diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..af3b9f02
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+---
+version: 2
+updates:
+ - package-ecosystem: "github-actions"
+ directory: "/"
+ schedule:
+ interval: "monthly"
+ groups:
+ github-actions:
+ patterns:
+ - "*"
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 13ce3b85..55eb1aa2 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -10,15 +10,16 @@ on:
- main
tags:
- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+ workflow_dispatch:
jobs:
build-docs:
name: Build & Upload Artifact
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- - uses: actions/setup-python@v3
+ - uses: actions/setup-python@v5
with:
python-version: "3.10"
@@ -31,13 +32,13 @@ jobs:
sudo apt install graphviz --yes
- name: Build Docs
- uses: aganders3/headless-gui@v1
+ uses: aganders3/headless-gui@v2
with:
run: make html
working-directory: ./docs
- name: Upload artifact
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
with:
name: docs
path: docs/_build
@@ -48,8 +49,8 @@ jobs:
needs: build-docs
if: contains(github.ref, 'tags')
steps:
- - uses: actions/checkout@v3
- - uses: actions/download-artifact@v3
+ - uses: actions/checkout@v4
+ - uses: actions/download-artifact@v4.3.0
with:
name: docs
diff --git a/.github/workflows/napari_hub_preview.yml b/.github/workflows/napari_hub_preview.yml
deleted file mode 100644
index c204ac45..00000000
--- a/.github/workflows/napari_hub_preview.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-name: napari hub Preview Page # we use this name to find your preview page artifact, so don't change it!
-# For more info on this action, see https://github.com/chanzuckerberg/napari-hub-preview-action/blob/main/action.yml
-
-on:
- pull_request:
- types: [ labeled ]
-
-jobs:
- preview-page:
- if: ${{ github.event.label.name == 'napari hub preview' }}
- name: Preview Page Deploy
- runs-on: ubuntu-latest
-
- steps:
- - name: Checkout repo
- uses: actions/checkout@v3
-
- - name: napari hub Preview Page Builder
- uses: chanzuckerberg/napari-hub-preview-action@v0.1
- with:
- hub-ref: main
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index df170bdf..77853f7e 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -12,6 +12,10 @@ on:
workflow_dispatch:
merge_group:
+concurrency:
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
+
jobs:
test:
name: ${{ matrix.platform }} py${{ matrix.python-version }}
@@ -20,13 +24,13 @@ jobs:
fail-fast: false
matrix:
platform: [ubuntu-latest, macos-latest, windows-latest]
- python-version: ['3.8', '3.9', '3.10']
+ python-version: ['3.10', '3.11', '3.12']
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
@@ -50,7 +54,7 @@ jobs:
run: python -m tox
- name: Upload pytest test results
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
with:
name: pytest-results-${{ matrix.platform }} py${{ matrix.python-version }}
path: reports/
@@ -58,13 +62,15 @@ jobs:
if: ${{ always() }}
- name: Coverage
- uses: codecov/codecov-action@v3
+ uses: codecov/codecov-action@v5
# Don't run coverage on merge queue CI to avoid duplicating reports
# to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155
if: github.event_name != 'merge_group'
with:
token: ${{ secrets.CODECOV_TOKEN }}
- fail_ci_if_error: true
+ fail_ci_if_error: false
+
+
deploy:
# this will run when you have tagged a commit, starting with "v*"
@@ -77,9 +83,9 @@ jobs:
permissions:
id-token: write
steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v4
- name: Set up Python
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v5
with:
python-version: "3.x"
- name: Install build
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 71aa4ae5..e592dea1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,18 +1,13 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.4.0
+ rev: v5.0.0
hooks:
- id: check-docstring-first
- id: end-of-file-fixer
- id: trailing-whitespace
- - repo: https://github.com/asottile/setup-cfg-fmt
- rev: v2.4.0
- hooks:
- - id: setup-cfg-fmt
-
- - repo: https://github.com/psf/black
- rev: 23.3.0
+ - repo: https://github.com/psf/black-pre-commit-mirror
+ rev: 25.1.0
hooks:
- id: black
@@ -22,14 +17,14 @@ repos:
- id: napari-plugin-checks
- repo: https://github.com/pre-commit/mirrors-mypy
- rev: v1.4.1
+ rev: v1.15.0
hooks:
- id: mypy
additional_dependencies: [numpy, matplotlib]
- - repo: https://github.com/charliermarsh/ruff-pre-commit
+ - repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
- rev: 'v0.0.276'
+ rev: 'v0.11.9'
hooks:
- id: ruff
diff --git a/MANIFEST.in b/MANIFEST.in
index d625d95e..7ce16f9b 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,6 +1,5 @@
include LICENSE
include README.md
-recursive-include * *.mplstyle
recursive-exclude * __pycache__
recursive-exclude * *.py[co]
diff --git a/README.md b/README.md
index 855c4991..fb7aa635 100644
--- a/README.md
+++ b/README.md
@@ -15,32 +15,7 @@ A plugin to create Matplotlib plots from napari layers
## Introduction
`napari-matplotlib` is a bridge between `napari` and `matplotlib`, making it easy to create publication quality `Matplotlib` plots based on the data loaded in `napari` layers.
-## Available widgets
-
-### `Slice`
-Plots 1D slices of data along a specified axis.
-
-
-### `Histogram`
-Plots histograms of individual image layers, or RGB histograms of an RGB image
-
-
-### `Scatter`
-Scatters the values of two similarly sized images layers against each other.
-
-
-## Installation
-
-You can install `napari-matplotlib` via [pip]:
-
- pip install napari-matplotlib
-
-
-
-To install latest development version :
-
- pip install git+https://github.com/matplotlib/napari-matplotlib.git
-
+Documentation can be found at https://napari-matplotlib.github.io/
## Contributing
diff --git a/docs/changelog.rst b/docs/changelog.rst
index a31a0d3a..60dd72ba 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -1,6 +1,99 @@
Changelog
=========
+2.1.0
+-----
+New features
+~~~~~~~~~~~~
+- Added a GUI element to manually set the number of bins in the histogram widgets.
+
+2.0.3
+-----
+Bug fixes
+~~~~~~~~~
+- Fix an error that happened when the histogram widget was open, but a layer that doesn't support
+ histogramming (e.g., a labels layer) was selected.
+
+2.0.2
+-----
+Dependencies
+~~~~~~~~~~~~
+napari-matplotlib now adheres to `SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_, and has:
+
+- Dropped support for Python 3.9
+- Added support for Python 3.12
+- Added a minimum required numpy verison of 1.23
+- Pinned the maximum napari version to ``< 0.5``.
+ Version 3.0 of ``napari-matplotlib`` will introduce support for ``napari`` version 0.5.
+
+2.0.1
+-----
+Bug fixes
+~~~~~~~~~
+- Fixed using the ``HistogramWidget`` with layers containing multiscale data.
+- Make sure ``HistogramWidget`` uses 100 bins (not 99) when floating point data is
+ selected.
+
+2.0.0
+-----
+Changes to custom theming
+~~~~~~~~~~~~~~~~~~~~~~~~~
+``napari-matplotlib`` now uses colours from the current napari theme to customise the
+Matplotlib plots. See `the example on creating a new napari theme
+<https://napari.org/stable/gallery/new_theme.html>`_ for a helpful guide on how to
+create custom napari themes.
+
+This means support for custom Matplotlib styles sheets has been removed.
+
+If you spot any issues with the new theming, please report them at
+https://github.com/matplotlib/napari-matplotlib/issues.
+
+Other changes
+~~~~~~~~~~~~~
+- Histogram bin sizes for integer-type data are now force to be an integer.
+- The ``HistogramWidget`` now has two vertical lines showing the contrast limits used
+ to render the selected layer in the main napari window.
+- Added an example gallery for the ``FeaturesHistogramWidget``.
+
+1.2.0
+-----
+Changes
+~~~~~~~
+- Dropped support for Python 3.8, and added support for Python 3.11.
+- Histogram plots of points and vector layers are now coloured with their napari colourmap.
+- Added support for Matplotlib 3.8
+
+1.1.0
+-----
+Additions
+~~~~~~~~~
+- Added a widget to draw a histogram of features.
+
+Changes
+~~~~~~~
+- The slice widget is now limited to slicing along the x/y dimensions. Support
+ for slicing along z has been removed for now to make the code simpler.
+- The slice widget now uses a slider to select the slice value.
+
+Bug fixes
+~~~~~~~~~
+- Fixed creating 1D slices of 2D images.
+- Removed the limitation that only the first 99 indices could be sliced using
+ the slice widget.
+
+1.0.2
+-----
+Bug fixes
+~~~~~~~~~
+- A full dataset is no longer read into memory when using ``HistogramWidget``.
+ Only the current slice is loaded.
+- Fixed compatibility with napari 0.4.18.
+
+Changes
+~~~~~~~
+- Histogram bin limits are now caclualted from the slice being histogrammed, and
+ not the whole dataset. This is as a result of the above bug fix.
+
1.0.1
-----
Bug fixes
diff --git a/docs/conf.py b/docs/conf.py
index 2517a59c..f1533830 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -13,7 +13,7 @@
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
-import qtgallery
+from sphinx_gallery import scrapers
# -- Project information -----------------------------------------------------
@@ -35,18 +35,58 @@
"sphinx.ext.intersphinx",
]
+
+def reset_napari(gallery_conf, fname): # type: ignore[no-untyped-def]
+ from napari.settings import get_settings
+ from qtpy.QtWidgets import QApplication
+
+ settings = get_settings()
+ settings.appearance.theme = "dark"
+
+ # Disabling `QApplication.exec_` means example scripts can call `exec_`
+ # (scripts work when run normally) without blocking example execution by
+ # sphinx-gallery. (from qtgallery)
+ QApplication.exec_ = lambda _: None
+
+
+def napari_scraper(block, block_vars, gallery_conf): # type: ignore[no-untyped-def]
+ """Basic napari window scraper.
