Add autoafids-quick functionality

autoafids/run_quick.py

@@ -0,0 +1,157 @@
+#!/usr/bin/env python3
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+from argparse import ArgumentParser
+from pathlib import Path
+
+IMAGE_MODALITY = {
+    "T1w": {"suffix": "T1w", "use_derivatives": False},
+    "T2w": {"suffix": "T2w", "use_derivatives": False},
+    "FLAIR": {"suffix": "flair", "use_derivatives": False},
+    "CT": {"suffix": "ct", "use_derivatives": False},
+}
+
+
+def check_conda_installation():
+    try:
+        conda_version = subprocess.run(
+            ["conda", "--version"], capture_output=True, text=True, check=True
+        )
+        print(f"Conda is installed (version: {conda_version.stdout.strip()})")
+        return True
+    except FileNotFoundError:
+        error_message = "Conda is not installed on your system or not found in PATH"
+        print(error_message)
+        return False
+
+
+def gen_parser():
+    parser = ArgumentParser(description="Run autoafids for a single subject.")
+
+    # command line arguments for autoafids-quick
+    parser.add_argument(
+        "-i",
+        "--input",
+        required=True,
+        help="File path to your input NIfTI image. Must have .nii.gz extension.",
+    )
+    parser.add_argument(
+        "-o", "--output", required=True, help="Path to your desired output folder."
+    )
+    parser.add_argument("-s", "--subject", required=True, help="SUBJECT ID (e.g., 001)")
+    parser.add_argument(
+        "-m",
+        "--modality",
+        required=True,
+        choices=list(IMAGE_MODALITY.keys()),
+        help="Image modality - chose between: " + ", ".join(IMAGE_MODALITY.keys()),
+    )
+    parser.add_argument(
+        "-n",
+        "--dry-run",
+        action="store_true",
+        help="Execute a dry run without actually running the full pipeline.",
+    )
+
+    return parser
+
+
+def main():
+
+    script_path = Path(__file__).resolve().parent / "run.py"
+
+    if not check_conda_installation():
+        print(
+            "Please activate conda and install snakebids to continue using autoafids quick."
+        )
+        sys.exit(1)
+
+    if "SNAKEMAKE_PROFILE" in os.environ:
+        del os.environ["SNAKEMAKE_PROFILE"]
+
+    args = gen_parser().parse_args()
+
+    with tempfile.TemporaryDirectory(prefix=None) as temp_dir:
+
+        # create temporary input directory within temp_dir
+        temp_input_dir = Path(temp_dir) / "input"
+        temp_input_dir.mkdir(parents=True, exist_ok=True)
+
+        temp_output_dir = Path(temp_dir) / "output"
+
+        # FIX 1: Correct BIDS structure -> sub-<subject>/anat
+        subject_folder = temp_input_dir / f"sub-{args.subject}" / "anat"
+        subject_folder.mkdir(parents=True, exist_ok=True)
+
+        # FIX 2: Fixed nested double quote syntax in f-string
+        input_filename = (
+            f"sub-{args.subject}_{IMAGE_MODALITY[args.modality]['suffix']}.nii.gz"
+        )
+
+        # add file name to the created subject folder
+        temp_input_file = subject_folder / input_filename
+
+        # copy the input file
+        shutil.copy(args.input, temp_input_file)
+
+        # run autoafids
+        command = [
+            str(script_path),
+            str(temp_input_dir),
+            str(temp_output_dir),
+            "participant",
+            "-c",
+            "all",
+            "--force-output",
+            "--nolock",
+            "--modality",
+            args.modality,
+            "--detect-with-nnlm",
+        ]
+
+        if args.dry_run:
+            command.append("-n")
+
+        if IMAGE_MODALITY[args.modality]["use_derivatives"]:
+            # need to have desc file in bids dir to use --derivatives
+            desc_file = temp_input_dir / "dataset_description.json"
+            desc_file.write_text(
+                '{"Name": "Generated Derivatives", '
+                '"BIDSVersion": "1.0.2", '
+                '"GeneratedBy": [{"Name": "autoafids-quick"}]}'
+            )
+            command.append("--derivatives")
+            command.append(str(temp_input_dir))
+
+        try:
+            subprocess.run(command, check=True)
+            print("autoafids ran successfully.")
+
+            # copy results from temp output to final output
+            temp_subject_dir = temp_output_dir / f"sub-{args.subject}"
+            final_output_dir = Path(args.output)
+
+            if temp_subject_dir.exists():
+                # create the final output structure
+                final_subject_dir = final_output_dir / f"sub-{args.subject}"
+
+                # copy the subject directory
+                if final_subject_dir.exists():
+                    shutil.rmtree(final_subject_dir)
+                final_output_dir.mkdir(parents=True, exist_ok=True)
+                shutil.copytree(temp_subject_dir, final_subject_dir)
+                print(f"Results copied to {final_subject_dir}")
+            else:
+                print(
+                    f"Warning: Expected output directory {temp_subject_dir} not found."
+                )
+
+        except subprocess.CalledProcessError as e:
+            print(f"Error: {e}")
+
+
+if __name__ == "__main__":
+    main()

docs/index.md

@@ -22,6 +22,7 @@ getting_started/conda
 
 usage/cli
 usage/useful_options
+usage/quick
 ```
 
 ```{toctree}

docs/usage/quick.md

@@ -0,0 +1,13 @@
+# Autoafids_quick
+
+`autoafids-quick` is designed to point directly to an input image from a single subject and generate an output folder. 
+
+## Autoafids-Quick Command-line interface
+
+```{argparse}
+---
+filename: ../autoafids/run_quick.py
+func: gen_parser
+prog: autoafids-quick
+---
+```

entrypoint_quick.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+exec /src/autoafids/run_quick.py "$@" 

pyproject.toml

@@ -7,7 +7,7 @@ license = "MIT"
 authors = [{name = "Alaa Taha", email = "ataha24@uwo.ca"}]
 requires-python = ">= 3.11, <3.13"
 dependencies = []
-scripts = { autoafids = "autoafids.run:app.run" }
+scripts = { autoafids = "autoafids.run:app.run", "autoafids-quick" = "autoafids.run_quick:main" }
 
 [build-system]
 build-backend = "hatchling.build"