Merge pull request #762 from tsalo/datasink-config

REF: Store global variables as DerivativesDataSink attributes

Author: effigies

niworkflows/interfaces/bids.py

@@ -498,12 +498,15 @@ class DerivativesDataSink(SimpleInterface):
     output_spec = _DerivativesDataSinkOutputSpec
     out_path_base = "niworkflows"
     _always_run = True
-    _allowed_entities = set(BIDS_DERIV_ENTITIES)
+    _config_entities = BIDS_DERIV_ENTITIES
+    _standard_spaces = STANDARD_SPACES
+    _file_patterns = BIDS_DERIV_PATTERNS
+    _default_dtypes = DEFAULT_DTYPES
 
     def __init__(self, allowed_entities=None, out_path_base=None, **inputs):
         """Initialize the SimpleInterface and extend inputs with custom entities."""
         self._allowed_entities = set(allowed_entities or []).union(
-            self._allowed_entities
+            set(self._config_entities)
         )
         if out_path_base:
             self.out_path_base = out_path_base
@@ -585,7 +588,7 @@ def _run_interface(self, runtime):
         space = out_entities.get("space")
         if resolution:
             # Standard spaces
-            if space in STANDARD_SPACES:
+            if space in self._standard_spaces:
                 res = _get_tf_resolution(space, resolution)
             else:  # TODO: Nonstandard?
                 res = "Unknown"
@@ -595,8 +598,8 @@ def _run_interface(self, runtime):
             out_entities["extension"] = out_entities["extension"][0]
 
         # Insert custom (non-BIDS) entities from allowed_entities.
-        custom_entities = set(out_entities.keys()) - set(BIDS_DERIV_ENTITIES)
-        patterns = BIDS_DERIV_PATTERNS
+        custom_entities = set(out_entities) - set(self._config_entities)
+        patterns = self._file_patterns
         if custom_entities:
             # Example: f"{key}-{{{key}}}" -> "task-{task}"
             custom_pat = "_".join(f"{key}-{{{key}}}" for key in sorted(custom_entities))
@@ -648,7 +651,7 @@ def _run_interface(self, runtime):
             is_nifti = out_file.name.endswith(
                 (".nii", ".nii.gz")
             ) and not out_file.name.endswith((".dtseries.nii", ".dtseries.nii.gz"))
-            data_dtype = self.inputs.data_dtype or DEFAULT_DTYPES[self.inputs.suffix]
+            data_dtype = self.inputs.data_dtype or self._default_dtypes[self.inputs.suffix]
             if is_nifti and any((self.inputs.check_hdr, data_dtype)):
                 nii = nb.load(orig_file)
 
@@ -667,7 +670,7 @@ def _run_interface(self, runtime):
                     xcodes = (1, 1)  # Derivative in its original scanner space
                     if self.inputs.space:
                         xcodes = (
-                            (4, 4) if self.inputs.space in STANDARD_SPACES else (2, 2)
+                            (4, 4) if self.inputs.space in self._standard_spaces else (2, 2)
                         )
 
                     curr_zooms = zooms = hdr.get_zooms()