[REF] Refactor converters (#1140)

* refactor converters (unfinished)

* some fixes

* some more fixes

* some more fixes 2

* some improvements

* some improvements 2

* try fixing oasis issues

* try fixing oasis issues again

* fix adni to bids and simplify genfi to bids

* work on API

* make API more uniform

* fix remaining bugs and continue uniformizing API

* finish refactoring

* fix call to find_image_path in adni_fmap

* warn when n_procs or subjects options are not implemented

* continue refactoring

* fix bad merge

* refine adni converter interface

* post rebase fixes

* fix bad rebase

* fix errors introduced while rebasing

* expose convert

clinica/iotools/converter_utils.py

@@ -1,6 +1,21 @@
 from os import PathLike
 from typing import List, Optional
 
+__all__ = ["replace_sequence_chars"]
+
+
+def replace_sequence_chars(sequence_name: str) -> str:
+    """Replace special characters in the sequence by underscores (as done for corresponding folder names in ADNI).
+
+    Args:
+        sequence_name: sequence to process
+
+    Returns: the new string
+    """
+    import re
+
+    return re.sub("[ /;*()<>:]", "_", sequence_name)
+
 
 class MissingModsTracker:
     """Class used for tracking the number of missing modalities in a database.

clinica/iotools/converters/__init__.py

@@ -0,0 +1,3 @@
+from .factory import convert
+
+__all__ = ["convert"]

clinica/iotools/converters/adni_to_bids/__init__.py

@@ -0,0 +1,3 @@
+from .adni_to_bids import convert
+
+__all__ = ["convert"]