+
+ Looks for any QtMainWindow instances and takes a screenshot of them.
+
+ `app.processEvents()` allows Qt events to propagateo and prevents hanging.
+ """
+ import napari
+
+ imgpath_iter = block_vars["image_path_iterator"]
+
+ if app := napari.qt.get_app():
+ app.processEvents()
+ else:
+ return ""
+
+ img_paths = []
+ for win, img_path in zip(
+ reversed(napari._qt.qt_main_window._QtMainWindow._instances),
+ imgpath_iter,
+ strict=False,
+ ):
+ img_paths.append(img_path)
+ win._window.screenshot(img_path, canvas_only=False)
+
+ napari.Viewer.close_all()
+ app.processEvents()
+
+ return scrapers.figure_rst(img_paths, gallery_conf["src_dir"])
+
+
sphinx_gallery_conf = {
"filename_pattern": ".",
- "image_scrapers": (qtgallery.qtscraper,),
- "reset_modules": (qtgallery.reset_qapp,),
+ "image_scrapers": (napari_scraper,),
+ "reset_modules": (reset_napari,),
}
+suppress_warnings = ["config.cache"]
-qtgallery_conf = {
- "xvfb_size": (640, 480),
- "xvfb_color_depth": 24,
- "xfvb_use_xauth": False,
- "xfvb_extra_args": [],
-}
numpydoc_show_class_members = False
automodapi_inheritance_diagram = True
diff --git a/docs/user_guide.rst b/docs/user_guide.rst
index 0872e540..253e3149 100644
--- a/docs/user_guide.rst
+++ b/docs/user_guide.rst
@@ -30,6 +30,7 @@ These widgets plot the data stored in the ``.features`` attribute of individual
Currently available are:
- 2D scatter plots of two features against each other.
+- Histograms of individual features.
To use these:
@@ -39,11 +40,6 @@ To use these:
Customising plots
-----------------
-`Matplotlib style sheets <https://matplotlib.org/stable/tutorials/introductory/customizing.html#defining-your-own-style>`__ can be used to customise
-the plots generated by ``napari-matplotlib``.
-To use a custom style sheet:
-
-1. Save it as ``napari-matplotlib.mplstyle``
-2. Put it in the Matplotlib configuration directory.
- The location of this directory varies on different computers,
- and can be found by calling :func:`matplotlib.get_configdir()`.
+``napari-matplotlib`` uses colours from the current napari theme to customise the
+Matplotlib plots. See `the example on creating a new napari theme
+<https://napari.org/stable/gallery/new_theme.html>`_ for a helpful guide.
diff --git a/examples/features_hist.py b/examples/features_hist.py
new file mode 100644
index 00000000..899ddef3
--- /dev/null
+++ b/examples/features_hist.py
@@ -0,0 +1,42 @@
+"""
+Hisogram of features
+====================
+"""
+
+import napari
+import numpy as np
+import numpy.typing as npt
+from skimage.measure import regionprops_table
+
+# make a test label image
+label_image: npt.NDArray[np.uint16] = np.zeros((100, 100), dtype=np.uint16)
+
+label_image[10:20, 10:20] = 1
+label_image[50:70, 50:70] = 2
+
+feature_table_1 = regionprops_table(
+ label_image, properties=("label", "area", "perimeter")
+)
+feature_table_1["index"] = feature_table_1["label"]
+
+# make the points data
+n_points = 100
+points_data = 100 * np.random.random((100, 2))
+points_features = {
+ "feature_0": np.random.random((n_points,)),
+ "feature_1": np.random.random((n_points,)),
+ "feature_2": np.random.random((n_points,)),
+}
+
+# create the viewer
+viewer = napari.Viewer()
+viewer.add_labels(label_image, features=feature_table_1)
+viewer.add_points(points_data, features=points_features)
+
+# make the widget
+viewer.window.add_plugin_dock_widget(
+ plugin_name="napari-matplotlib", widget_name="FeaturesHistogram"
+)
+
+if __name__ == "__main__":
+ napari.run()
diff --git a/examples/histogram.py b/examples/histogram.py
index ccda491a..b9ceb377 100644
--- a/examples/histogram.py
+++ b/examples/histogram.py
@@ -2,6 +2,7 @@
Histograms
==========
"""
+
import napari
viewer = napari.Viewer()
diff --git a/examples/scatter.py b/examples/scatter.py
index cd812401..00e01ec9 100644
--- a/examples/scatter.py
+++ b/examples/scatter.py
@@ -2,6 +2,7 @@
Scatter plots
=============
"""
+
import napari
viewer = napari.Viewer()
diff --git a/examples/slice.py b/examples/slice.py
index 3e43443e..242a16cc 100644
--- a/examples/slice.py
+++ b/examples/slice.py
@@ -2,6 +2,7 @@
1D slices
=========
"""
+
import napari
viewer = napari.Viewer()
diff --git a/pyproject.toml b/pyproject.toml
index 7c7dbbdd..f76831a3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,19 +1,34 @@
[build-system]
-requires = ["setuptools", "wheel", "setuptools_scm"]
+requires = ["setuptools", "setuptools_scm"]
build-backend = "setuptools.build_meta"
[tool.setuptools_scm]
write_to = "src/napari_matplotlib/_version.py"
[tool.pytest.ini_options]
-qt_api = "pyqt6"
-addopts = "--mpl"
filterwarnings = [
"error",
+ "ignore:(?s).*Pyarrow will become a required dependency of pandas",
# Coming from vispy
"ignore:distutils Version classes are deprecated:DeprecationWarning",
"ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning",
+ # Coming from pydantic via napari
+ "ignore:Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.:DeprecationWarning",
+ # Until we stop supporting older numpy versions (<2.1)
+ "ignore:(?s).*`newshape` keyword argument is deprecated.*$:DeprecationWarning",
+]
+qt_api = "pyqt6"
+addopts = [
+ "--mpl",
+ "--mpl-baseline-relative",
+ "--strict-config",
+ "--strict-markers",
+ "-ra",
]
+minversion = "7"
+testpaths = ["src/napari_matplotlib/tests"]
+log_cli_level = "INFO"
+xfail_strict = true
[tool.black]
line-length = 79
@@ -23,8 +38,11 @@ profile = "black"
line_length = 79
[tool.ruff]
-target-version = "py38"
-select = ["I", "UP", "F", "E", "W", "D"]
+target-version = "py310"
+fix = true
+
+[tool.ruff.lint]
+select = ["B", "I", "UP", "F", "E", "W", "D"]
ignore = [
"D100", # Missing docstring in public module
"D104", # Missing docstring in public package
@@ -34,37 +52,25 @@ ignore = [
"D401", # First line of docstring should be in imperative mood
]
-fix = true
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
"docs/*" = ["D"]
"examples/*" = ["D"]
"src/napari_matplotlib/tests/*" = ["D"]
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.mypy]
-python_version = "3.8"
+python_version = "3.12"
# Block below are checks that form part of mypy 'strict' mode
-warn_unused_configs = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-strict_equality = true
-strict_concatenate = true
-check_untyped_defs = true
+strict = true
disallow_subclassing_any = false # TODO: fix
-disallow_untyped_decorators = true
-disallow_any_generics = true
-disallow_untyped_calls = true
-disallow_incomplete_defs = true
-disallow_untyped_defs = true
-no_implicit_reexport = true
-warn_return_any = false # TODO: fix
+warn_return_any = false # TODO: fix
ignore_missing_imports = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+
[[tool.mypy.overrides]]
-module = [
- "napari_matplotlib/tests/*",
-]
+module = ["napari_matplotlib/tests/*"]
disallow_untyped_defs = false
diff --git a/setup.cfg b/setup.cfg
index dfd52347..a3709e66 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
[metadata]
-name = napari_matplotlib
+name = napari-matplotlib
description = A plugin to use Matplotlib with napari
long_description = file: README.md
long_description_content_type = text/markdown
@@ -9,7 +9,7 @@ author_email = d.stansby@ucl.ac.uk
license = BSD-3-Clause
license_files = LICENSE
classifiers =
- Development Status :: 3 - Alpha
+ Development Status :: 5 - Production/Stable
Framework :: napari
Intended Audience :: Developers
License :: OSI Approved :: BSD License
@@ -28,10 +28,10 @@ project_urls =
packages = find:
install_requires =
matplotlib
- napari<0.4.18
- numpy
+ napari>=0.5
+ numpy>=1.23
tinycss2
-python_requires = >=3.8
+python_requires = >=3.10
include_package_data = True
package_dir =
=src
@@ -49,13 +49,13 @@ napari.manifest =
docs =
napari[all]
numpydoc
+ pydantic<2
pydata-sphinx-theme
- qtgallery
sphinx
sphinx-automodapi
sphinx-gallery
testing =
- napari[pyqt6-experimental]
+ napari[pyqt6_experimental]>=0.4.18
pooch
pyqt6
pytest
diff --git a/src/napari_matplotlib/base.py b/src/napari_matplotlib/base.py
index 792b5aff..ca69a548 100644
--- a/src/napari_matplotlib/base.py
+++ b/src/napari_matplotlib/base.py
@@ -1,26 +1,22 @@
import os
from pathlib import Path
-from typing import List, Optional, Tuple
-import matplotlib
import matplotlib.style as mplstyle
import napari
-from matplotlib.backends.backend_qtagg import (
- FigureCanvas,
+from matplotlib.backends.backend_qtagg import ( # type: ignore[attr-defined]
+ FigureCanvasQTAgg,
NavigationToolbar2QT,
)
from matplotlib.figure import Figure
+from napari.utils.events import Event
+from napari.utils.theme import get_theme
from qtpy.QtGui import QIcon
from qtpy.QtWidgets import QLabel, QVBoxLayout, QWidget
-from .util import Interval, from_napari_css_get_size_of
+from .util import Interval, from_napari_css_get_size_of, style_sheet_from_theme
__all__ = ["BaseNapariMPLWidget", "NapariMPLWidget", "SingleAxesWidget"]
-_CUSTOM_STYLE_PATH = (
- Path(matplotlib.get_configdir()) / "napari-matplotlib.mplstyle"
-)
-
class BaseNapariMPLWidget(QWidget):
"""
@@ -41,24 +37,21 @@ class BaseNapariMPLWidget(QWidget):
def __init__(
self,
napari_viewer: napari.Viewer,
- parent: Optional[QWidget] = None,
+ parent: QWidget | None = None,
):
super().__init__(parent=parent)
self.viewer = napari_viewer
- self._mpl_style_sheet_path: Optional[Path] = None
+ self.napari_theme_style_sheet = style_sheet_from_theme(
+ get_theme(napari_viewer.theme)
+ )
# Sets figure.* style
- with mplstyle.context(self.mpl_style_sheet_path):
- self.canvas = FigureCanvas()
+ with mplstyle.context(self.napari_theme_style_sheet):
+ self.canvas = FigureCanvasQTAgg() # type: ignore[no-untyped-call]
self.canvas.figure.set_layout_engine("constrained")
- self.toolbar = NapariNavigationToolbar(
- self.canvas, parent=self
- ) # type: ignore[no-untyped-call]
+ self.toolbar = NapariNavigationToolbar(self.canvas, parent=self)
self._replace_toolbar_icons()
- # callback to update when napari theme changed
- # TODO: this isn't working completely (see issue #140)
- # most of our styling respects the theme change but not all
self.viewer.events.theme.connect(self._on_napari_theme_changed)
self.setLayout(QVBoxLayout())
@@ -70,24 +63,6 @@ def figure(self) -> Figure:
"""Matplotlib figure."""
return self.canvas.figure
- @property
- def mpl_style_sheet_path(self) -> Path:
- """
- Path to the set Matplotlib style sheet.
- """
- if self._mpl_style_sheet_path is not None:
- return self._mpl_style_sheet_path
- elif (_CUSTOM_STYLE_PATH).exists():
- return _CUSTOM_STYLE_PATH
- elif self._napari_theme_has_light_bg():
- return Path(__file__).parent / "styles" / "light.mplstyle"
- else:
- return Path(__file__).parent / "styles" / "dark.mplstyle"
-
- @mpl_style_sheet_path.setter
- def mpl_style_sheet_path(self, path: Path) -> None:
- self._mpl_style_sheet_path = Path(path)
-
def add_single_axes(self) -> None:
"""
Add a single Axes to the figure.
@@ -96,13 +71,21 @@ def add_single_axes(self) -> None:
"""
# Sets axes.* style.
# Does not set any text styling set by axes.* keys
- with mplstyle.context(self.mpl_style_sheet_path):
- self.axes = self.figure.subplots()
+ with mplstyle.context(self.napari_theme_style_sheet):
+ self.axes = self.figure.add_subplot()
- def _on_napari_theme_changed(self) -> None:
+ def _on_napari_theme_changed(self, event: Event) -> None:
"""
Called when the napari theme is changed.
+
+ Parameters
+ ----------
+ event : napari.utils.events.Event
+ Event that triggered the callback.
"""
+ self.napari_theme_style_sheet = style_sheet_from_theme(
+ get_theme(event.value)
+ )
self._replace_toolbar_icons()
def _napari_theme_has_light_bg(self) -> bool:
@@ -114,7 +97,7 @@ def _napari_theme_has_light_bg(self) -> bool:
bool
True if theme's background colour has hsl lighter than 50%, False if darker.
"""
- theme = napari.utils.theme.get_theme(self.viewer.theme, as_dict=False)
+ theme = napari.utils.theme.get_theme(self.viewer.theme)
_, _, bg_lightness = theme.background.as_hsl_tuple()
return bg_lightness > 0.5
@@ -184,16 +167,16 @@ class NapariMPLWidget(BaseNapariMPLWidget):
#: Number of layers taken as input
n_layers_input = Interval(None, None)
#: Type of layer taken as input
- input_layer_types: Tuple[napari.layers.Layer, ...] = (napari.layers.Layer,)
+ input_layer_types: tuple[napari.layers.Layer, ...] = (napari.layers.Layer,)
def __init__(
self,
napari_viewer: napari.viewer.Viewer,
- parent: Optional[QWidget] = None,
+ parent: QWidget | None = None,
):
super().__init__(napari_viewer=napari_viewer, parent=parent)
self._setup_callbacks()
- self.layers: List[napari.layers.Layer] = []
+ self.layers: list[napari.layers.Layer] = []
helper_text = self.n_layers_input._helper_text
if helper_text is not None:
@@ -213,15 +196,18 @@ def current_z(self) -> int:
"""
return self.viewer.dims.current_step[0]
- def _on_napari_theme_changed(self) -> None:
+ def _on_napari_theme_changed(self, event: Event) -> None:
"""Update MPL toolbar and axis styling when `napari.Viewer.theme` is changed.
- Note:
- At the moment we only handle the default 'light' and 'dark' napari themes.
+ Parameters
+ ----------
+ event : napari.utils.events.Event
+ Event that triggered the callback.
"""
- super()._on_napari_theme_changed()
- self.clear()
- self.draw()
+ super()._on_napari_theme_changed(event)
+ # use self._draw instead of self.draw to cope with redraw while there are no
+ # layers, this makes the self.clear() obsolete
+ self._draw()
def _setup_callbacks(self) -> None:
"""
@@ -238,6 +224,15 @@ def _setup_callbacks(self) -> None:
self._update_layers
)
+ @property
+ def _valid_layer_selection(self) -> bool:
+ """
+ Return `True` if layer selection is valid.
+ """
+ return self.n_selected_layers in self.n_layers_input and all(
+ isinstance(layer, self.input_layer_types) for layer in self.layers
+ )
+
def _update_layers(self, event: napari.utils.events.Event) -> None:
"""
Update the ``layers`` attribute with currently selected layers and re-draw.
@@ -245,7 +240,8 @@ def _update_layers(self, event: napari.utils.events.Event) -> None:
self.layers = list(self.viewer.layers.selection)
self.layers = sorted(self.layers, key=lambda layer: layer.name)
self.on_update_layers()
- self._draw()
+ if self._valid_layer_selection:
+ self._draw()
def _draw(self) -> None:
"""
@@ -254,13 +250,12 @@ def _draw(self) -> None:
"""
# Clearing axes sets new defaults, so need to make sure style is applied when
# this happens
- with mplstyle.context(self.mpl_style_sheet_path):
+ with mplstyle.context(self.napari_theme_style_sheet):
+ # everything should be done in the style context
self.clear()
- if self.n_selected_layers in self.n_layers_input and all(
- isinstance(layer, self.input_layer_types) for layer in self.layers
- ):
- self.draw()
- self.canvas.draw()
+ if self._valid_layer_selection:
+ self.draw()
+ self.canvas.draw() # type: ignore[no-untyped-call]
def clear(self) -> None:
"""
@@ -293,7 +288,7 @@ class SingleAxesWidget(NapariMPLWidget):
def __init__(
self,
napari_viewer: napari.viewer.Viewer,
- parent: Optional[QWidget] = None,
+ parent: QWidget | None = None,
):
super().__init__(napari_viewer=napari_viewer, parent=parent)
self.add_single_axes()
@@ -302,15 +297,15 @@ def clear(self) -> None:
"""
Clear the axes.
"""
- with mplstyle.context(self.mpl_style_sheet_path):
+ with mplstyle.context(self.napari_theme_style_sheet):
self.axes.clear()
class NapariNavigationToolbar(NavigationToolbar2QT):
"""Custom Toolbar style for Napari."""
- def __init__(self, *args, **kwargs): # type: ignore[no-untyped-def]
- super().__init__(*args, **kwargs)
+ def __init__(self, *args, **kwargs) -> None: # type: ignore[no-untyped-def]
+ super().__init__(*args, **kwargs) # type: ignore[no-untyped-call]
self.setIconSize(
from_napari_css_get_size_of(
"QtViewerPushButton", fallback=(28, 28)
@@ -319,7 +314,7 @@ def __init__(self, *args, **kwargs): # type: ignore[no-untyped-def]
def _update_buttons_checked(self) -> None:
"""Update toggle tool icons when selected/unselected."""
