feat: Add legacy flag to switch between pre and post MED_2D

darwin/cli.py

@@ -100,7 +100,7 @@ def _run(args: Namespace, parser: ArgumentParser) -> None:
         print(__version__)
 
     elif args.command == "convert":
-        f.convert(args.format, args.files, args.output_dir)
+        f.convert(args.format, args.files, args.output_dir, legacy=args.legacy)
     elif args.command == "dataset":
         if args.action == "remote":
             f.list_remote_datasets(args.all, args.team)
@@ -167,11 +167,13 @@ def _run(args: Namespace, parser: ArgumentParser) -> None:
                 args.import_annotators,
                 args.import_reviewers,
                 args.overwrite,
-                isotropic=args.isotropic,
+                legacy=args.legacy,
                 cpu_limit=args.cpu_limit,
             )
         elif args.action == "convert":
-            f.dataset_convert(args.dataset, args.format, args.output_dir)
+            f.dataset_convert(
+                args.dataset, args.format, args.output_dir, legacy=args.legacy
+            )
         elif args.action == "set-file-status":
             f.set_file_status(args.dataset, args.status, args.files)
         elif args.action == "delete-files":

darwin/cli_functions.py

@@ -853,7 +853,7 @@ def dataset_import(
     import_annotators: bool = False,
     import_reviewers: bool = False,
     overwrite: bool = False,
-    isotropic: bool = False,
+    legacy: bool = False,
     use_multi_cpu: bool = False,
     cpu_limit: Optional[int] = None,
 ) -> None:
@@ -887,7 +887,7 @@ def dataset_import(
     overwrite : bool, default: False
         If ``True`` it will bypass a warning that the import will overwrite the current annotations if any are present.
         If ``False`` this warning will be skipped and the import will overwrite the current annotations without warning.
-    isotropic : bool, default: False
+    legacy : bool, default: False
         If ``True`` it will not resize the annotations to be isotropic.
         If ``False`` it will resize the annotations to be isotropic.
     use_multi_cpu : bool, default: False
@@ -901,8 +901,8 @@ def dataset_import(
     try:
         importer: ImportParser = get_importer(format)
 
-        if format == "nifti" and isotropic:
-            importer = partial(importer, isotropic=True)
+        if format == "nifti" and legacy:
+            importer = partial(importer, legacy=True)
 
         dataset: RemoteDataset = client.get_remote_dataset(
             dataset_identifier=dataset_slug
@@ -1172,7 +1172,10 @@ def validate_schemas(
 
 
 def dataset_convert(
-    dataset_identifier: str, format: str, output_dir: Optional[PathLike] = None
+    dataset_identifier: str,
+    format: str,
+    output_dir: Optional[PathLike] = None,
+    legacy: bool = False,
 ) -> None:
     """
     Converts the annotations from the given dataset to the given format.
@@ -1188,12 +1191,20 @@ def dataset_convert(
     output_dir : Optional[PathLike], default: None
         The folder where the exported annotation files will be. If None it will be the inside the
         annotations folder of the dataset under 'other_formats/{format}'.
+    legacy : bool, default: False
+        This flag is only for the nifti format.
+        If True, it will not export the annotations using legacy calculations.
+        If False, it will resize the annotations using the new calculation by dividing with pixdims.
     """
     identifier: DatasetIdentifier = DatasetIdentifier.parse(dataset_identifier)
     client: Client = _load_client(team_slug=identifier.team_slug)
 
     try:
         parser: ExportParser = get_exporter(format)
+
+        if format == "nifti" and legacy:
+            parser = partial(parser, legacy=True)
+
         dataset: RemoteDataset = client.get_remote_dataset(
             dataset_identifier=identifier
         )
@@ -1224,7 +1235,9 @@ def dataset_convert(
         _error(f"No dataset with name '{e.name}'")
 
 
-def convert(format: str, files: List[PathLike], output_dir: Path) -> None:
+def convert(
+    format: str, files: List[PathLike], output_dir: Path, legacy: bool = False
+) -> None:
     """
     Converts the given files to the specified format.
 
@@ -1236,9 +1249,15 @@ def convert(format: str, files: List[PathLike], output_dir: Path) -> None:
         List of files to be converted.
     output_dir: Path
         Folder where the exported annotations will be placed.
+    legacy: bool, default: False
+        This flag is only for the nifti format.
+        If True, it will not export the annotations using legacy calculations.
+        If False, it will resize the annotations using the new calculation by dividing with pixdims.
     """
     try:
         parser: ExportParser = get_exporter(format)
+        if format == "nifti" and legacy:
+            parser = partial(parser, legacy=True)
     except ExporterNotFoundError:
         _error(f"Unsupported export format, currently supported: {export_formats}")
     except AttributeError:

darwin/exporter/formats/nifti.py

@@ -44,7 +44,11 @@ class Volume:
     from_raster_layer: bool
 
 
-def export(annotation_files: Iterable[dt.AnnotationFile], output_dir: Path) -> None:
+def export(
+    annotation_files: Iterable[dt.AnnotationFile],
+    output_dir: Path,
+    legacy: bool = False,
+) -> None:
     """
     Exports the given ``AnnotationFile``\\s into nifti format inside of the given
     ``output_dir``. Deletes everything within ``output_dir/masks`` before writting to it.
@@ -55,13 +59,23 @@ def export(annotation_files: Iterable[dt.AnnotationFile], output_dir: Path) -> N
         The ``AnnotationFile``\\s to be exported.
     output_dir : Path
         The folder where the new instance mask files will be.
+    legacy : bool, default=False
+        If ``True``, the exporter will use the legacy calculation.
+        If ``False``, the exporter will use the new calculation by dividing with pixdims.
+
 
