pass None for default preprocessing config

brainglobe_template_builder/preprocess.py

@@ -18,7 +18,10 @@
 )
 from brainglobe_template_builder.utils.cropping import crop_to_mask
 from brainglobe_template_builder.utils.masking import create_mask
-from brainglobe_template_builder.utils.preproc_config import PreprocConfig
+from brainglobe_template_builder.utils.preproc_config import (
+    MaskConfig,
+    PreprocConfig,
+)
 from brainglobe_template_builder.validate import validate_input_csv
 
 logger = logging.getLogger(__name__)
@@ -158,7 +161,9 @@ def _process_subject(
     }
 
 
-def preprocess(standardised_csv: Path, config: Path | PreprocConfig) -> None:
+def preprocess(
+    standardised_csv: Path, config: Path | PreprocConfig | None = None
+) -> None:
     """Process nifti files in ASR orientation to create output images +
     masks ready for template creation.
 
@@ -189,12 +194,19 @@ def preprocess(standardised_csv: Path, config: Path | PreprocConfig) -> None:
     standardised_csv : Path
         Standardised csv file path. One row per sample, each with a
         unique 'subject_id' - this is created via `standardise`.
-    config : Path | PreprocConfig
+    config : Path | PreprocConfig | None
         Config yaml file path, or PreprocConfig object. Contains settings for
-        pre-processing steps.
+        pre-processing steps. Defaults to None, which will use defaults.
     """
 
-    if isinstance(config, Path):
+    if not config:
+        # use default mask and padding, and default to outputting
+        # into sibling folder of `standardised/`
+        preproc_config = PreprocConfig(
+            output_dir=standardised_csv.parent.parent,
+            mask=MaskConfig(),
+        )
+    elif isinstance(config, Path):
         with open(config) as f:
             config_yaml = yaml.safe_load(f)
         preproc_config = PreprocConfig.model_validate(config_yaml)

docs/source/conf.py

@@ -90,6 +90,8 @@
 # during sphinx-build linkcheck
 linkcheck_ignore = [
     "https://opensource.org/license/*",  # to avoid odd 403 error
+    "https://zenodo.org/badge/*",  # avoid 403 error
+    "https://doi.org/*",  # avoid 403 error
 ]
 
 # -- Options for HTML output -------------------------------------------------

tests/test_unit/test_preprocess.py

@@ -93,23 +93,27 @@ def test_preprocess_use_input(
 
 @pytest.mark.parametrize(
     "config_type",
-    ["config_file", "PreprocConfig object"],
+    ["config_file", "PreprocConfig object", "None"],
 )
 @pytest.mark.usefixtures("mock_fancylog_datetime")
 def test_preprocess(
     write_standardised_test_data: tuple[Path, Path], config_type: str
 ) -> None:
-    """Test that preprocess creates expected directories and files - both
-    with a config yaml file path as input OR a PreprocConfig object."""
+    """Test that preprocess creates expected directories and files - with
+    a config yaml file path as input, a PreprocConfig object OR None."""
     csv_path, config_path = write_standardised_test_data
 
-    config: Path | PreprocConfig
+    config: Path | PreprocConfig | None
     if config_type == "config_file":
         config = config_path
-    else:
+    elif config_type == "PreprocConfig object":
         with open(config_path) as f:
             config_yaml = yaml.safe_load(f)
         config = PreprocConfig.model_validate(config_yaml)
+    elif config_type == "None":
+        config = None
+    else:
+        raise ValueError("Testing with invalid config")
 
     preprocess(csv_path, config)