- super()._update_buttons_checked()
+ super()._update_buttons_checked() # type: ignore[no-untyped-call]
icon_dir = self.parentWidget()._get_path_to_icon()
# changes pan/zoom icons depending on state (checked or not)
diff --git a/src/napari_matplotlib/features.py b/src/napari_matplotlib/features.py
new file mode 100644
index 00000000..34abf104
--- /dev/null
+++ b/src/napari_matplotlib/features.py
@@ -0,0 +1,9 @@
+from napari.layers import Labels, Points, Shapes, Tracks, Vectors
+
+FEATURES_LAYER_TYPES = (
+ Labels,
+ Points,
+ Shapes,
+ Tracks,
+ Vectors,
+)
diff --git a/src/napari_matplotlib/histogram.py b/src/napari_matplotlib/histogram.py
index 39ad41a3..85bba9d2 100644
--- a/src/napari_matplotlib/histogram.py
+++ b/src/napari_matplotlib/histogram.py
@@ -1,17 +1,58 @@
-from typing import Optional
+from typing import Any, cast
import napari
import numpy as np
-from qtpy.QtWidgets import QWidget
+import numpy.typing as npt
+from matplotlib.container import BarContainer
+from napari.layers import Image
+from napari.layers._multiscale_data import MultiScaleData
+from qtpy.QtWidgets import (
+ QComboBox,
+ QFormLayout,
+ QGroupBox,
+ QLabel,
+ QSpinBox,
+ QVBoxLayout,
+ QWidget,
+)
from .base import SingleAxesWidget
+from .features import FEATURES_LAYER_TYPES
from .util import Interval
-__all__ = ["HistogramWidget"]
+__all__ = ["HistogramWidget", "FeaturesHistogramWidget"]
_COLORS = {"r": "tab:red", "g": "tab:green", "b": "tab:blue"}
+def _get_bins(
+ data: npt.NDArray[Any],
+ num_bins: int = 100,
+) -> npt.NDArray[np.floating]:
+ """Create evenly spaced bins with a given interval.
+
+ Parameters
+ ----------
+ data : napari.layers.Layer.data
+ Napari layer data.
+ num_bins : integer, optional
+ Number of evenly-spaced bins to create. Defaults to 100.
+
+ Returns
+ -------
+ bin_edges : numpy.ndarray
+ Array of evenly spaced bin edges.
+ """
+ if data.dtype.kind in {"i", "u"}:
+ # Make sure integer data types have integer sized bins
+ step = np.ceil(np.ptp(data) / num_bins)
+ return np.arange(np.min(data), np.max(data) + step, step)
+ else:
+ # For other data types we can use exactly `num_bins` bins
+ # (and `num_bins` + 1 bin edges)
+ return np.linspace(np.min(data), np.max(data), num_bins + 1)
+
+
class HistogramWidget(SingleAxesWidget):
"""
Display a histogram of the currently selected layer.
@@ -23,36 +64,251 @@ class HistogramWidget(SingleAxesWidget):
def __init__(
self,
napari_viewer: napari.viewer.Viewer,
- parent: Optional[QWidget] = None,
+ parent: QWidget | None = None,
):
super().__init__(napari_viewer, parent=parent)
+
+ num_bins_widget = QSpinBox()
+ num_bins_widget.setRange(1, 100_000)
+ num_bins_widget.setValue(101)
+ num_bins_widget.setWrapping(False)
+ num_bins_widget.setKeyboardTracking(False)
+
+ # Set bins widget layout
+ bins_selection_layout = QFormLayout()
+ bins_selection_layout.addRow("num bins", num_bins_widget)
+
+ # Group the widgets and add to main layout
+ params_widget_group = QGroupBox("Params")
+ params_widget_group_layout = QVBoxLayout()
+ params_widget_group_layout.addLayout(bins_selection_layout)
+ params_widget_group.setLayout(params_widget_group_layout)
+ self.layout().addWidget(params_widget_group)
+
+ # Add callbacks
+ num_bins_widget.valueChanged.connect(self._draw)
+
+ # Store widgets for later usage
+ self.num_bins_widget = num_bins_widget
+
self._update_layers(None)
+ self.viewer.events.theme.connect(self._on_napari_theme_changed)
- def draw(self) -> None:
+ def on_update_layers(self) -> None:
"""
- Clear the axes and histogram the currently selected layer/slice.
+ Called when the selected layers are updated.
"""
- layer = self.layers[0]
- bins = np.linspace(np.min(layer.data), np.max(layer.data), 100)
+ super().on_update_layers()
+ if self._valid_layer_selection:
+ self.layers[0].events.contrast_limits.connect(
+ self._update_contrast_lims
+ )
+
+ if not self.layers:
+ return
+
+ # Reset the num bins based on new layer data
+ layer_data = self._get_layer_data(self.layers[0])
+ self._set_widget_nums_bins(data=layer_data)
+
+ def _update_contrast_lims(self) -> None:
+ for lim, line in zip(
+ self.layers[0].contrast_limits, self._contrast_lines, strict=False
+ ):
+ line.set_xdata(lim)
+
+ self.figure.canvas.draw()
+
+ def _set_widget_nums_bins(self, data: npt.NDArray[Any]) -> None:
+ """Update num_bins widget with bins determined from the image data"""
+ bins = _get_bins(data)
+ self.num_bins_widget.setValue(bins.size - 1)
+
+ def _get_layer_data(self, layer: napari.layers.Layer) -> npt.NDArray[Any]:
+ """Get the data associated with a given layer"""
+ data = layer.data
- if layer.data.ndim - layer.rgb == 3:
+ if isinstance(layer.data, MultiScaleData):
+ data = data[layer.data_level]
+
+ if layer.ndim - layer.rgb == 3:
# 3D data, can be single channel or RGB
- data = layer.data[self.current_z]
+ # Slice in z dimension
+ data = data[self.current_z]
self.axes.set_title(f"z={self.current_z}")
- else:
- data = layer.data
+
+ # Read data into memory if it's a dask array
+ data = np.asarray(data)
+
+ return data
+
+ def draw(self) -> None:
+ """
+ Clear the axes and histogram the currently selected layer/slice.
+ """
+ layer: Image = self.layers[0]
+ data = self._get_layer_data(layer)
+
+ # Important to calculate bins after slicing 3D data, to avoid reading
+ # whole cube into memory.
+ bins = _get_bins(
+ data,
+ num_bins=self.num_bins_widget.value(),
+ )
if layer.rgb:
# Histogram RGB channels independently
for i, c in enumerate("rgb"):
self.axes.hist(
data[..., i].ravel(),
- bins=bins,
+ bins=bins.tolist(),
label=c,
histtype="step",
color=_COLORS[c],
)
else:
- self.axes.hist(data.ravel(), bins=bins, label=layer.name)
+ self.axes.hist(data.ravel(), bins=bins.tolist(), label=layer.name)
+ self._contrast_lines = [
+ self.axes.axvline(lim, color="white")
+ for lim in layer.contrast_limits
+ ]
self.axes.legend()
+
+
+class FeaturesHistogramWidget(SingleAxesWidget):
+ """
+ Display a histogram of selected feature attached to selected layer.
+ """
+
+ n_layers_input = Interval(1, 1)
+ # All layers that have a .features attributes
+ input_layer_types = FEATURES_LAYER_TYPES
+
+ def __init__(
+ self,
+ napari_viewer: napari.viewer.Viewer,
+ parent: QWidget | None = None,
+ ):
+ super().__init__(napari_viewer, parent=parent)
+
+ self.layout().addLayout(QVBoxLayout())
+ self._key_selection_widget = QComboBox()
+ self.layout().addWidget(QLabel("Key:"))
+ self.layout().addWidget(self._key_selection_widget)
+
+ self._key_selection_widget.currentTextChanged.connect(
+ self._set_axis_keys
+ )
+
+ self._update_layers(None)
+
+ @property
+ def x_axis_key(self) -> str | None:
+ """Key to access x axis data from the FeaturesTable"""
+ return self._x_axis_key
+
+ @x_axis_key.setter
+ def x_axis_key(self, key: str | None) -> None:
+ self._x_axis_key = key
+ self._draw()
+
+ def _set_axis_keys(self, x_axis_key: str) -> None:
+ """Set both axis keys and then redraw the plot"""
+ self._x_axis_key = x_axis_key
+ self._draw()
+
+ def _get_valid_axis_keys(self) -> list[str]:
+ """
+ Get the valid axis keys from the layer FeatureTable.
+
+ Returns
+ -------
+ axis_keys : List[str]
+ The valid axis keys in the FeatureTable. If the table is empty
+ or there isn't a table, returns an empty list.
+ """
+ if len(self.layers) == 0 or not (hasattr(self.layers[0], "features")):
+ return []
+ else:
+ return self.layers[0].features.keys()
+
+ def _get_data(self) -> tuple[npt.NDArray[Any] | None, str]:
+ """Get the plot data.
+
+ Returns
+ -------
+ data : List[np.ndarray]
+ List contains X and Y columns from the FeatureTable. Returns
+ an empty array if nothing to plot.
+ x_axis_name : str
+ The title to display on the x axis. Returns
+ an empty string if nothing to plot.
+ """
+ if not hasattr(self.layers[0], "features"):
+ # if the selected layer doesn't have a featuretable,
+ # skip draw
+ return None, ""
+
+ feature_table = self.layers[0].features
+
+ if (len(feature_table) == 0) or (self.x_axis_key is None):
+ return None, ""
+
+ data = feature_table[self.x_axis_key]
+ x_axis_name = self.x_axis_key.replace("_", " ")
+
+ return data, x_axis_name
+
+ def on_update_layers(self) -> None:
+ """
+ Called when the layer selection changes by ``self.update_layers()``.
+ """
+ # reset the axis keys
+ self._x_axis_key = None
+
+ # Clear combobox
+ self._key_selection_widget.clear()
+ self._key_selection_widget.addItems(self._get_valid_axis_keys())
+
+ def draw(self) -> None:
+ """Clear the axes and histogram the currently selected layer/slice."""
