[MISC] openneuro demo, add run argument, use pybids database...

.vscode/settings.json

@@ -9,5 +9,6 @@
         "eyemask",
         "filefolder"
     ],
-    "autoDocstring.docstringFormat": "sphinx"
+    "autoDocstring.docstringFormat": "sphinx",
+    "esbonio.sphinx.confDir": ""
 }

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean clean-build clean-pyc clean-test coverage dist docs help install lint lint/flake8 lint/black Dockerfile_dev
+.PHONY: clean clean-build clean-pyc clean-test coverage dist  help install
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -52,6 +52,38 @@ clean-test: ## remove test and coverage artifacts
 clean-models: ## remove pretrained models
 	rm -fr models/
 
+
+## INSTALL
+
+install: clean models ## install the package to the active Python's site-packages
+	pip install .
+
+install_dev: clean models ## install the package and development dependencies to the active Python's site-packages
+	pip install -e .[dev]
+
+release: dist ## package and upload a release
+	twine upload dist/*
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+
+## PRE-TRAINED MODELS
+models: models/dataset1_guided_fixations.h5 models/dataset5_free_viewing.h5 ## gets all pretrained models from OSF
+
+models/dataset1_guided_fixations.h5:
+	mkdir -p models
+	wget -q https://osf.io/download/cqf74/ -O models/dataset1_guided_fixations.h5
+
+models/dataset5_free_viewing.h5:
+	mkdir -p models
+	wget -q https://osf.io/download/89nky/ -O models/dataset5_free_viewing.h5
+
+
+## STYLE
+
 lint/flake8: ## check style with flake8
 	flake8 bidsmreye tests
 lint/black: ## check style with black
@@ -61,6 +93,13 @@ lint/mypy: ## check style with mypy
 
 lint: lint/black lint/mypy lint/flake8  ## check style
 
+validate_cff: ## Validate the citation file
+	cffconvert --validate
+
+
+## DOC
+.PHONY: docs
+
 docs: ## generate Sphinx HTML documentation, including API docs
 	rm -f docs/source/bidsmreye.rst
 	rm -f docs/source/modules.rst
@@ -72,23 +111,6 @@ docs: ## generate Sphinx HTML documentation, including API docs
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
-release: dist ## package and upload a release
-	twine upload dist/*
-
-dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
-	ls -l dist
-
-install: clean models ## install the package to the active Python's site-packages
-	pip install .
-
-install_dev: clean models ## install the package and development dependencies to the active Python's site-packages
-	pip install .[dev]
-
-
-validate_cff: ## Validate the citation file
-	cffconvert --validate
 
 ## TESTS
 
@@ -102,53 +124,131 @@ tests/data/moae_fmriprep: ## gets fmriprep preprocessed data of the SPM MOAE dat
 	rm download
 	mv moae_fmriprep tests/data/moae_fmriprep
 
-## PRE-TRAINED MODELS
-models: models/dataset1_guided_fixations.h5 models/dataset5_free_viewing.h5 ## gets all pretrained models from OSF
-
-models/dataset1_guided_fixations.h5:
-	mkdir -p models
-	wget -q https://osf.io/download/cqf74/ -O models/dataset1_guided_fixations.h5
-
-models/dataset5_free_viewing.h5:
-	mkdir -p models
-	wget -q https://osf.io/download/89nky/ -O models/dataset5_free_viewing.h5
-
 
 ## DEMO
+.PHONY: clean-demo
+
+clean-demo:
+	rm -fr outputs/moae_fmriprep
 
-demo: clean-demo ## demo: runs all demo steps on MOAE dataset
-	make prepare_data
-	make combine
-	make generalize
+demo: clean-demo tests/data/moae_fmriprep models/dataset1_guided_fixations.h5 ## demo: runs all demo steps on MOAE dataset
+	bidsmreye 	--action all \
+				--verbosity INFO \
+				--debug true \
+				--reset_database true \
+				$$PWD/tests/data/moae_fmriprep \
+				$$PWD/outputs/moae_fmriprep/derivatives \
+				participant
 
-prepare_data: tests/data/moae_fmriprep models/dataset1_guided_fixations.h5 ## demo: prepares the data of MOAE dataset
+prepare: tests/data/moae_fmriprep models/dataset1_guided_fixations.h5 ## demo: prepares the data of MOAE dataset
 	bidsmreye 	--action prepare \
 				--verbosity INFO \
 				--debug true \
+				--reset_database true \
 				$$PWD/tests/data/moae_fmriprep \
-				$$PWD/outputs participant
+				$$PWD/outputs/moae_fmriprep/derivatives \
+				participant
 
 combine: ## demo: combines data and dummy labels of MOAE dataset
 	bidsmreye 	--action combine \
 				--verbosity INFO \
 				--debug true \
+				--reset_database true \
 				$$PWD/tests/data/moae_fmriprep \
-				$$PWD/outputs participant
+				$$PWD/outputs/moae_fmriprep/derivatives \
+				participant
 
