From a9c46ee37bb1226ea19f5e9c023d80b33cb4206a Mon Sep 17 00:00:00 2001
From: marshallxu <marshall.xu@uq.edu.au>
Date: Tue, 3 Sep 2024 19:25:39 +1000
Subject: [PATCH 1/2] sync with upstream

---
 recipes/vesselboost/build.sh | 38 +++++++++++++++++++++++++++++++-----
 1 file changed, 33 insertions(+), 5 deletions(-)

diff --git a/recipes/vesselboost/build.sh b/recipes/vesselboost/build.sh
index d56e1cfd..82a1258c 100755
--- a/recipes/vesselboost/build.sh
+++ b/recipes/vesselboost/build.sh
@@ -1,5 +1,5 @@
 export toolName='vesselboost'
-export toolVersion='1.0.0'
+export toolVersion='1.0.1'
 
 if [ "$1" != "" ]; then
     echo "Entering Debug mode"
@@ -9,11 +9,33 @@ fi
 source ../main_setup.sh
 
 neurodocker generate ${neurodocker_buildMode} \
---base-image pytorch/pytorch:1.13.1-cuda11.6-cudnn8-runtime \
+--base-image pytorch/pytorch:2.4.0-cuda11.8-cudnn9-runtime `# Ubuntu 22.04 base image`\
 --pkg-manager apt \
 --env DEBIAN_FRONTEND=noninteractive \
---install git vim \
---workdir=/opt \
+--workdir='/opt/code' \
+--install build-essential libxslt1.1 libhdf5-103 libboost-program-options1.74.0 libpugixml1v5 vim dos2unix git cmake g++ libhdf5-dev libxml2-dev libxslt1-dev libboost-all-dev libfftw3-dev libpugixml-dev \
+--run='git clone https://github.com/ismrmrd/ismrmrd.git && \
+    cd ./ismrmrd && \
+    cmake . && \
+    make -j $(nproc) && \
+    make install' \
+--run='git clone https://github.com/ismrmrd/siemens_to_ismrmrd.git && \
+    cd siemens_to_ismrmrd && \
+    mkdir build && \
+    cd build && \
+    cmake .. && \
+    make -j $(nproc) && \
+    make install' \
+--run='pip3 install h5py ismrmrd matplotlib pydicom pynetdicom nibabel' \
+--run='git clone https://github.com/ismrmrd/ismrmrd-python-tools.git && \
+    cd ismrmrd-python-tools && \
+    pip3 install --no-cache-dir .' \
+--run='git clone https://github.com/kspaceKelvin/python-ismrmrd-server && \
+    find /opt/code/python-ismrmrd-server -name "*.sh" -exec chmod +x {} \; && \
+    find /opt/code/python-ismrmrd-server -name "*.sh" | xargs dos2unix' \
+--copy invertcontrast.py /opt/code/python-ismrmrd-server/invertcontrast.py \
+--entrypoint='python3 /opt/code/python-ismrmrd-server/main.py -v -r -H=0.0.0.0 -p=9002 -l=/tmp/python-ismrmrd-server.log -s -S=/tmp/share/saved_data' \
+--workdir='/opt' \
 --run='git clone https://github.com/KMarshallX/VesselBoost.git && \
     cd VesselBoost && \
     git checkout e1f628369f181b67fa880c1e6a8edf29885f9717' \
@@ -29,6 +51,12 @@ neurodocker generate ${neurodocker_buildMode} \
 --copy README.md /README.md \
 > ${toolName}_${toolVersion}.Dockerfile 
 
+
+
+
+
+
+
 if [ "$1" != "" ]; then
    ./../main_build.sh
-fi
+fi
\ No newline at end of file

From 4d178f9a9823fe168d10cc1b3c293957b02a54c7 Mon Sep 17 00:00:00 2001
From: marshallxu <marshall.xu@uq.edu.au>
Date: Mon, 9 Sep 2024 13:07:57 +1000
Subject: [PATCH 2/2] update VesselBoost_OpenRecon

---
 recipes/vesselboost/build.sh | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/recipes/vesselboost/build.sh b/recipes/vesselboost/build.sh
index 82a1258c..87fa1655 100755
--- a/recipes/vesselboost/build.sh
+++ b/recipes/vesselboost/build.sh
@@ -33,12 +33,10 @@ neurodocker generate ${neurodocker_buildMode} \
 --run='git clone https://github.com/kspaceKelvin/python-ismrmrd-server && \
     find /opt/code/python-ismrmrd-server -name "*.sh" -exec chmod +x {} \; && \
     find /opt/code/python-ismrmrd-server -name "*.sh" | xargs dos2unix' \
---copy invertcontrast.py /opt/code/python-ismrmrd-server/invertcontrast.py \
 --entrypoint='python3 /opt/code/python-ismrmrd-server/main.py -v -r -H=0.0.0.0 -p=9002 -l=/tmp/python-ismrmrd-server.log -s -S=/tmp/share/saved_data' \
 --workdir='/opt' \
 --run='git clone https://github.com/KMarshallX/VesselBoost.git && \
-    cd VesselBoost && \
-    git checkout e1f628369f181b67fa880c1e6a8edf29885f9717' \
+    cd VesselBoost' \
 --workdir='/opt/VesselBoost/' \
 --run='pip install -r requirements.txt ' \
 --workdir='/opt/VesselBoost/saved_models' \
@@ -53,7 +51,7 @@ neurodocker generate ${neurodocker_buildMode} \
 
 
 
-
+# --copy invertcontrast.py /opt/code/python-ismrmrd-server/invertcontrast.py \