phasorpy 0.5__cp313-cp313-win_amd64.whl → 0.6__cp313-cp313-win_amd64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- phasorpy/__init__.py +2 -3
- phasorpy/_phasorpy.cp313-win_amd64.pyd +0 -0
- phasorpy/_phasorpy.pyx +185 -2
- phasorpy/_utils.py +121 -9
- phasorpy/cli.py +56 -3
- phasorpy/cluster.py +42 -6
- phasorpy/components.py +226 -55
- phasorpy/experimental.py +312 -0
- phasorpy/io/__init__.py +137 -0
- phasorpy/io/_flimlabs.py +350 -0
- phasorpy/io/_leica.py +329 -0
- phasorpy/io/_ometiff.py +445 -0
- phasorpy/io/_other.py +782 -0
- phasorpy/io/_simfcs.py +627 -0
- phasorpy/phasor.py +307 -1
- phasorpy/plot/__init__.py +27 -0
- phasorpy/plot/_functions.py +717 -0
- phasorpy/plot/_lifetime_plots.py +553 -0
- phasorpy/plot/_phasorplot.py +1119 -0
- phasorpy/plot/_phasorplot_fret.py +559 -0
- phasorpy/utils.py +84 -296
- {phasorpy-0.5.dist-info → phasorpy-0.6.dist-info}/METADATA +2 -2
- phasorpy-0.6.dist-info/RECORD +34 -0
- {phasorpy-0.5.dist-info → phasorpy-0.6.dist-info}/WHEEL +1 -1
- phasorpy/_io.py +0 -2655
- phasorpy/io.py +0 -9
- phasorpy/plot.py +0 -2318
- phasorpy/version.py +0 -80
- phasorpy-0.5.dist-info/RECORD +0 -26
- {phasorpy-0.5.dist-info → phasorpy-0.6.dist-info}/entry_points.txt +0 -0
- {phasorpy-0.5.dist-info → phasorpy-0.6.dist-info}/licenses/LICENSE.txt +0 -0
- {phasorpy-0.5.dist-info → phasorpy-0.6.dist-info}/top_level.txt +0 -0
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"""PhasorPlot class."""
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from __future__ import annotations
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__all__ = ['PhasorPlot']
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import math
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import os
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from collections.abc import Sequence
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from typing import TYPE_CHECKING
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if TYPE_CHECKING:
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from .._typing import Any, ArrayLike, NDArray, IO
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from matplotlib.axes import Axes
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from matplotlib.figure import Figure
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import numpy
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from matplotlib import pyplot
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from matplotlib.font_manager import FontProperties
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from matplotlib.lines import Line2D
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from matplotlib.patches import Arc, Circle, Ellipse, FancyArrowPatch, Polygon
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from matplotlib.path import Path
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from matplotlib.patheffects import AbstractPathEffect
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from .._phasorpy import _intersect_circle_circle, _intersect_circle_line
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from .._utils import (
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dilate_coordinates,
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parse_kwargs,
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phasor_from_polar_scalar,
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phasor_to_polar_scalar,
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sort_coordinates,
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update_kwargs,
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)
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from ..phasor import (
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phasor_from_lifetime,
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phasor_semicircle,
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phasor_to_apparent_lifetime,
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phasor_transform,
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)
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GRID_COLOR = '0.5'
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GRID_LINESTYLE = ':'
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GRID_LINESTYLE_MAJOR = '-'
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GRID_LINEWIDH = 1.0
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GRID_LINEWIDH_MINOR = 0.5
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GRID_FILL = False
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class PhasorPlot:
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"""Phasor plot.
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Create publication quality visualizations of phasor coordinates.
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Parameters
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----------
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allquadrants : bool, optional
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Show all quadrants of phasor space.
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By default, only the first quadrant with universal semicircle is shown.
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ax : matplotlib axes, optional
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Matplotlib axes used for plotting.
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By default, a new subplot axes is created.
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frequency : float, optional
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Laser pulse or modulation frequency in MHz.
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grid : bool, optional, default: True
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Display polar grid or universal semicircle.
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**kwargs
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Additional properties to set on `ax`.
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See Also
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--------
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phasorpy.plot.plot_phasor
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:ref:`sphx_glr_tutorials_api_phasorpy_phasorplot.py`
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"""
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_ax: Axes
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"""Matplotlib axes."""
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_limits: tuple[tuple[float, float], tuple[float, float]]
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"""Axes limits (xmin, xmax), (ymin, ymax)."""
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_full: bool
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"""Show all quadrants of phasor space."""
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_semicircle_ticks: SemicircleTicks | None
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"""Last SemicircleTicks instance created."""
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_frequency: float
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"""Laser pulse or modulation frequency in MHz."""
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def __init__(
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self,
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/,
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allquadrants: bool | None = None,
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ax: Axes | None = None,
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*,
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frequency: float | None = None,
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grid: bool = True,
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**kwargs: Any,
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) -> None:
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# initialize empty phasor plot
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self._ax = pyplot.subplots()[1] if ax is None else ax
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self._ax.format_coord = ( # type: ignore[method-assign]
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self._on_format_coord
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)
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self._semicircle_ticks = None
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self._full = bool(allquadrants)
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if self._full:
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xlim = (-1.05, 1.05)
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ylim = (-1.05, 1.05)
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xticks: tuple[float, ...] = (-1.0, -0.5, 0.0, 0.5, 1.0)
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yticks: tuple[float, ...] = (-1.0, -0.5, 0.0, 0.5, 1.0)
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if grid:
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self.polar_grid()
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else:
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xlim = (-0.05, 1.05)
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ylim = (-0.05, 0.7)
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xticks = (0.0, 0.2, 0.4, 0.6, 0.8, 1.0)
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yticks = (0.0, 0.2, 0.4, 0.6)
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if grid:
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self.semicircle(frequency=frequency)
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title = 'Phasor plot'
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if frequency is not None:
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self._frequency = float(frequency)
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title += f' ({frequency:g} MHz)'
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else:
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self._frequency = 0.0
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update_kwargs(
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kwargs,
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title=title,
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xlabel='G, real',
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ylabel='S, imag',
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aspect='equal',
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xlim=xlim,
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ylim=ylim,
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xticks=xticks,
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yticks=yticks,
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)
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self._limits = (kwargs['xlim'], kwargs['ylim'])
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self._ax.set(**kwargs)
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@property
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def ax(self) -> Axes:
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"""Matplotlib :py:class:`matplotlib.axes.Axes`."""
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return self._ax
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@property
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def fig(self) -> Figure | None:
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"""Matplotlib :py:class:`matplotlib.figure.Figure`."""
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try:
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# matplotlib >= 3.10.0
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return self._ax.get_figure(root=True)
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except TypeError:
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return self._ax.get_figure() # type: ignore[return-value]
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@property
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def dataunit_to_point(self) -> float:
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"""Factor to convert data to point unit."""
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fig = self.fig
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assert fig is not None
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length = fig.bbox_inches.height * self._ax.get_position().height * 72.0
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vrange: float = numpy.diff(self._ax.get_ylim()).item()
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return length / vrange
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def show(self) -> None:
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"""Display all open figures. Call :py:func:`matplotlib.pyplot.show`."""
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# self.fig.show()
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pyplot.show()
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def save(
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self,
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file: str | os.PathLike[Any] | IO[bytes] | None,
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/,
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**kwargs: Any,
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) -> None:
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"""Save current figure to file.
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Parameters
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----------
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file : str, path-like, or binary file-like
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Path or Python file-like object to write the current figure to.
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**kwargs
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Additional keyword arguments passed to
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:py:func:`matplotlib:pyplot.savefig`.
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"""
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pyplot.savefig(file, **kwargs)
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def plot(
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self,
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real: ArrayLike,
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imag: ArrayLike,
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/,
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fmt: str = 'o',
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*,
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label: Sequence[str] | None = None,
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**kwargs: Any,
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) -> list[Line2D]:
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"""Plot imaginary versus real coordinates as markers or lines.
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Parameters
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----------
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real : array_like
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Real component of phasor coordinates.
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Must be one or two dimensional.
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imag : array_like
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Imaginary component of phasor coordinates.
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Must be of same shape as `real`.
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fmt : str, optional, default: 'o'
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Matplotlib style format string.
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label : sequence of str, optional
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Plot label.
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May be a sequence if phasor coordinates are two dimensional arrays.
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**kwargs
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Additional parameters passed to
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:py:meth:`matplotlib.axes.Axes.plot`.
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Returns
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-------
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list[matplotlib.lines.Line2D]
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Lines representing data plotted last.
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"""
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lines = []
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if fmt == 'o':
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if 'marker' in kwargs:
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fmt = ''
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if 'linestyle' not in kwargs and 'ls' not in kwargs:
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kwargs['linestyle'] = ''
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args = (fmt,) if fmt else ()
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ax = self._ax
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if label is not None and (
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isinstance(label, str) or not isinstance(label, Sequence)
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):
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label = (label,)
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for (
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i,
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(re, im),
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) in enumerate(
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zip(
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numpy.atleast_2d(numpy.asarray(real)),
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numpy.atleast_2d(numpy.asarray(imag)),
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)
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):
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lbl = None
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if label is not None:
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try:
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lbl = label[i]
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except IndexError:
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pass
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lines = ax.plot(re, im, *args, label=lbl, **kwargs)
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if label is not None:
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ax.legend()
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self._reset_limits()
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return lines
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def _histogram2d(
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self,
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real: ArrayLike,
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imag: ArrayLike,
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**kwargs: Any,
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) -> tuple[NDArray[Any], NDArray[Any], NDArray[Any]]:
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"""Return two-dimensional histogram of imag versus real coordinates."""
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update_kwargs(kwargs, range=self._limits)
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(xmin, xmax), (ymin, ymax) = kwargs['range']
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assert xmax > xmin and ymax > ymin
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bins = kwargs.get('bins', 128)
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if isinstance(bins, int):
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assert bins > 0
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aspect = (xmax - xmin) / (ymax - ymin)
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if aspect > 1:
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bins = (bins, max(int(bins / aspect), 1))
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else:
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bins = (max(int(bins * aspect), 1), bins)
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kwargs['bins'] = bins
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return numpy.histogram2d(
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numpy.asanyarray(real).reshape(-1),
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numpy.asanyarray(imag).reshape(-1),
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**kwargs,
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)
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def _reset_limits(self) -> None:
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"""Reset axes limits."""
