ome-arrow 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

ome_arrow/meta.py

@@ -12,8 +12,10 @@ OME_ARROW_TAG_VERSION = ome_arrow_version
 # OME_ARROW_STRUCT: ome-arrow record (describes one image/value).
 #  - type/version: quick identity & evolution.
 #  - id/name/acquisition_datetime: identity & provenance.
+#  - image_type: open-ended image kind (e.g., "image", "label").
 #  - pixels_meta: pixels struct (sizes, units, channels).
 #  - planes: list of planes struct entries, one per (t,c,z).
+#  - chunk_grid/chunks: optional chunked pixels (TCZYX-aware), stored as Arrow lists.
 #  - masks: reserved for future labels/ROIs (placeholder).
 OME_ARROW_STRUCT: pa.StructType = pa.struct(
     [
@@ -21,6 +23,7 @@ OME_ARROW_STRUCT: pa.StructType = pa.struct(
         pa.field("version", pa.string()),  # e.g., "1.0.0"
         pa.field("id", pa.string()),  # stable image identifier
         pa.field("name", pa.string()),  # human label
+        pa.field("image_type", pa.string()),  # open-ended (e.g., "image", "label")
         pa.field("acquisition_datetime", pa.timestamp("us")),
         # PIXELS: OME-like "Pixels" header summarizing shape & scale.
         #  - dimension_order: hint like "XYZCT" (or "XYCT" when Z==1).
@@ -68,6 +71,44 @@ OME_ARROW_STRUCT: pa.StructType = pa.struct(
                 ]
             ),
         ),
+        # CHUNK GRID: optional chunking metadata for random access.
+        #  - order: axis order for the full array, e.g., "TCZYX".
+        #  - chunk_*: chunk sizes for each axis (defaults to 1 for T/C).
+        #  - chunk_order: order used to flatten chunk pixels (default "ZYX").
+        pa.field(
+            "chunk_grid",
+            pa.struct(
+                [
+                    pa.field("order", pa.string()),
+                    pa.field("chunk_t", pa.int32()),
+                    pa.field("chunk_c", pa.int16()),
+                    pa.field("chunk_z", pa.int32()),
+                    pa.field("chunk_y", pa.int32()),
+                    pa.field("chunk_x", pa.int32()),
+                    pa.field("chunk_order", pa.string()),
+                ]
+            ),
+        ),
+        # CHUNKS: list of chunk entries (Arrow-native, no binary payloads).
+        #  - pixels flattened in chunk_order (default "ZYX").
+        pa.field(
+            "chunks",
+            pa.list_(
+                pa.struct(
+                    [
+                        pa.field("t", pa.int32()),
+                        pa.field("c", pa.int16()),
+                        pa.field("z", pa.int32()),
+                        pa.field("y", pa.int32()),
+                        pa.field("x", pa.int32()),
+                        pa.field("shape_z", pa.int32()),
+                        pa.field("shape_y", pa.int32()),
+                        pa.field("shape_x", pa.int32()),
+                        pa.field("pixels", pa.list_(pa.uint16())),
+                    ]
+                )
+            ),
+        ),
         # PLANES: one 2D image plane for a specific (t, c, z).
         #  - pixels: flattened numeric list (Y*X) for analysis-ready computation.
         pa.field(

ome_arrow/transform.py

@@ -8,6 +8,7 @@ from typing import Any, Dict, Iterable, List, Optional, Tuple
 import numpy as np
 import pyarrow as pa
 
+from ome_arrow.ingest import _build_chunks_from_planes, _normalize_chunk_shape
 from ome_arrow.meta import OME_ARROW_STRUCT
 
 
@@ -179,4 +180,37 @@ def slice_ome_arrow(
     rec_out["pixels_meta"] = pm_out
     rec_out["planes"] = planes_out
 