     Returns
     -------
     sends output volumes, image_id and output_dir to the write_output_volume_to_disk function
 
     """
 
+    if legacy:
+        console.print(
+            "Legacy flag is set to True. Annotations will be resized using legacy calculations.",
+            style="bold blue",
+        )
+
     video_annotations = list(annotation_files)
     for video_annotation in video_annotations:
         image_id = check_for_error_and_return_imageid(video_annotation, output_dir)
@@ -92,10 +106,10 @@ def export(annotation_files: Iterable[dt.AnnotationFile], output_dir: Path) -> N
         ]
         if polygon_annotations:
             populate_output_volumes_from_polygons(
-                polygon_annotations, slot_map, output_volumes
+                polygon_annotations, slot_map, output_volumes, legacy=legacy
             )
         write_output_volume_to_disk(
-            output_volumes, image_id=image_id, output_dir=output_dir
+            output_volumes, image_id=image_id, output_dir=output_dir, legacy=legacy
         )
         # Need to map raster layers to SeriesInstanceUIDs
         if mask_present:
@@ -124,7 +138,10 @@ def export(annotation_files: Iterable[dt.AnnotationFile], output_dir: Path) -> N
                     output_volumes=raster_output_volumes,
                 )
             write_output_volume_to_disk(
-                raster_output_volumes, image_id=image_id, output_dir=output_dir
+                raster_output_volumes,
+                image_id=image_id,
+                output_dir=output_dir,
+                legacy=legacy,
             )
 
 
@@ -302,6 +319,7 @@ def populate_output_volumes_from_polygons(
     annotations: List[Union[dt.Annotation, dt.VideoAnnotation]],
     slot_map: Dict,
     output_volumes: Dict,
+    legacy: bool = False,
 ):
     """
     Populates the output volumes with the given polygon annotations. The annotations are converted into masks
@@ -315,6 +333,9 @@ def populate_output_volumes_from_polygons(
         Dictionary of the different slots within the annotation file
     output_volumes : Dict
         Volumes created from the build_output_volumes file
+    legacy : bool, default=False
+        If ``True``, the exporter will use the legacy calculation.
+        If ``False``, the exporter will use the new calculation by dividing with pixdims.
     """
     for annotation in annotations:
         slot_name = annotation.slot_names[0]
@@ -341,7 +362,7 @@ def populate_output_volumes_from_polygons(
             if "paths" in frame_data:
                 # Dealing with a complex polygon
                 polygons = [
-                    shift_polygon_coords(polygon_path, pixdims)
+                    shift_polygon_coords(polygon_path, pixdims, legacy=legacy)
                     for polygon_path in frame_data["paths"]
                 ]
             else:
@@ -412,7 +433,10 @@ def populate_output_volumes_from_raster_layer(
 
 
 def write_output_volume_to_disk(
-    output_volumes: Dict, image_id: str, output_dir: Union[str, Path]
+    output_volumes: Dict,
+    image_id: str,
+    output_dir: Union[str, Path],
+    legacy: bool = False,
 ) -> None:
     """Writes the given output volumes to disk.
 
@@ -424,6 +448,9 @@ def write_output_volume_to_disk(
         The specific image id
     output_dir : Union[str, Path]
         The output directory to write the volumes to
+    legacy : bool, default=False
+        If ``True``, the exporter will use the legacy calculation.
+        If ``False``, the exporter will use the new calculation by dividing with pixdims.
 
     Returns
     -------
@@ -446,7 +473,7 @@ def unnest_dict_to_list(d: Dict) -> List:
             dataobj=np.flip(volume.pixel_array, (0, 1, 2)).astype(np.int16),
             affine=volume.affine,
         )
-        if volume.original_affine is not None:
+        if legacy and volume.original_affine is not None:
             orig_ornt = io_orientation(
                 volume.original_affine
             )  # Get orientation of current affine
@@ -464,14 +491,19 @@ def unnest_dict_to_list(d: Dict) -> List:
         nib.save(img=img, filename=output_path)
 
 
-def shift_polygon_coords(polygon: List[Dict], pixdim: List[Number]) -> List:
-    # Need to make it clear that we flip x/y because we need to take the transpose later.
-    if pixdim[1] > pixdim[0]:
-        return [{"x": p["y"], "y": p["x"] * pixdim[1] / pixdim[0]} for p in polygon]
-    elif pixdim[1] < pixdim[0]:
-        return [{"x": p["y"] * pixdim[0] / pixdim[1], "y": p["x"]} for p in polygon]
+def shift_polygon_coords(
+    polygon: List[Dict], pixdim: List[Number], legacy: bool = False
+) -> List:
+    if legacy:
+        # Need to make it clear that we flip x/y because we need to take the transpose later.
+        if pixdim[1] > pixdim[0]:
+            return [{"x": p["y"], "y": p["x"] * pixdim[1] / pixdim[0]} for p in polygon]
+        elif pixdim[1] < pixdim[0]:
+            return [{"x": p["y"] * pixdim[0] / pixdim[1], "y": p["x"]} for p in polygon]
+        else:
+            return [{"x": p["y"], "y": p["x"]} for p in polygon]
     else:
-        return [{"x": p["y"], "y": p["x"]} for p in polygon]
+        return [{"x": p["y"] // pixdim[1], "y": p["x"] // pixdim[0]} for p in polygon]
 
 
 def get_view_idx(frame_idx: int, groups: List) -> int: