Removed API-facing flag (#983)

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, legacy=args.legacy)
+        f.convert(args.format, args.files, args.output_dir)
     elif args.command == "dataset":
         if args.action == "remote":
             f.list_remote_datasets(args.all, args.team)
@@ -173,12 +173,13 @@ def _run(args: Namespace, parser: ArgumentParser) -> None:
                 args.import_annotators,
                 args.import_reviewers,
                 args.overwrite,
-                legacy=args.legacy,
                 cpu_limit=args.cpu_limit,
             )
         elif args.action == "convert":
             f.dataset_convert(
-                args.dataset, args.format, args.output_dir, legacy=args.legacy
+                args.dataset,
+                args.format,
+                args.output_dir,
             )
         elif args.action == "set-file-status":
             f.set_file_status(args.dataset, args.status, args.files)

darwin/cli_functions.py

@@ -5,7 +5,6 @@
 import os
 import sys
 import traceback
-from functools import partial
 from glob import glob
 from itertools import tee
 from pathlib import Path
@@ -888,7 +887,6 @@ def dataset_import(
     import_annotators: bool = False,
     import_reviewers: bool = False,
     overwrite: bool = False,
-    legacy: bool = False,
     use_multi_cpu: bool = False,
     cpu_limit: Optional[int] = None,
 ) -> None:
@@ -922,9 +920,6 @@ 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.
-    legacy : bool, default: False
-        If ``True`` it will resize the annotations to be isotropic.
-        If ``False`` it will not resize the annotations to be isotropic.
     use_multi_cpu : bool, default: False
         If ``True`` it will use all multiple CPUs to speed up the import process.
     cpu_limit : Optional[int], default: Core count - 2
@@ -955,7 +950,6 @@ def dataset_import(
             overwrite,
             use_multi_cpu,
             cpu_limit,
-            legacy,
         )
 
     except ImporterNotFoundError:
@@ -1211,7 +1205,6 @@ def dataset_convert(
     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.
@@ -1227,10 +1220,6 @@ 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 resize the annotations by dividing by pixdims.
-        If False, it will not export the annotations using legacy calculations
     """
     identifier: DatasetIdentifier = DatasetIdentifier.parse(dataset_identifier)
     client: Client = _load_client(team_slug=identifier.team_slug)
@@ -1269,7 +1258,9 @@ def dataset_convert(
 
 
 def convert(
-    format: str, files: List[PathLike], output_dir: Path, legacy: bool = False
+    format: str,
+    files: List[PathLike],
+    output_dir: Path,
 ) -> None:
     """
     Converts the given files to the specified format.
@@ -1282,15 +1273,9 @@ def convert(
         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 resize the annotations by dividing by pixdims
-        If False, it will not export the annotations using legacy calculations.
     """
     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

@@ -59,7 +59,6 @@ class Volume:
 def export(
     annotation_files: Iterable[dt.AnnotationFile],
     output_dir: Path,
-    legacy: Optional[bool] = None,
 ) -> None:
     """
     Exports the given ``AnnotationFile``\\s into nifti format inside of the given
@@ -71,23 +70,12 @@ def export(
         The ``AnnotationFile``\\s to be exported.
     output_dir : Path
         The folder where the new instance mask files will be.
-    legacy : bool, default=None
-        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 is not None:
-        console.print(
-            "The `legacy` flag is now non-functional and will be deprecated soon. The annotation conversion process now automatically detects if legacy annotation scaling is required.",
-            style="warning",
-        )
-
     video_annotations = list(annotation_files)
     for video_annotation in video_annotations:
         try:

