napari-ome-arrow 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

napari_ome_arrow/_reader_types.py

@@ -0,0 +1,11 @@
+"""Shared reader type aliases."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any, Union
+
+import numpy as np
+
+PathLike = Union[str, Path]
+LayerData = tuple[np.ndarray, dict[str, Any], str]

napari_ome_arrow/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.3'
-__version_tuple__ = version_tuple = (0, 0, 3)
+__version__ = version = '0.0.5'
+__version_tuple__ = version_tuple = (0, 0, 5)
 
 __commit_id__ = commit_id = None

napari_ome_arrow/napari.yaml

@@ -12,6 +12,9 @@ contributions:
         - "*.ome.parquet"
         - "*.parquet"
         - "*.pq"
+        # OME-Vortex
+        - "*.ome.vortex"
+        - "*.vortex"
         # OME-TIFF
         - "*.ome.tif"
         - "*.ome.tiff"

{napari_ome_arrow-0.0.3.dist-info → napari_ome_arrow-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-ome-arrow
-Version: 0.0.3
+Version: 0.0.5
 Summary: A Napari plugin for OME-Arrow and OME-Parquet bioimage data
 License: 
         Copyright (c) 2025, Dave Bunten
@@ -51,7 +51,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: magicgui
 Requires-Dist: numpy
-Requires-Dist: ome-arrow>=0.0.2
+Requires-Dist: ome-arrow>=0.0.3
 Requires-Dist: qtpy>=2.4
 Requires-Dist: scikit-image
 Provides-Extra: all
@@ -65,6 +65,8 @@ Provides-Extra: pyside6
 Requires-Dist: napari[pyside6]; extra == "pyside6"
 Requires-Dist: pyside6>=6.6; extra == "pyside6"
 Requires-Dist: qtpy>=2.4; extra == "pyside6"
+Provides-Extra: vortex
+Requires-Dist: vortex-data; extra == "vortex"
 Dynamic: license-file
 
 # napari-ome-arrow
@@ -74,6 +76,7 @@ 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.
 
@@ -82,6 +85,7 @@ It provides a single, explicit pathway for loading OME-style bioimage data:
 - **OME-TIFF** (`.ome.tif`, `.ome.tiff`, `.tif`, `.tiff`)
 - **OME-Zarr** (`.ome.zarr`, `.zarr` stores and URLs)
 - **OME-Parquet** (`.ome.parquet`, `.parquet`, `.pq`)
+- **OME-Vortex** (`.ome.vortex`, `.vortex`)
 - **Bio-Formats–style stack patterns** (paths containing `<`, `>`, or `*`)
 - A simple **`.npy` fallback** for quick testing / ad-hoc arrays
 
@@ -126,8 +130,11 @@ 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.
+- ✅ **Grid view for multi-row OME-Parquet / OME-Vortex**
+  When a Parquet or Vortex 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` or `NAPARI_OME_ARROW_VORTEX_COLUMN` to pick which image column to visualize.
+
+- ✅ **Stack scale prompt + override**
+  When loading image stacks (stack patterns), napari prompts for voxel spacing only if no scale metadata or `NAPARI_OME_ARROW_STACK_SCALE` override is present and a Qt UI is available (headless runs skip the prompt). To avoid the prompt, set `NAPARI_OME_ARROW_STACK_SCALE` using `Z,Y,X` or `T,C,Z,Y,X`.
 
 ______________________________________________________________________
 
@@ -153,13 +160,19 @@ To install latest development version :
 pip install git+https://github.com/wayscience/napari-ome-arrow.git
 ```
 
+To enable OME-Vortex support via OME-Arrow, install the optional extra:
+
+```bash
+pip install "napari-ome-arrow[vortex]"
+```
+
 ## Usage
 
 ### From the napari GUI
 
 1. Install the plugin (see above).
 1. Start napari.
-1. Drag and drop an OME-TIFF, OME-Zarr, OME-Parquet file, or stack pattern into the viewer.
+1. Drag and drop an OME-TIFF, OME-Zarr, OME-Parquet, OME-Vortex file, a stack pattern, or a multi-select stack (e.g. `img_000.tif` ... `img_123.tif`) into the viewer.
 1. When prompted, choose **Image** or **Labels**.
 
 The plugin will:
@@ -167,6 +180,7 @@ The plugin will:
 - load the data through `OMEArrow`,
 - map channels and axes appropriately, and
 - automatically switch to 3D if there is a Z-stack.
+- When multiple files look like a numbered stack, treat them as a single stack rather than independent layers.
 
 ### From the command line
 
@@ -183,6 +197,12 @@ NAPARI_OME_ARROW_LAYER_TYPE=labels napari my_labels.ome.parquet
 NAPARI_OME_ARROW_LAYER_TYPE=image \\
 NAPARI_OME_ARROW_PARQUET_COLUMN=Image_FileName_OrigDNA_OMEArrow_ORIG \\
 napari tests/data/cytodataframe/BR00117006.ome.parquet
+
+# Prefill stack voxel spacing for stack patterns (Z,Y,X or T,C,Z,Y,X)
+NAPARI_OME_ARROW_STACK_SCALE=1.0,0.108,0.108 napari "stack/z<000-120>.tif"
+
+# Prefill stack voxel spacing for multi-file stacks (use a pattern or glob on CLI)
+NAPARI_OME_ARROW_STACK_SCALE=1.0,0.108,0.108 napari "stack/img_<000-120>.tif"
 ```
 
