Dev (#1)

* add: basic gear to change the name of a nifti image (not working)

* fix: rename_and_copy_file

* fix: parser auto-detect

* updates up to 15-03-2024

* add: useful commands md

* remove unused variables from Dockerfile

* add: more useful commands

* moved files and folders in .gitignore

* modified run.py - nnUNet_predict command (local)

* generated manifest.json - adding the variables from Dockerfile

* generated config.json to run the gear locally

* generated files before running

* temporary call to the command

* fix: correct path for nnunet in useful commands

* add: --gpus device=0 to run the inference on GPU - not working

* version 0.0.0

.dockerignore

@@ -0,0 +1,13 @@
+# Exclude everything
+**
+
+# Except package dirs, run.py, tests, .git and README
+!README.md
+!requirements.txt
+!manifest.json
+!run.py
+!fw_gear_aeye
+!nnUNet
+
+# Re-ignore pycache which might be inside package dir
+**/__pycache__

.gitignore

@@ -0,0 +1,137 @@
+# Custom folders/files to ignore
+templates/
+*.nii.gz
+input/
+output/
+work/
+nnUNet/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.input_map.json

@@ -0,0 +1 @@
+{"/flywheel/v0/input/nifti/I_Kopf_t1_mpr_tra_iso_p2.nii.gz": "input/nifti/I_Kopf_t1_mpr_tra_iso_p2.nii.gz"}

Dockerfile

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+# Template
+# Contains pytorch, torchvision, cuda, cudnn
+FROM nvcr.io/nvidia/pytorch:24.02-py3
+
+# Mantainer
+LABEL maintainer="Jaime Barranco @jaimebarran"
+
+# Install Flywheel
+RUN pip install flywheel-sdk --break-system-packages \
+    && pip install nnunet
+
+# nnUNet dir
+ARG resources="/opt/nnunet_resources"
+ENV nnUNet_raw_data_base=$resources"/nnUNet_raw_data_base"
+ENV nnUNet_preprocessed=$resources"/nnUNet_preprocessed"
+ENV RESULTS_FOLDER=$resources"/nnUNet_trained_models"
+
+# Set environment variables and workdir
+ENV FLYWHEEL="/flywheel/v0"
+WORKDIR ${FLYWHEEL}
+
+# Installing main dependencies
+COPY requirements.txt ${FLYWHEEL}/requirements.txt
+RUN pip install --no-cache-dir -r $FLYWHEEL/requirements.txt
+
+# Installing the current project (most likely to change, above layer can be cached)
+COPY README.md ${FLYWHEEL}/README.md
+COPY manifest.json ${FLYWHEEL}/manifest.json
+COPY run.py ${FLYWHEEL}/run.py
+COPY fw_gear_aeye ${FLYWHEEL}/fw_gear_aeye
+COPY nnUNet/nnUNet_raw_data_base $resources"/nnUNet_raw_data_base"
+COPY nnUNet/nnUNet_preprocessed $resources"/nnUNet_preprocessed"
+COPY nnUNet/nnUNet_trained_models $resources"/nnUNet_trained_models"
+
+# Configure entrypoint
+RUN chmod a+x ${FLYWHEEL}/run.py
+ENTRYPOINT ["python3","/flywheel/v0/run.py"]