+    chunk_grid_in = row.get("chunk_grid") or {}
+    if chunk_grid_in or row.get("chunks"):
+        chunk_shape = (
+            int(chunk_grid_in.get("chunk_z", 1)),
+            int(chunk_grid_in.get("chunk_y", 512)),
+            int(chunk_grid_in.get("chunk_x", 512)),
+        )
+        chunk_order = str(chunk_grid_in.get("chunk_order") or "ZYX")
+        chunks_out = _build_chunks_from_planes(
+            planes=planes_out,
+            size_t=new_st,
+            size_c=new_sc,
+            size_z=new_sz,
+            size_y=new_sy,
+            size_x=new_sx,
+            chunk_shape=chunk_shape,
+            chunk_order=chunk_order,
+        )
+        cz, cy, cx = _normalize_chunk_shape(chunk_shape, new_sz, new_sy, new_sx)
+        rec_out["chunk_grid"] = {
+            "order": "TCZYX",
+            "chunk_t": 1,
+            "chunk_c": 1,
+            "chunk_z": cz,
+            "chunk_y": cy,
+            "chunk_x": cx,
+            "chunk_order": chunk_order,
+        }
+        rec_out["chunks"] = chunks_out
+    else:
+        rec_out["chunk_grid"] = row.get("chunk_grid")
+        rec_out["chunks"] = row.get("chunks")
+
     return pa.scalar(rec_out, type=OME_ARROW_STRUCT)

ome_arrow/view.py

@@ -23,6 +23,8 @@ except ImportError:  # pragma: no cover - exercised when viz extra missing
 if TYPE_CHECKING:
     import pyvista
 
+from ome_arrow.export import plane_from_chunks
+
 
 def view_matplotlib(
     data: dict[str, object] | pa.StructScalar,
@@ -33,29 +35,25 @@ def view_matplotlib(
     cmap: str = "gray",
     show: bool = True,
 ) -> tuple[Figure, Axes, AxesImage]:
-    if isinstance(data, pa.StructScalar):
-        data = data.as_py()
-
-    pm = data["pixels_meta"]
-    sx, sy = int(pm["size_x"]), int(pm["size_y"])
+    """Render a single (t, c, z) plane with Matplotlib.
+
+    Args:
+        data: OME-Arrow row or dict containing pixels_meta and planes.
+        tcz: (t, c, z) indices of the plane to render.
+        autoscale: If True, infer vmin/vmax from the image data.
+        vmin: Explicit lower display limit for intensity scaling.
+        vmax: Explicit upper display limit for intensity scaling.
+        cmap: Matplotlib colormap name.
+        show: Whether to display the plot immediately.
+
+    Returns:
+        A tuple of (figure, axes, image) from Matplotlib.
+
+    Raises:
+        ValueError: If the requested plane is missing or pixel sizes mismatch.
+    """
     t, c, z = (int(x) for x in tcz)
-
-    plane = next(
-        (
-            p
-            for p in data["planes"]
-            if int(p["t"]) == t and int(p["c"]) == c and int(p["z"]) == z
-        ),
-        None,
-    )
-    if plane is None:
-        raise ValueError(f"plane (t={t}, c={c}, z={z}) not found")
-
-    pix = plane["pixels"]
-    if len(pix) != sx * sy:
-        raise ValueError(f"pixels len {len(pix)} != size_x*size_y ({sx * sy})")
-
-    img = np.asarray(pix, dtype=np.uint16).reshape(sy, sx).copy()
+    img = plane_from_chunks(data, t=t, c=c, z=z, dtype=np.uint16).copy()
 
     if (vmin is None or vmax is None) and autoscale:
         lo, hi = int(img.min()), int(img.max())

{ome_arrow-0.0.4.dist-info → ome_arrow-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ome-arrow
-Version: 0.0.4
+Version: 0.0.6
 Summary: Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
 Author: Dave Bunten
 Classifier: Programming Language :: Python :: 3 :: Only
@@ -28,9 +28,11 @@ Requires-Dist: pyvista>=0.46.4; extra == "viz"
 Requires-Dist: trame>=3.12; extra == "viz"
 Requires-Dist: trame-vtk>=2.10; extra == "viz"
 Requires-Dist: trame-vuetify>=3.1; extra == "viz"
+Provides-Extra: vortex
+Requires-Dist: vortex-data>=0.56; extra == "vortex"
 Dynamic: license-file
 
-<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
+<img width="600" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
 