+ # get the colormap from the layer depending on its type
+ if isinstance(self.layers[0], napari.layers.Points):
+ colormap = self.layers[0].face_colormap
+ if self.x_axis_key:
+ self.layers[0].face_color = self.x_axis_key
+ elif isinstance(self.layers[0], napari.layers.Vectors):
+ colormap = self.layers[0].edge_colormap
+ if self.x_axis_key:
+ self.layers[0].edge_color = self.x_axis_key
+ else:
+ colormap = None
+
+ # apply new colors to the layer
+ self.viewer.layers[self.layers[0].name].refresh_colors(True)
+ self.viewer.layers[self.layers[0].name].refresh()
+
+ # Draw the histogram
+ data, x_axis_name = self._get_data()
+
+ if data is None:
+ return
+
+ bins = _get_bins(data)
+
+ _, bins, patches = self.axes.hist(data, bins=bins.tolist())
+ patches = cast(BarContainer, patches)
+
+ # recolor the histogram plot
+ if colormap is not None:
+ self.bins_norm = (bins - bins.min()) / (bins.max() - bins.min())
+ colors = colormap.map(self.bins_norm)
+
+ # Set histogram style:
+ for idx, patch in enumerate(patches):
+ patch.set_facecolor(colors[idx])
+
+ # set ax labels
+ self.axes.set_xlabel(x_axis_name)
+ self.axes.set_ylabel("Counts [#]")
diff --git a/src/napari_matplotlib/napari.yaml b/src/napari_matplotlib/napari.yaml
index b736592b..71af0ca6 100644
--- a/src/napari_matplotlib/napari.yaml
+++ b/src/napari_matplotlib/napari.yaml
@@ -14,6 +14,10 @@ contributions:
python_name: napari_matplotlib:FeaturesScatterWidget
title: Make a scatter plot of layer features
+ - id: napari-matplotlib.features_histogram
+ python_name: napari_matplotlib:FeaturesHistogramWidget
+ title: Plot feature histograms
+
- id: napari-matplotlib.slice
python_name: napari_matplotlib:SliceWidget
title: Plot a 1D slice
@@ -28,5 +32,8 @@ contributions:
- command: napari-matplotlib.features_scatter
display_name: FeaturesScatter
+ - command: napari-matplotlib.features_histogram
+ display_name: FeaturesHistogram
+
- command: napari-matplotlib.slice
display_name: 1D slice
diff --git a/src/napari_matplotlib/scatter.py b/src/napari_matplotlib/scatter.py
index db86c7f3..98ebe928 100644
--- a/src/napari_matplotlib/scatter.py
+++ b/src/napari_matplotlib/scatter.py
@@ -1,10 +1,11 @@
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any
import napari
import numpy.typing as npt
from qtpy.QtWidgets import QComboBox, QLabel, QVBoxLayout, QWidget
from .base import SingleAxesWidget
+from .features import FEATURES_LAYER_TYPES
from .util import Interval
__all__ = ["ScatterBaseWidget", "ScatterWidget", "FeaturesScatterWidget"]
@@ -39,7 +40,7 @@ def draw(self) -> None:
self.axes.set_xlabel(x_axis_name)
self.axes.set_ylabel(y_axis_name)
- def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
+ def _get_data(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
"""
Get the plot data.
@@ -66,7 +67,7 @@ class ScatterWidget(ScatterBaseWidget):
n_layers_input = Interval(2, 2)
input_layer_types = (napari.layers.Image,)
- def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
+ def _get_data(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
"""
Get the plot data.
@@ -94,24 +95,18 @@ class FeaturesScatterWidget(ScatterBaseWidget):
n_layers_input = Interval(1, 1)
# All layers that have a .features attributes
- input_layer_types = (
- napari.layers.Labels,
- napari.layers.Points,
- napari.layers.Shapes,
- napari.layers.Tracks,
- napari.layers.Vectors,
- )
+ input_layer_types = FEATURES_LAYER_TYPES
def __init__(
self,
napari_viewer: napari.viewer.Viewer,
- parent: Optional[QWidget] = None,
+ parent: QWidget | None = None,
):
super().__init__(napari_viewer, parent=parent)
self.layout().addLayout(QVBoxLayout())
- self._selectors: Dict[str, QComboBox] = {}
+ self._selectors: dict[str, QComboBox] = {}
for dim in ["x", "y"]:
self._selectors[dim] = QComboBox()
# Re-draw when combo boxes are updated
@@ -123,7 +118,7 @@ def __init__(
self._update_layers(None)
@property
- def x_axis_key(self) -> Union[str, None]:
+ def x_axis_key(self) -> str | None:
"""
Key for the x-axis data.
"""
@@ -138,7 +133,7 @@ def x_axis_key(self, key: str) -> None:
self._draw()
@property
- def y_axis_key(self) -> Union[str, None]:
+ def y_axis_key(self) -> str | None:
"""
Key for the y-axis data.
"""
@@ -152,7 +147,7 @@ def y_axis_key(self, key: str) -> None:
self._selectors["y"].setCurrentText(key)
self._draw()
- def _get_valid_axis_keys(self) -> List[str]:
+ def _get_valid_axis_keys(self) -> list[str]:
"""
Get the valid axis keys from the layer FeatureTable.
@@ -191,7 +186,7 @@ def draw(self) -> None:
if self._ready_to_scatter():
super().draw()
- def _get_data(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
+ def _get_data(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any], str, str]:
"""
Get the plot data from the ``features`` attribute of the first
selected layer.
diff --git a/src/napari_matplotlib/slice.py b/src/napari_matplotlib/slice.py
index e3aa80b2..1924bf2b 100644
--- a/src/napari_matplotlib/slice.py
+++ b/src/napari_matplotlib/slice.py
@@ -1,19 +1,23 @@
-from typing import Any, Dict, Optional, Tuple
+from typing import Any
import matplotlib.ticker as mticker
import napari
import numpy as np
import numpy.typing as npt
-from qtpy.QtWidgets import QComboBox, QHBoxLayout, QLabel, QSpinBox, QWidget
+from qtpy.QtCore import Qt
+from qtpy.QtWidgets import (
+ QComboBox,
+ QLabel,
+ QSlider,
+ QVBoxLayout,
+ QWidget,
+)
from .base import SingleAxesWidget
from .util import Interval
__all__ = ["SliceWidget"]
-_dims_sel = ["x", "y"]
-_dims = ["x", "y", "z"]
-
class SliceWidget(SingleAxesWidget):
"""
@@ -26,33 +30,51 @@ class SliceWidget(SingleAxesWidget):
def __init__(
self,
napari_viewer: napari.viewer.Viewer,
- parent: Optional[QWidget] = None,
+ parent: QWidget | None = None,
):
# Setup figure/axes
super().__init__(napari_viewer, parent=parent)
- button_layout = QHBoxLayout()
- self.layout().addLayout(button_layout)
-
self.dim_selector = QComboBox()
+ self.dim_selector.addItems(["x", "y"])
+
+ self.slice_selector = QSlider(orientation=Qt.Orientation.Horizontal)
+
+ # Create widget layout
+ button_layout = QVBoxLayout()
button_layout.addWidget(QLabel("Slice axis:"))
button_layout.addWidget(self.dim_selector)
- self.dim_selector.addItems(_dims)
-
- self.slice_selectors = {}
- for d in _dims_sel:
- self.slice_selectors[d] = QSpinBox()
- button_layout.addWidget(QLabel(f"{d}:"))
- button_layout.addWidget(self.slice_selectors[d])
+ button_layout.addWidget(self.slice_selector)
+ self.layout().addLayout(button_layout)
# Setup callbacks
- # Re-draw when any of the combon/spin boxes are updated
+ # Re-draw when any of the combo/slider is updated
self.dim_selector.currentTextChanged.connect(self._draw)
- for d in _dims_sel:
- self.slice_selectors[d].textChanged.connect(self._draw)
+ self.slice_selector.valueChanged.connect(self._draw)
self._update_layers(None)
+ def on_update_layers(self) -> None:
+ """
+ Called when layer selection is updated.
+ """
+ if not len(self.layers):
+ return
+ if self.current_dim_name == "x":
+ max = self._layer.data.shape[-2]
+ elif self.current_dim_name == "y":
+ max = self._layer.data.shape[-1]
+ else:
+ raise RuntimeError("dim name must be x or y")
+ self.slice_selector.setRange(0, max - 1)
+
+ @property
+ def _slice_width(self) -> int:
+ """
+ Width of the slice being plotted.
+ """
+ return self._layer.data.shape[self.current_dim_index]
+
@property
def _layer(self) -> napari.layers.Layer:
"""
@@ -61,7 +83,7 @@ def _layer(self) -> napari.layers.Layer:
return self.layers[0]
@property
- def current_dim(self) -> str:
+ def current_dim_name(self) -> str:
"""
Currently selected slice dimension.
"""
@@ -74,36 +96,40 @@ def current_dim_index(self) -> int:
"""
# Note the reversed list because in napari the z-axis is the first
# numpy axis
- return _dims[::-1].index(self.current_dim)
+ return self._dim_names.index(self.current_dim_name)
@property
- def _selector_values(self) -> Dict[str, int]:
+ def _dim_names(self) -> list[str]:
"""
- Values of the slice selectors.
+ List of dimension names. This is a property as it varies depending on the
+ dimensionality of the currently selected data.
"""
- return {d: self.slice_selectors[d].value() for d in _dims_sel}
-
- def _get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
+ if self._layer.data.ndim == 2:
+ return ["y", "x"]
+ elif self._layer.data.ndim == 3:
+ return ["z", "y", "x"]
+ else:
+ raise RuntimeError("Don't know how to handle ndim != 2 or 3")
+
+ def _get_xy(self) -> tuple[npt.NDArray[Any], npt.NDArray[Any]]:
"""
Get data for plotting.