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try:
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self._ax.set(xlim=self._limits[0], ylim=self._limits[1])
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except AttributeError:
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pass
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def hist2d(
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self,
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real: ArrayLike,
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imag: ArrayLike,
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**kwargs: Any,
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) -> None:
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"""Plot two-dimensional histogram of imag versus real coordinates.
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Parameters
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----------
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real : array_like
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Real component of phasor coordinates.
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imag : array_like
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Imaginary component of phasor coordinates.
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Must be of same shape as `real`.
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**kwargs
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Additional parameters passed to :py:meth:`numpy.histogram2d`
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and :py:meth:`matplotlib.axes.Axes.pcolormesh`.
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"""
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kwargs_hist2d = parse_kwargs(
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kwargs, 'bins', 'range', 'density', 'weights'
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)
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h, xedges, yedges = self._histogram2d(real, imag, **kwargs_hist2d)
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update_kwargs(kwargs, cmap='Blues', norm='log')
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cmin = kwargs.pop('cmin', 1)
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cmax = kwargs.pop('cmax', None)
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if cmin is not None:
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h[h < cmin] = None
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if cmax is not None:
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h[h > cmax] = None
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self._ax.pcolormesh(xedges, yedges, h.T, **kwargs)
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self._reset_limits()
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def contour(
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self,
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real: ArrayLike,
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imag: ArrayLike,
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/,
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**kwargs: Any,
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) -> None:
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"""Plot contours of imag versus real coordinates (not implemented).
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Parameters
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----------
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real : array_like
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Real component of phasor coordinates.
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imag : array_like
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Imaginary component of phasor coordinates.
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Must be of same shape as `real`.
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**kwargs
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Additional parameters passed to :py:func:`numpy.histogram2d`
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and :py:meth:`matplotlib.axes.Axes.contour`.
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"""
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if 'cmap' not in kwargs and 'colors' not in kwargs:
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kwargs['cmap'] = 'Blues'
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update_kwargs(kwargs, norm='log')
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kwargs_hist2d = parse_kwargs(
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kwargs, 'bins', 'range', 'density', 'weights'
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)
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+
h, xedges, yedges = self._histogram2d(real, imag, **kwargs_hist2d)
|
359
|
+
xedges = xedges[:-1] + ((xedges[1] - xedges[0]) / 2.0)
|
360
|
+
yedges = yedges[:-1] + ((yedges[1] - yedges[0]) / 2.0)
|
361
|
+
self._ax.contour(xedges, yedges, h.T, **kwargs)
|
362
|
+
self._reset_limits()
|
363
|
+
|
364
|
+
def imshow(
|
365
|
+
self,
|
366
|
+
image: ArrayLike,
|
367
|
+
/,
|
368
|
+
**kwargs: Any,
|
369
|
+
) -> None:
|
370
|
+
"""Plot an image, for example, a 2D histogram (not implemented).
|
371
|
+
|
372
|
+
Parameters
|
373
|
+
----------
|
374
|
+
image : array_like
|
375
|
+
Image to display.
|
376
|
+
**kwargs
|
377
|
+
Additional parameters passed to
|
378
|
+
:py:meth:`matplotlib.axes.Axes.imshow`.
|
379
|
+
|
380
|
+
"""
|
381
|
+
raise NotImplementedError
|
382
|
+
|
383
|
+
def components(
|
384
|
+
self,
|
385
|
+
real: ArrayLike,
|
386
|
+
imag: ArrayLike,
|
387
|
+
/,
|
388
|
+
fraction: ArrayLike | None = None,
|
389
|
+
labels: Sequence[str] | None = None,
|
390
|
+
label_offset: float | None = None,
|
391
|
+
**kwargs: Any,
|
392
|
+
) -> None:
|
393
|
+
"""Plot linear combinations of phasor coordinates or ranges thereof.
|
394
|
+
|
395
|
+
Parameters
|
396
|
+
----------
|
397
|
+
real : (N,) array_like
|
398
|
+
Real component of phasor coordinates.
|
399
|
+
imag : (N,) array_like
|
400
|
+
Imaginary component of phasor coordinates.
|
401
|
+
fraction : (N,) array_like, optional
|
402
|
+
Weight associated with each component.
|
403
|
+
If None (default), outline the polygon area of possible linear
|
404
|
+
combinations of components.
|
405
|
+
Else, draw lines from the component coordinates to the weighted
|
406
|
+
average.
|
407
|
+
labels : Sequence of str, optional
|
408
|
+
Text label for each component.
|
409
|
+
label_offset : float, optional
|
410
|
+
Distance of text label to component coordinate.
