Upsample

dacapo/experiments/datasplits/datasets/arrays/resampled_array_config.py

@@ -9,6 +9,7 @@
 from xarray_multiscale import windowed_mean
 import numpy as np
 import dask.array as da
+from skimage.transform import rescale
 
 from typing import Sequence
 
@@ -62,20 +63,52 @@ def preprocess(self, array: Array) -> Array:
         Preprocess an array by resampling it to the desired voxel size.
         """
         if self.downsample is not None:
-            downsample = Coordinate(self.downsample)
+            downsample = list(self.downsample)
+            for i, axis_name in enumerate(array.axis_names):
+                if "^" in axis_name:
+                    downsample = downsample[:i] + [1] + downsample[i:]
             return Array(
                 data=downscale_dask(
                     adjust_shape(array.data, downsample),
                     windowed_mean,
                     scale_factors=downsample,
                 ),
                 offset=array.offset,
-                voxel_size=array.voxel_size * downsample,
+                voxel_size=array.voxel_size * self.downsample,
                 axis_names=array.axis_names,
                 units=array.units,
             )
         elif self.upsample is not None:
-            raise NotImplementedError("Upsampling not yet implemented")
+            upsample = list(self.upsample)
+            for i, axis_name in enumerate(array.axis_names):
+                if "^" in axis_name:
+                    upsample = upsample[:i] + [1] + upsample[i:]
+
+            depth = [int(x > 1) for x in upsample]
+            trim_slicing = tuple(
+                slice(d * s, (-d * s)) if d > 1 else slice(None)
+                for d, s in zip(depth, upsample)
+            )
+
+            rescaled_arr = da.map_overlap(
+                lambda x: rescale(
+                    x, upsample, order=int(self.interp_order), preserve_range=True
+                )[trim_slicing],
+                array.data,
+                depth=depth,
+                boundary="reflect",
+                trim=False,
+                dtype=array.data.dtype,
+                chunks=tuple(c * u for c, u in zip(array.data.chunksize, upsample)),
+            )
+
+            return Array(
+                data=rescaled_arr,
+                offset=array.offset,
+                voxel_size=array.voxel_size / self.upsample,
+                axis_names=array.axis_names,
+                units=array.units,
+            )
 
     def array(self, mode: str = "r") -> Array:
         source_array = self.source_array_config.array(mode)

dacapo/experiments/datasplits/simple_config.py

@@ -45,7 +45,7 @@ def get_paths(self, group_name: str) -> list[Path]:
             ), f"Found raw data at {level_1} and {level_2}"
             return [Path(x).parent for x in level_1_matches]
         elif len(level_2_matches) > 0:
-            return [Path(x) for x in level_2_matches]
+            return [Path(x).parent for x in level_2_matches]
 
         raise Exception(f"No raw data found at {level_0} or {level_1} or {level_2}")