Add option to change output mip level.

python/ouroboros/helpers/coordinates.py

@@ -52,7 +52,7 @@ def convert_points_between_volumes(
     Parameters
     ----------
         points : np.ndarray
-            The points to convert.
+            The points to convert. (N, 3)
         source_shape : tuple
             The shape of the volume that the points are currently in.
         target_shape : tuple

python/ouroboros/helpers/options.py

@@ -32,6 +32,8 @@ class SliceOptions(CommonOptions):
     connect_start_and_end: bool = (
         False  # Whether to connect the start and end of the given annotation points
     )
+    annotation_mip_level: int = 0  # MIP level for the annotation layer
+    output_mip_level: int = 0  # MIP level for the output image layer
 
     @field_serializer("bounding_box_params")
     def serialize_bounding_box_params(self, value: BoundingBoxParams):

python/ouroboros/helpers/volume_cache.py

@@ -219,3 +219,25 @@ def get_resolution_um(self, mip: int):
 
     def flush_cache(self):
         self.cv.cache.flush()
+
+
+def get_mip_volume_sizes(source_url: str) -> dict:
+    """
+    Get the volume sizes for all available MIPs.
+
+    Parameters:
+    ----------
+        source_url (str): The URL of the cloud volume.
+
+    Returns:
+    -------
+        dict: A dictionary containing the volume sizes for all available MIPs.
+    """
+
+    try:
+        cv = CloudVolumeInterface(source_url)
+        result = {mip: cv.get_volume_shape(mip) for mip in cv.available_mips}
+    except BaseException:
+        return {}
+
+    return result

python/ouroboros/pipeline/slices_geom_pipeline.py

@@ -1,16 +1,18 @@
+from ouroboros.helpers.coordinates import convert_points_between_volumes
 from ouroboros.helpers.slice import calculate_slice_rects
 from ouroboros.helpers.spline import Spline
+from ouroboros.helpers.volume_cache import get_mip_volume_sizes
 from .pipeline import PipelineStep
 from ouroboros.helpers.options import SliceOptions
 import numpy as np
 
 
 class SlicesGeometryPipelineStep(PipelineStep):
     def __init__(self) -> None:
-        super().__init__(inputs=("slice_options", "sample_points"))
+        super().__init__(inputs=("slice_options", "sample_points", "source_url"))
 
     def _process(self, input_data: tuple[any]) -> None | str:
-        config, sample_points, pipeline_input = input_data
+        config, sample_points, source_url, pipeline_input = input_data
 
         # Verify that a config object is provided
         if not isinstance(config, SliceOptions):
@@ -20,6 +22,30 @@ def _process(self, input_data: tuple[any]) -> None | str:
         if not isinstance(sample_points, np.ndarray):
             return "Input data must contain an array of sample points."
 
+        # Rescale the sample points if the option is enabled
+        if config.annotation_mip_level != config.output_mip_level:
+            mip_sizes = get_mip_volume_sizes(source_url)
+
+            if len(mip_sizes) == 0:
+                return "Failed to get the mip sizes from the volume."
+
+            if (
+                config.annotation_mip_level not in mip_sizes
+                or config.output_mip_level not in mip_sizes
+            ):
+                return "The specified mip levels are not present in the volume."
+
+            sample_points = convert_points_between_volumes(
+                sample_points,
+                mip_sizes[config.annotation_mip_level],
+                mip_sizes[config.output_mip_level],
+            )
+
+            # Update the pipeline input with the rescaled sample points
+            # Note: this ensures that the rescaled sample points are saved to the JSON file,
+            # which is important for the backprojection step
+            pipeline_input.sample_points = sample_points
+
         spline = Spline(sample_points, degree=3)
 
         # Plot equidistant points along the spline

python/ouroboros/pipeline/volume_cache_pipeline.py

@@ -35,6 +35,7 @@ def _process(self, input_data: tuple[any]) -> None | str:
             link_rects,
             cloud_volume_interface,
             flush_cache=config.flush_cache,
+            mip=config.output_mip_level,
         )
 
         # Update the pipeline input with the volume cache

python/test/helpers/test_volume_cache.py

@@ -3,6 +3,7 @@
 from ouroboros.helpers.volume_cache import (
     VolumeCache,
     CloudVolumeInterface,
+    get_mip_volume_sizes,
 )
 from ouroboros.helpers.bounding_boxes import BoundingBox
 
@@ -15,7 +16,7 @@ def mock_cloud_volume():
         mock_cv.dtype = "uint8"
         mock_cv.shape = (100, 100, 100, 3)
         mock_cv.cache.flush = MagicMock()
-        mock_cv.mip_volume_size = lambda mip: (100, 100, 100, 3)
+        mock_cv.mip_volume_size = lambda mip: (100, 100, 100)
         yield mock_cv
 
 
@@ -115,7 +116,7 @@ def test_cloud_volume_interface_to_dict(cloud_volume_interface):
 
 def test_cloud_volume_interface_get_volume_shape(cloud_volume_interface):
     shape = cloud_volume_interface.get_volume_shape(0)
-    assert shape == (100, 100, 100, 3)
+    assert shape == (100, 100, 100)
 
 
 def test_cloud_volume_interface_get_resolution_nm(cloud_volume_interface):
@@ -154,7 +155,7 @@ def test_volume_cache_get_available_mips(volume_cache):
 
 
 def test_volume_cache_get_shape(volume_cache):
-    assert volume_cache.get_volume_shape() == (100, 100, 100, 3)
+    assert volume_cache.get_volume_shape() == (100, 100, 100)
 
 
 def test_request_volume_for_slice(volume_cache):
@@ -186,3 +187,22 @@ def mock_download_func(volume_index, bounding_box, parallel):
         assert processing_data[1] == volume_cache.bounding_boxes[0]
         assert processing_data[2] == [0]
         assert processing_data[3] == 0
+
+
+def test_get_mip_volume_sizes(mock_cloud_volume):
+    with patch.object(mock_cloud_volume, "mip_volume_size") as mock_mip_volume_size:
+        mock_mip_volume_size.return_value = (100, 100, 100)
+
+        sizes = get_mip_volume_sizes("test_source_url")
+
+        assert sizes == {0: (100, 100, 100), 1: (100, 100, 100), 2: (100, 100, 100)}
+
+
+def test_get_mip_volume_sizes_error(mock_cloud_volume):
+    with patch.object(mock_cloud_volume, "mip_volume_size") as mock_mip_volume_size:
+        mock_mip_volume_size.return_value = (100, 100, 100)
+        mock_mip_volume_size.side_effect = Exception
+
+        sizes = get_mip_volume_sizes("test_source_url")
+
+        assert sizes == {}

src/renderer/src/interfaces/options.tsx

@@ -172,6 +172,8 @@ export class SliceOptionsFile extends CompoundEntry {
 			new Entry('slice_height', 'Slice Height', 120, 'number'),
 			new Entry('output_file_folder', 'Output File Folder', './', 'filePath'),
 			new Entry('output_file_name', 'Output File Name', 'sample', 'string'),
+			new Entry('annotation_mip_level', 'Annotation MIP Level', 0, 'number'),
+			new Entry('output_mip_level', 'Output MIP Level', 0, 'number'),
 			new Entry('dist_between_slices', 'Distance Between Slices', 1, 'number'),
 			new Entry('make_single_file', 'Output Single File', true, 'boolean'),
 			new Entry('connect_start_and_end', 'Connect Endpoints', false, 'boolean'),