|
411
|
+
**kwargs
|
412
|
+
Additional parameters passed to
|
413
|
+
:py:class:`matplotlib.patches.Polygon`,
|
414
|
+
:py:class:`matplotlib.lines.Line2D`, or
|
415
|
+
:py:class:`matplotlib.axes.Axes.annotate`
|
416
|
+
|
417
|
+
"""
|
418
|
+
# TODO: use convex hull for outline
|
419
|
+
# TODO: improve automatic placement of labels
|
420
|
+
# TODO: catch more annotate properties?
|
421
|
+
real, imag, indices = sort_coordinates(real, imag)
|
422
|
+
|
423
|
+
label_ = kwargs.pop('label', None)
|
424
|
+
marker = kwargs.pop('marker', None)
|
425
|
+
color = kwargs.pop('color', None)
|
426
|
+
fontsize = kwargs.pop('fontsize', 12)
|
427
|
+
fontweight = kwargs.pop('fontweight', 'bold')
|
428
|
+
horizontalalignment = kwargs.pop('horizontalalignment', 'center')
|
429
|
+
verticalalignment = kwargs.pop('verticalalignment', 'center')
|
430
|
+
if label_offset is None:
|
431
|
+
label_offset = numpy.diff(self._ax.get_xlim()).item() * 0.04
|
432
|
+
|
433
|
+
if labels is not None:
|
434
|
+
if len(labels) != real.size:
|
435
|
+
raise ValueError(
|
436
|
+
f'number labels={len(labels)} != components={real.size}'
|
437
|
+
)
|
438
|
+
labels = [labels[i] for i in indices]
|
439
|
+
textposition = dilate_coordinates(real, imag, label_offset)
|
440
|
+
for label, re, im, x, y in zip(labels, real, imag, *textposition):
|
441
|
+
if not label:
|
442
|
+
continue
|
443
|
+
self._ax.annotate(
|
444
|
+
label,
|
445
|
+
(re, im),
|
446
|
+
xytext=(x, y),
|
447
|
+
color=color,
|
448
|
+
fontsize=fontsize,
|
449
|
+
fontweight=fontweight,
|
450
|
+
horizontalalignment=horizontalalignment,
|
451
|
+
verticalalignment=verticalalignment,
|
452
|
+
)
|
453
|
+
|
454
|
+
if fraction is None:
|
455
|
+
update_kwargs(
|
456
|
+
kwargs,
|
457
|
+
edgecolor=GRID_COLOR if color is None else color,
|
458
|
+
linestyle=GRID_LINESTYLE,
|
459
|
+
linewidth=GRID_LINEWIDH,
|
460
|
+
fill=GRID_FILL,
|
461
|
+
)
|
462
|
+
self._ax.add_patch(Polygon(numpy.vstack((real, imag)).T, **kwargs))
|
463
|
+
if marker is not None:
|
464
|
+
self._ax.plot(
|
465
|
+
real,
|
466
|
+
imag,
|
467
|
+
marker=marker,
|
468
|
+
linestyle='',
|
469
|
+
color=color,
|
470
|
+
label=label_,
|
471
|
+
)
|
472
|
+
if label_ is not None:
|
473
|
+
self._ax.legend()
|
474
|
+
return
|
475
|
+
|
476
|
+
fraction = numpy.asarray(fraction)[indices]
|
477
|
+
update_kwargs(
|
478
|
+
kwargs,
|
479
|
+
color=GRID_COLOR if color is None else color,
|
480
|
+
linestyle=GRID_LINESTYLE,
|
481
|
+
linewidth=GRID_LINEWIDH,
|
482
|
+
)
|
483
|
+
center_re, center_im = numpy.average(
|
484
|
+
numpy.vstack((real, imag)), axis=-1, weights=fraction
|
485
|
+
)
|
486
|
+
for re, im in zip(real, imag):
|
487
|
+
self._ax.add_line(
|
488
|
+
Line2D([center_re, re], [center_im, im], **kwargs)
|
489
|
+
)
|
490
|
+
if marker is not None:
|
491
|
+
self._ax.plot(real, imag, marker=marker, linestyle='', color=color)
|
492
|
+
self._ax.plot(
|
493
|
+
center_re,
|
494
|
+
center_im,
|
495
|
+
marker=marker,
|
496
|
+
linestyle='',
|
497
|
+
color=color,
|
498
|
+
label=label_,
|
499
|
+
)
|
500
|
+
if label_ is not None:
|
501
|
+
self._ax.legend()
|
502
|
+
|
503
|
+
def line(
|
504
|
+
self,
|
505
|
+
real: ArrayLike,
|
506
|
+
imag: ArrayLike,
|
507
|
+
/,
|
508
|
+
**kwargs: Any,
|
509
|
+
) -> list[Line2D]:
|
510
|
+
"""Draw grid line.
|
511
|
+
|
512
|
+
Parameters
|
513
|
+
----------
|
514
|
+
real : array_like, shape (n, )
|
515
|
+
Real components of line start and end coordinates.
|
516
|
+
imag : array_like, shape (n, )
|
517
|
+
Imaginary components of line start and end coordinates.
|
518
|
+
**kwargs
|
519
|
+
Additional parameters passed to
|
520
|
+
:py:class:`matplotlib.lines.Line2D`.