"""
- x = np.arange(self._layer.data.shape[self.current_dim_index])
-
- vals = self._selector_values
- vals.update({"z": self.current_z})
+ val = self.slice_selector.value()
slices = []
- for d in _dims:
- if d == self.current_dim:
+ for dim_name in self._dim_names:
+ if dim_name == self.current_dim_name:
# Select all data along this axis
slices.append(slice(None))
+ elif dim_name == "z":
+ # Only select the currently viewed z-index
+ slices.append(slice(self.current_z, self.current_z + 1))
else:
# Select specific index
- val = vals[d]
slices.append(slice(val, val + 1))
- # Reverse since z is the first axis in napari
- slices = slices[::-1]
+ x = np.arange(self._slice_width)
y = self._layer.data[tuple(slices)].ravel()
return x, y
@@ -115,7 +141,7 @@ def draw(self) -> None:
x, y = self._get_xy()
self.axes.plot(x, y)
- self.axes.set_xlabel(self.current_dim)
+ self.axes.set_xlabel(self.current_dim_name)
self.axes.set_title(self._layer.name)
# Make sure all ticks lie on integer values
self.axes.xaxis.set_major_locator(
diff --git a/src/napari_matplotlib/styles/README.md b/src/napari_matplotlib/styles/README.md
deleted file mode 100644
index 79d3c417..00000000
--- a/src/napari_matplotlib/styles/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-This folder contains default built-in Matplotlib style sheets.
-See https://matplotlib.org/stable/tutorials/introductory/customizing.html#defining-your-own-style
-for more info on Matplotlib style sheets.
diff --git a/src/napari_matplotlib/styles/dark.mplstyle b/src/napari_matplotlib/styles/dark.mplstyle
deleted file mode 100644
index 1658f9b4..00000000
--- a/src/napari_matplotlib/styles/dark.mplstyle
+++ /dev/null
@@ -1,12 +0,0 @@
-# Dark-theme napari colour scheme for matplotlib plots
-
-# text (very light grey - almost white): #f0f1f2
-# foreground (mid grey): #414851
-# background (dark blue-gray): #262930
-
-figure.facecolor : none
-axes.labelcolor : f0f1f2
-axes.facecolor : none
-axes.edgecolor : 414851
-xtick.color : f0f1f2
-ytick.color : f0f1f2
diff --git a/src/napari_matplotlib/styles/light.mplstyle b/src/napari_matplotlib/styles/light.mplstyle
deleted file mode 100644
index 3b8d7d1d..00000000
--- a/src/napari_matplotlib/styles/light.mplstyle
+++ /dev/null
@@ -1,12 +0,0 @@
-# Light-theme napari colour scheme for matplotlib plots
-
-# text (very dark grey - almost black): #3b3a39
-# foreground (mid grey): #d6d0ce
-# background (brownish beige): #efebe9
-
-figure.facecolor : none
-axes.labelcolor : 3b3a39
-axes.facecolor : none
-axes.edgecolor : d6d0ce
-xtick.color : 3b3a39
-ytick.color : 3b3a39
diff --git a/src/napari_matplotlib/tests/baseline/test_custom_theme.png b/src/napari_matplotlib/tests/baseline/test_custom_theme.png
index 65c43a49..ffa4635b 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_custom_theme.png and b/src/napari_matplotlib/tests/baseline/test_custom_theme.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_feature_histogram.png b/src/napari_matplotlib/tests/baseline/test_feature_histogram.png
new file mode 100644
index 00000000..1892af44
Binary files /dev/null and b/src/napari_matplotlib/tests/baseline/test_feature_histogram.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_feature_histogram_points.png b/src/napari_matplotlib/tests/baseline/test_feature_histogram_points.png
new file mode 100644
index 00000000..88a28f79
Binary files /dev/null and b/src/napari_matplotlib/tests/baseline/test_feature_histogram_points.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_feature_histogram_vectors.png b/src/napari_matplotlib/tests/baseline/test_feature_histogram_vectors.png
new file mode 100644
index 00000000..857d9344
Binary files /dev/null and b/src/napari_matplotlib/tests/baseline/test_feature_histogram_vectors.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_histogram_2D.png b/src/napari_matplotlib/tests/baseline/test_histogram_2D.png
index b76d1e10..b9096e4d 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_histogram_2D.png and b/src/napari_matplotlib/tests/baseline/test_histogram_2D.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png b/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png
new file mode 100644
index 00000000..98e3cde1
Binary files /dev/null and b/src/napari_matplotlib/tests/baseline/test_histogram_2D_bins.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_histogram_3D.png b/src/napari_matplotlib/tests/baseline/test_histogram_3D.png
index 2dffdcb2..ec4ad96d 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_histogram_3D.png and b/src/napari_matplotlib/tests/baseline/test_histogram_3D.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_slice_2D.png b/src/napari_matplotlib/tests/baseline/test_slice_2D.png
index 5b73091c..c1e67637 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_slice_2D.png and b/src/napari_matplotlib/tests/baseline/test_slice_2D.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_slice_3D.png b/src/napari_matplotlib/tests/baseline/test_slice_3D.png
index 43c8c3b6..046293f3 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_slice_3D.png and b/src/napari_matplotlib/tests/baseline/test_slice_3D.png differ
diff --git a/src/napari_matplotlib/tests/data/test_theme.mplstyle b/src/napari_matplotlib/tests/data/test_theme.mplstyle
deleted file mode 100644
index 2f94b31f..00000000
--- a/src/napari_matplotlib/tests/data/test_theme.mplstyle
+++ /dev/null
@@ -1,15 +0,0 @@
-# Dark-theme napari colour scheme for matplotlib plots
-
-#f4b8b2 # light red
-#b2e4f4 # light blue
-#0aa3fc # dark blue
-#008939 # dark green
-
-figure.facecolor : f4b8b2 # light red
-axes.facecolor : b2e4f4 # light blue
-axes.edgecolor : 0aa3fc # dark blue
-
-xtick.color : 008939 # dark green
-xtick.labelcolor : 008939 # dark green
-ytick.color : 008939 # dark green
-ytick.labelcolor : 008939 # dark green
diff --git a/src/napari_matplotlib/tests/scatter/baseline/test_features_scatter_widget_2D.png b/src/napari_matplotlib/tests/scatter/baseline/test_features_scatter_widget_2D.png
index 269ebd01..9237dbdc 100644
Binary files a/src/napari_matplotlib/tests/scatter/baseline/test_features_scatter_widget_2D.png and b/src/napari_matplotlib/tests/scatter/baseline/test_features_scatter_widget_2D.png differ
diff --git a/src/napari_matplotlib/tests/scatter/baseline/test_scatter_2D.png b/src/napari_matplotlib/tests/scatter/baseline/test_scatter_2D.png
index 3b550666..a11bda5f 100644
Binary files a/src/napari_matplotlib/tests/scatter/baseline/test_scatter_2D.png and b/src/napari_matplotlib/tests/scatter/baseline/test_scatter_2D.png differ
diff --git a/src/napari_matplotlib/tests/scatter/baseline/test_scatter_3D.png b/src/napari_matplotlib/tests/scatter/baseline/test_scatter_3D.png
index 27e7d673..cd42a8a2 100644
Binary files a/src/napari_matplotlib/tests/scatter/baseline/test_scatter_3D.png and b/src/napari_matplotlib/tests/scatter/baseline/test_scatter_3D.png differ
diff --git a/src/napari_matplotlib/tests/scatter/test_scatter.py b/src/napari_matplotlib/tests/scatter/test_scatter.py
index a225863d..0c60660c 100644
--- a/src/napari_matplotlib/tests/scatter/test_scatter.py
+++ b/src/napari_matplotlib/tests/scatter/test_scatter.py
@@ -15,7 +15,9 @@ def test_scatter_2D(make_napari_viewer, astronaut_data):
viewer.add_image(astronaut_data[0], **astronaut_data[1], name="astronaut")
viewer.add_image(
- astronaut_data[0] * -1, **astronaut_data[1], name="astronaut_reversed"
+ astronaut_data[0] * -1.0,
+ **astronaut_data[1],
+ name="astronaut_reversed",
)
# De-select existing selection
viewer.layers.selection.clear()
@@ -36,7 +38,7 @@ def test_scatter_3D(make_napari_viewer, brain_data):
viewer.add_image(brain_data[0], **brain_data[1], name="brain")
viewer.add_image(
- brain_data[0] * -1, **brain_data[1], name="brain_reversed"
+ brain_data[0] * -1.0, **brain_data[1], name="brain_reversed"
)
# De-select existing selection
viewer.layers.selection.clear()
diff --git a/src/napari_matplotlib/tests/scatter/test_scatter_features.py b/src/napari_matplotlib/tests/scatter/test_scatter_features.py
index b5a396fd..3ede1e28 100644
--- a/src/napari_matplotlib/tests/scatter/test_scatter_features.py
+++ b/src/napari_matplotlib/tests/scatter/test_scatter_features.py
@@ -1,5 +1,5 @@
from copy import deepcopy
-from typing import Any, Dict, Tuple
+from typing import Any
import numpy as np
import numpy.typing as npt
@@ -34,7 +34,7 @@ def test_features_scatter_widget_2D(
def make_labels_layer_with_features() -> (
- Tuple[npt.NDArray[np.uint16], Dict[str, Any]]
+ tuple[npt.NDArray[np.uint16], dict[str, Any]]
):
label_image: npt.NDArray[np.uint16] = np.zeros((100, 100), dtype=np.uint16)
for label_value, start_index in enumerate([10, 30, 50], start=1):
diff --git a/src/napari_matplotlib/tests/test_histogram.py b/src/napari_matplotlib/tests/test_histogram.py
index 4d170014..435973ba 100644
--- a/src/napari_matplotlib/tests/test_histogram.py
