Filled Circle Markers

Create a signal

import hyperspy.api as hs
import matplotlib as mpl
import numpy as np

# Create a Signal2D with 2 navigation dimensions
rng = np.random.default_rng(0)
data = np.ones((25, 25, 100, 100))
s = hs.signals.Signal2D(data)

This first example shows how to draw static filled circles

# Define the position of the circles
offsets = rng.random((10, 2)) * 100

m = hs.plot.markers.Points(
    sizes=20,
    offsets=offsets,
    facecolors="red",
    )

s.plot()
s.add_marker(m)

• 
• 

/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(

Dynamic Filled Circle Markers

This second example shows how to draw dynamic filled circles, whose size, color and position change depending on the navigation position

s2 = hs.signals.Signal2D(data)

offsets = np.empty(s.axes_manager.navigation_shape, dtype=object)
sizes = np.empty(s.axes_manager.navigation_shape, dtype=object)
colors = list(mpl.colors.TABLEAU_COLORS.values())[:10]

for ind in np.ndindex(offsets.shape):
    offsets[ind] = rng.random((10, 2)) * 100
    sizes[ind] = rng.random((10, )) * 50

m = hs.plot.markers.Points(
    sizes=sizes,
    offsets=offsets,
    facecolors=colors,
    )

s2.plot()
s2.add_marker(m)

• 
• 

/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(
/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/site-packages/rsciio/utils/rgb_tools.py:62: VisibleDeprecationWarning: The module `rsciio.utils.rgb_tools` has been renamed to `rsciio.utils.rgb` and it will be removed in version 1.0.
  warnings.warn(

sphinx_gallery_thumbnail_number = 2