|
521
|
+
|
522
|
+
Returns
|
523
|
+
-------
|
524
|
+
list[matplotlib.lines.Line2D]
|
525
|
+
List containing plotted line.
|
526
|
+
|
527
|
+
"""
|
528
|
+
update_kwargs(
|
529
|
+
kwargs,
|
530
|
+
color=GRID_COLOR,
|
531
|
+
linestyle=GRID_LINESTYLE,
|
532
|
+
linewidth=GRID_LINEWIDH,
|
533
|
+
)
|
534
|
+
return [self._ax.add_line(Line2D(real, imag, **kwargs))]
|
535
|
+
|
536
|
+
def circle(
|
537
|
+
self,
|
538
|
+
real: float,
|
539
|
+
imag: float,
|
540
|
+
/,
|
541
|
+
radius: float,
|
542
|
+
**kwargs: Any,
|
543
|
+
) -> None:
|
544
|
+
"""Draw grid circle of radius around center.
|
545
|
+
|
546
|
+
Parameters
|
547
|
+
----------
|
548
|
+
real : float
|
549
|
+
Real component of circle center coordinate.
|
550
|
+
imag : float
|
551
|
+
Imaginary component of circle center coordinate.
|
552
|
+
radius : float
|
553
|
+
Circle radius.
|
554
|
+
**kwargs
|
555
|
+
Additional parameters passed to
|
556
|
+
:py:class:`matplotlib.patches.Circle`.
|
557
|
+
|
558
|
+
"""
|
559
|
+
update_kwargs(
|
560
|
+
kwargs,
|
561
|
+
color=GRID_COLOR,
|
562
|
+
linestyle=GRID_LINESTYLE,
|
563
|
+
linewidth=GRID_LINEWIDH,
|
564
|
+
fill=GRID_FILL,
|
565
|
+
)
|
566
|
+
self._ax.add_patch(Circle((real, imag), radius, **kwargs))
|
567
|
+
|
568
|
+
def arrow(
|
569
|
+
self,
|
570
|
+
point0: ArrayLike,
|
571
|
+
point1: ArrayLike,
|
572
|
+
/,
|
573
|
+
*,
|
574
|
+
angle: float | None = None,
|
575
|
+
**kwargs: Any,
|
576
|
+
) -> None:
|
577
|
+
"""Draw arrow between points.
|
578
|
+
|
579
|
+
By default, draw a straight arrow with a `'-|>'` style, a mutation
|
580
|
+
scale of 20, and a miter join style.
|
581
|
+
|
582
|
+
Parameters
|
583
|
+
----------
|
584
|
+
point0 : array_like
|
585
|
+
X and y coordinates of start point of arrow.
|
586
|
+
point1 : array_like
|
587
|
+
X and y coordinates of end point of arrow.
|
588
|
+
angle : float, optional
|
589
|
+
Angle in radians, controlling curvature of line between points.
|
590
|
+
If None (default), draw a straight line.
|
591
|
+
**kwargs
|
592
|
+
Additional parameters passed to
|
593
|
+
:py:class:`matplotlib.patches.FancyArrowPatch`.
|
594
|
+
|
595
|
+
"""
|
596
|
+
arrowstyle = kwargs.pop('arrowstyle', '-|>')
|
597
|
+
mutation_scale = kwargs.pop('mutation_scale', 20)
|
598
|
+
joinstyle = kwargs.pop('joinstyle', 'miter')
|
599
|
+
if angle is not None:
|
600
|
+
kwargs['connectionstyle'] = f'arc3,rad={math.tan(angle / 4.0)}'
|
601
|
+
|
602
|
+
patch = FancyArrowPatch(
|
603
|
+
point0, # type: ignore[arg-type]
|
604
|
+
point1, # type: ignore[arg-type]
|
605
|
+
arrowstyle=arrowstyle,
|
606
|
+
mutation_scale=mutation_scale,
|
607
|
+
# capstyle='projecting',
|
608
|
+
joinstyle=joinstyle,
|
609
|
+
**kwargs,
|
610
|
+
)
|
611
|
+
self._ax.add_patch(patch)
|
612
|
+
|
613
|
+
def cursor(
|
614
|
+
self,
|
615
|
+
real: float,
|
616
|
+
imag: float,
|
617
|
+
/,
|
618
|
+
real_limit: float | None = None,
|
619
|
+
imag_limit: float | None = None,
|
620
|
+
radius: float | None = None,
|
621
|
+
radius_minor: float | None = None,
|
622
|
+
angle: float | None = None,
|
623
|
+
align_semicircle: bool = False,
|
624
|
+
**kwargs: Any,
|
625
|
+
) -> None:
|
626
|
+
"""Plot phase and modulation grid lines and arcs at phasor coordinates.
|
627
|
+
|
628
|
+
Parameters
|
629
|
+
----------
|
630
|
+
real : float
|
631
|
+
Real component of phasor coordinate.
|
632
|
+
imag : float
|
633
|
+
Imaginary component of phasor coordinate.
|
634
|
+
real_limit : float, optional
|
635
|
+
Real component of limiting phasor coordinate.
