntu.sh
@@ -1,9 +1,10 @@
 #!/usr/bin/env bash
 [ -f .bashrc ] && . .bashrc
 set -ev
+INSTALL_DIR="${1:-/opt}"
 # SIRF
-git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b docker /opt/SIRF-SuperBuild
-pushd /opt/SIRF-SuperBuild
+git clone https://github.com/CCPPETMR/SIRF-SuperBuild --recursive -b docker $INSTALL_DIR/SIRF-SuperBuild
+pushd $INSTALL_DIR/SIRF-SuperBuild
 
 echo $BUILD_FLAGS $EXTRA_BUILD_FLAGS
 cmake $BUILD_FLAGS $EXTRA_BUILD_FLAGS .

From dbc65af445350713684b92ecbb5a69e2bc9ff7e9 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Sat, 2 Mar 2019 02:11:22 +0000
Subject: [PATCH 16/16] add siemens_to_ismrmrd essentials

---
 docker/build_system-ubuntu.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docker/build_system-ubuntu.sh b/docker/build_system-ubuntu.sh
index 9a36fa24..00baf3ba 100755
--- a/docker/build_system-ubuntu.sh
+++ b/docker/build_system-ubuntu.sh
@@ -7,4 +7,9 @@ apt-get install -yq --no-install-recommends \
   libfftw3-dev         \
   libhdf5-serial-dev   \
   swig
+
+# siemens_to_ismrmrd external dependencies
+apt-get install -yq --no-install-recommends \
+  libxml2-dev          \
+  libxslt-dev
 apt-get clean