Implement BIDS Exec (#9)

.github/workflows/boutiques.yml

@@ -0,0 +1,58 @@
+name: "Tests - Boutique"
+on:
+  # Trigger the workflow on push or pull request, but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v1
+
+      - uses: BSFishy/pip-action@v1
+        with:
+          packages: |
+            boutiques
+
+      - name: Download test data
+        shell: bash -el {0}
+        run: |
+          curl -L https://github.com/rob-luke/BIDS-NIRS-Tapping/archive/master.zip --output data.zip
+          pwd
+          unzip data.zip -d ./example_data
+          ls
+
+      - name: Where are we and whats around
+        run: |
+          pwd
+          ls
+
+      - name: Run bosh
+        run: |
+          bosh exec launch fnirsapp_qr.json example_invocation.json --debug
+
+      - name: Where are we and whats around
+        run: |
+          pwd
+          ls
+          ls example_data
+          ls example_data/BIDS-NIRS-Tapping-master
+          ls example_data/BIDS-NIRS-Tapping-master/derivatives
+          ls example_data/BIDS-NIRS-Tapping-master/derivatives/fnirs-app-quality-reports
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: Bosh output
+          path: |
+            /home/runner/work/fnirs-apps-quality-reports/fnirs-apps-quality-reports/*bosh*
+            example_data/BIDS-NIRS-Tapping-master/derivatives/fnirs-app-quality-reports/*

.github/workflows/tests.yml

@@ -41,10 +41,10 @@ jobs:
         run: docker build --progress=plain -t test .
 
       - name: Run docker image
-        run: docker run -v /home/runner/example_data/BIDS-NIRS-Tapping-master/:/bids_dataset test --participant_label 03
+        run: docker run -v /home/runner/example_data/BIDS-NIRS-Tapping-master/:/bids_dataset test --subject-label 03
 
       - name: Run docker image
-        run: docker run -v /home/runner/example_data/BIDS-NIRS-Tapping-master/:/bids_dataset test --participant_label 03 --pp_threshold 0.6
+        run: docker run -v /home/runner/example_data/BIDS-NIRS-Tapping-master/:/bids_dataset test --subject-label 03 --pp-threshold 0.6
 
       - name: Run docker image
-        run: docker run -v /home/runner/example_data/BIDS-NIRS-Tapping-master/:/bids_dataset test --participant_label 03 --pp_threshold 0.6 --sci_threshold 0.8
+        run: docker run -v /home/runner/example_data/BIDS-NIRS-Tapping-master/:/bids_dataset test --subject-label 03 --pp-threshold 0.6 --sci-threshold 0.8

Dockerfile

@@ -14,6 +14,7 @@ RUN pip install https://github.com/nilearn/nilearn/archive/main.zip
 RUN pip install mne-nirs
 RUN pip install h5py
 
-COPY run.py /run.py
+COPY fnirsapp_qr.py /run.py
+RUN chmod +x /run.py
 
 ENTRYPOINT ["/run.py"]

example_invocation.json

@@ -0,0 +1,13 @@
+{
+    "input_datasets": "/home/runner/work/fnirs-apps-quality-reports/fnirs-apps-quality-reports/example_data/BIDS-NIRS-Tapping-master",
+    "output_location": "/home/runner/work/fnirs-apps-quality-reports/fnirs-apps-quality-reports/example_data/BIDS-NIRS-Tapping-master/derivatives/fnirs-app-quality-reports",
+    "subject_label": [
+        "01",
+        "02"
+    ],
+    "task_label": [
+        "tapping"
+    ],
+    "pp_threshold": 0.6,
+    "sci_threshold": 0.7
+}

fnirsapp_qr.json

@@ -0,0 +1,100 @@
+{
+    "name": "fNIRS Apps: Quality Reports",
+    "description": "A GLM pipeline for quality reports",
+    "author": "Robert Luke",
+    "tool-version": "v0.1.0",
+    "schema-version": "0.5",
+    "command-line": "/run.py [InputDataset] [OutputLocation] [SubjectLabel] [TaskLabel] [SCIThreshold] [PeakPowerThreshold]",
+    "container-image": {
+        "image": "ghcr.io/rob-luke/fnirs-apps-quality-reports/app",
+        "index": "ghcr.io",
+        "type": "docker",
+        "entrypoint": true
+    },
+    "inputs": [
+        {
+            "command-line-flag": "--input-datasets",
+            "id": "input_datasets",
+            "description": "The directory with the input dataset formatted according to the BIDS standard.",
+            "name": "input-datasets",
+            "optional": true,
+            "type": "File",
+            "value-key": "[InputDataset]"
+        },
+        {
+            "command-line-flag": "--output-location",
+            "id": "output_location",
+            "description": "The directory where the output files should be stored.",
+            "name": "output-location",
+            "optional": true,
+            "type": "File",
+            "value-key": "[OutputLocation]"
+        },
+        {
+            "command-line-flag": "--subject-label",
+            "description": "The label(s) of the subjects(s) that should be analyzed. The label corresponds to sub-<subject_label> from the BIDS spec (so it does not include \"sub-\"). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list.",
+            "id": "subject_label",
+            "name": "subject-label",
+            "optional": true,
+            "type": "String",
+            "list": true,
+            "value-key": "[SubjectLabel]"
+        },
+        {
+            "command-line-flag": "--task-label",
+            "description": "The label(s) of the tasks(s) that should be analyzed. The label corresponds to task-<subject_label> from the BIDS spec. If this parameter is not provided all tasks should be analyzed. Multiple tasks can be specified with a space separated list.",
+            "id": "task_label",
+            "name": "task-label",
+            "optional": true,
+            "type": "String",
+            "list": true,
+            "value-key": "[TaskLabel]"
+        },
+        {
+            "command-line-flag": "--sci-threshold",
+            "id": "sci_threshold",
+            "name": "sci-threshold",
+            "optional": true,
+            "type": "Number",
+            "value-key": "[SCIThreshold]"
+        },
+        {
+            "command-line-flag": "--pp-threshold",
+            "id": "pp_threshold",
+            "name": "pp-threshold",
+            "optional": true,
+            "type": "Number",
+            "value-key": "[PeakPowerThreshold]"
+        }
+    ],
+    "output-files": [
+        {
+            "id": "output_directory",
+            "name": "BIDS derivatives directory",
+            "optional": false,
+            "path-template": "[OutputLocation]"
+        }
+    ],
+    "suggested-resources": {
+        "cpu-cores": 1,
+        "ram": 1,
+        "walltime-estimate": 60
+    },
+    "tags": {
+        "domain": [
+            "neuroimaging",
+            "fnirs",
+            "quality",
+            "bids"
+        ]
+    },
+    "error-codes": [
+        {
+            "code": 1,
+            "description": "Crashed"
+        }
+    ],
+    "custom": {
+        "BIDSAppSpecVersion": "Draft"
+    }
+}