|
636
|
+
imag_limit : float, optional
|
637
|
+
Imaginary component of limiting phasor coordinate.
|
638
|
+
radius : float, optional
|
639
|
+
Radius of circle limiting phase and modulation grid lines and arcs.
|
640
|
+
radius_minor : float, optional
|
641
|
+
Radius of elliptic cursor along semi-minor axis.
|
642
|
+
By default, `radius_minor` is equal to `radius`, that is,
|
643
|
+
the ellipse is circular.
|
644
|
+
angle : float, optional
|
645
|
+
Rotation angle of semi-major axis of elliptic cursor in radians.
|
646
|
+
If None (default), orient ellipse cursor according to
|
647
|
+
`align_semicircle`.
|
648
|
+
align_semicircle : bool, optional
|
649
|
+
Determines elliptic cursor orientation if `angle` is not provided.
|
650
|
+
If true, align the minor axis of the ellipse with the closest
|
651
|
+
tangent on the universal semicircle, else align to the unit circle.
|
652
|
+
**kwargs
|
653
|
+
Additional parameters passed to
|
654
|
+
:py:class:`matplotlib.lines.Line2D`,
|
655
|
+
:py:class:`matplotlib.patches.Circle`,
|
656
|
+
:py:class:`matplotlib.patches.Ellipse`, or
|
657
|
+
:py:class:`matplotlib.patches.Arc`.
|
658
|
+
|
659
|
+
See Also
|
660
|
+
--------
|
661
|
+
phasorpy.plot.PhasorPlot.polar_cursor
|
662
|
+
|
663
|
+
"""
|
664
|
+
if real_limit is not None and imag_limit is not None:
|
665
|
+
return self.polar_cursor(
|
666
|
+
*phasor_to_polar_scalar(real, imag),
|
667
|
+
*phasor_to_polar_scalar(real_limit, imag_limit),
|
668
|
+
radius=radius,
|
669
|
+
radius_minor=radius_minor,
|
670
|
+
angle=angle,
|
671
|
+
align_semicircle=align_semicircle,
|
672
|
+
**kwargs,
|
673
|
+
)
|
674
|
+
return self.polar_cursor(
|
675
|
+
*phasor_to_polar_scalar(real, imag),
|
676
|
+
radius=radius,
|
677
|
+
radius_minor=radius_minor,
|
678
|
+
angle=angle,
|
679
|
+
align_semicircle=align_semicircle,
|
680
|
+
# _circle_only=True,
|
681
|
+
**kwargs,
|
682
|
+
)
|
683
|
+
|
684
|
+
def polar_cursor(
|
685
|
+
self,
|
686
|
+
phase: float | None = None,
|
687
|
+
modulation: float | None = None,
|
688
|
+
phase_limit: float | None = None,
|
689
|
+
modulation_limit: float | None = None,
|
690
|
+
radius: float | None = None,
|
691
|
+
radius_minor: float | None = None,
|
692
|
+
angle: float | None = None,
|
693
|
+
align_semicircle: bool = False,
|
694
|
+
**kwargs: Any,
|
695
|
+
) -> None:
|
696
|
+
"""Plot phase and modulation grid lines and arcs.
|
697
|
+
|
698
|
+
Parameters
|
699
|
+
----------
|
700
|
+
phase : float, optional
|
701
|
+
Angular component of polar coordinate in radians.
|
702
|
+
modulation : float, optional
|
703
|
+
Radial component of polar coordinate.
|
704
|
+
phase_limit : float, optional
|
705
|
+
Angular component of limiting polar coordinate (in radians).
|
706
|
+
Modulation grid arcs are drawn between `phase` and `phase_limit`.
|
707
|
+
modulation_limit : float, optional
|
708
|
+
Radial component of limiting polar coordinate.
|
709
|
+
Phase grid lines are drawn from `modulation` to `modulation_limit`.
|
710
|
+
radius : float, optional
|
711
|
+
Radius of circle limiting phase and modulation grid lines and arcs.
|
712
|
+
radius_minor : float, optional
|
713
|
+
Radius of elliptic cursor along semi-minor axis.
|
714
|
+
By default, `radius_minor` is equal to `radius`, that is,
|
715
|
+
the ellipse is circular.
|
716
|
+
angle : float, optional
|
717
|
+
Rotation angle of semi-major axis of elliptic cursor in radians.
|
718
|
+
If None (default), orient ellipse cursor according to
|
719
|
+
`align_semicircle`.
|
720
|
+
align_semicircle : bool, optional
|
721
|
+
Determines elliptic cursor orientation if `angle` is not provided.
|
722
|
+
If true, align the minor axis of the ellipse with the closest
|
723
|
+
tangent on the universal semicircle, else align to the unit circle.
|
724
|
+
**kwargs
|
725
|
+
Additional parameters passed to
|
726
|
+
:py:class:`matplotlib.lines.Line2D`,
|
727
|
+
:py:class:`matplotlib.patches.Circle`,
|
728
|
+
:py:class:`matplotlib.patches.Ellipse`, or
|
729
|
+
:py:class:`matplotlib.patches.Arc`.