darwin/importer/importer.py

@@ -3,7 +3,6 @@
 import json
 import copy
 from collections import defaultdict
-from functools import partial
 from logging import getLogger
 from multiprocessing import cpu_count
 from pathlib import Path
@@ -1158,7 +1157,6 @@ def import_annotations(  # noqa: C901
     overwrite: bool = False,
     use_multi_cpu: bool = False,
     cpu_limit: Optional[int] = None,
-    legacy: Optional[bool] = None,
 ) -> None:
     """
     Imports the given given Annotations into the given Dataset.
@@ -1200,9 +1198,6 @@ def import_annotations(  # noqa: C901
         If ``cpu_limit`` is greater than the number of available CPU cores, it will be set to the number of available cores.
         If ``cpu_limit`` is less than 1, it will be set to CPU count - 2.
         If ``cpu_limit`` is omitted, it will be set to CPU count - 2.
-    legacy : bool, default: False
-        If ``True`` will use the legacy isotropic transformation to resize annotations
-        If ``False`` will not use the legacy isotropic transformation to resize annotations
     Raises
     -------
     ValueError
@@ -1215,12 +1210,6 @@ def import_annotations(  # noqa: C901
     """
     console = Console(theme=_console_theme())
 
-    if legacy is not None:
-        console.print(
-            "The `legacy` flag is now non-functional and will be deprecated soon. The annotation import process now automatically detects if legacy annotation scaling is required.",
-            style="warning",
-        )
-
     if append and delete_for_empty:
         raise IncompatibleOptions(
             "The options 'append' and 'delete_for_empty' cannot be used together. Use only one of them."
@@ -2072,9 +2061,6 @@ def _get_annotation_format(
     annotation_format : str
         The annotation format of the importer used to parse local files
     """
-    # This `if` block is temporary, but necessary while we migrate NifTI imports between the legacy method & the new method
-    if isinstance(importer, partial):
-        return importer.func.__module__.split(".")[3]
     return importer.__module__.split(".")[3]
 
 

darwin/options.py

@@ -60,14 +60,6 @@ def __init__(self) -> None:
             nargs="+",
             help="Annotation files (or folders) to convert.",
         )
-        parser_convert.add_argument(
-            "--legacy",
-            type=lambda x: (str(x).lower() == "true") if x is not None else None,
-            nargs="?",
-            const=True,
-            default=None,
-            help="The legacy flag is now non-functional and will be deprecated soon. The annotation conversion process now automatically detects if legacy annotation scaling is required.",
-        )
         parser_convert.add_argument(
             "output_dir", type=str, help="Where to store output files."
         )
@@ -381,14 +373,6 @@ def __init__(self) -> None:
             action="store_true",
             help="Bypass warnings about overwiting existing annotations.",
         )
-        parser_import.add_argument(
-            "--legacy",
-            type=lambda x: (str(x).lower() == "true") if x is not None else None,
-            nargs="?",
-            const=True,
-            default=None,
-            help="The legacy flag is now non-functional and will be deprecated soon. The annotation import process now automatically detects if legacy annotation scaling is required.",
-        )
 
         # Cpu limit for multiprocessing tasks
         def cpu_default_types(input: Any) -> Optional[int]:  # type: ignore
@@ -418,14 +402,6 @@ def cpu_default_types(input: Any) -> Optional[int]:  # type: ignore
         parser_convert.add_argument(
             "format", type=str, help="Annotation format to convert to."
         )
-        parser_convert.add_argument(
-            "--legacy",
-            type=lambda x: (str(x).lower() == "true") if x is not None else None,
-            nargs="?",
-            const=True,
-            default=None,
-            help="The legacy flag is now non-functional and will be deprecated soon. The annotation conversion process now automatically detects if legacy annotation scaling is required.",
-        )
         parser_convert.add_argument(
             "-o", "--output_dir", type=str, help="Where to store output files."
         )

tests/darwin/importer/importer_test.py

@@ -1,6 +1,5 @@
 import json
 import tempfile
-from functools import partial
 from pathlib import Path
 from typing import List, Tuple
 from unittest.mock import MagicMock, Mock, _patch, patch
@@ -2145,12 +2144,6 @@ def test__get_annotation_format():
     assert _get_annotation_format(get_importer("superannotate")) == "superannotate"
 
 
-def test__get_annotation_format_with_partial():
-    nifti_importer = get_importer("nifti")
-    legacy_nifti_importer = partial(nifti_importer, legacy=True)
-    assert _get_annotation_format(legacy_nifti_importer) == "nifti"
-
-
 def test_no_verify_warning_for_single_slotted_items():
     bounding_box_class = dt.AnnotationClass(
         name="class1", annotation_type="bounding_box"