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Commit bb0bb27

Browse filesBrowse files
clewis7kushalkolar
clewis7
and
kushalkolar
authored
sphinx gallery (#509)
* start sphinx gallery * relevant file changes * progress * edit setup.py to include missing dependencies * attempt to fix rtd * remove large heatmap example that breaks rtd * fix linter, attempt to fix quickstart bug * fix gridplot examples and gallery structure * remove nbsphinx * remove nbsphinx and quickstart.ipynb from docs * remove init files from examples * update examples and conf.py * add animation examples, edit conf.py, fix scatter examples * add sklearn to docs, example needs it * Update setup.py * Update setup.py * remove from gallery, kills readthedocs runner * update canvas size so thumbnails render better * change scatter examples, remove sklearn from docs dependencies * add iris scatter examples, exclude from screenshot tests * add more animation examples, add to tests * add simple multigraphic gridplot example * add simple event, fix multigraphic gridplot * Update line3d_animation.py * add simple event example * minor changes * replace screenshots and fix small bug * fix scatter examples for CI build * fix screenshots * add sklearn as docs dependency, include iris scatter examples in gallery * Update examples/desktop/misc/simple_event.py Co-authored-by: Kushal Kolar <kushalkolar@gmail.com> * update screenshots --------- Co-authored-by: Kushal Kolar <kushalkolar@gmail.com>
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‎docs/source/conf.py

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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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import os
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# need to force offscreen rendering before importing fpl
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# otherwise fpl tries to select glfw canvas
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os.environ["WGPU_FORCE_OFFSCREEN"] = "1"
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import fastplotlib
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from pygfx.utils.gallery_scraper import find_examples_for_gallery
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from pathlib import Path
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import sys
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from sphinx_gallery.sorting import ExplicitOrder
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import imageio.v3 as iio
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ROOT_DIR = Path(__file__).parents[1].parents[0] # repo root
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EXAMPLES_DIR = Path.joinpath(ROOT_DIR, "examples", "desktop")
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sys.path.insert(0, str(ROOT_DIR))
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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"sphinx.ext.viewcode",
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"sphinx_copybutton",
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"sphinx_design",
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"sphinx_gallery.gen_gallery"
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]
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sphinx_gallery_conf = {
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"gallery_dirs": "_gallery",
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"backreferences_dir": "_gallery/backreferences",
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"doc_module": ("fastplotlib",),
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"image_scrapers": ("pygfx",),
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"remove_config_comments": True,
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"subsection_order": ExplicitOrder(
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[
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"../../examples/desktop/image",
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"../../examples/desktop/gridplot",
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"../../examples/desktop/line",
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"../../examples/desktop/line_collection",
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"../../examples/desktop/scatter",
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"../../examples/desktop/heatmap",
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"../../examples/desktop/misc"
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]
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),
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"ignore_pattern": r'__init__\.py',
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"nested_sections": False,
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"thumbnail_size": (250, 250)
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}
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extra_conf = find_examples_for_gallery(EXAMPLES_DIR)
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sphinx_gallery_conf.update(extra_conf)
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# download imageio examples for the gallery
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iio.imread("imageio:clock.png")
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iio.imread("imageio:astronaut.png")
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iio.imread("imageio:coffee.png")
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iio.imread("imageio:hubble_deep_field.png")
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autosummary_generate = True
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templates_path = ["_templates"]
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}
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html_theme_options = {
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"source_repository": "https://github.com/kushalkolar/fastplotlib",
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"source_repository": "https://github.com/fastplotlib/fastplotlib",
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"source_branch": "main",
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"source_directory": "docs/",
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}

‎docs/source/index.rst

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Utils <api/utils>
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GPU <api/gpu>
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.. toctree::
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:caption: Gallery
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:maxdepth: 1
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Gallery <_gallery/index>
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Summary
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=======
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‎examples/README.rst

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Examples that use fastplotlib
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=============================

‎examples/desktop/gridplot/__init__.py renamed to ‎examples/desktop/README.rst

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‎examples/desktop/gridplot/README.rst

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GridPlot Examples
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=================

‎examples/desktop/gridplot/gridplot.py

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"""
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GridPlot Simple
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============
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===============
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Example showing simple 2x2 GridPlot with Standard images from imageio.
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"""
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# test_example = true
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# sphinx_gallery_pygfx_docs = 'screenshot'
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import fastplotlib as fpl
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import imageio.v3 as iio
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fig = fpl.Figure(shape=(2, 2))
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figure = fpl.Figure(shape=(2, 2))
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im = iio.imread("imageio:clock.png")
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im2 = iio.imread("imageio:astronaut.png")
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im3 = iio.imread("imageio:coffee.png")
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im4 = iio.imread("imageio:hubble_deep_field.png")
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fig[0, 0].add_image(data=im)
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fig[0, 1].add_image(data=im2)
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fig[1, 0].add_image(data=im3)
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fig[1, 1].add_image(data=im4)
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figure[0, 0].add_image(data=im)
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figure[0, 1].add_image(data=im2)
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figure[1, 0].add_image(data=im3)
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figure[1, 1].add_image(data=im4)
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fig.show()
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figure.show()
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fig.canvas.set_logical_size(800, 800)
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figure.canvas.set_logical_size(700, 560)
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for subplot in fig:
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for subplot in figure:
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subplot.auto_scale()
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# NOTE: `if __name__ == "__main__"` is NOT how to use fastplotlib interactively
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# please see our docs for using fastplotlib interactively in ipython and jupyter
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if __name__ == "__main__":
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print(__doc__)
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fpl.run()

‎examples/desktop/gridplot/gridplot_non_square.py

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"""
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GridPlot Simple
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============
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GridPlot Non-Square Example
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===========================
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Example showing simple 2x2 GridPlot with Standard images from imageio.
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"""
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# test_example = true
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# sphinx_gallery_pygfx_docs = 'screenshot'
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import fastplotlib as fpl
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import imageio.v3 as iio
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fig = fpl.Figure(shape=(2, 2), controller_ids="sync")
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figure = fpl.Figure(shape=(2, 2), controller_ids="sync")
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im = iio.imread("imageio:clock.png")
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im2 = iio.imread("imageio:astronaut.png")
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im3 = iio.imread("imageio:coffee.png")
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fig[0, 0].add_image(data=im)
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fig[0, 1].add_image(data=im2)
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fig[1, 0].add_image(data=im3)
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figure[0, 0].add_image(data=im)
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figure[0, 1].add_image(data=im2)
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figure[1, 0].add_image(data=im3)
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fig.show()
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figure.show()
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fig.canvas.set_logical_size(800, 800)
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figure.canvas.set_logical_size(700, 560)
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for subplot in fig:
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for subplot in figure:
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subplot.auto_scale()
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# NOTE: `if __name__ == "__main__"` is NOT how to use fastplotlib interactively
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# please see our docs for using fastplotlib interactively in ipython and jupyter
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if __name__ == "__main__":
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print(__doc__)
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fpl.run()