 ## Contributing

napari_ome_arrow-0.0.5.dist-info/RECORD

@@ -0,0 +1,15 @@
+napari_ome_arrow/__init__.py,sha256=hfpJMmD3HYHJH-0lh-esO04Pe57u8YbK4OO_qcx1b8o,236
+napari_ome_arrow/_reader.py,sha256=jOWj5w8GZyp7oiCPRf3mJ7l_pNgbAzqcz8kec4b-z4k,11894
+napari_ome_arrow/_reader_infer.py,sha256=fp4n7MQoys3rl37lTZU1RJBLj8bHxw1O9D9SC4oj8OQ,6303
+napari_ome_arrow/_reader_napari.py,sha256=mf29u86pUrYDfayLKJrAi2X-9RnrpLrh7iaVnOizS2s,2696
+napari_ome_arrow/_reader_omearrow.py,sha256=DC9hHyv0o49HcYO3jEsHCdxEo3AWNoKep4sEXxfPtHM,14913
+napari_ome_arrow/_reader_stack.py,sha256=uZ46tZ4A68TKupN5RPvYLgEFmY0tCi1ZZu59X8QkTqY,22945
+napari_ome_arrow/_reader_types.py,sha256=FUWVUb2oKP9PiC9WZDnyi5LQTli2LgeEfyBdWA2_Crg,226
+napari_ome_arrow/_version.py,sha256=YRV1ohn6CdKEhsUOmFFMmr5UTjMv4Ydw3WJGxF2BHBs,704
+napari_ome_arrow/napari.yaml,sha256=LO5bEgu2lp2X0GwfSdQfFcfDgvGuXDcibhniDbrKxFE,634
+napari_ome_arrow-0.0.5.dist-info/licenses/LICENSE,sha256=RuLVTR9eFL6OX1phw5Ue8tdGrhgoG9ZErP6QrxrUlaE,1486
+napari_ome_arrow-0.0.5.dist-info/METADATA,sha256=2R29BjUisN1JZts2HUiNGoZx5LYXo4rLQDhITHRJbDM,9854
+napari_ome_arrow-0.0.5.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+napari_ome_arrow-0.0.5.dist-info/entry_points.txt,sha256=ZNpIZF-jrixFQlUNA1kR_jCBsBDxvoIrmc_lrQqu8VE,66
+napari_ome_arrow-0.0.5.dist-info/top_level.txt,sha256=IRsRRK6uFbyipfWh77Br3G4_6uvSYp8CL01RjMN6Mzk,17
+napari_ome_arrow-0.0.5.dist-info/RECORD,,

{napari_ome_arrow-0.0.3.dist-info → napari_ome_arrow-0.0.5.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
 

napari_ome_arrow-0.0.3.dist-info/RECORD

@@ -1,10 +0,0 @@
-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=pBZsQt6tlL02W-ri--X_4JCubpAK7jjCSnOmUp_isjc,704
-napari_ome_arrow/napari.yaml,sha256=L64Y_YyvIlkOBgP2b8HciimyE3xmzfo9ASj5o-wu9gI,567
-napari_ome_arrow-0.0.3.dist-info/licenses/LICENSE,sha256=RuLVTR9eFL6OX1phw5Ue8tdGrhgoG9ZErP6QrxrUlaE,1486
-napari_ome_arrow-0.0.3.dist-info/METADATA,sha256=ABKwECGALgq03J4rmVonPtxUoP_EUxrkySZ7PIjgR6I,8596
-napari_ome_arrow-0.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napari_ome_arrow-0.0.3.dist-info/entry_points.txt,sha256=ZNpIZF-jrixFQlUNA1kR_jCBsBDxvoIrmc_lrQqu8VE,66
-napari_ome_arrow-0.0.3.dist-info/top_level.txt,sha256=IRsRRK6uFbyipfWh77Br3G4_6uvSYp8CL01RjMN6Mzk,17
-napari_ome_arrow-0.0.3.dist-info/RECORD,,