 generalize: ## demo: predicts labels of MOAE dataset
 	bidsmreye 	--model guided_fixations \
 				--action generalize \
 				--verbosity INFO \
 				--debug true \
+				--reset_database true \
 				$$PWD/tests/data/moae_fmriprep \
-				$$PWD/outputs participant
+				$$PWD/outputs/moae_fmriprep/derivatives \
+				participant
+
+
+## Openneuro data
+.PHONY: get_ds002799_dat
+
+clean-ds002799:
+	rm -fr outputs/ds002799/derivatives
+
+tests/data/data_ds002799:
+	datalad install -s ///openneuro/ds002799 tests/data/ds002799
+
+get_ds002799: tests/data/data_ds002799
+	cd tests/data/ds002799/derivatives/fmriprep && \
+	datalad get sub-30[27]/ses-*/func/*run-*preproc*bold*
+
+ds002799_prepare: get_ds002799 models/dataset1_guided_fixations.h5
+	bidsmreye 	--action prepare \
+				--verbosity INFO \
+				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+				$$PWD/outputs/ds002799/derivatives \
+				participant \
+				--participant_label 302 307 \
+				--space MNI152NLin2009cAsym T1w \
+				--run 1 2
+
+ds002799_combine:
+	bidsmreye 	--action combine \
+				--verbosity INFO \
+				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+				$$PWD/outputs/ds002799/derivatives \
+				participant \
+				--participant_label 302 307 \
+				--space MNI152NLin2009cAsym T1w \
+				--run 1 2
+
+ds002799_generalize:
+	bidsmreye 	--action generalize \
+				--verbosity INFO \
+				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+				$$PWD/outputs/ds002799/derivatives \
+				participant \
+				--participant_label 302 307 \
+				--space MNI152NLin2009cAsym T1w \
+				--run 1 2
+
+ds002799: clean-ds002799
+	bidsmreye 	--action all \
+				--verbosity INFO \
+				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+				$$PWD/outputs/ds002799/derivatives \
+				participant \
+				--participant_label 302 307 \
+				--space MNI152NLin2009cAsym T1w \
+				--run 1 2
 
-clean-demo:
-	rm -fr outputs/bidsmreye
 
 ## DOCKER
+.PHONY: docker/Dockerfile docker/Dockerfile_dev
+
+docker/Dockerfile: ## Dockerfile for the bidsmreye docker image
+	docker run --rm repronim/neurodocker:0.7.0 generate docker \
+	--base debian:stretch-slim \
+	--pkg-manager apt \
+	--install "git wget make" \
+	--miniconda \
+		create_env="bidsmreye" \
+		conda_install="python=3.9 pip" \
+		activate="true" \
+		pip_install="git+https://github.com/cpp-lln-lab/bidsMReye.git" \
+	--run "mkdir -p /home/neuro/bidsMReye" \
+	--copy Makefile /home/neuro/bidsMReye \
+	--workdir /home/neuro/bidsMReye \
+ 	--run "make models" \
+	--copy ./docker/entrypoint.sh /neurodocker/startup.sh \
+	--run "chmod +x /neurodocker/startup.sh" \
+	--cmd bidsmreye \
+	> docker/Dockerfile
 
-Dockerfile:
+docker_build: docker/Dockerfile
+	docker build --tag cpplab/bidsmreye:latest --file docker/Dockerfile .
+
+docker/Dockerfile_dev: ## Dockerfile for the bidsmreye docker image using local pacakge
 	docker run --rm repronim/neurodocker:0.7.0 generate docker \
 	--base debian:stretch-slim \
 	--pkg-manager apt \
@@ -163,59 +263,52 @@ Dockerfile:
  	--run "make models" \
 	--miniconda \
 		use_env="bidsmreye" \
-		pip_install="git+https://github.com/cpp-lln-lab/bidsMReye.git" \
-	--copy ./docker_entrypoint.sh /neurodocker/startup.sh \
+		pip_install="." \
+	--copy ./docker/entrypoint.sh /neurodocker/startup.sh \
 	--run "chmod +x /neurodocker/startup.sh" \
 	--cmd bidsmreye \
-	> Dockerfile
+	> docker/Dockerfile_dev
 
-Docker_dev_build: Dockerfile_dev
-	docker build --tag bidsmreye:dev --file Dockerfile_dev .
+docker_dev_build: docker/Dockerfile_dev
+	docker build --tag cpplab/bidsmreye:dev --file docker/Dockerfile_dev .
 
-Docker_dev_build_no_cache: Dockerfile_dev
-	docker build --tag bidsmreye:dev --no-cache --file Dockerfile_dev .
+docker_dev_build_no_cache: docker/Dockerfile_dev
+	docker build --tag bidsmreye:dev --no-cache --file docker/Dockerfile_dev .
 
-Docker_demo: Docker_dev_build clean-demo
+docker_demo: Docker_build clean-demo
 	make Docker_prepare_data
 	make Docker_combine
 	make Docker_generalize
 
-Docker_prepare_data:
+docker_prepare_data:
 	docker run --rm -it \
 				--user "$(id -u):$(id -g)" \
 				-v $$PWD/tests/data/moae_fmriprep:/home/neuro/data \
 				-v $$PWD/outputs:/home/neuro/outputs \
-				bidsmreye:dev \
+				bidsmreye:latest \
 				/home/neuro/data/ \
 				/home/neuro/outputs/ \
 				participant \
-				--action prepare \
-				--space T1w \
-				--task auditory
+				--action prepare
 
-Docker_combine:
+docker_combine:
 	docker run --rm -it \
 				--user "$(id -u):$(id -g)" \
 				-v $$PWD/tests/data/moae_fmriprep:/home/neuro/data \
 				-v $$PWD/outputs:/home/neuro/outputs \
-				bidsmreye:dev \
+				bidsmreye:latest \
 				/home/neuro/data/ \
 				/home/neuro/outputs/ \
 				participant \
-				--action combine \
-				--space T1w \
-				--task auditory
+				--action combine
 
-Docker_generalize:
+docker_generalize:
 	docker run --rm -it \
 				--user "$(id -u):$(id -g)" \
 				-v $$PWD/tests/data/moae_fmriprep:/home/neuro/data \
 				-v $$PWD/outputs:/home/neuro/outputs \
-				bidsmreye:dev \
+				bidsmreye:latest \
 				/home/neuro/data/ \
 				/home/neuro/outputs/ \
 				participant \
-				--action generalize \
-				--space T1w \
-				--model guided_fixations \
-				--task auditory
+				--action generalize