napari-ome-arrow 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

napari_ome_arrow/_reader.py

@@ -11,6 +11,7 @@ Behavior:
 
 from __future__ import annotations
 
+import math
 import os
 import warnings
 from collections.abc import Sequence
@@ -18,7 +19,9 @@ from pathlib import Path
 from typing import Any, Union
 
 import numpy as np
+import pyarrow as pa
 from ome_arrow.core import OMEArrow
+from ome_arrow.meta import OME_ARROW_STRUCT
 
 PathLike = Union[str, Path]
 LayerData = tuple[np.ndarray, dict[str, Any], str]
@@ -170,6 +173,124 @@ def _looks_like_ome_source(path_str: str) -> bool:
     )
 
 
+# --------------------------------------------------------------------- #
+#  OME-Parquet helpers (multi-row grid)
+# --------------------------------------------------------------------- #
+
+
+def _find_ome_parquet_columns(table: pa.Table) -> list[str]:
+    """Return struct columns matching the OME-Arrow schema."""
+    import pyarrow as pa
+
+    expected_fields = {f.name for f in OME_ARROW_STRUCT}
+    names: list[str] = []
+    for name, col in zip(table.column_names, table.columns, strict=False):
+        if (
+            pa.types.is_struct(col.type)
+            and {f.name for f in col.type} == expected_fields
+        ):
+            names.append(name)
+    return names
+
+
+def _enable_grid(n_layers: int) -> None:
+    """Switch current viewer into grid view when possible."""
+    if n_layers <= 1:
+        return
+    try:
+        import napari
+
+        viewer = napari.current_viewer()
+    except Exception:
+        return
+    if viewer is None:
+        return
+
+    cols = math.ceil(math.sqrt(n_layers))
+    rows = math.ceil(n_layers / cols)
+    try:
+        viewer.grid.enabled = True
+        viewer.grid.shape = (rows, cols)
+    except Exception:
+        # grid is best-effort; ignore if unavailable
+        return
+
+
+def _read_parquet_rows(src: str, mode: str) -> list[LayerData] | None:
+    """
+    Specialized path for multi-row OME-Parquet:
+    create one layer per row and enable napari grid view.
+    """
+    s = src.lower()
+    if not (s.endswith((".ome.parquet", ".parquet", ".pq"))):
+        return None
+
+    try:
+        import pyarrow as pa
+        import pyarrow.parquet as pq
+    except Exception:
+        return None
+
+    table = pq.read_table(src)
+    ome_cols = _find_ome_parquet_columns(table)
+    if not ome_cols or table.num_rows <= 1:
+        return None
+
+    override = os.environ.get("NAPARI_OME_ARROW_PARQUET_COLUMN")
+    if override:
+        matched = [c for c in ome_cols if c.lower() == override.lower()]
+        selected = matched[0] if matched else ome_cols[0]
+        if not matched:
+            warnings.warn(
+                f"Column '{override}' not found in {Path(src).name}; using {selected!r}.",
+                stacklevel=2,
+            )
+    else:
+        selected = ome_cols[0]
+
+    column = table[selected]
+    layers: list[LayerData] = []
+
+    for idx in range(table.num_rows):
+        try:
+            record = column.slice(idx, 1).to_pylist()[0]
+            scalar = pa.scalar(record, type=OME_ARROW_STRUCT)
+            arr = OMEArrow(scalar).export(
+                how="numpy", dtype=np.uint16, strict=False
+            )
+        except Exception as e:  # pragma: no cover - warn and skip bad rows
+            warnings.warn(
+                f"Skipping row {idx} in column '{selected}': {e}",
+                stacklevel=2,
+            )
+            continue
+
+        add_kwargs: dict[str, Any] = {
+            "name": f"{Path(src).name}[{selected}][row {idx}]"
+        }
+        if mode == "image":
+            if arr.ndim >= 5:
+                add_kwargs["channel_axis"] = 1  # TCZYX
+            elif arr.ndim == 4:
+                add_kwargs["channel_axis"] = 0  # CZYX
+            layer_type = "image"
+        else:
+            if arr.ndim == 5:
+                arr = arr[:, 0, ...]
+            elif arr.ndim == 4:
+                arr = arr[0, ...]
+            arr = _as_labels(arr)
+            add_kwargs.setdefault("opacity", 0.7)
+            layer_type = "labels"
+
+        _maybe_set_viewer_3d(arr)
+        layers.append((arr, add_kwargs, layer_type))
+
+    if layers:
+        _enable_grid(len(layers))
+    return layers or None
+
+
 # --------------------------------------------------------------------- #
 #  napari entry point: napari_get_reader
 # --------------------------------------------------------------------- #
@@ -319,6 +440,10 @@ def reader_function(
 
     for src in paths:
         try:
+            parquet_layers = _read_parquet_rows(src, mode)
+            if parquet_layers is not None:
+                layers.extend(parquet_layers)
+                continue
             layers.append(_read_one(src, mode=mode))
         except Exception as e:
             warnings.warn(

napari_ome_arrow/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.2'
-__version_tuple__ = version_tuple = (0, 0, 2)
+__version__ = version = '0.0.4'
+__version_tuple__ = version_tuple = (0, 0, 4)
 
 __commit_id__ = commit_id = None

{napari_ome_arrow-0.0.2.dist-info → napari_ome_arrow-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-ome-arrow
-Version: 0.0.2
+Version: 0.0.4
 Summary: A Napari plugin for OME-Arrow and OME-Parquet bioimage data
 License: 
         Copyright (c) 2025, Dave Bunten
@@ -74,6 +74,7 @@ Dynamic: license-file
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-ome-arrow.svg?color=green)](https://python.org)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ome-arrow)](https://napari-hub.org/plugins/napari-ome-arrow)
 [![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17613571.svg)](https://doi.org/10.5281/zenodo.17613571)
 
 `napari-ome-arrow` is a minimal plugin for [napari](https://napari.org) that opens image data through the [OME-Arrow](https://github.com/wayscience/ome-arrow) toolkit.
 
