A starter project for new Gadgetron developers
License: MIT License
The Gadgetron is an open source project for medical image reconstruction. If you find the Gadgetron useful in your research, please cite this paper:
Hansen MS, Sørensen TS. Gadgetron: An Open Source Framework for Medical Image Reconstruction. Magn Reson Med. 2013 Jun;69(6):1768-76.
Documentation for the project is available at https://gadgetron.readthedocs.io
The Gadgetron is available under a modified MIT license. Please read LICENSE file for licensing details.
When using VSCode Devcontainers as a development and debugging environment, there is currently an issue with running Gadgetron on the default port due to an address binding collision. To reproduce, start the devcontainer via "F1->Reopen in container", then press F5 to build and start the gadgetron:
06-07 14:07:19.999 DEBUG [gadgetron_paths.cpp:117] Executable path: "/opt/conda/envs/gadgetron/bin/gadgetron"
06-07 14:07:19.999 DEBUG [gadgetron_paths.cpp:123] Default Gadgetron home: "/opt/conda/envs/gadgetron"
06-07 14:07:19.999 WARNING [initialization.cpp:38] Environment variable 'OMP_WAIT_POLICY' not set to 'PASSIVE'.
06-07 14:07:19.999 WARNING [initialization.cpp:39] Gadgetron may experience serious performance issues under heavy load (multiple simultaneous reconstructions, etc.)
06-07 14:07:19.999 INFO [main.cpp:90] Gadgetron 4.4.7 [a0318d1349dce1b9799cb9f6b4486c6cfc5e0c7f]
06-07 14:07:20.000 DEBUG [storage.cpp:68] Found storage server: /opt/conda/envs/gadgetron/bin/mrd-storage-server
06-07 14:07:20.000 INFO [storage.cpp:69] Starting storage server on port 9112
06-07 14:07:20.001 INFO [storage.cpp:28] Verifying connectivity to storage server...
{"level":"info","time":"2023-06-07T14:07:20.098Z","message":"Listening on port 9112"}
{"level":"info","requestId":"e1eb6eaf-2206-4122-affd-b503fec7b3e4","status":200,"method":"GET","path":"/healthcheck","query":"","latencyMs":0.441,"time":"2023-06-07T14:07:20.202Z","message":"request completed"}
06-07 14:07:20.202 INFO [storage.cpp:33] Received successful response from storage server.
06-07 14:07:20.202 INFO [main.cpp:99] Running on port 9002
06-07 14:07:20.202 INFO [Server.cpp:25] Gadgetron home directory: "/opt/conda/envs/gadgetron"
06-07 14:07:20.202 INFO [Server.cpp:26] Gadgetron working directory: "/tmp/gadgetron/"
06-07 14:07:20.203 ERROR [main.cpp:136] bind: Address already in use [system:98 at /opt/conda/envs/gadgetron/include/boost/asio/detail/reactive_socket_service.hpp:161 in function 'bind']
Support for building doxygen documentation as well as creation of a readthedocs account for this project is needed.
The longest part of initializing the devcontainer for this project is configuration of the oot working environment. We should build and host the interstitial tag "gadgetron_dev_cuda_oot" (as well as a non-cuda version) so that starting the devcontainer doesnt require building the conda environment.
Adding a code coverage measurement and associated indicator on the front readme page based on test cases would allow at-a-glance views of whether the gadgets within the starter project (or derivatives) are fully tested.
OS: PopOS 22.04, NVIDIA GPU drivers. Cloned repository, reopened in dev container. Container construction failed with below error.
#0 12.91 Setting up python3.8-minimal (3.8.10-0ubuntu1~20.04.8) ...
