Added a simple CLI using typer

brainles_preprocessing/cli.py

@@ -0,0 +1,155 @@
+from typing import Optional
+from pathlib import Path
+import typer
+from typing_extensions import Annotated
+from importlib.metadata import version
+
+
+from brainles_preprocessing.modality import Modality, CenterModality
+from brainles_preprocessing.normalization.percentile_normalizer import (
+    PercentileNormalizer,
+)
+from brainles_preprocessing.preprocessor import Preprocessor
+
+
+def version_callback(value: bool):
+    __version__ = version("brainles_preprocessing")
+    if value:
+        typer.echo(f"Preprocessor CLI v{__version__}")
+        raise typer.Exit()
+
+
+app = typer.Typer(
+    context_settings={"help_option_names": ["-h", "--help"]}, add_completion=False
+)
+
+
+@app.command()
+def main(
+    input_t1c: Annotated[
+        str,
+        typer.Option(
+            "-t1c",
+            "--input_t1c",
+            help="The path to the T1c image",
+        ),
+    ],
+    input_t1: Annotated[
+        str,
+        typer.Option(
+            "-t1",
+            "--input_t1",
+            help="The path to the T1 image",
+        ),
+    ],
+    input_t2: Annotated[
+        str,
+        typer.Option(
+            "-t2",
+            "--input_t2",
+            help="The path to the T2 image",
+        ),
+    ],
+    input_fla: Annotated[
+        str,
+        typer.Option(
+            "-fl",
+            "--input_fla",
+            help="The path to the FLAIR image",
+        ),
+    ],
+    output_dir: Annotated[
+        str,
+        typer.Option(
+            "-o",
+            "--output_dir",
+            help="The path to the output directory",
+        ),
+    ],
+    input_atlas: Annotated[
+        Optional[str],
+        typer.Option(
+            "-a",
+            "--input_atlas",
+            help="The path to the atlas image",
+        ),
+    ] = "SRI24 BraTS atlas",
+    version: Annotated[
+        Optional[bool],
+        typer.Option(
+            "-v",
+            "--version",
+            callback=version_callback,
+            is_eager=True,
+            help="Print the version and exit.",
+        ),
+    ] = None,
+):
+    """
+    Preprocess the input images according to the BraTS protocol.
+    """
+
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # specify a normalizer
+    percentile_normalizer = PercentileNormalizer(
+        lower_percentile=0.1,
+        upper_percentile=99.9,
+        lower_limit=0,
+        upper_limit=1,
+    )
+
+    # define center and moving modalities
+    center = CenterModality(
+        modality_name="t1c",
+        input_path=input_t1c,
+        normalizer=percentile_normalizer,
+        # specify the output paths for the raw and normalized images of each step - here only for atlas registered and brain extraction
+        raw_skull_output_path=output_dir / "t1c_skull_raw.nii.gz",
+        raw_bet_output_path=output_dir / "t1c_bet_raw.nii.gz",
+        raw_defaced_output_path=output_dir / "t1c_defaced_raw.nii.gz",
+        normalized_skull_output_path=output_dir / "t1c_skull_normalized.nii.gz",
+        normalized_bet_output_path=output_dir / "t1c_bet_normalized.nii.gz",
+        normalized_defaced_output_path=output_dir / "t1c_defaced_normalized.nii.gz",
+        # specify output paths for the brain extraction and defacing masks
+        bet_mask_output_path=output_dir / "t1c_bet_mask.nii.gz",
+        defacing_mask_output_path=output_dir / "t1c_defacing_mask.nii.gz",
+    )
+
+    for modality in ["t1", "t2", "fla"]:
+        moving_modalities = [
+            Modality(
+                modality_name=modality,
+                input_path=eval(f"input_{modality}"),
+                normalizer=percentile_normalizer,
+                # specify the output paths for the raw and normalized images of each step - here only for atlas registered and brain extraction
+                raw_skull_output_path=output_dir / f"{modality}_skull_raw.nii.gz",
+                raw_bet_output_path=output_dir / f"{modality}_bet_raw.nii.gz",
+                raw_defaced_output_path=output_dir / f"{modality}_defaced_raw.nii.gz",
+                normalized_skull_output_path=output_dir
+                / f"{modality}_skull_normalized.nii.gz",
+                normalized_bet_output_path=output_dir
+                / f"{modality}_bet_normalized.nii.gz",
+                normalized_defaced_output_path=output_dir
+                / f"{modality}_defaced_normalized.nii.gz",
+            )
+        ]
+
+    # if the input atlas is the SRI24 BraTS atlas, set it to None, because it will be picked up through the package
+    if input_atlas == "SRI24 BraTS atlas":
+        input_atlas = None
+
+    # instantiate and run the preprocessor using defaults for registration/ brain extraction/ defacing backends
+    preprocessor = Preprocessor(
+        center_modality=center,
+        moving_modalities=moving_modalities,
+        temp_folder=output_dir / "temp",
+        input_atlas=input_atlas,
+    )
+
+    preprocessor.run()
+
+
+if __name__ == "__main__":
+    app()

brainles_preprocessing/modality.py

@@ -407,7 +407,6 @@ def deface(
             category=DeprecationWarning,
         )
         if isinstance(defacer, QuickshearDefacer):
-
             defaced_dir_path = Path(defaced_dir_path)
             atlas_mask_path = (
                 defaced_dir_path / f"atlas__{self.modality_name}_deface_mask.nii.gz"
@@ -595,7 +594,6 @@ def deface(
         """
 
         if isinstance(defacer, QuickshearDefacer):
-
             defaced_dir_path = Path(defaced_dir_path)
             atlas_mask_path = (
                 defaced_dir_path / f"atlas__{self.modality_name}_deface_mask.nii.gz"

brainles_preprocessing/preprocessor.py

@@ -379,9 +379,9 @@ def run_atlas_correction(
                 dst=str(center_atlas_corrected_path),
             )
             # save step result
-            self.center_modality.steps[PreprocessorSteps.ATLAS_CORRECTED] = (
-                center_atlas_corrected_path
-            )
+            self.center_modality.steps[
+                PreprocessorSteps.ATLAS_CORRECTED
+            ] = center_atlas_corrected_path
 
         self._save_output(
             src=atlas_correction_dir,

pyproject.toml

@@ -54,6 +54,8 @@ ttictoc = "^0.5.6"
 pathlib = "^1.0.1"
 nibabel = ">=3.2.1"
 numpy = "^1.23.0"
+typer = "^0.15.0"
+black = "^22.1.0"
 
 # registration
 antspyx = "^0.4.2"
@@ -86,3 +88,6 @@ Sphinx = ">=7.0.0"
 sphinx-copybutton = ">=0.5.2"
 sphinx-rtd-theme = ">=1.3.0"
 myst-parser = ">=2.0.0"
+
+[tool.poetry.scripts]
+preprocessor = "brainles_preprocessing.cli:app"

tests/registrator_base.py

@@ -6,7 +6,6 @@
 
 
 class RegistratorBase:
-
     @abstractmethod
     def get_registrator(self):
         pass