|
730
|
+
|
731
|
+
See Also
|
732
|
+
--------
|
733
|
+
phasorpy.plot.PhasorPlot.cursor
|
734
|
+
|
735
|
+
"""
|
736
|
+
update_kwargs(
|
737
|
+
kwargs,
|
738
|
+
color=GRID_COLOR,
|
739
|
+
linestyle=GRID_LINESTYLE,
|
740
|
+
linewidth=GRID_LINEWIDH,
|
741
|
+
fill=GRID_FILL,
|
742
|
+
)
|
743
|
+
_circle_only = kwargs.pop('_circle_only', False)
|
744
|
+
ax = self._ax
|
745
|
+
if radius is not None and phase is not None and modulation is not None:
|
746
|
+
x = modulation * math.cos(phase)
|
747
|
+
y = modulation * math.sin(phase)
|
748
|
+
if radius_minor is not None and radius_minor != radius:
|
749
|
+
if angle is None:
|
750
|
+
if align_semicircle:
|
751
|
+
angle = math.atan2(y, x - 0.5)
|
752
|
+
else:
|
753
|
+
angle = phase
|
754
|
+
angle = math.degrees(angle)
|
755
|
+
ax.add_patch(
|
756
|
+
Ellipse(
|
757
|
+
(x, y),
|
758
|
+
radius * 2,
|
759
|
+
radius_minor * 2,
|
760
|
+
angle=angle,
|
761
|
+
**kwargs,
|
762
|
+
)
|
763
|
+
)
|
764
|
+
# TODO: implement gridlines intersecting with ellipse
|
765
|
+
return None
|
766
|
+
ax.add_patch(Circle((x, y), radius, **kwargs))
|
767
|
+
if _circle_only:
|
768
|
+
return None
|
769
|
+
del kwargs['fill']
|
770
|
+
x0, y0, x1, y1 = _intersect_circle_line(x, y, radius, 0, 0, x, y)
|
771
|
+
ax.add_line(Line2D((x0, x1), (y0, y1), **kwargs))
|
772
|
+
x0, y0, x1, y1 = _intersect_circle_circle(
|
773
|
+
0, 0, modulation, x, y, radius
|
774
|
+
)
|
775
|
+
ax.add_patch(
|
776
|
+
Arc(
|
777
|
+
(0, 0),
|
778
|
+
modulation * 2,
|
779
|
+
modulation * 2,
|
780
|
+
theta1=math.degrees(math.atan2(y0, x0)),
|
781
|
+
theta2=math.degrees(math.atan2(y1, x1)),
|
782
|
+
fill=False,
|
783
|
+
**kwargs,
|
784
|
+
)
|
785
|
+
)
|
786
|
+
return None
|
787
|
+
|
788
|
+
del kwargs['fill']
|
789
|
+
for phi in (phase, phase_limit):
|
790
|
+
if phi is not None:
|
791
|
+
if modulation is not None and modulation_limit is not None:
|
792
|
+
x0 = modulation * math.cos(phi)
|
793
|
+
y0 = modulation * math.sin(phi)
|
794
|
+
x1 = modulation_limit * math.cos(phi)
|
795
|
+
y1 = modulation_limit * math.sin(phi)
|
796
|
+
else:
|
797
|
+
x0 = 0
|
798
|
+
y0 = 0
|
799
|
+
x1 = math.cos(phi)
|
800
|
+
y1 = math.sin(phi)
|
801
|
+
ax.add_line(Line2D((x0, x1), (y0, y1), **kwargs))
|
802
|
+
for mod in (modulation, modulation_limit):
|
803
|
+
if mod is not None:
|
804
|
+
if phase is not None and phase_limit is not None:
|
805
|
+
theta1 = math.degrees(min(phase, phase_limit))
|
806
|
+
theta2 = math.degrees(max(phase, phase_limit))
|
807
|
+
else:
|
808
|
+
theta1 = 0.0
|
809
|
+
theta2 = 360.0 if self._full else 90.0
|
810
|
+
ax.add_patch(
|
811
|
+
Arc(
|
812
|
+
(0, 0),
|
813
|
+
mod * 2,
|
814
|
+
mod * 2,
|
815
|
+
theta1=theta1,
|
816
|
+
theta2=theta2,
|
817
|
+
fill=False, # filling arc objects is not supported
|
818
|
+
**kwargs,
|
819
|
+
)
|
820
|
+
)
|
821
|
+
return None
|
822
|
+
|
823
|
+
def polar_grid(self, **kwargs: Any) -> None:
|
824
|
+
"""Draw polar coordinate system.
|
825
|
+
|
826
|
+
Parameters
|
827
|
+
----------
|
828
|
+
**kwargs
|
829
|
+
Parameters passed to
|
830
|
+
:py:class:`matplotlib.patches.Circle` and
|
831
|
+
:py:class:`matplotlib.lines.Line2D`.
