[DAR-5371] Removed NifTI export pixdim scaling

darwin/cli_functions.py

@@ -1059,7 +1059,7 @@ def set_file_status(dataset_slug: str, status: str, files: List[str]) -> None:
     files: List[str]
         Names of the files we want to update.
     """
-    available_statuses = ["archived", "clear", "new", "restore-archived", "complete"]
+    available_statuses = ["archived", "new", "restore-archived", "complete"]
     if status not in available_statuses:
         _error(
             f"Invalid status '{status}', available statuses: {', '.join(available_statuses)}"
@@ -1075,8 +1075,6 @@ def set_file_status(dataset_slug: str, status: str, files: List[str]) -> None:
         )
         if status == "archived":
             dataset.archive(items)
-        elif status == "clear":
-            dataset.reset(items)
         elif status == "new":
             dataset.move_to_new(items)
         elif status == "restore-archived":

darwin/dataset/remote_dataset.py

@@ -467,68 +467,57 @@ def fetch_remote_files(
         """
 
     @abstractmethod
-    def archive(self, items: Iterator[DatasetItem]) -> None:
+    def archive(self, items: Iterable[DatasetItem]) -> None:
         """
         Archives (soft-deletion) the given ``DatasetItem``\\s belonging to this ``RemoteDataset``.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be archived.
         """
 
     @abstractmethod
-    def restore_archived(self, items: Iterator[DatasetItem]) -> None:
+    def restore_archived(self, items: Iterable[DatasetItem]) -> None:
         """
         Restores the archived ``DatasetItem``\\s that belong to this ``RemoteDataset``.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be restored.
         """
 
     @abstractmethod
-    def move_to_new(self, items: Iterator[DatasetItem]) -> None:
+    def move_to_new(self, items: Iterable[DatasetItem]) -> None:
         """
         Changes the given ``DatasetItem``\\s status to ``new``.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s whose status will change.
         """
 
     @abstractmethod
-    def reset(self, items: Iterator[DatasetItem]) -> None:
-        """
-        Resets the given ``DatasetItem``\\s.
-
-        Parameters
-        ----------
-        items : Iterator[DatasetItem]
-            The ``DatasetItem``\\s to be reset.
-        """
-
-    @abstractmethod
-    def complete(self, items: Iterator[DatasetItem]) -> None:
+    def complete(self, items: Iterable[DatasetItem]) -> None:
         """
         Completes the given ``DatasetItem``\\s.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be completed.
         """
 
     @abstractmethod
-    def delete_items(self, items: Iterator[DatasetItem]) -> None:
+    def delete_items(self, items: Iterable[DatasetItem]) -> None:
         """
         Deletes the given ``DatasetItem``\\s.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be deleted.
         """
 

darwin/dataset/remote_dataset_v2.py

@@ -10,6 +10,7 @@
     Sequence,
     Tuple,
     Union,
+    Iterable,
 )
 import numpy as np
 from pydantic import ValidationError
@@ -362,13 +363,13 @@ def fetch_remote_files(
             else:
                 return
 
-    def archive(self, items: Iterator[DatasetItem]) -> None:
+    def archive(self, items: Iterable[DatasetItem]) -> None:
         """
         Archives (soft-deletion) the given ``DatasetItem``\\s belonging to this ``RemoteDataset``.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be archived.
         """
         payload: Dict[str, Any] = {
@@ -379,13 +380,13 @@ def archive(self, items: Iterator[DatasetItem]) -> None:
         }
         self.client.api_v2.archive_items(payload, team_slug=self.team)
 
-    def restore_archived(self, items: Iterator[DatasetItem]) -> None:
+    def restore_archived(self, items: Iterable[DatasetItem]) -> None:
         """
         Restores the archived ``DatasetItem``\\s that belong to this ``RemoteDataset``.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be restored.
         """
         payload: Dict[str, Any] = {
@@ -396,13 +397,13 @@ def restore_archived(self, items: Iterator[DatasetItem]) -> None:
         }
         self.client.api_v2.restore_archived_items(payload, team_slug=self.team)
 
-    def move_to_new(self, items: Iterator[DatasetItem]) -> None:
+    def move_to_new(self, items: Iterable[DatasetItem]) -> None:
         """
         Changes the given ``DatasetItem``\\s status to ``new``.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s whose status will change.
         """
 
@@ -417,25 +418,13 @@ def move_to_new(self, items: Iterator[DatasetItem]) -> None:
             team_slug=self.team,
         )
 
-    def reset(self, items: Iterator[DatasetItem]) -> None:
-        """
-        Deprecated
-        Resets the  given ``DatasetItem``\\s.
-
-        Parameters
-        ----------
-        items : Iterator[DatasetItem]
-            The ``DatasetItem``\\s to be resetted.
-        """
-        raise ValueError("Reset is deprecated for version 2 datasets")
-
-    def complete(self, items: Iterator[DatasetItem]) -> None:
+    def complete(self, items: Iterable[DatasetItem]) -> None:
         """
         Completes the given ``DatasetItem``\\s.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be completed.
         """
         (workflow_id, stages) = self._fetch_stages("complete")
@@ -449,13 +438,13 @@ def complete(self, items: Iterator[DatasetItem]) -> None:
             team_slug=self.team,
         )
 
-    def delete_items(self, items: Iterator[DatasetItem]) -> None:
+    def delete_items(self, items: Iterable[DatasetItem]) -> None:
         """
         Deletes the given ``DatasetItem``\\s.
 