@@ -126,6 +127,9 @@ It provides a single, explicit pathway for loading OME-style bioimage data:
   - respects `NAPARI_OME_ARROW_LAYER_TYPE`, and
   - defaults to `"image"` if the variable is not set.
 
+- ✅ **Grid view for multi-row OME-Parquet**
+  When a Parquet file contains multiple OME-Arrow rows, each row is loaded as its own layer and the viewer is switched to napari’s grid mode. Set `NAPARI_OME_ARROW_PARQUET_COLUMN` to pick which image column to visualize.
+
 ______________________________________________________________________
 
 This [napari] plugin was generated with [copier] using the [napari-plugin-template] (None).
@@ -175,6 +179,11 @@ NAPARI_OME_ARROW_LAYER_TYPE=image napari my_data.ome.tif
 
 # Load as labels (segmentation)
 NAPARI_OME_ARROW_LAYER_TYPE=labels napari my_labels.ome.parquet
+
+# Pick a specific column in a multi-row OME-Parquet and show in grid mode
+NAPARI_OME_ARROW_LAYER_TYPE=image \\
+NAPARI_OME_ARROW_PARQUET_COLUMN=Image_FileName_OrigDNA_OMEArrow_ORIG \\
+napari tests/data/cytodataframe/BR00117006.ome.parquet
 ```
 
 ## Contributing

napari_ome_arrow-0.0.4.dist-info/RECORD

@@ -0,0 +1,10 @@
+napari_ome_arrow/__init__.py,sha256=hfpJMmD3HYHJH-0lh-esO04Pe57u8YbK4OO_qcx1b8o,236
+napari_ome_arrow/_reader.py,sha256=JobcKfWGscMonX9u7cu_SdZtZL_Hbcj8-Uu1whuFe0o,14230
+napari_ome_arrow/_version.py,sha256=QlXZ5JTjE_pgpDaeHk0GTExkc75xUZFmd0hA7kGYCJ0,704
+napari_ome_arrow/napari.yaml,sha256=L64Y_YyvIlkOBgP2b8HciimyE3xmzfo9ASj5o-wu9gI,567
+napari_ome_arrow-0.0.4.dist-info/licenses/LICENSE,sha256=RuLVTR9eFL6OX1phw5Ue8tdGrhgoG9ZErP6QrxrUlaE,1486
+napari_ome_arrow-0.0.4.dist-info/METADATA,sha256=WC_VSHA8ZJ102297ls1_rQQThkhLbo97AcruYpPKZpU,8719
+napari_ome_arrow-0.0.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napari_ome_arrow-0.0.4.dist-info/entry_points.txt,sha256=ZNpIZF-jrixFQlUNA1kR_jCBsBDxvoIrmc_lrQqu8VE,66
+napari_ome_arrow-0.0.4.dist-info/top_level.txt,sha256=IRsRRK6uFbyipfWh77Br3G4_6uvSYp8CL01RjMN6Mzk,17
+napari_ome_arrow-0.0.4.dist-info/RECORD,,

napari_ome_arrow-0.0.2.dist-info/RECORD

@@ -1,10 +0,0 @@
-napari_ome_arrow/__init__.py,sha256=hfpJMmD3HYHJH-0lh-esO04Pe57u8YbK4OO_qcx1b8o,236
-napari_ome_arrow/_reader.py,sha256=98vYiA5zK19sLCywWRKXJESmd3DbULIvpDJeiIg7raA,10398
-napari_ome_arrow/_version.py,sha256=huLsL1iGeXWQKZ8bjwDdIWC7JOkj3wnzBh-HFMZl1PY,704
-napari_ome_arrow/napari.yaml,sha256=L64Y_YyvIlkOBgP2b8HciimyE3xmzfo9ASj5o-wu9gI,567
-napari_ome_arrow-0.0.2.dist-info/licenses/LICENSE,sha256=RuLVTR9eFL6OX1phw5Ue8tdGrhgoG9ZErP6QrxrUlaE,1486
-napari_ome_arrow-0.0.2.dist-info/METADATA,sha256=3WRgK92QSCD5CT0k4FcY9bcRtCqm09QZdwZ1A_zWE-E,8087
-napari_ome_arrow-0.0.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napari_ome_arrow-0.0.2.dist-info/entry_points.txt,sha256=ZNpIZF-jrixFQlUNA1kR_jCBsBDxvoIrmc_lrQqu8VE,66
-napari_ome_arrow-0.0.2.dist-info/top_level.txt,sha256=IRsRRK6uFbyipfWh77Br3G4_6uvSYp8CL01RjMN6Mzk,17
-napari_ome_arrow-0.0.2.dist-info/RECORD,,