‎examples/desktop/gridplot/multigraphic_gridplot.py

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"""
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Multi-Graphic GridPlot
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======================
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Example showing a Figure with multiple subplots and multiple graphic types.
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"""
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# test_example = true
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# sphinx_gallery_pygfx_docs = 'screenshot'
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import fastplotlib as fpl
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import numpy as np
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import imageio.v3 as iio
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from itertools import product
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# define figure
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figure = fpl.Figure(shape=(2, 2), names=[["image-overlay", "circles"], ["line-stack", "scatter"]])
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img = iio.imread("imageio:coffee.png")
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# add image to subplot
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figure["image-overlay"].add_image(data=img)
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# generate overlay
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# empty array for overlay, shape is [nrows, ncols, RGBA]
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overlay = np.zeros(shape=(*img.shape[:2], 4), dtype=np.float32)
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# set the blue values of some pixels with an alpha > 1
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overlay[img[:, :, -1] > 200] = np.array([0.0, 0.0, 1.0, 0.6]).astype(np.float32)
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# add overlay to image
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figure["image-overlay"].add_image(data=overlay)
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# generate some circles
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def make_circle(center, radius: float, n_points: int = 75) -> np.ndarray:
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theta = np.linspace(0, 2 * np.pi, n_points)
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xs = radius * np.sin(theta)
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ys = radius * np.cos(theta)
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return np.column_stack([xs, ys]) + center
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spatial_dims = (50, 50)
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# this makes 16 circles, so we can create 16 cmap values, so it will use these values to set the
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# color of the line based by using the cmap as a LUT with the corresponding cmap_transform
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circles = list()
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for center in product(range(0, spatial_dims[0], 15), range(0, spatial_dims[1], 15)):
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circles.append(make_circle(center, 5, n_points=75))
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# things like class labels, cluster labels, etc.
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cmap_transform = [
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0, 1, 1, 2,
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0, 0, 1, 1,
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2, 2, 8, 3,
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1, 9, 1, 5
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]
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# add an image to overlay the circles on
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img2 = np.ones((60, 60))
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figure["circles"].add_image(data=img2)
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# add the circles to the figure
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figure["circles"].add_line_collection(
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circles,
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cmap="tab10",
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cmap_transform=cmap_transform,
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thickness=3,
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alpha=0.5,
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name="circles-graphic"
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)
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# move the circles graphic so that it is centered over the image
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figure["circles"]["circles-graphic"].offset = np.array([7, 7, 2])
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# generate some sine data
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# linspace, create 100 evenly spaced x values from -10 to 10
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xs = np.linspace(-10, 10, 100)
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# sine wave
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ys = np.sin(xs)
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sine = np.dstack([xs, ys])[0]
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# make 10 identical waves
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sine_waves = 10 * [sine]
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# add the line stack to the figure
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figure["line-stack"].add_line_stack(data=sine_waves, cmap="Wistia", separation=1)
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figure["line-stack"].auto_scale(maintain_aspect=True)
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# generate some scatter data
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# create a gaussian cloud of 500 points
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n_points = 500
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mean = [0, 0] # mean of the Gaussian distribution
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covariance = [[1, 0], [0, 1]] # covariance matrix
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gaussian_cloud = np.random.multivariate_normal(mean, covariance, n_points)
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gaussian_cloud2 = np.random.multivariate_normal(mean, covariance, n_points)
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# add the scatter graphics to the figure
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figure["scatter"].add_scatter(data=gaussian_cloud, sizes=1, cmap="jet")
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figure["scatter"].add_scatter(data=gaussian_cloud2, colors="r", sizes=1)
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figure.show()
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figure.canvas.set_logical_size(700, 560)
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# NOTE: `if __name__ == "__main__"` is NOT how to use fastplotlib interactively
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# please see our docs for using fastplotlib interactively in ipython and jupyter
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if __name__ == "__main__":
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print(__doc__)
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fpl.run()
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‎examples/desktop/heatmap/README.rst

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Heatmap Examples
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================

‎examples/desktop/heatmap/__init__.py

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‎examples/desktop/heatmap/heatmap.py

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"""
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# sphinx_gallery_pygfx_docs = 'screenshot'
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import numpy as np
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fig = fpl.Figure()
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figure = fpl.Figure()
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xs = np.linspace(0, 1_000, 10_000, dtype=np.float32)
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data = np.vstack([sine * i for i in range(20_000)])
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# plot the image data
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img = fig[0, 0].add_image(data=data, name="heatmap")
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img = figure[0, 0].add_image(data=data, name="heatmap")
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fig.show()
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figure.show()
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fig.canvas.set_logical_size(1500, 1500)
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figure.canvas.set_logical_size(700, 560)
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fig[0, 0].auto_scale()
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figure[0, 0].auto_scale()
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# NOTE: `if __name__ == "__main__"` is NOT how to use fastplotlib interactively
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# please see our docs for using fastplotlib interactively in ipython and jupyter
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if __name__ == "__main__":
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print(__doc__)
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fpl.run()

‎examples/desktop/heatmap/heatmap_cmap.py

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Change the cmap of a heatmap
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"""
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# test_example = false
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# sphinx_gallery_pygfx_docs = 'hidden'
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import numpy as np
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fig = fpl.Figure()
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figure = fpl.Figure()
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xs = np.linspace(0, 1_000, 10_000, dtype=np.float32)
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data = np.vstack([sine * i for i in range(20_000)])
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# plot the image data
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img = fig[0, 0].add_image(data=data, name="heatmap")
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img = figure[0, 0].add_image(data=data, name="heatmap")
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fig.show()
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figure.show()
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fig.canvas.set_logical_size(1500, 1500)
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figure.canvas.set_logical_size(700, 560)
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fig[0, 0].auto_scale()
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figure[0, 0].auto_scale()
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img.cmap = "viridis"
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# NOTE: `if __name__ == "__main__"` is NOT how to use fastplotlib interactively
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# please see our docs for using fastplotlib interactively in ipython and jupyter
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if __name__ == "__main__":
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print(__doc__)
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fpl.run()

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