+++ b/src/napari_matplotlib/tests/test_histogram.py
@@ -1,8 +1,27 @@
from copy import deepcopy
+import numpy as np
import pytest
-from napari_matplotlib import HistogramWidget
+from napari_matplotlib import FeaturesHistogramWidget, HistogramWidget
+from napari_matplotlib.tests.helpers import (
+ assert_figures_equal,
+ assert_figures_not_equal,
+)
+
+
+@pytest.mark.mpl_image_compare
+def test_histogram_2D_bins(make_napari_viewer, astronaut_data):
+ viewer = make_napari_viewer()
+ viewer.theme = "light"
+ viewer.add_image(astronaut_data[0], **astronaut_data[1])
+ widget = HistogramWidget(viewer)
+ viewer.window.add_dock_widget(widget)
+ widget.num_bins_widget.setValue(25)
+ fig = widget.figure
+ # Need to return a copy, as original figure is too eagerley garbage
+ # collected by the widget
+ return deepcopy(fig)
@pytest.mark.mpl_image_compare
@@ -28,3 +47,108 @@ def test_histogram_3D(make_napari_viewer, brain_data):
# Need to return a copy, as original figure is too eagerley garbage
# collected by the widget
return deepcopy(fig)
+
+
+def test_feature_histogram(make_napari_viewer):
+ n_points = 1000
+ random_points = np.random.random((n_points, 3)) * 10
+ random_directions = np.random.random((n_points, 3)) * 10
+ random_vectors = np.stack([random_points, random_directions], axis=1)
+ feature1 = np.random.random(n_points)
+ feature2 = np.random.normal(size=n_points)
+
+ viewer = make_napari_viewer()
+ viewer.add_points(
+ random_points,
+ properties={"feature1": feature1, "feature2": feature2},
+ name="points1",
+ )
+ viewer.add_vectors(
+ random_vectors,
+ properties={"feature1": feature1, "feature2": feature2},
+ name="vectors1",
+ )
+
+ widget = FeaturesHistogramWidget(viewer)
+ viewer.window.add_dock_widget(widget)
+
+ # Check whether changing the selected key changes the plot
+ widget._set_axis_keys("feature1")
+ fig1 = deepcopy(widget.figure)
+
+ widget._set_axis_keys("feature2")
+ assert_figures_not_equal(widget.figure, fig1)
+
+ # check whether selecting a different layer produces the same plot
+ viewer.layers.selection.clear()
+ viewer.layers.selection.add(viewer.layers[1])
+ assert_figures_equal(widget.figure, fig1)
+
+
+@pytest.mark.mpl_image_compare
+def test_feature_histogram_vectors(make_napari_viewer):
+ n_points = 1000
+ np.random.seed(42)
+ random_points = np.random.random((n_points, 3)) * 10
+ random_directions = np.random.random((n_points, 3)) * 10
+ random_vectors = np.stack([random_points, random_directions], axis=1)
+ feature1 = np.random.random(n_points)
+
+ viewer = make_napari_viewer()
+ viewer.add_vectors(
+ random_vectors,
+ properties={"feature1": feature1},
+ name="vectors1",
+ )
+
+ widget = FeaturesHistogramWidget(viewer)
+ viewer.window.add_dock_widget(widget)
+ widget._set_axis_keys("feature1")
+
+ fig = FeaturesHistogramWidget(viewer).figure
+ return deepcopy(fig)
+
+
+@pytest.mark.mpl_image_compare
+def test_feature_histogram_points(make_napari_viewer):
+ np.random.seed(0)
+ n_points = 1000
+ random_points = np.random.random((n_points, 3)) * 10
+ feature1 = np.random.random(n_points)
+
+ viewer = make_napari_viewer()
+ viewer.add_points(
+ random_points,
+ properties={"feature1": feature1},
+ name="points1",
+ )
+
+ widget = FeaturesHistogramWidget(viewer)
+ viewer.window.add_dock_widget(widget)
+ widget._set_axis_keys("feature1")
+
+ fig = FeaturesHistogramWidget(viewer).figure
+ return deepcopy(fig)
+
+
+def test_change_layer(make_napari_viewer, brain_data, astronaut_data):
+ viewer = make_napari_viewer()
+ widget = HistogramWidget(viewer)
+
+ viewer.add_image(brain_data[0], **brain_data[1])
+ viewer.add_image(astronaut_data[0], **astronaut_data[1])
+
+ # Select first layer
+ viewer.layers.selection.clear()
+ viewer.layers.selection.add(viewer.layers[0])
+ fig1 = deepcopy(widget.figure)
+
+ # Re-selecting first layer should produce identical plot
+ viewer.layers.selection.clear()
+ viewer.layers.selection.add(viewer.layers[0])
+ assert_figures_equal(widget.figure, fig1)
+
+ # Plotting the second layer should produce a different plot
+ viewer.layers.selection.clear()
+ viewer.layers.selection.add(viewer.layers[1])
+ assert_figures_not_equal(widget.figure, fig1)
diff --git a/src/napari_matplotlib/tests/test_layer_changes.py b/src/napari_matplotlib/tests/test_layer_changes.py
index bdd6c600..15958c07 100644
--- a/src/napari_matplotlib/tests/test_layer_changes.py
+++ b/src/napari_matplotlib/tests/test_layer_changes.py
@@ -1,5 +1,5 @@
from copy import deepcopy
-from typing import Any, Dict, Tuple, Type
+from typing import Any
import numpy as np
import numpy.typing as npt
@@ -61,8 +61,8 @@ def test_change_features_layer(
def assert_features_plot_changes(
viewer: Viewer,
- widget_cls: Type[NapariMPLWidget],
- data: Tuple[npt.NDArray[np.generic], Dict[str, Any]],
+ widget_cls: type[NapariMPLWidget],
+ data: tuple[npt.NDArray[np.generic], dict[str, Any]],
) -> None:
"""
When the selected layer is changed, make sure the plot generated
diff --git a/src/napari_matplotlib/tests/test_slice.py b/src/napari_matplotlib/tests/test_slice.py
index 412e71c3..368a7ded 100644
--- a/src/napari_matplotlib/tests/test_slice.py
+++ b/src/napari_matplotlib/tests/test_slice.py
@@ -9,9 +9,13 @@
def test_slice_3D(make_napari_viewer, brain_data):
viewer = make_napari_viewer()
viewer.theme = "light"
- viewer.add_image(brain_data[0], **brain_data[1])
+
+ data = brain_data[0]
+ assert data.ndim == 3, data.shape
+ viewer.add_image(data, **brain_data[1])
+
axis = viewer.dims.last_used
- slice_no = brain_data[0].shape[0] - 1
+ slice_no = data.shape[0] - 1
viewer.dims.set_current_step(axis, slice_no)
fig = SliceWidget(viewer).figure
# Need to return a copy, as original figure is too eagerley garbage
@@ -23,8 +27,37 @@ def test_slice_3D(make_napari_viewer, brain_data):
def test_slice_2D(make_napari_viewer, astronaut_data):
viewer = make_napari_viewer()
viewer.theme = "light"
- viewer.add_image(astronaut_data[0], **astronaut_data[1])
+
+ # Take first RGB channel
+ data = astronaut_data[0][:, :, 0]
+ assert data.ndim == 2, data.shape
+ viewer.add_image(data)
+
fig = SliceWidget(viewer).figure
# Need to return a copy, as original figure is too eagerley garbage
# collected by the widget
return deepcopy(fig)
+
+
+def test_slice_axes(make_napari_viewer, astronaut_data):
+ viewer = make_napari_viewer()
+ viewer.theme = "light"
+
+ # Take first RGB channel
+ data = astronaut_data[0][:256, :, 0]
+ # Shape:
+ # x: 0 > 512
+ # y: 0 > 256
+ assert data.ndim == 2, data.shape
+ # Make sure data isn't square for later tests
+ assert data.shape[0] != data.shape[1]
+ viewer.add_image(data)
+
+ widget = SliceWidget(viewer)
+ assert widget._dim_names == ["y", "x"]
+ assert widget.current_dim_name == "x"
+ assert widget.slice_selector.value() == 0
+ assert widget.slice_selector.minimum() == 0
+ assert widget.slice_selector.maximum() == data.shape[0] - 1
+ # x/y are flipped in napari
+ assert widget._slice_width == data.shape[1]
diff --git a/src/napari_matplotlib/tests/test_theme.py b/src/napari_matplotlib/tests/test_theme.py
index a3642f8f..5fedc43d 100644
--- a/src/napari_matplotlib/tests/test_theme.py
+++ b/src/napari_matplotlib/tests/test_theme.py
@@ -1,15 +1,8 @@
-import os
-import shutil
-from copy import deepcopy
-from pathlib import Path
-
-import matplotlib
import napari
import numpy as np
import pytest
-from matplotlib.colors import to_rgba
-from napari_matplotlib import HistogramWidget, ScatterWidget
+from napari_matplotlib import ScatterWidget
from napari_matplotlib.base import NapariMPLWidget
@@ -36,10 +29,12 @@ def _mock_up_theme() -> None:
Based on:
https://napari.org/stable/gallery/new_theme.html
"""
- blue_theme = napari.utils.theme.get_theme("dark", False)
- blue_theme.name = "blue"
+ blue_theme = napari.utils.theme.get_theme("dark")
+ blue_theme.label = "blue"
blue_theme.background = "#4169e1" # my favourite shade of blue
- napari.utils.theme.register_theme("blue", blue_theme)
+ napari.utils.theme.register_theme(
+ "blue", blue_theme, source="napari-mpl-tests"
+ )
def test_theme_background_check(make_napari_viewer):
@@ -125,66 +120,3 @@ def test_no_theme_side_effects(make_napari_viewer):
unrelated_figure.tight_layout()
return unrelated_figure
-
-
-@pytest.mark.mpl_image_compare
-def test_custom_theme(make_napari_viewer, theme_path, brain_data):
- viewer = make_napari_viewer()
- viewer.theme = "dark"
-
- widget = ScatterWidget(viewer)
- widget.mpl_style_sheet_path = theme_path
-
- viewer.add_image(brain_data[0], **brain_data[1], name="brain")
- viewer.add_image(
- brain_data[0] * -1, **brain_data[1], name="brain_reversed"
- )
-
- viewer.layers.selection.clear()
- viewer.layers.selection.add(viewer.layers[0])
- viewer.layers.selection.add(viewer.layers[1])
-
- return deepcopy(widget.figure)
-
-
-def find_mpl_stylesheet(name: str) -> Path:
- """Find the built-in matplotlib stylesheet."""
