[DAR-4672][External] Replaced no_legacy with legacy & swapped def…

…ault scaling behaviour of `NifTI` importer (#958)

* Replaced  with

* Test coverage

darwin/cli_functions.py

@@ -919,8 +919,8 @@ def dataset_import(
         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 not resize the annotations to be isotropic.
-        If ``False`` it will resize the annotations to be isotropic.
+        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
@@ -931,7 +931,6 @@ def dataset_import(
 
     try:
         importer: ImportParser = get_importer(format)
-
         if format == "nifti" and legacy:
             importer = partial(importer, legacy=True)
 
@@ -954,7 +953,7 @@ def dataset_import(
             overwrite,
             use_multi_cpu,
             cpu_limit,
-            no_legacy=False if legacy else True,
+            legacy,
         )
 
     except ImporterNotFoundError:
@@ -1228,8 +1227,8 @@ def dataset_convert(
         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.
+        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)
@@ -1286,8 +1285,8 @@ def convert(
         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.
+        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)

darwin/importer/importer.py

@@ -1092,7 +1092,7 @@ def import_annotations(  # noqa: C901
     overwrite: bool = False,
     use_multi_cpu: bool = False,
     cpu_limit: Optional[int] = None,
-    no_legacy: Optional[bool] = False,
+    legacy: Optional[bool] = False,
 ) -> None:
     """
     Imports the given given Annotations into the given Dataset.
@@ -1134,9 +1134,9 @@ 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.
-    no_legacy : bool, default: False
-        If ``True`` will not use the legacy isotropic transformation to resize annotations
-        If ``False`` will use the legacy isotropic transformation to resize annotations
+    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
@@ -1154,7 +1154,7 @@ def import_annotations(  # noqa: C901
     # CLI-initiated imports will raise an AttributeError because of the partial function
     # This block handles SDK-initiated imports
     try:
-        if importer.__module__ == "darwin.importer.formats.nifti" and not no_legacy:
+        if importer.__module__ == "darwin.importer.formats.nifti" and legacy:
             importer = partial(importer, legacy=True)
     except AttributeError:
         pass

darwin/options.py

@@ -61,10 +61,10 @@ def __init__(self) -> None:
             help="Annotation files (or folders) to convert.",
         )
         parser_convert.add_argument(
-            "--no-legacy",
-            action="store_false",
-            dest="legacy",
-            help="Do not convert annotation using legacy process (isotropic transformation).",
+            "--legacy",
+            action="store_true",
+            default=False,
+            help="Import annotation files using legacy process (isotropic transformation).",
         )
         parser_convert.add_argument(
             "output_dir", type=str, help="Where to store output files."
@@ -375,10 +375,10 @@ def __init__(self) -> None:
             help="Bypass warnings about overwiting existing annotations.",
         )
         parser_import.add_argument(
-            "--no-legacy",
-            action="store_false",
-            dest="legacy",
-            help="Do not importing annotation files using legacy process (isotropic transformation).",
+            "--legacy",
+            action="store_true",
+            default=False,
+            help="Import annotation files using legacy process (isotropic transformation).",
         )
 
         # Cpu limit for multiprocessing tasks
@@ -410,9 +410,10 @@ def cpu_default_types(input: Any) -> Optional[int]:  # type: ignore
             "format", type=str, help="Annotation format to convert to."
         )
         parser_convert.add_argument(
-            "legacy",
+            "--legacy",
             action="store_true",
-            help="Convert annotation using legacy process (isotropic transformation).",
+            default=False,
+            help="Import annotation files using legacy process (isotropic transformation).",
         )
         parser_convert.add_argument(
             "-o", "--output_dir", type=str, help="Where to store output files."

tests/darwin/data/nifti/legacy/.v7/metadata.json

@@ -0,0 +1,44 @@
+{
+  "version": "1.0",
+  "schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/metadata/1.0/schema.json",
+  "classes": [
+    {
+      "name": "Reference_sBAT",
+      "type": "polygon",
+      "description": null,
+      "color": "rgba(0,255,170,1.0)",
+      "sub_types": [
+        "text",
+        "inference"
+      ],
+      "properties": [],
+      "sub_types_settings": {
+        "inference": {},
+        "text": {}
+      }
+    }
+  ],
+  "properties": [
+    {
+      "name": "item-level-ss",
+      "type": "single_select",
+      "description": "What is this?",
+      "required": false,
+      "property_values": [
+        {
+          "value": "1",
+          "color": "rgba(238,240,241,1.0)"
+        },
+        {
+          "value": "2",
+          "color": "rgba(255,0,214,1.0)"
+        },
+        {
+          "value": "3",
+          "color": "rgba(173,255,0,1.0)"
+        }
+      ],
+      "granularity": "item"
+    }
+  ]
+}