Add 3D mask visualization capabilities (#200)

* add 3d segmentation masks for test dataset

* add 3d mask visualization capabilities

* [pre-commit.ci lite] apply automatic fixes

* changes from coderabbit review

* changes based on copilot review

* linting

* add checkbox to toggle the mask when present

* add mask text label

Co-Authored-By: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

* notebook update

* notebook update

* [pre-commit.ci lite] apply automatic fixes

* fix scrolling within 2d windows

* update notebook

* linting

* readd static snapshots for 2d

* linting

* remove empty cell from notebook

* changes based on jenna's review

Co-Authored-By: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
Co-authored-by: Jenna Tomkinson <107513215+jenna-tomkinson@users.noreply.github.com>

Author: 3 people

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
     -   id: codespell
         exclude: |
@@ -50,7 +50,7 @@ repos:
     hooks:
     -   id: actionlint
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.4"
+    rev: "v0.15.5"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
@@ -76,6 +76,7 @@ repos:
     hooks:
     -   id: coverage-xml
     -   id: coverage-badge
+        stages: [manual]
         additional_dependencies:
         -   setuptools<81
         args: ["-o", "media/coverage-badge.svg"]

docs/src/examples/cytodataframe_at_a_glance.ipynb

@@ -354,3 +354,15 @@
 )
 
 cdf[["ImageNumber", "ObjectNumber", "FileName_Nuclei"]][:3]
+# +
+# %%time
+
+# read 3d images with segmentation masks and show the
+# segmentation masks are also 3D.
+cdf = CytoDataFrame(
+    data=pathlib.Path(cp_3d_path) / "output/MyExpt_RealsizeNuclei.csv",
+    data_context_dir=str(pathlib.Path(cp_3d_path) / "input"),
+    data_mask_context_dir=str(pathlib.Path(cp_3d_path) / "output/masks"),
+)
+
+cdf[["ImageNumber", "ObjectNumber", "FileName_Nuclei"]][:3]