Add OME-Arrow demonstration notebook

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.21.0"
+    rev: "v2.21.1"
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/codespell-project/codespell
@@ -50,7 +50,7 @@ repos:
     hooks:
     -   id: actionlint
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.8"
+    rev: "v0.15.10"
     hooks:
     -   id: ruff-format
     -   id: ruff-check

docs/src/examples.md

@@ -1,5 +1,8 @@
 # Examples
 
+Featured example:
+[OME Arrow and CytoDataFrame](examples/omearrow_and_cytodataframe)
+
 ```{toctree}
 ---
 caption: "List of examples"

docs/src/examples/omearrow_and_cytodataframe.py

@@ -0,0 +1,58 @@
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.17.3
+#   kernelspec:
+#     display_name: cytodataframe-shAZamSV-py3.12
+#     language: python
+#     name: python3
+# ---
+
+# # OME-Arrow and CytoDataFrame
+#
+# This notebook demonstrates how [OME-Arrow](https://github.com/WayScience/ome-arrow) works in context with CytoDataFrame.
+
+# + colab={"base_uri": "https://localhost:8080/", "height": 423} id="Y5e85t05nSLt" outputId="a0807c7c-4705-41a2-83b2-9fb7287c40f9"
+import pyarrow as pa
+import pyarrow.parquet as pq
+from ome_arrow import OMEArrow
+
+from cytodataframe import CytoDataFrame
+
+# load a tiff using OME Arrow
+oa_img = OMEArrow(
+    "../../../tests/data/cytotable/JUMP_plate_BR00117006/images/orig/r01c01f01p01-ch2sk1fk1fl1.tiff"
+)
+oa_img
+
+# + colab={"base_uri": "https://localhost:8080/", "height": 423} id="wkCpuZEBosNV" outputId="4adee883-9707-40a4-92ab-2ee748bbcf76"
+# make a "slice" (crop) from the overall image
+oa_img_slice = oa_img.slice(x_min=240, x_max=310, y_min=360, y_max=430)
+oa_img_slice
+
+# + colab={"base_uri": "https://localhost:8080/"} id="ZZ8LWIuQqQqz" outputId="f82de1df-3240-4dba-d0a0-6a4ce973f299"
+# show the OME Arrow struct
+oa_img_slice.data
+
+# + colab={"base_uri": "https://localhost:8080/", "height": 1000} id="zcaDHeNorxCt" outputId="e64c061b-c56e-462b-dfe0-c73de76df0d3"
+# create a pyarrow table for writing the data
+table = pa.table(
+    {
+        # two columns, two values each, both int64 type
+        "metadata_1": pa.array([0, 2], type=pa.int64()),
+        "feature_1": pa.array([1, 2], type=pa.int64()),
+        # add an image column with repeated entries based on the image slice
+        "image": pa.repeat(oa_img_slice.data, 2),
+    }
+)
+
+# write a parquet table
+pq.write_table(table, "example.ome.parquet")
+
+# read the parquet table with cytodataframe
+# (showing the OME-Arrow image that was written)
+CytoDataFrame("example.ome.parquet")

pyproject.toml

@@ -110,12 +110,16 @@ lint.select = [
 ]
 # Ignore `E402` and `F401` (unused imports) in all `__init__.py` files
 lint.per-file-ignores."__init__.py" = [ "E402", "F401" ]
-lint.per-file-ignores."docs/src/examples/cytodataframe_at_a_glance.py" = [ "E402" ]
+lint.per-file-ignores."docs/src/examples/*.py" = [ "E402", "E501" ]
 lint.per-file-ignores."src/cytodataframe/*.py" = [ "ANN401", "PLC0415" ]
 lint.per-file-ignores."src/cytodataframe/image.py" = [ "PLR2004" ]
 # ignore typing rules for tests
 lint.per-file-ignores."tests/*" = [ "ANN201", "PLR0913", "PLR2004", "SIM105" ]
 
+# specify where version replacement is performed
+[tool.bandit]
+exclude_dirs = [ "tests" ]
+
 [tool.pytest]
 ini_options.addopts = "--cov=src/cytodataframe --cov-report=term-missing:skip-covered --no-cov-on-fail"
 
@@ -130,10 +134,6 @@ run.omit = [
 [tool.jupytext]
 formats = "ipynb,py:light"
 
-# specify where version replacement is performed
-[tool.bandit]
-exclude_dirs = [ "tests" ]
-
 [tool.poe]
 # note: quarto commands below expect quarto installed on the local system.
 # see here for more information: https://quarto.org/docs/download/