[FIX] ADNI-to-BIDS fmap conversion : delete real/imaginary files properly, enable converting to the same folder for fmap

clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fmap.py

@@ -168,20 +168,43 @@ def compute_fmap_path(
     # Exceptions
     # ==========
     conversion_errors = [
-        ("006_S_4485", "m84"),
-        ("123_S_4127", "m96"),
-        # Eq_1
-        ("094_S_4503", "m24"),
-        ("009_S_4388", "m72"),
-        ("036_S_6088", "bl"),
-        ("036_S_6134", "bl"),
-        ("016_S_6802", "bl"),
-        ("016_S_6816", "bl"),
-        ("126_S_4891", "m84"),
-        ("177_S_6448", "m24"),
-        ("023_S_4115", "m126"),
         # Multiple images
         ("029_S_2395", "m72"),
+        # Real/Imaginary
+        ("002_S_1261", "m60"),
+        ("002_S_1261", "m72"),
+        ("002_S_1261", "m84"),
+        ("002_S_1261", "m96"),
+        ("006_S_4485", "bl"),
+        ("006_S_4485", "m03"),
+        ("006_S_4485", "m06"),
+        ("006_S_4485", "m12"),
+        ("006_S_4485", "m24"),
+        ("006_S_4485", "m48"),
+        # Unrecognized BIDSCase
+        ("006_S_4485", "m78"),
+        ("009_S_4388", "m03"),
+        ("009_S_4388", "m06"),
+        ("009_S_4388", "m12"),
+        ("009_S_4388", "m24"),
+        ("009_S_4388", "m48"),
+        ("023_S_4115", "bl"),
+        ("023_S_4115", "m03"),
+        ("023_S_4115", "m06"),
+        ("023_S_4115", "m12"),
+        ("023_S_4115", "m24"),
+        ("023_S_4115", "m48"),
+        ("123_S_4127", "bl"),
+        ("123_S_4127", "m12"),
+        ("123_S_4127", "m24"),
+        ("123_S_4127", "m36"),
+        # Missing EchoTime Keys
+        ("006_S_4485", "m90"),
+        ("036_S_6088", "m12"),
+        ("123_S_4127", "m84"),
+        # Missing DICOMS
+        ("023_S_4115", "m126"),
+        ("177_S_6448", "m24"),
     ]
 
     # Removing known exceptions from images to convert
@@ -250,6 +273,7 @@ def fmap_image(
 
 
 class BIDSFMAPCase(str, Enum):
+    ALREADY_RENAMED = "already_renamed"
     EMPTY_FOLDER = "empty_folder"
     ONE_PHASE_TWO_MAGNITUDES = "one_phase_two_magnitudes"
     TWO_PHASES_TWO_MAGNITUDES = "two_phases_two_magnitudes"
@@ -295,6 +319,8 @@ def rename_files(fmap_path: Path, case: BIDSFMAPCase):
 
 
 def fmap_case_handler_factory(case: BIDSFMAPCase) -> Callable:
+    if case == BIDSFMAPCase.ALREADY_RENAMED:
+        return already_renamed_handler
     if case == BIDSFMAPCase.EMPTY_FOLDER:
         return empty_folder_handler
     if case == BIDSFMAPCase.ONE_PHASE_TWO_MAGNITUDES:
@@ -333,6 +359,14 @@ def check_json_contains_keys(json_file: Path, keys: Iterable[str]) -> bool:
     return True
 
 
+def already_renamed_handler(fmap_path: Path):
+    cprint(
+        f"Files for subject {fmap_path.parent.parent.name},"
+        f"session {fmap_path.parent.name} were already renamed.",
+        lvl="info",
+    )
+
+
 def empty_folder_handler(fmap_path: Path):
     cprint(
         f"Folder for subject {fmap_path.parent.parent.name},"
@@ -409,6 +443,8 @@ def infer_case_fmap(fmap_path: Path) -> BIDSFMAPCase:
 
     if nb_files == 0:
         return BIDSFMAPCase.EMPTY_FOLDER
+    elif all([re.search(r"magnitude|phase", f) for f in files]):
+        return BIDSFMAPCase.ALREADY_RENAMED
     elif nb_files == 4:
         if extensions == {""}:
             return BIDSFMAPCase.DIRECT_FIELDMAPS

clinica/iotools/converters/adni_to_bids/adni_utils.py

@@ -1,6 +1,6 @@
 from enum import Enum, auto
 from pathlib import Path
-from typing import List, Optional, Tuple, Union
+from typing import Iterable, List, Optional, Tuple, Union
 
