make the image more like a cmd

It now uses WORKDIR, ENTRYPOINT and CMD to make the image work more like
a shell command.

It tries to translate paths between the native session and the docker
image, so you can tab-complete to make the T1 and T2 arguments.

It's a bit smaller too.

README updated.

.dockerignore

@@ -0,0 +1,2 @@
+atlases
+build

Dockerfile

@@ -41,9 +41,14 @@ RUN apt-get install -y \
 	libgstreamer1.0-dev libqt4-dev
 
 COPY . /usr/src/structural-pipeline
+
 RUN ls /usr/src/structural-pipeline \
     && NUM_CPUS=${THREADS:-`cat /proc/cpuinfo | grep processor | wc -l`} \
     && echo "Maximum number of build threads = $NUM_CPUS" \
     && cd /usr/src/structural-pipeline \
     && ./setup.sh -j $NUM_CPUS
 
+WORKDIR /data
+ENTRYPOINT ["/usr/src/structural-pipeline/dhcp-pipeline.sh"]
+CMD ["-help"]
+

dhcp-pipeline.sh

@@ -64,6 +64,7 @@ command=$@
 subjectID=$1
 sessionID=$2
 age=$3
+shift; shift; shift;
 
 # alias for the specific session
 subj=$subjectID-$sessionID
@@ -75,7 +76,6 @@ minimal=1
 noreorient=0
 cleanup=1
 
-shift; shift; shift;
 while [ $# -gt 0 ]; do
   case "$1" in
     -T2)  shift; T2=$1; ;;
@@ -92,6 +92,24 @@ while [ $# -gt 0 ]; do
   shift
 done
 
+# consider the case where the user is running us inside docker with an
+# argument like:
+#
+#	-T2 data/T1w.nii.gz
+#
+# the user's data directory will be mapped to /data, and that's out WORKDIR,
+# so we need to remove the leading data/ component for the path to be valid
+#
+# we don't want to make this change unless we have to, so only drop the first
+# pathname component if the file named by T2 does not exist and	T2 is a 
+# relative path
+
+if [[ "$T2" != /* && ! -f "$T2" ]]; then
+  T1=${T1#*/}
+  T2=${T2#*/}
+fi
+
+
 ################ Checks ################
 
 [ "$T2" != "-" -a "$T2" != "" ] || { echo "T2 image not provided!" >&2; exit 1; }