Testing is good

.github/workflows/petdeface.yaml

@@ -0,0 +1,26 @@
+name: petdeface
+on:
+  workflow_call:
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        type: boolean
+        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+        required: false
+        default: false
+
+jobs:
+  test_petdeface:
+    runs-on: ubuntu-latest
+    name: Test petdeface
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Poetry
+        run: pipx install poetry
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: poetry
+      - run: poetry install
+      - name: Run All Tests
+        run: poetry run make testall

.gitignore

@@ -26,5 +26,13 @@ scratch.txt
 # ignore scratch folder
 scratch/
 
+# ignore scripts folder, for now
+scripts/
+
 # integration testing scripts using unpublishable dicoms
 integration_testing.sh
+
+petdeface/Dockerfile
+petdeface/README.md
+petdeface/pyproject.toml
+petdeface/README.md

Makefile

@@ -0,0 +1,19 @@
+# Quickly run black on all python files in this repository, local version of the pre-commit hook
+black:
+	for file in `find . -name "*.py"`; do \
+		black $$file; \
+	done
+
+testlayoutsverbose:
+	pytest tests/test_dir_layouts.py -s -vv
+
+testlayouts:
+	pytest tests/test_dir_layouts.py
+
+# run all tests
+testall: testlayouts
+.PHONY: testall
+
+# install python dependencies
+pythondeps:
+	pip install --upgrade pip && pip install  -e .

petdeface/petdeface.py

@@ -253,7 +253,11 @@ def init_single_subject_wf(subject_id: str, bids_dir: str) -> Workflow:
     t1w_wf = Workflow(name="t1w_wf")
     unique_t1w_best_matches = sorted(set(t1w_best_matches))
     for j, t1w_file in enumerate(unique_t1w_best_matches):
-        ses_id = re.search("/ses-(.+?)/", t1w_file).group(1)
+        ses_id = re.search("/ses-(.+?)/", t1w_file)
+        if ses_id:
+            ses_id = f".ses-{ses_id.group(1)}_"
+        else:
+            ses_id = ""
         deface_t1w = Node(
             Mideface(in_file=t1w_file),
             name=f"deface_t1w{j}",
@@ -264,10 +268,10 @@ def init_single_subject_wf(subject_id: str, bids_dir: str) -> Workflow:
                     deface_t1w,
                     datasink,
                     [
-                        ("out_file", f"sub-{subject_id}.ses-{ses_id}.anat"),
+                        ("out_file", f"sub-{subject_id}{ses_id}.anat"),
                         (
                             "out_facemask",
-                            f"sub-{subject_id}.ses-{ses_id}.anat.@facemask",
+                            f"sub-{subject_id}{ses_id}.anat.@facemask",
                         ),
                     ],
                 ),

pyproject.toml

@@ -24,6 +24,7 @@ black = "^23.7.0"
 flake8 = "^6.1.0"
 isort = "^5.12.0"
 pre-commit = "^3.3.3"
+pytest = "^7.4.2"
 
 [tool.isort]
 profile = "black"

scripts/integration_testing.sh

@@ -0,0 +1,46 @@
+#! /usr/bin/env bash
+
+SCRIPT_PATH=$(dirname $(realpath -s $0))
+REPO_PATH=$(dirname $SCRIPT_PATH)
+
+while getopts 'r' flag
+do
+    case "$flag" in
+        r) rebuildimage=true ;;
+    esac
+
+    case "$flag" in
+        o) outputdir=${OPTARG} ;;
+    esac
+
+done
+
+if [[ -n "$rebuildimage" ]]
+#if $rebuildimage
+then
+    echo "rebuilding docker image"
+    pushd $REPO_PATH
+    docker build . -t petdeface
+else
+    echo "Using existing petdeface docker image"
+fi
+
+shift $(($OPTIND - 1))
+INPUT_DIR=$1
+OUTPUT_DIR=$2
+
+echo Removing contents of existing output directory at $OUTPUT_DIR
+mkdir -p $OUTPUT_DIR
+rm -rf $OUTPUT_DIR/*
+
+echo running the following command:
+echo python3 petdeface/petdeface.py $INPUT_DIR \
+--output $OUTPUT_DIR \
+--n_procs 16 \
+--skip_bids_validator \
+
+
+python3 petdeface/petdeface.py $INPUT_DIR \
+--output $OUTPUT_DIR \
+--n_procs 16 \
+--skip_bids_validator \

