napari-ome-arrow 0.0.2__tar.gz → 0.0.3__tar.gz

{napari_ome_arrow-0.0.2 → napari_ome_arrow-0.0.3}/.github/workflows/publish-pypi.yml

@@ -16,7 +16,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Fetch tags

{napari_ome_arrow-0.0.2 → napari_ome_arrow-0.0.3}/.github/workflows/run-tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       # checks out the repo
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       # run pre-commit
       - name: Python setup
         uses: actions/setup-python@v6
@@ -40,7 +40,7 @@ jobs:
       OS: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Python setup
         uses: actions/setup-python@v6
         with:

{napari_ome_arrow-0.0.2 → napari_ome_arrow-0.0.3}/.pre-commit-config.yaml

@@ -39,12 +39,12 @@ repos:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.14.5"
+    rev: "v0.14.7"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.8
+    rev: v1.7.9
     hooks:
     -   id: actionlint
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update

{napari_ome_arrow-0.0.2 → napari_ome_arrow-0.0.3}/CITATION.cff

@@ -60,3 +60,68 @@ references:
       - description: "OME Model Documentation — OME-TIFF Sample Data"
         type: url
         value: "https://ome-model.readthedocs.io/en/stable/ome-tiff/data.html"
+  - authors:
+      - family-names: Chandrasekaran
+        given-names: Srinivas Niranj
+      - family-names: Cimini
+        given-names: Beth A.
+      - family-names: Goodale
+        given-names: Amy
+      - family-names: Miller
+        given-names: Lisa
+      - family-names: Kost-Alimova
+        given-names: Maria
+      - family-names: Jamali
+        given-names: Nasim
+      - family-names: Doench
+        given-names: John G.
+      - family-names: Fritchman
+        given-names: Briana
+      - family-names: Skepner
+        given-names: Adam
+      - family-names: Melanson
+        given-names: Michelle
+      - family-names: Kalinin
+        given-names: Alexandr A.
+      - family-names: Arevalo
+        given-names: John
+      - family-names: Haghighi
+        given-names: Marzieh
+      - family-names: Caicedo
+        given-names: Juan C.
+      - family-names: Kuhn
+        given-names: Daniel
+      - family-names: Hernandez
+        given-names: Desiree
+      - family-names: Berstler
+        given-names: James
+      - family-names: Shafqat-Abbasi
+        given-names: Hamdah
+      - family-names: Root
+        given-names: David E.
+      - family-names: Swalley
+        given-names: Susanne E.
+      - family-names: Garg
+        given-names: Sakshi
+      - family-names: Singh
+        given-names: Shantanu
+      - family-names: Carpenter
+        given-names: Anne E.
+    date-accessed: "2024-08-21"
+    title: >-
+      Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
+    type: article
+    issn: 1548-7105
+    issue: 6
+    journal: Nature Methods
+    pages: 1114-1121
+    volume: 21
+    url: https://doi.org/10.1038/s41592-024-02241-6
+    date-published: "2024-06-01"
+    identifiers:
+      - type: doi
+        value: 10.1038/s41592-024-02241-6
+    notes: >-
+      JUMP (cpg0000-jump-pilot) was used to help demonstrate napari-ome-arrow's
+      ability to parse various image data (specifically, plate BR00117006).
+      https://github.com/broadinstitute/cellpainting-gallery

{napari_ome_arrow-0.0.2/src/napari_ome_arrow.egg-info → napari_ome_arrow-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-ome-arrow
-Version: 0.0.2
+Version: 0.0.3
 Summary: A Napari plugin for OME-Arrow and OME-Parquet bioimage data
 License: 
         Copyright (c) 2025, Dave Bunten
@@ -126,6 +126,9 @@ 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 +178,11 @@ 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-0.0.2 → napari_ome_arrow-0.0.3}/README.md

@@ -57,6 +57,9 @@ 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).
@@ -106,6 +109,11 @@ 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-0.0.2 → napari_ome_arrow-0.0.3}/src/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-0.0.2 → napari_ome_arrow-0.0.3}/src/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 = '0.0.3'
+__version_tuple__ = version_tuple = (0, 0, 3)
 
-__commit_id__ = commit_id = 'g6635efe48'
+__commit_id__ = commit_id = 'g837da2b31'

{napari_ome_arrow-0.0.2 → napari_ome_arrow-0.0.3/src/napari_ome_arrow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-ome-arrow
-Version: 0.0.2
+Version: 0.0.3
 Summary: A Napari plugin for OME-Arrow and OME-Parquet bioimage data
 License: 
         Copyright (c) 2025, Dave Bunten
@@ -126,6 +126,9 @@ 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 +178,11 @@ 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