Merge pull request #65 from janelia-cellmap/rewrite

Rewrite

Author: rhoadesScholar

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 # https://peps.python.org/pep-0621/
 [project]
 name = "cellmap-data"
-description = "Utility for loading CellMap data for machine learning training, utilizing PyTorch, Xarray, TensorStore, and PyDantic."
+description = "Utility for loading CellMap data for machine learning training, utilizing PyTorch and zarr."
 readme = "README.md"
 requires-python = ">=3.11"
 license = { text = "BSD 3-Clause License" }
@@ -28,18 +28,10 @@ dependencies = [
     "torchvision",
     "numpy",
     "matplotlib",
-    "pydantic_ome_ngff",
-    "xarray_ome_ngff",
-    "tensorstore",
-    # "xarray=2024.10.0",
-    "xarray-tensorstore==0.1.5",
+    "zarr>=2.0,<3.0",
     "universal_pathlib>=0.2.0",
     "fsspec[s3,http]",
-    "neuroglancer",
-    "h5py", # Only needed until the new cellmap-flow is released
-    # "cellmap-flow",
     "ipython",
-    # "py_distance_transforms",
     "scipy",
     "tqdm",
 ]

src/cellmap_data/__init__.py

@@ -12,8 +12,6 @@
 __author__ = "Jeff Rhoades"
 __email__ = "rhoadesj@hhmi.org"
 
-from .base_dataset import CellMapBaseDataset
-from .base_image import CellMapImageBase
 from .dataloader import CellMapDataLoader
 from .dataset import CellMapDataset
 from .dataset_writer import CellMapDatasetWriter
@@ -22,20 +20,16 @@
 from .image import CellMapImage
 from .image_writer import ImageWriter
 from .multidataset import CellMapMultiDataset
-from .mutable_sampler import MutableSubsetRandomSampler
-from .subdataset import CellMapSubset
+from .sampler import ClassBalancedSampler
 
 __all__ = [
-    "CellMapBaseDataset",
-    "CellMapImageBase",
     "CellMapDataLoader",
     "CellMapDataset",
     "CellMapDatasetWriter",
     "CellMapDataSplit",
     "CellMapImage",
     "ImageWriter",
     "CellMapMultiDataset",
-    "CellMapSubset",
     "EmptyImage",
-    "MutableSubsetRandomSampler",
+    "ClassBalancedSampler",
 ]