52 pipeline should halt if bad t1ws are present or more generally if not bids valid

data/participants.tsv

@@ -1,2 +1,2 @@
 participant_id	height	weight	age	gender
-sub-01	178	58	28	male
+sub-01	178	58	28	male

petdeface/petdeface.py

@@ -31,10 +31,12 @@
     from mideface import ApplyMideface
     from mideface import Mideface
     from pet import WeightedAverage
+    from utils import run_validator
 except ModuleNotFoundError:
     from .mideface import ApplyMideface
     from .mideface import Mideface
     from .pet import WeightedAverage
+    from .utils import run_validator
 
 
 # collect version from pyproject.toml
@@ -207,6 +209,10 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
     else:
         args = args
 
+    # first check to see if the dataset is bids valid
+    if not args.skip_bids_validator:
+        run_validator(args.bids_dir)
+
     if not check_valid_fs_license() and not locate_freesurfer_license().exists():
         raise Exception("You need a valid FreeSurfer license to proceed!")
 
@@ -255,6 +261,8 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
 
     petdeface_wf = Workflow(name="petdeface_wf", base_dir=output_dir)
 
+    missing_file_errors = []
+
     for subject_id in subjects:
         try:
             single_subject_wf = init_single_subject_wf(
@@ -265,12 +273,20 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
                 session_label=args.session_label,
                 session_label_exclude=args.session_label_exclude,
             )
-        except FileNotFoundError:
+        except FileNotFoundError as error:
             single_subject_wf = None
-
+            missing_file_errors.append(str(error))
         if single_subject_wf:
             petdeface_wf.add_nodes([single_subject_wf])
 
+    if (
+        missing_file_errors
+    ):  # todo add conditional later for cases where a template t1w is used
+        raise FileNotFoundError(
+            "The following subjects are missing t1w images:\n"
+            + "\n".join(missing_file_errors)
+        )
+
     try:
         petdeface_wf.write_graph("petdeface.dot", graph2use="colored", simple_form=True)
     except OSError as Err:
@@ -748,7 +764,7 @@ def __init__(
         anat_only=False,
         subject="",
         n_procs=2,
-        skip_bids_validator=True,
+        skip_bids_validator=False,
         remove_existing=True,
         placement="adjacent",
         preview_pics=True,

petdeface/utils.py

@@ -0,0 +1,50 @@
+import subprocess
+from pathlib import Path
+import json
+import sys
+
+
+class InvalidBIDSDataset(Exception):
+    def __init__(self, message, errors):
+        super().__init__(message)
+        self.errors = errors
+        print(f"{message}\n{errors}")
+
+
+def deno_validator_installed():
+    get_help = subprocess.run(
+        "bids-validator-deno --help", shell=True, capture_output=True
+    )
+    if get_help.returncode == 0:
+        return True
+    else:
+        return False
+
+
+def run_validator(bids_path):
+    bids_path = Path(bids_path)
+    if bids_path.exists():
+        pass
+    else:
+        raise FileNotFoundError(bids_path)
+    if deno_validator_installed():
+        command = f"bids-validator-deno {bids_path.resolve()} --ignoreWarnings --json --no-color"
+        run_validator = subprocess.run(command, shell=True, capture_output=True)
+        json_output = json.loads(run_validator.stdout.decode("utf-8"))
+        # since we've ignored warnings any issue in issue is an error
+        issues = json_output.get("issues").get("issues")
+        formatted_errors = ""
+        for issue in issues:
+            formatted_errors += "\n" + json.dumps(issue, indent=4)
+        if formatted_errors != "":
+            raise InvalidBIDSDataset(
+                message=f"Dataset at {bids_path} is invalid, see:",
+                errors=formatted_errors,
+            )
+
+    else:
+        raise Exception(
+            f"bids-validator-deno not found"
+            + "\nskip validation with --skip_bids_validator"
+            + "\nor install with pip install bids-validator-deno"
+        )

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "petdeface"
-version = "0.2.2"
+version = "0.2.3"
 description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace."
 authors = ["Martin Nørgaard <[email protected]>", "Anthony Galassi <[email protected]>", "Murat Bilgel <[email protected]>"]
 license = "MIT"
@@ -19,6 +19,9 @@ python = ">=3.10, <4.0"
 setuptools = "^68.1.2"
 petutils = "^0.0.1"
 niworkflows = "^1.11.0"
+niftifixer = {git = "https://github.com/openneuropet/nifti_fixer.git"}
+bids-validator-deno = "^2.0.5"
+
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.7.0"

tests/test_dir_layouts.py

@@ -3,6 +3,7 @@
 import shutil
 import bids
 from petdeface.petdeface import PetDeface
+from petdeface.utils import InvalidBIDSDataset
 from os import cpu_count
 from bids.layout import BIDSLayout
 import subprocess
@@ -34,6 +35,7 @@ def test_anat_in_first_session_folder():
             / "derivatives"
             / "petdeface",
             n_procs=nthreads,
+            preview_pics=False,
         )
         petdeface.run()
 
@@ -80,6 +82,7 @@ def test_anat_in_each_session_folder():
             / "derivatives"
             / "petdeface",
             n_procs=nthreads,
+            preview_pics=False,
         )
         petdeface.run()
 
@@ -117,5 +120,54 @@ def test_anat_in_subject_folder():
             / "derivatives"
             / "petdeface",
             n_procs=nthreads,
+            preview_pics=False,
         )
         petdeface.run()
+
+def test_no_anat():
+    # create a temporary directory to copy the existing dataset into
+    with tempfile.TemporaryDirectory() as tmpdir:
+        shutil.copytree(data_dir, Path(tmpdir) / "no_anat")
+
+        subject_folder = Path(tmpdir) / "no_anat" / "sub-01"
+        # next we delete the anat fold in the subject folder
+        shutil.rmtree(subject_folder / "ses-baseline" / "anat")
+
+        # run petdeface on the copied dataset
+        petdeface = PetDeface(
+            Path(tmpdir) / "no_anat",
+            output_dir=Path(tmpdir)
+            / "no_anat_defaced"
+            / "derivatives"
+            / "petdeface",
+            n_procs=nthreads,
+        )
+
+        # now we want to assert that this pipeline crashes and print the error
+        with pytest.raises(FileNotFoundError) as exc_info:
+            petdeface.run()
+
+def test_invalid_bids():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        shutil.copytree(data_dir, Path(tmpdir) / "invalid")
+        # rename the files in the pet folder to a different subject id
+        subject_folder = Path(tmpdir) / "invalid" / "sub-01"
+        pet_folder = subject_folder / "ses-baseline" / "pet"
+        for file in pet_folder.glob("sub-01_*"):
+            shutil.move(
+                file,
+                pet_folder / file.name.replace("sub-01", "sub-01-bestsubject")
+            )
+
+        # run petdeface on the invalid dataset
+        petdeface = PetDeface(
+            Path(tmpdir) / "invalid",
+            output_dir=Path(tmpdir) / "invalid_defaced" / "derivatives" / "petdeface",
+            n_procs=nthreads,
+        )
+
+        # Run it and see what error gets raised
+        with pytest.raises(InvalidBIDSDataset) as exc_info:
+            petdeface.run()
+        assert "Dataset at" in str(exc_info.value)
+