wip

brainglobe_workflows/registration_script.py

@@ -0,0 +1,54 @@
+import os
+from pathlib import Path
+import subprocess
+import json
+from typing import Dict, Union
+
+Pathlike = Union[str, bytes, os.PathLike]
+# TODO: use pydantic or attrs, and/or a dataclass, for this??
+def _default_config():
+	defaults = {
+        "sample_data_path"
+    }
+
+def _validate_config(config_dict: Dict[str]):
+	expected_keys = [
+		"sample_data_path",
+		"output_path",
+		"voxel size",
+		"orientation"
+		"atlas"
+		]
+	expected_types = [
+		Pathlike,
+    ]
+	for key, type in zip(expected_keys, expected_types):
+        assert key in config_dict.keys()
+
+
+def example_workflow():
+	input_config_path = Path(os.environ("BRAINGLOBE_REGISTRATION_CONFIG_PATH"))
+	if input_config_path.exists():
+		config = json.loads(input_config_path)
+	else:
+		config = _default_config()
+	input_data = read_from_config(config)
+	preprocessed_data = process(input_data) # if required
+	results = run_main_tool(prepocessed_data)
+	save(results)
+
+if __name__ == "__main__":
+	example_workflow()
+
+"""
+To run brainreg, you need to pass:
+    * The path to the sample data
+    * The path to the directory to save the results
+    * The voxel sizes
+    * The orientation
+    * The atlas to use
+
+We put this all together in a single command:
+
+brainreg test_brain brainreg_output -v 50 40 40  --orientation psl --atlas allen_mouse_50um
+"""