add method section

code/_parsers.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser, HelpFormatter
 
 from _version import __version__
-from defaults import supported_batches
+from defaults import CAT_VERSION, MCR_VERSION, supported_batches
 
 
 def _base_parser(
@@ -17,7 +17,11 @@ def _base_parser(
         "--version",
         action="version",
         help="Show program's version number and exit.",
-        version=__version__,
+        version=f"""
+        BIDS app: {__version__};
+        CAT12: {CAT_VERSION};
+        MATLAB MCR: {MCR_VERSION}
+""",
     )
     parser.add_argument(
         "bids_dir",

code/data/methods/template.jinja

@@ -0,0 +1,8 @@
+These results were generated with the BIDS app for Computational Anatomy Toolbox
+(BIDS app: {{version}}; CAT12: {{cat_version}}; MATLAB MCR: {{mcr_version}})
+
+The following steps were followed.
+
+1. ...
+
+2. ...

code/defaults.py

@@ -2,6 +2,11 @@
 
 from __future__ import annotations
 
+import os
+
+MCR_VERSION = os.getenv("MCR_VERSION")
+CAT_VERSION = " ".join(os.getenv("CAT_VERSION")[1:10].split("_"))
+
 
 def log_levels() -> list[str]:
     """Return a list of log levels."""
@@ -16,9 +21,7 @@ def supported_batches() -> list[str]:
         "segment_long",
         "segment_enigma",
         "resample",
-        "tfce",
         "get_IQR",
-        "smooth",
         "get_TIV",
         "get_quality",
         "get_ROI_values",
@@ -31,13 +34,13 @@ def supported_batches() -> list[str]:
 # cat_standalone_segment_long.m
 
 # cat_standalone_resample.m
-# cat_standalone_tfce.m
 # cat_standalone_get_IQR.m
-# cat_standalone_smooth.m
 # cat_standalone_get_TIV.m
 # cat_standalone_get_quality.m
 # cat_standalone_get_ROI_values.m
 
 # WON'T DO
+# cat_standalone_smooth.m
+# cat_standalone_tfce.m
 # cat_standalone_dicom2nii.m
 # cat_standalone_deface.m

code/main.py

@@ -19,6 +19,7 @@
 )
 from cat_logging import cat12_log
 from defaults import log_levels
+from methods import generate_method_section
 from rich import print
 from rich_argparse import RichHelpFormatter
 from utils import progress_bar
@@ -118,6 +119,8 @@ def main():
 
         logger.info(f"{segment_type=} - using batch {batch}.")
 
+        generate_method_section(output_dir=output_dir, batch=batch)
+
         text = "processing subjects"
         with progress_bar(text=text) as progress:
 

code/methods.py

@@ -0,0 +1,38 @@
+"""Module responsible for generating method section."""
+
+from pathlib import Path
+
+from _version import __version__
+from defaults import CAT_VERSION, MCR_VERSION
+from jinja2 import Environment, FileSystemLoader, select_autoescape
+
+
+def generate_method_section(
+    output_dir: Path,
+    version: str = __version__,
+    cat_version: str = CAT_VERSION,
+    mcr_version: str = MCR_VERSION,
+    batch: str = None,
+) -> None:
+    """Add a method section to the output dataset."""
+    env = Environment(
+        loader=FileSystemLoader(Path(__file__).parent),
+        autoescape=select_autoescape(),
+        lstrip_blocks=True,
+        trim_blocks=True,
+    )
+
+    template = env.get_template("data/methods/template.jinja")
+
+    output_file = output_dir / "logs" / "CITATION.md"
+    output_file.parent.mkdir(parents=True, exist_ok=True)
+
+    data = {
+        "version": version,
+        "cat_version": cat_version,
+        "mcr_version": mcr_version,
+        "batch": batch,
+    }
+
+    with open(output_file, "w") as f:
+        print(template.render(data=data), file=f)

code/requirements.txt

@@ -1,3 +1,4 @@
 rich_argparse
 pybids
 nibabel
+jinja2

makefile

@@ -7,6 +7,9 @@ tests/data/MoAEpilot:
 build:
 	docker build . --tag cat12
 
+version:
+	docker run --rm -it cat12 . . participant --version
+
 view:
 	docker run --rm -it cat12 . . participant view tfce --verbose 3