tests/test_dir_layouts.py

@@ -0,0 +1,120 @@
+import pytest
+from pathlib import Path
+import shutil
+import bids
+from petdeface.petdeface import PetDeface
+from os import cpu_count
+from bids.layout import BIDSLayout
+
+import tempfile
+
+# collect test bids dataset from data directory
+data_dir = Path(__file__).parent.parent / "data"
+
+# get number of cores, use all but one
+nthreads = cpu_count() - 1
+
+layout = BIDSLayout(data_dir, validate=True)
+
+if layout:
+    pass
+
+
+def test_anat_in_first_session_folder():
+    # create a temporary directory to copy the existing dataset into
+    with tempfile.TemporaryDirectory() as tmpdir:
+        shutil.copytree(data_dir, Path(tmpdir) / "anat_in_first_session_folder")
+
+        # run petdeface on the copied dataset
+        petdeface = PetDeface(
+            Path(tmpdir) / "anat_in_first_session_folder",
+            output_dir=Path(tmpdir)
+            / "anat_in_first_session_folder_defaced"
+            / "derivatives"
+            / "petdeface",
+            n_procs=nthreads,
+        )
+        petdeface.run()
+
+
+def test_anat_in_each_session_folder():
+    # create a temporary directory to copy the existing dataset into
+    with tempfile.TemporaryDirectory() as tmpdir:
+        shutil.copytree(data_dir, Path(tmpdir) / "anat_in_each_session_folder")
+
+        # create a second session
+        second_session_folder = (
+            Path(tmpdir) / "anat_in_each_session_folder" / "sub-01" / "ses-second"
+        )
+        second_session_folder.mkdir(parents=True, exist_ok=True)
+
+        shutil.copytree(
+            Path(tmpdir) / "anat_in_each_session_folder" / "sub-01" / "ses-baseline",
+            second_session_folder,
+            dirs_exist_ok=True,
+        )
+
+        # replace the ses- entities in the files in the newly created second session folder
+        for file in second_session_folder.glob("pet/*"):
+            shutil.move(
+                file,
+                second_session_folder
+                / "pet"
+                / file.name.replace("ses-baseline_", "ses-second_"),
+            )
+
+        for file in second_session_folder.glob("anat/*"):
+            shutil.move(
+                file,
+                second_session_folder
+                / "anat"
+                / file.name.replace("ses-baseline_", "ses-second_"),
+            )
+
+        # run petdeface on the copied dataset
+        petdeface = PetDeface(
+            Path(tmpdir) / "anat_in_each_session_folder",
+            output_dir=Path(tmpdir)
+            / "anat_in_each_session_folder_defaced"
+            / "derivatives"
+            / "petdeface",
+            n_procs=nthreads,
+        )
+        petdeface.run()
+
+
+def test_anat_in_subject_folder():
+    # create a temporary directory to copy the existing dataset into
+    with tempfile.TemporaryDirectory() as tmpdir:
+        shutil.copytree(data_dir, Path(tmpdir) / "anat_in_subject_folder")
+
+        original_anat_folder = (
+            Path(tmpdir) / "anat_in_subject_folder" / "sub-01" / "ses-baseline" / "anat"
+        )
+        subject_folder = Path(tmpdir) / "anat_in_subject_folder" / "sub-01"
+        # now we move the anatomical folder in the first session of our test data into the subject level folder
+        shutil.move(original_anat_folder, subject_folder)
+
+        # and next remove the ses- entities from the files in the newly created anat folder
+        for file in Path(tmpdir).glob(
+            "anat_in_subject_folder/sub-01/anat/sub-01_ses-baseline_*"
+        ):
+            shutil.move(
+                file,
+                Path(tmpdir)
+                / "anat_in_subject_folder"
+                / "sub-01"
+                / "anat"
+                / file.name.replace("ses-baseline_", ""),
+            )
+
+        # run petdeface on the copied dataset
+        petdeface = PetDeface(
+            Path(tmpdir) / "anat_in_subject_folder",
+            output_dir=Path(tmpdir)
+            / "anat_in_subject_folder_defaced"
+            / "derivatives"
+            / "petdeface",
+            n_procs=nthreads,
+        )
+        petdeface.run()