commands.md

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+# Useful commands
+
+## Docker
+
+- Build docker image
+
+    `docker build --no-cache -t jaimebarran/fw_gear_aeye_test .`
+
+- Push docker image
+
+    `docker push jaimebarran/fw_gear_aeye_test`
+
+- Run docker image interactively (local image)
+
+    `docker run -it --rm docker.io/jaimebarran/fw_gear_aeye_interactive /bin/bash`
+
+- Run docker image interactively (remote image)
+
+    `docker run -it --rm jaimebarran/fw_gear_aeye_interactive /bin/bash`
+
+- List images
+
+    `docker images` or `docker image ls`
+
+- List containers
+
+    `docker ps -a` or `docker container ls -a`
+
+- Remove image
+
+    `docker rmi <image_id>`
+
+- Remove container
+
+    `docker rm <container_id>`
+
+- Prune images
+
+    `docker image prune`
+
+- Prune containers
+
+    `docker container prune`
+
+## Flywheel
+
+- Log in
+
+    `fw login {FW_API_KEY}`
+
+- Test local gear
+
+    `fw gear local --nifti=input/nifti/I_Kopf_t1_mpr_tra_iso_p2.nii.gz --measurement="auto-detect" --debug=true`
+
+- Upload gear
+
+    `fw gear upload`
+
+### Flywheel beta
+
+- Log in
+
+    `fw-beta login --api-key=${FW_API_KEY}`
+
+- Validate the manifest
+
+    `fw-beta gear --validate manifest.json`
+
+- Build the gear - this runs `docker build` and then extracts the `ENV` inside the Docker container and adds it to the `manifest.json`
+
+    `fw-beta gear build`
+
+- Create the gear `config.json` (needed to later run the gear locally)
+
+    `fw-beta gear config --create`
+
+- List the configuration options for this specific gear
+
+    `fw-beta gear config --show`
+
+- Configure the local job (specify the input and config options)
+
+    `fw-beta gear config -i nifti=input/nifti/<filename> -c debug=True`
+
+- Run the gear locally
+
+    `fw-beta gear run --rm`
+
+## nnUNet
+
+- Test to see if it is installed
+
+    `nnUNet_predict -h`
+
+- Run nnUNet locally
+
+    ```bash
+    nnUNet_predict -i "/home/jaimebarranco/Downloads/nnUNet_inference/input" -o "/home/jaimebarranco/Downloads/nnUNet_inference/output" -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_fullres -p nnUNetPlansv2.1 -t Task313_Eye
+    ```
+
+- Run nnUNet through Docker pushed image
+
+    ```bash
+    docker run --rm --gpus device=0 --shm-size=10gb -v /home/jaimebarranco/Desktop/nnUNet:/opt/nnunet_resources jaimebarran/fw_gear_aeye_interactive:latest nnUNet_predict -i /opt/nnunet_resources/nnUNet_inference/input -o /opt/nnunet_resources/nnUNet_inference/output -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_fullres -p nnUNetPlansv2.1 -t Task313_Eye
+    ```
+
+- Run nnUNet through Docker pushed image with trained model
+
+    ```bash
+    docker run --rm --gpus device=0 --shm-size=10gb -v /home/jaimebarranco/Downloads/nnUNet_inference:/tmp jaimebarran/fw_gear_aeye_interactive:latest nnUNet_predict -i /tmp/input -o /tmp/output -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_fullres -p nnUNetPlansv2.1 -t Task313_Eye
+    ```
+
+- Last command but with CDI
+
+    ```bash
+    docker run --rm --shm-size=10gb --runtime=nvidia -v /home/jaimebarranco/Downloads/nnUNet_inference:/tmp jaimebarran/fw_gear_aeye_interactive:latest
+    -e NVIDIA_VISIBLE_DEVICES=nvidia.com/gpu=all nnUNet_predict -i /tmp/input -o /tmp/output -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes 
+    -m 3d_fullres -p nnUNetPlansv2.1 -t Task313_Eye
+    ```
+
+- Last command but with CDI set in etc/nvidia-container-runtime/config.toml > nvidia-container-runtime > mode = "cdi" instead of "auto"
+
+    ```bash
+    docker run --rm --shm-size=10gb --runtime=nvidia -v /home/jaimebarranco/Downloads/nnUNet_inference:/tmp jaimebarran/fw_gear_aeye_interactive:latest
+    -e NVIDIA_VISIBLE_DEVICES=all nnUNet_predict -i /tmp/input -o /tmp/output -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes 
+    -m 3d_fullres -p nnUNetPlansv2.1 -t Task313_Eye
+    ```
+
+- Export environment variables (required)
+
+  - nnUNet_raw
+
+    `export nnUNet_raw="/home/jaimebarranco/Desktop/nnUNet/nnUNet_raw_data"`
+
+  - nnUNet_preprocessed
+
+    `export nnUNet_preprocessed="/home/jaimebarranco/Desktop/nnUNet/nnUNet_preprocessed"`
+
+  - nnUNet_results
+
+    `export nnUNet_results="/home/jaimebarranco/Desktop/nnUNet/nnUNet_trained_models"`
+
+## File permissions
+
+- Change file permissions
+
+    `sudo chmod -R a+rw /mnt/sda1/Repos/flywheel/aeye_flywheel/output/input/`
+
+- Change file owner
+
+    `sudo chown jaimebarranco output/input/I_Kopf_t1_mpr_tra_iso_p2.nii.gz`

config.json

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+{
+    "config": {
+        "measurement": "T1",
+        "debug": true
+    },
+    "inputs": {
+        "nifti": {
+            "base": "file",
+            "location": {
+                "name": "I_Kopf_t1_mpr_tra_iso_p2.nii.gz",
+                "path": "/flywheel/v0/input/nifti/I_Kopf_t1_mpr_tra_iso_p2.nii.gz"
+            },
+            "object": {
+                "size": 8703369,
+                "type": null,
+                "mimetype": "application/octet-stream",
+                "modality": null,
+                "classification": {},
+                "tags": [],
+                "info": {},
+                "zip_member_count": null,
+                "version": 1,
+                "file_id": "",
+                "origin": {
+                    "type": "user",
+                    "id": ""
+                }
+            }
+        }
+    },
+    "destination": {}
+}