Merge pull request #143 from BrainLesion/138-feature-citation-reminder

138 feature citation reminder

Author: neuronflow

README.md

@@ -111,9 +111,25 @@ For further information please have a look at our [Jupyter Notebook tutorials](h
 
 
 
+## Citation
 
+> [!IMPORTANT]
+> If you use `brainles-preprocessing` in your research, please cite it to support the development!
 
-<!-- TODO citation -->
+Kofler, F., Rosier, M., Astaraki, M., Möller, H., Mekki, I. I., Buchner, J. A., Schmick, A., Pfiffer, A., Oswald, E., Zimmer, L., Rosa, E. de la, Pati, S., Canisius, J., Piffer, A., Baid, U., Valizadeh, M., Linardos, A., Peeken, J. C., Shit, S., … Menze, B. (2025). *BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis* [arXiv preprint arXiv:2507.09036](https://doi.org/10.48550/arXiv.2507.09036)
+
+
+```
+@misc{kofler2025brainlesionsuiteflexibleuserfriendly,
+      title={BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis}, 
+      author={Florian Kofler and Marcel Rosier and Mehdi Astaraki and Hendrik Möller and Ilhem Isra Mekki and Josef A. Buchner and Anton Schmick and Arianna Pfiffer and Eva Oswald and Lucas Zimmer and Ezequiel de la Rosa and Sarthak Pati and Julian Canisius and Arianna Piffer and Ujjwal Baid and Mahyar Valizadeh and Akis Linardos and Jan C. Peeken and Surprosanna Shit and Felix Steinbauer and Daniel Rueckert and Rolf Heckemann and Spyridon Bakas and Jan Kirschke and Constantin von See and Ivan Ezhov and Marie Piraud and Benedikt Wiestler and Bjoern Menze},
+      year={2025},
+      eprint={2507.09036},
+      archivePrefix={arXiv},
+      primaryClass={cs.CV},
+      url={https://arxiv.org/abs/2507.09036}, 
+}
+```
 
 ## Documentation
 We provide a (WIP) documentation. Have a look [here](https://brainles-preprocessing.readthedocs.io/en/latest/?badge=latest)

brainles_preprocessing/preprocessor/preprocessor.py

@@ -22,6 +22,7 @@
 )
 from brainles_preprocessing.registration import ANTsRegistrator
 from brainles_preprocessing.registration.registrator import Registrator
+from brainles_preprocessing.utils.citation_reminder import citation_reminder
 from brainles_preprocessing.utils.logging_utils import LoggingManager
 
 logging_man = LoggingManager(name=__name__)
@@ -45,6 +46,7 @@ class BasePreprocessor(ABC):
 
     """
 
+    @citation_reminder
     def __init__(
         self,
         center_modality: CenterModality,

brainles_preprocessing/registration/ANTs/ANTs.py

@@ -241,7 +241,7 @@ def inverse_transform(
             fixed_image_path (str or Path): Path to the fixed image.
             moving_image_path (str or Path): Path to the moving image.
             transformed_image_path (str or Path): Path to the transformed image (output).
-           matrix_path (str or Path or List[str | Path]): Path to the transformation matrix or a list of matrices.
+            matrix_path (str or Path or List[str | Path]): Path to the transformation matrix or a list of matrices.
             log_file_path (str or Path): Path to the log file.
             interpolator (str): Interpolator to use for the transformation. Default is 'nearestNeighbor'.
             **kwargs: Additional transformation parameters to update the instantiated defaults.

brainles_preprocessing/utils/citation_reminder.py

@@ -0,0 +1,41 @@
+import functools
+import os
+
+from rich.console import Console
+
+CITATION_LINK = "https://github.com/BrainLesion/preprocessing#citation"
+
+
+def citation_reminder(func):
+    """
+    Decorator to remind users to cite brainles-preprocessing.
+
+    The reminder is shown when the environment variable
+    `BRAINLES_PREPROCESSING_CITATION_REMINDER` is set to "true" (default).
+    To disable the reminder, set the environment variable to "false".
+
+    Environment variable used:
+    - BRAINLES_PREPROCESSING_CITATION_REMINDER: Controls whether the reminder is shown.
+    """
+
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        if (
+            os.environ.get("BRAINLES_PREPROCESSING_CITATION_REMINDER", "true").lower()
+            == "true"
+        ):
+            console = Console()
+            console.rule("Thank you for using [bold]brainles-preprocessing[/bold]")
+            console.print(
+                "Please support our development by citing",
+                justify="center",
+            )
+            console.print(
+                f"{CITATION_LINK} -- Thank you!",
+                justify="center",
+            )
+            console.rule()
+            console.line()
+        return func(*args, **kwargs)
+
+    return wrapper