 ![PyPI - Version](https://img.shields.io/pypi/v/ome-arrow)
 [![Build Status](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml?query=branch%3Amain)
@@ -104,6 +106,9 @@ oa_image.view(how="pyvista")
 # Export to OME-Parquet.
 # We can also export OME-TIFF, OME-Zarr or NumPy arrays.
 oa_image.export(how="ome-parquet", out="your_image.ome.parquet")
+
+# Export to Vortex (install extras: `pip install 'ome-arrow[vortex]'`).
+oa_image.export(how="vortex", out="your_image.vortex")
 ```
 
 ## Contributing, Development, and Testing

ome_arrow-0.0.6.dist-info/RECORD

@@ -0,0 +1,14 @@
+ome_arrow/__init__.py,sha256=WWenJP9XxLZNGQPVOEFBDlDM1kSvj_QdHssrET6UuNQ,644
+ome_arrow/_version.py,sha256=7MyqQ3iPP2mJruPfRYGCNCq1z7_Nk7c-eyYecYITxsY,704
+ome_arrow/core.py,sha256=K1-jfojhqYkn3h-0AdmBQYFza0wtFqduJs6K7aw4Kuc,21303
+ome_arrow/export.py,sha256=XbKVIeMLbPshgo_OGO3e0PRqtZ3vEx_JAGyF9oUmZJw,26024
+ome_arrow/ingest.py,sha256=CptjVXXL8YzfHKlKqyoA-ani5SLbFlQSUVPqOXlPhXA,46931
+ome_arrow/meta.py,sha256=peIx6NLriaFpGBx9Y3NyTHLfGAg91v9YQpoBzrveKFQ,6031
+ome_arrow/transform.py,sha256=X3gKZkgTDNQSBcU3_YmJRav8JIBrDdYJci3PbFZ4t38,7200
+ome_arrow/utils.py,sha256=XHovcqmjqoiBpKvXY47-_yUwf07f8zVE_F9BR_VKaPU,2383
+ome_arrow/view.py,sha256=j9dpmSnVbiukwH6asFhCJ_WVRxwyCAdTeLiUnv_xvcE,10187
+ome_arrow-0.0.6.dist-info/licenses/LICENSE,sha256=9-2Pyhu3vTt2RJU8DorHQtHeNO_e5RLeFJTyOU4hOi4,1508
+ome_arrow-0.0.6.dist-info/METADATA,sha256=VWirz2ueYrPLOrsNj1EC2BGcsPtLpJU6Jay_NW_irZ8,6110
+ome_arrow-0.0.6.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+ome_arrow-0.0.6.dist-info/top_level.txt,sha256=aWOtkGXo_pfU-yy82guzGhz8Zh2h2nFl8Kc5qdzMGuE,10
+ome_arrow-0.0.6.dist-info/RECORD,,

{ome_arrow-0.0.4.dist-info → ome_arrow-0.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

ome_arrow-0.0.4.dist-info/RECORD

@@ -1,14 +0,0 @@
-ome_arrow/__init__.py,sha256=DfQsw8l0mx1Qt3YiiMv2SUljKETP3wS5hrD5eBbjMDM,583
-ome_arrow/_version.py,sha256=QlXZ5JTjE_pgpDaeHk0GTExkc75xUZFmd0hA7kGYCJ0,704
-ome_arrow/core.py,sha256=pTKmzKFXF5d4nSJpXQxlS71UA23P7TLHrX2eA0IxgUg,18594
-ome_arrow/export.py,sha256=CCTnEdHko4Z0i5LEHuNGFLznWSsPyAFcS42H5nHU22Q,14875
-ome_arrow/ingest.py,sha256=7N-M_NYOskHjs59Yhd4j8QXnKC5ykBXM7cT9Ap2chz8,32032
-ome_arrow/meta.py,sha256=qeD0e_ItAQyZDT7ypkBU0rBh9oHIu2ziz9MCfPpPp9g,4199
-ome_arrow/transform.py,sha256=0275_Mn1mlGXSWJ86llch8JoJyvqEOfvG-ub1dUWFNI,5997
-ome_arrow/utils.py,sha256=XHovcqmjqoiBpKvXY47-_yUwf07f8zVE_F9BR_VKaPU,2383
-ome_arrow/view.py,sha256=O4sIF8CZ4if-tV-rr2-yyG8WB5jHN9jq8HKvS-Ielnw,10034
-ome_arrow-0.0.4.dist-info/licenses/LICENSE,sha256=9-2Pyhu3vTt2RJU8DorHQtHeNO_e5RLeFJTyOU4hOi4,1508
-ome_arrow-0.0.4.dist-info/METADATA,sha256=2al9lOlUBjuximxy-1L9TsbVkFC46o0_zR3T1EnFRtU,5908
-ome_arrow-0.0.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-ome_arrow-0.0.4.dist-info/top_level.txt,sha256=aWOtkGXo_pfU-yy82guzGhz8Zh2h2nFl8Kc5qdzMGuE,10
-ome_arrow-0.0.4.dist-info/RECORD,,