run.py → fnirsapp_qr.py

@@ -15,10 +15,10 @@
 import os
 import subprocess
 
-__version__ = "v0.0.13"
+__version__ = "v0.1.0"
 
 
-def run(command, env={}):
+def fnirsapp_qr(command, env={}):
     merged_env = os.environ
     merged_env.update(env)
     process = subprocess.Popen(command, stdout=subprocess.PIPE,
@@ -35,27 +35,29 @@ def run(command, env={}):
 
 
 parser = argparse.ArgumentParser(description='Quality Reports')
-parser.add_argument('--bids_dir', default="/bids_dataset", type=str,
+parser.add_argument('--input-datasets', default="/bids_dataset", type=str,
                     help='The directory with the input dataset '
                     'formatted according to the BIDS standard.')
-parser.add_argument('--sci_threshold', type=float, default=0.0,
-                    help='Threshold below which a channel is marked as bad.')
-parser.add_argument('--pp_threshold', type=float, default=0.0,
-                    help='Threshold below which a channel is marked as bad.')
-parser.add_argument('--participant_label',
+parser.add_argument('--output-location', default="/bids_dataset/derivatives/fnirs-apps-quality-reports",
+                    type=str, help='The directory where the output files should be stored.')
+parser.add_argument('--subject-label',
                     help='The label(s) of the participant(s) that should be '
                     'analyzed. The label corresponds to '
-                    'sub-<participant_label> from the BIDS spec (so it does '
+                    'sub-<subject-label> from the BIDS spec (so it does '
                     'not include "sub-"). If this parameter is not provided '
                     'all subjects should be analyzed. Multiple participants '
                     'can be specified with a space separated list.',
                     nargs="+")
-parser.add_argument('--task_label',
+parser.add_argument('--task-label',
                     help='The label(s) of the tasks(s) that should be '
                     'analyzed. If this parameter is not provided '
                     'all tasks should be analyzed. Multiple tasks '
                     'can be specified with a space separated list.',
                     nargs="+")
+parser.add_argument('--sci-threshold', type=float, default=0.0,
+                    help='Threshold below which a channel is marked as bad.')
+parser.add_argument('--pp-threshold', type=float, default=0.0,
+                    help='Threshold below which a channel is marked as bad.')
 parser.add_argument('-v', '--version', action='version',
                     version='BIDS-App Scalp Coupling Index version '
                     f'{__version__}')
@@ -69,11 +71,11 @@ def run(command, env={}):
 
 ids = []
 # only for a subset of subjects
-if args.participant_label:
-    ids = args.participant_label
+if args.subject_label:
+    ids = args.subject_label
 # for all subjects
 else:
-    subject_dirs = glob(op.join(args.bids_dir, "sub-*"))
+    subject_dirs = glob(op.join(args.input_datasets, "sub-*"))
     ids = [subject_dir.split("-")[-1] for
            subject_dir in subject_dirs]
     print(f"No participants specified, processing {ids}")
@@ -83,7 +85,7 @@ def run(command, env={}):
 if args.task_label:
     tasks = args.task_label
 else:
-    all_snirfs = glob(f"{args.bids_dir}/**/*_nirs.snirf", recursive=True)
+    all_snirfs = glob(f"{args.input_datasets}/**/*_nirs.snirf", recursive=True)
     for a in all_snirfs:
         s = a.split("_task-")[1]
         s = s.split("_nirs.snirf")[0]
@@ -198,11 +200,11 @@ def summarise_odpsd(raw, report):
 ########################################
 
 print(" ")
-Path(f"{args.bids_dir}/derivatives/fnirs-apps-quality-reports/").\
+Path(f"{args.output_location}/").\
     mkdir(parents=True, exist_ok=True)
 for id in ids:
     report = mne.Report(verbose=True, raw_psd=True)
-    report.parse_folder(f"{args.bids_dir}/sub-{id}", render_bem=False)
+    report.parse_folder(f"{args.input_datasets}/sub-{id}", render_bem=False)
     for idx, fname in enumerate(report.fnames):
         if mne.report._endswith(fname, 'nirs'):
             raw = mne.io.read_raw_snirf(fname)
@@ -215,7 +217,7 @@ def summarise_odpsd(raw, report):
             raw, report = summarise_sci(raw, report, threshold=args.sci_threshold)
             raw, report = summarise_montage(raw, report)
 
-            report.save(f"{args.bids_dir}/derivatives/fnirs-apps-quality-reports/"
+            report.save(f"{args.output_location}/"
                         f"report_basic_{id}.html",
                         overwrite=True, open_browser=False)