 import pandas as pd
 
@@ -1369,6 +1369,61 @@ def paths_to_bids(
     return output_file_treated
 
 
+def _get_images_with_suffix(
+    folder: Path,
+    suffixes: Iterable[str],
+) -> Iterable[Path]:
+    import re
+
+    if suffixes:
+        rgx = re.compile(r"|".join(suffixes))
+        images = list(filter(rgx.search, [f.name for f in folder.iterdir()]))
+        return [folder / image for image in images]
+    return []
+
+
+def _remove_existing_images_if_necessary(
+    folder: Path,
+    suffixes: Iterable[str],
+    mod_to_update: bool = False,
+) -> bool:
+    """Returns whether it was possible to delete the existing images or not."""
+    from clinica.utils.stream import cprint
+
+    images_to_remove = _get_images_with_suffix(folder, suffixes)
+    if not images_to_remove:
+        return True
+    elif mod_to_update:
+        cprint(f"Removing old images : {images_to_remove}", lvl="info")
+        for path_to_unlink in images_to_remove:
+            (path_to_unlink).unlink()
+        return True
+    cprint(
+        f"There already exist images : {images_to_remove}. "
+        "The parameter 'mod_to_update' is set to False so that "
+        "they cannot be overwritten.",
+        lvl="warning",
+    )
+    return False
+
+
+def _remove_files_with_unsupported_suffixes(
+    folder: Path, suffixes: Iterable[str]
+) -> Iterable[Path]:
+    from clinica.utils.stream import cprint
+
+    invalid_suffix_images = _get_images_with_suffix(folder, suffixes)
+    for image_to_remove in invalid_suffix_images:
+        cprint(
+            f"Image with bad suffix {', '.join(suffixes)} was generated by dcm2nix. These are not"
+            f"supported by Clinica so the image will NOT be converted.",
+            lvl="warning",
+        )
+        cprint(f"Removing image {folder / image_to_remove}", lvl="info")
+        (folder / image_to_remove).unlink()
+    return [folder / image for image in invalid_suffix_images]
+
+
 def create_file(
     image: pd.Series, modality: str, bids_dir: Path, mod_to_update: bool
 ) -> Optional[Path]:
@@ -1495,6 +1550,7 @@ def create_file(
         modality = image.Tracer.lower()
 
     if not image.Path:
+        # todo : check for message redundancy
         cprint(
             f"[{modality.upper()}] No path specified for {subject} in session {viscode}",
             lvl="info",
@@ -1524,18 +1580,13 @@ def create_file(
     )
     output_path.mkdir(parents=True, exist_ok=True)
 
-    # If updated mode is selected, check if an old image is existing and remove it
-    for image_to_remove in output_path.glob(f"{output_filename}*"):
-        if not mod_to_update:
-            cprint(
-                f"There exists already an image at {image_to_remove}. "
-                "The parameter 'mod_to_update' is set to False such that "
-                "images cannot be overwritten.",
-                lvl="warning",
-            )
-            return None
-        cprint(f"Removing old image {image_to_remove}...", lvl="info")
-        image_to_remove.unlink()
+    # Check if old images exist and if updated mode is set to TRUE remove them
+    if not _remove_existing_images_if_necessary(
+        output_path,
+        (modality_specific[modality]["output_filename"], "magnitude", "phase"),
+        mod_to_update,
+    ):
+        return None
 
     try:
         os.makedirs(output_path)
@@ -1571,32 +1622,10 @@ def create_file(
             os.rename(trigger_time, no_trigger_time)
 
         # Removing images with unsupported suffixes if generated by dcm2niix
-        for suffix in (
-            "ADC",
-            "real",
-            "imaginary",
-            "e1_real",
-            "e1_imaginary",
-            "e2_real",
-            "e2_imaginary",
-        ):
-            file_with_bad_suffix = output_path / f"{output_filename}_{suffix}"
-            if any(
-                [
-                    file_with_bad_suffix.with_suffix(s).exists()
-                    for s in (".nii", ".nii.gz")
-                ]
-            ):
-                cprint(
-                    f"Image with bad suffix {suffix} was generated by dcm2niix "
-                    f"for subject {subject} and session {session} : "
-                    f"{file_with_bad_suffix.with_suffix('.nii.gz')}. This image will NOT "
-                    "be converted as the suffix is not supported by Clinica.",
-                    lvl="warning",
-                )
-                for file_to_delete in output_path.glob(f"{output_filename}_{suffix}*"):
-                    cprint(f"Deleting file {file_to_delete}.", lvl="info")
-                    os.remove(file_to_delete)
+        # todo : maybe later use output to remind user what failed
+        _remove_files_with_unsupported_suffixes(
+            output_path, ("ADC", "real", "imaginary")
+        )
 
         # Conditions to check if output NIFTI files exists,
         # and, if DWI, if .bvec and .bval files are also present