#0 13.00 Traceback (most recent call last):
#0 13.00 File "/usr/lib/python3.8/py_compile.py", line 215, in <module>
#0 13.00 sys.exit(main())
[2023-06-10T01:37:46.897Z]
#0 13.00 File "/usr/lib/python3.8/py_compile.py", line 207, in main
#0 13.00 compile(filename, doraise=True)
#0 13.00 File "/usr/lib/python3.8/py_compile.py", line 172, in compile
#0 13.00 importlib._bootstrap_external._write_atomic(cfile, bytecode, mode)
#0 13.00 File "<frozen importlib._bootstrap_external>", line 186, in _write_atomic
#0 13.00 PermissionError: [Errno 13] Permission denied: '/usr/lib/python3.8/__pycache__/__future__.cpython-38.pyc.139716894588576'
#0 13.00 dpkg: error processing package python3.8-minimal (--configure):
#0 13.00 installed python3.8-minimal package post-installation script subprocess returned error exit status 1
#0 13.01 Errors were encountered while processing:
#0 13.01 python3.8-minimal
#0 13.02 E: Sub-process /usr/bin/dpkg returned an error code (1)
------
[2023-06-10T01:37:46.897Z] ERROR: failed to solve: executor failed running [/bin/sh -c cd /tmp/build-features/common_1 && chmod +x ./install.sh && ./install.sh]: exit code: 100
[2023-06-10T01:37:46.901Z] Stop (14193 ms): Run: docker buildx build --load --build-arg BUILDKIT_INLINE_CACHE=1 -f /tmp/vsch-calderds/container-features/0.245.2-1686361052630/Dockerfile-with-features -t vsc-gadgetron-starter-056c3c374dfa0779d7e7bb885ddee9a2 --target dev_containers_target_stage --cache-from ghcr.io/andrew-dupuis/gadgetron-starter/gadgetron_ubuntu_dev_cuda_oot:latest --build-context dev_containers_feature_content_source=/tmp/vsch-calderds/container-features/0.245.2-1686361052630 --build-arg _DEV_CONTAINERS_BASE_IMAGE=gadgetron_dev_cuda_oot --build-arg _DEV_CONTAINERS_IMAGE_USER=root --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp /home/calderds/Projects/Coding/gadgetron-starter
[2023-06-10T01:37:46.903Z] Error: Command failed: docker buildx build --load --build-arg BUILDKIT_INLINE_CACHE=1 -f /tmp/vsch-calderds/container-features/0.245.2-1686361052630/Dockerfile-with-features -t vsc-gadgetron-starter-056c3c374dfa0779d7e7bb885ddee9a2 --target dev_containers_target_stage --cache-from ghcr.io/andrew-dupuis/gadgetron-starter/gadgetron_ubuntu_dev_cuda_oot:latest --build-context dev_containers_feature_content_source=/tmp/vsch-calderds/container-features/0.245.2-1686361052630 --build-arg _DEV_CONTAINERS_BASE_IMAGE=gadgetron_dev_cuda_oot --build-arg _DEV_CONTAINERS_IMAGE_USER=root --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp /home/calderds/Projects/Coding/gadgetron-starter
[2023-06-10T01:37:46.903Z] at HS (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:256:1490)
[2023-06-10T01:37:46.903Z] at processTicksAndRejections (node:internal/process/task_queues:96:5)
[2023-06-10T01:37:46.903Z] at async Cu (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:255:2801)
[2023-06-10T01:37:46.903Z] at async Zw (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:255:1779)
[2023-06-10T01:37:46.903Z] at async KS (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:261:2006)
[2023-06-10T01:37:46.903Z] at async co (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:261:3110)
[2023-06-10T01:37:46.903Z] at async LP (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:360:9352)
[2023-06-10T01:37:46.903Z] at async DP (/home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js:360:9108)
[2023-06-10T01:37:46.907Z] Stop (14500 ms): Run: /usr/share/code/code /home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/calderds/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --workspace-folder /home/calderds/Projects/Coding/gadgetron-starter --workspace-mount-consistency cached --id-label devcontainer.local_folder=/home/calderds/Projects/Coding/gadgetron-starter --log-level debug --log-format json --config /home/calderds/Projects/Coding/gadgetron-starter/.devcontainer/devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root true
[2023-06-10T01:37:46.907Z] Exit code 1
[2023-06-10T01:37:46.911Z] Command failed: /usr/share/code/code /home/calderds/.vscode/extensions/ms-vscode-remote.remote-containers-0.245.2/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/calderds/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --workspace-folder /home/calderds/Projects/Coding/gadgetron-starter --workspace-mount-consistency cached --id-label devcontainer.local_folder=/home/calderds/Projects/Coding/gadgetron-starter --log-level debug --log-format json --config /home/calderds/Projects/Coding/gadgetron-starter/.devcontainer/devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root true
[2023-06-10T01:37:46.911Z] Exit code 1
A test needs to be written for the StorageServer Saving and Loading example gadgets - possibly an xml config that saves the incoming data then immediately loads it back and checks for consistency.
There is an issue building within the OOT environment due to cmake looking for MKL within a specific static path. There are four lines in the dockerfile that address this in a very friable way currently, but we should find a real solution within the cmakelists file itself that avoids the following dir crations and symlinks:
RUN sudo mkdir /opt/intel &&\
sudo mkdir /opt/intel/mkl &&\
sudo mkdir /opt/intel/mkl/lib &&\
sudo mkdir /opt/intel/mkl/lib/intel64 &&\
sudo ln -s /opt/conda/envs/gadgetron/lib/libmkl_intel_lp64.so /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.so && \
sudo ln -s /opt/conda/envs/gadgetron/lib/libmkl_gnu_thread.so /opt/intel/mkl/lib/intel64/libmkl_gnu_thread.so && \
sudo ln -s /opt/conda/envs/gadgetron/lib/libmkl_core.so /opt/intel/mkl/lib/intel64/libmkl_core.so
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