- return Path(matplotlib.__path__[0]) / f"mpl-data/stylelib/{name}.mplstyle"
-
-
-def test_custom_stylesheet(make_napari_viewer, image_data):
- """
- Test that a stylesheet in the current directory is given precidence.
-
- Do this by copying over a stylesheet from matplotlib's built in styles,
- naming it correctly, and checking the colours are as expected.
- """
- # Copy Solarize_Light2 as if it was a user-overriden stylesheet.
- style_sheet_path = (
- Path(matplotlib.get_configdir()) / "napari-matplotlib.mplstyle"
- )
- if style_sheet_path.exists():
- pytest.skip("Won't ovewrite existing custom style sheet.")
- shutil.copy(
- find_mpl_stylesheet("Solarize_Light2"),
- style_sheet_path,
- )
-
- try:
- viewer = make_napari_viewer()
- viewer.add_image(image_data[0], **image_data[1])
- widget = HistogramWidget(viewer)
- assert widget.mpl_style_sheet_path == style_sheet_path
- ax = widget.figure.gca()
-
- # The axes should have a light brownish grey background:
- assert ax.get_facecolor() == to_rgba("#eee8d5")
- assert ax.patch.get_facecolor() == to_rgba("#eee8d5")
-
- # The figure background and axis gridlines are light yellow:
- assert widget.figure.patch.get_facecolor() == to_rgba("#fdf6e3")
- for gridline in ax.get_xgridlines() + ax.get_ygridlines():
- assert gridline.get_visible() is True
- assert gridline.get_color() == "#fdf6e3"
- finally:
- os.remove(style_sheet_path)
diff --git a/src/napari_matplotlib/tests/test_util.py b/src/napari_matplotlib/tests/test_util.py
index a8792d41..e966cc26 100644
--- a/src/napari_matplotlib/tests/test_util.py
+++ b/src/napari_matplotlib/tests/test_util.py
@@ -26,7 +26,7 @@ def test_interval():
assert 10 not in interval
with pytest.raises(ValueError, match="must be an integer"):
- "string" in interval # type: ignore
+ assert "string" in interval # type: ignore[operator]
with pytest.raises(ValueError, match="must be <= upper_bound"):
Interval(5, 3)
@@ -69,7 +69,10 @@ def test_fallback_if_missing_dimensions(mocker):
test_css = " Flobble { background-color: rgb(0, 97, 163); } "
mocker.patch("napari.qt.get_current_stylesheet").return_value = test_css
with pytest.warns(RuntimeWarning, match="Unable to find DimensionToken"):
- assert from_napari_css_get_size_of("Flobble", (1, 2)) == QSize(1, 2)
+ with pytest.warns(RuntimeWarning, match="Unable to find Flobble"):
+ assert from_napari_css_get_size_of("Flobble", (1, 2)) == QSize(
+ 1, 2
+ )
def test_fallback_if_prelude_not_in_css():
diff --git a/src/napari_matplotlib/util.py b/src/napari_matplotlib/util.py
index 2aa15ddd..8d4150c3 100644
--- a/src/napari_matplotlib/util.py
+++ b/src/napari_matplotlib/util.py
@@ -1,8 +1,8 @@
-from typing import List, Optional, Tuple, Union
from warnings import warn
import napari.qt
import tinycss2
+from napari.utils.theme import Theme
from qtpy.QtCore import QSize
@@ -11,7 +11,7 @@ class Interval:
An integer interval.
"""
- def __init__(self, lower_bound: Optional[int], upper_bound: Optional[int]):
+ def __init__(self, lower_bound: int | None, upper_bound: int | None):
"""
Parameters
----------
@@ -47,7 +47,7 @@ def __contains__(self, val: int) -> bool:
return True
@property
- def _helper_text(self) -> Optional[str]:
+ def _helper_text(self) -> str | None:
"""
Helper text for widgets.
"""
@@ -76,7 +76,7 @@ def _helper_text(self) -> Optional[str]:
return helper_text
-def _has_id(nodes: List[tinycss2.ast.Node], id_name: str) -> bool:
+def _has_id(nodes: list[tinycss2.ast.Node], id_name: str) -> bool:
"""
Is `id_name` in IdentTokens in the list of CSS `nodes`?
"""
@@ -85,9 +85,7 @@ def _has_id(nodes: List[tinycss2.ast.Node], id_name: str) -> bool:
)
-def _get_dimension(
- nodes: List[tinycss2.ast.Node], id_name: str
-) -> Union[int, None]:
+def _get_dimension(nodes: list[tinycss2.ast.Node], id_name: str) -> int | None:
"""
Get the value of the DimensionToken for the IdentToken `id_name`.
@@ -96,19 +94,23 @@ def _get_dimension(
None if no IdentToken is found.
"""
cleaned_nodes = [node for node in nodes if node.type != "whitespace"]
- for name, _, value, _ in zip(*(iter(cleaned_nodes),) * 4):
+ for name, _, value, _ in zip(*(iter(cleaned_nodes),) * 4, strict=False):
if (
name.type == "ident"
and value.type == "dimension"
and name.value == id_name
):
return value.int_value
- warn(f"Unable to find DimensionToken for {id_name}", RuntimeWarning)
+ warn(
+ f"Unable to find DimensionToken for {id_name}",
+ RuntimeWarning,
+ stacklevel=1,
+ )
return None
def from_napari_css_get_size_of(
- qt_element_name: str, fallback: Tuple[int, int]
+ qt_element_name: str, fallback: tuple[int, int]
) -> QSize:
"""
Get the size of `qt_element_name` from napari's current stylesheet.
@@ -136,5 +138,52 @@ def from_napari_css_get_size_of(
f"Unable to find {qt_element_name} or unable to find its size in "
f"the current Napari stylesheet, falling back to {fallback}",
RuntimeWarning,
+ stacklevel=1,
)
return QSize(*fallback)
+
+
+def style_sheet_from_theme(theme: Theme) -> dict[str, str]:
+ """Translate napari theme to a matplotlib style dictionary.
+
+ Parameters
+ ----------
+ theme : napari.utils.theme.Theme
+ Napari theme object representing the theme of the current viewer.
+
+ Returns
+ -------
+ Dict[str, str]
+ Matplotlib compatible style dictionary.
+ """
+ return {
+ "axes.edgecolor": theme.secondary.as_hex(),
+ # BUG: could be the same as napari canvas, but facecolors do not get
+ # updated upon redraw for what ever reason
+ #'axes.facecolor':theme.canvas.as_hex(),
+ "axes.facecolor": "none",
+ "axes.labelcolor": theme.text.as_hex(),
+ "boxplot.boxprops.color": theme.text.as_hex(),
+ "boxplot.capprops.color": theme.text.as_hex(),
+ "boxplot.flierprops.markeredgecolor": theme.text.as_hex(),
+ "boxplot.whiskerprops.color": theme.text.as_hex(),
+ "figure.edgecolor": theme.secondary.as_hex(),
+ # BUG: should be the same as napari background, but facecolors do not get
+ # updated upon redraw for what ever reason
+ #'figure.facecolor':theme.background.as_hex(),
+ "figure.facecolor": "none",
+ "grid.color": theme.foreground.as_hex(),
+ # COMMENT: the hard coded colors are to match the previous behaviour
+ # alternativly we could use the theme to style the legend as well
+ #'legend.edgecolor':theme.secondary.as_hex(),
+ "legend.edgecolor": "black",
+ #'legend.facecolor':theme.background.as_hex(),
+ "legend.facecolor": "white",
+ #'legend.labelcolor':theme.text.as_hex()
+ "legend.labelcolor": "black",
+ "text.color": theme.text.as_hex(),
+ "xtick.color": theme.secondary.as_hex(),
+ "xtick.labelcolor": theme.text.as_hex(),
+ "ytick.color": theme.secondary.as_hex(),
+ "ytick.labelcolor": theme.text.as_hex(),
+ }
diff --git a/tox.ini b/tox.ini
index 298887e1..f4aed6a8 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,19 +1,14 @@
[tox]
-envlist = py{38,39,310}
+envlist = py{310,311,312}
isolated_build = true
[gh-actions]
python =
- 3.8: py38
- 3.9: py39
3.10: py310
+ 3.11: py311
+ 3.12: py312
[testenv]
extras = testing
-allowlist_externals =
- cp
- ls
commands =
- cp -R {toxinidir}/src/napari_matplotlib/tests/baseline {envdir}/baseline
- ls {toxinidir}/src/napari_matplotlib/tests/baseline
python -m pytest --mpl --mpl-generate-summary=html --mpl-results-path={toxinidir}/reports -v --color=yes --cov=napari_matplotlib --cov-report=xml