feat: new, safe, documented PrecomputedInfoSpec

.coveragerc

@@ -6,8 +6,9 @@ omit =
   zetta_utils/mazepa_layer_processing/**/*.py
   zetta_utils/tensor_mapping/*.py
   zetta_utils/tensor_mapping/**/*.py
-  zetta_utils/convnet/architecture/deprecated/*.py
-  zetta_utils/convnet/architecture/deprecated/**/*.py
+  zetta_utils/**/deprecated.py
+  zetta_utils/**/deprecated/*.py
+  zetta_utils/**/deprecated/**/*.py
   zetta_utils/viz/*.py
   zetta_utils/viz/**/*.py
   zetta_utils/internal/*.py

docs/source/subchunkable_apply_flow_quick_start_guide.rst

@@ -196,7 +196,7 @@ Precomputed volumes require an *infofile* that contains information about things
 
 .. collapse:: infofiles in zetta_utils
 
-   In ``zetta_utils``, infofiles are handled by ``zetta_utils.layer.volumetric.precomputed`` module, which is used by ``zetta_utils.layer.volumetric.cloudvol`` and ``zetta_utils.layer.volumetric.tensorstore`` (both instances of ``VolumetricBackend``). While changing the contents of the infofiles within Python (rather than passing in arguments into `build_cv_layer`) is outside the scope of this guide and is something that you shouldn't need to do, here is the example code for reading the content (with ``cvl`` as before):
+   In ``zetta_utils``, infofiles are handled by ``zetta_utils.layer.precomputed`` module, which is used by ``zetta_utils.layer.volumetric.cloudvol`` and ``zetta_utils.layer.volumetric.tensorstore`` (both instances of ``VolumetricBackend``). While changing the contents of the infofiles within Python (rather than passing in arguments into `build_cv_layer`) is outside the scope of this guide and is something that you shouldn't need to do, here is the example code for reading the content (with ``cvl`` as before):
 
      >>> cvl.backend.get_bounds(Vec3D(4, 4, 40)) # get bound at resolution
      VolumetricIndex(resolution=Vec3D(4, 4, 40), bbox=BBox3D(bounds=((0, 1048576), (0, 524288), (0, 282560)), unit='nm', pprint_px_resolution=(1, 1, 1)), chunk_id=0, allow_slice_rounding=False)

scripts/assign_synapses.py

@@ -31,9 +31,9 @@
 
 import zetta_utils.tensor_ops.convert as convert
 from zetta_utils.geometry import BBox3D, Vec3D
+from zetta_utils.layer.precomputed import PrecomputedInfoSpec, PrecomputedVolumeDType
 from zetta_utils.layer.volumetric import VolumetricIndex, VolumetricLayer
 from zetta_utils.layer.volumetric.cloudvol import build_cv_layer
-from zetta_utils.layer.volumetric.precomputed import PrecomputedInfoSpec
 
 # Configuration
 resolution = Vec3D(8, 8, 42)  # working resolution
@@ -56,28 +56,20 @@ def make_layer(
     bbox: BBox3D,
     resolution: Vec3D,
     path: str,
-    data_type: str = "int32",
+    data_type: PrecomputedVolumeDType = "int32",
     chunk_sizes: Sequence[Sequence[int]] = [[256, 256, 32]],
 ) -> VolumetricLayer:
     return build_cv_layer(
         path=path,
         on_info_exists="overwrite",
         index_resolution=resolution,
-        info_field_overrides={
-            "type": "image",
-            "data_type": data_type,
-            "num_channels": 1,
-            "scales": [
-                {
-                    "encoding": "raw",
-                    "resolution": list(resolution),
-                    "size": list(bbox.shape),
-                    "chunk_sizes": chunk_sizes,
-                    "voxel_offset": list(bbox.start),
-                    "key": "_".join(str(i) for i in resolution),
-                }
-            ],
-        },
+        info_type="image",
+        info_data_type=data_type,
+        info_num_channels=1,
+        info_encoding="raw",
+        info_scales=[resolution],
+        info_chunk_size=chunk_sizes[0],
+        info_bbox=bbox,
         cv_kwargs={"non_aligned_writes": True},
     )
 
@@ -87,7 +79,7 @@ def load_volume(path: str, scale_index: int = 0) -> Tuple[VolumetricLayer, BBox3
     Load a CloudVolume given the path, and optionally, which scale (resolution) is desired.
     Return the CloudVolume, and a BBox3D describing the data bounds.
     """
-    spec = PrecomputedInfoSpec(reference_path=path)
+    spec = PrecomputedInfoSpec(info_path=path)
     info = spec.make_info()
     assert info is not None
     scale = info["scales"][scale_index]

scripts/find_contacts.py

@@ -17,7 +17,7 @@
 from zetta_utils.geometry import BBox3D, Vec3D
 from zetta_utils.layer.volumetric import VolumetricIndex, VolumetricLayer
 from zetta_utils.layer.volumetric.cloudvol import build_cv_layer
-from zetta_utils.layer.volumetric.precomputed import PrecomputedInfoSpec
+from zetta_utils.layer.volumetric.deprecated import PrecomputedInfoSpec
 
 client: CAVEclient
 
@@ -290,24 +290,14 @@ def find_contact_clusters(cell_ids, cell1, cell2, n=2):
     data_resolution=resolution,
     allow_slice_rounding=True,
     interpolation_mode="segmentation",
-    info_voxel_offset=volume_index.start,
-    info_dataset_size=volume_index.shape,
-    info_chunk_size=[128, 128, 40],
+    info_type="segmentation",
+    info_data_type="int32",
+    info_num_channels=1,
     on_info_exists="overwrite",
-    info_add_scales_ref={
-        "chunk_sizes": [128, 128, 40],
-        "encoding": "raw",
-        "resolution": resolution,
-        "size": volume_index.shape,
-        "voxel_offset": volume_index.start,
-    },
-    info_add_scales=[resolution],
-    # info_add_scales_mode = 'replace',
-    info_field_overrides={
-        "type": "segmentation",
-        "data_type": "int32",
-        "num_channels": 1,
-    },
+    info_scales=[resolution],
+    info_encoding="raw",
+    info_chunk_size=[128, 128, 40],
+    info_bbox=volume_index.bbox,
 )
 enable_stdout()
 shape = (1, *volume_index.shape)