         Parameters
         ----------
-        items : Iterator[DatasetItem]
+        items : Iterable[DatasetItem]
             The ``DatasetItem``\\s to be deleted.
         """
         self.client.api_v2.delete_items(

darwin/exporter/formats/nifti.py

@@ -3,7 +3,6 @@
 import re
 from dataclasses import dataclass
 from enum import Enum
-from numbers import Number
 from pathlib import Path
 from typing import Dict, Iterable, List, Optional, Tuple, Union
 
@@ -538,7 +537,7 @@ def _get_reoriented_nifti_image(
 
 
 def shift_polygon_coords(
-    polygon: List[Dict], pixdim: List[Number], legacy: bool = False
+    polygon: List[Dict], pixdim: List[float], legacy: bool = False
 ) -> List:
     if legacy:
         # Need to make it clear that we flip x/y because we need to take the transpose later.
@@ -549,7 +548,7 @@ def shift_polygon_coords(
         else:
             return [{"x": p["y"], "y": p["x"]} for p in polygon]
     else:
-        return [{"x": p["y"] // pixdim[1], "y": p["x"] // pixdim[0]} for p in polygon]
+        return [{"x": p["y"], "y": p["x"]} for p in polygon]
 
 
 def get_view_idx(frame_idx: int, groups: List) -> int:

tests/darwin/cli_functions_test.py

@@ -289,25 +289,6 @@ def test_calls_dataset_archive(
                     )
                     mock.assert_called_once_with(fetch_remote_files_mock.return_value)
 
-    def test_calls_dataset_clear(
-        self, dataset_identifier: str, remote_dataset: RemoteDataset
-    ):
-        with patch.object(
-            Client, "get_remote_dataset", return_value=remote_dataset
-        ) as get_remote_dataset_mock:
-            with patch.object(
-                RemoteDatasetV2, "fetch_remote_files"
-            ) as fetch_remote_files_mock:
-                with patch.object(RemoteDatasetV2, "reset") as mock:
-                    set_file_status(dataset_identifier, "clear", ["one.jpg", "two.jpg"])
-                    get_remote_dataset_mock.assert_called_once_with(
-                        dataset_identifier=dataset_identifier
-                    )
-                    fetch_remote_files_mock.assert_called_once_with(
-                        {"item_names": "one.jpg,two.jpg"}
-                    )
-                    mock.assert_called_once_with(fetch_remote_files_mock.return_value)
-
     def test_calls_dataset_new(
         self, dataset_identifier: str, remote_dataset: RemoteDataset
     ):

tests/darwin/exporter/formats/export_nifti_test.py

@@ -169,3 +169,58 @@ def test_export_creates_file_for_polygons_and_masks(
                 # Empty the directory for the next test
                 for output_file in video_annotation_files[video_annotation_file]:
                     (Path(tmpdir) / output_file).unlink()
+
+
+def test_shift_polygon_coords_legacy():
+    """Test the `shift_polygon_coords` function in legacy mode with different pixdim ratios."""
+    # Case 1: pixdim[1] > pixdim[0]
+    polygon = [{"x": 10, "y": 20}, {"x": 30, "y": 40}, {"x": 50, "y": 60}]
+    pixdim = [1.0, 2.0, 1.0]
+    result = nifti.shift_polygon_coords(polygon, pixdim, legacy=True)
+    expected = [
+        {"x": 20, "y": 20},
+        {"x": 40, "y": 60},
+        {"x": 60, "y": 100},
+    ]
+    assert result == expected
+
+    # Case 2: pixdim[1] < pixdim[0]
+    polygon = [{"x": 10, "y": 20}, {"x": 30, "y": 40}, {"x": 50, "y": 60}]
+    pixdim = [2.0, 1.0, 1.0]
+    result = nifti.shift_polygon_coords(polygon, pixdim, legacy=True)
+    expected = [
+        {"x": 40, "y": 10},
+        {"x": 80, "y": 30},
+        {"x": 120, "y": 50},
+    ]
+    assert result == expected
+
+    # Case 3: pixdim[1] == pixdim[0]
+    polygon = [{"x": 10, "y": 20}, {"x": 30, "y": 40}, {"x": 50, "y": 60}]
+    pixdim = [1.0, 1.0, 1.0]
+    result = nifti.shift_polygon_coords(polygon, pixdim, legacy=True)
+    expected = [
+        {"x": 20, "y": 10},
+        {"x": 40, "y": 30},
+        {"x": 60, "y": 50},
+    ]
+    assert result == expected
+
+
+def test_shift_polygon_coords_no_legacy():
+    """Test the `shift_polygon_coords` function in non-legacy mode."""
+    polygon = [{"x": 10, "y": 20}, {"x": 30, "y": 40}, {"x": 50, "y": 60}]
+    pixdim = [2.0, 1.0, 1.0]
+    result = nifti.shift_polygon_coords(polygon, pixdim, legacy=False)
+    expected = [{"x": 20, "y": 10}, {"x": 40, "y": 30}, {"x": 60, "y": 50}]
+    assert result == expected
+
+
+def test_shift_polygon_coords_empty_polygon():
+    """Test the `shift_polygon_coords` function with an empty polygon."""
+    empty_polygon = []
+    pixdim = [1.0, 1.0, 1.0]
+    result = nifti.shift_polygon_coords(empty_polygon, pixdim, legacy=True)
+    assert result == []
+    result = nifti.shift_polygon_coords(empty_polygon, pixdim, legacy=False)
+    assert result == []