|
832
|
+
|
833
|
+
"""
|
834
|
+
ax = self._ax
|
835
|
+
# major gridlines
|
836
|
+
kwargs_copy = kwargs.copy()
|
837
|
+
update_kwargs(
|
838
|
+
kwargs,
|
839
|
+
color=GRID_COLOR,
|
840
|
+
linestyle=GRID_LINESTYLE_MAJOR,
|
841
|
+
linewidth=GRID_LINEWIDH,
|
842
|
+
# fill=GRID_FILL,
|
843
|
+
)
|
844
|
+
ax.add_line(Line2D([-1, 1], [0, 0], **kwargs))
|
845
|
+
ax.add_line(Line2D([0, 0], [-1, 1], **kwargs))
|
846
|
+
ax.add_patch(Circle((0, 0), 1, fill=False, **kwargs))
|
847
|
+
# minor gridlines
|
848
|
+
kwargs = kwargs_copy
|
849
|
+
update_kwargs(
|
850
|
+
kwargs,
|
851
|
+
color=GRID_COLOR,
|
852
|
+
linestyle=GRID_LINESTYLE,
|
853
|
+
linewidth=GRID_LINEWIDH_MINOR,
|
854
|
+
)
|
855
|
+
for r in (1 / 3, 2 / 3):
|
856
|
+
ax.add_patch(Circle((0, 0), r, fill=False, **kwargs))
|
857
|
+
for a in (3, 6):
|
858
|
+
x = math.cos(math.pi / a)
|
859
|
+
y = math.sin(math.pi / a)
|
860
|
+
ax.add_line(Line2D([-x, x], [-y, y], **kwargs))
|
861
|
+
ax.add_line(Line2D([-x, x], [y, -y], **kwargs))
|
862
|
+
|
863
|
+
def semicircle(
|
864
|
+
self,
|
865
|
+
frequency: float | None = None,
|
866
|
+
*,
|
867
|
+
polar_reference: tuple[float, float] | None = None,
|
868
|
+
phasor_reference: tuple[float, float] | None = None,
|
869
|
+
lifetime: Sequence[float] | None = None,
|
870
|
+
labels: Sequence[str] | None = None,
|
871
|
+
show_circle: bool = True,
|
872
|
+
use_lines: bool = False,
|
873
|
+
**kwargs: Any,
|
874
|
+
) -> list[Line2D]:
|
875
|
+
"""Draw universal semicircle.
|
876
|
+
|
877
|
+
Parameters
|
878
|
+
----------
|
879
|
+
frequency : float, optional
|
880
|
+
Laser pulse or modulation frequency in MHz.
|
881
|
+
polar_reference : (float, float), optional, default: (0, 1)
|
882
|
+
Polar coordinates of zero lifetime.
|
883
|
+
phasor_reference : (float, float), optional, default: (1, 0)
|
884
|
+
Phasor coordinates of zero lifetime.
|
885
|
+
Alternative to `polar_reference`.
|
886
|
+
lifetime : sequence of float, optional
|
887
|
+
Single component lifetimes at which to draw ticks and labels.
|
888
|
+
Only applies when `frequency` is specified.
|
889
|
+
labels : sequence of str, optional
|
890
|
+
Tick labels. By default, the values of `lifetime`.
|
891
|
+
Only applies when `frequency` and `lifetime` are specified.
|
892
|
+
show_circle : bool, optional, default: True
|
893
|
+
Draw universal semicircle.
|
894
|
+
use_lines : bool, optional, default: False
|
895
|
+
Draw universal semicircle using lines instead of arc.
|
896
|
+
**kwargs
|
897
|
+
Additional parameters passed to
|
898
|
+
:py:class:`matplotlib.lines.Line2D` or
|
899
|
+
:py:class:`matplotlib.patches.Arc` and
|
900
|
+
:py:meth:`matplotlib.axes.Axes.plot`.
|
901
|
+
|
902
|
+
Returns
|
903
|
+
-------
|
904
|
+
list[matplotlib.lines.Line2D]
|
905
|
+
Lines representing plotted semicircle and ticks.
|
906
|
+
|
907
|
+
"""
|
908
|
+
if frequency is not None:
|
909
|
+
self._frequency = float(frequency)
|
910
|
+
|
911
|
+
update_kwargs(
|
912
|
+
kwargs,
|
913
|
+
color=GRID_COLOR,
|
914
|
+
linestyle=GRID_LINESTYLE_MAJOR,
|
915
|
+
linewidth=GRID_LINEWIDH,
|
916
|
+
)
|
917
|
+
if phasor_reference is not None:
|
918
|
+
polar_reference = phasor_to_polar_scalar(*phasor_reference)
|
919
|
+
if polar_reference is None:
|
920
|
+
polar_reference = (0.0, 1.0)
|
921
|
+
if phasor_reference is None:
|
922
|
+
phasor_reference = phasor_from_polar_scalar(*polar_reference)
|
923
|
+
ax = self._ax
|
924
|
+
|
925
|
+
lines = []
|
926
|
+
|
927
|
+
if show_circle:
|
928
|
+
if use_lines:
|
929
|
+
lines = [
|
930
|
+
ax.add_line(
|
931
|
+
Line2D(
|
932
|
+
*phasor_transform(
|
933
|
+
*phasor_semicircle(), *polar_reference
|
934
|
+
),
|
935
|
+
**kwargs,
|
936
|
+
)
|
937
|
+
)
|
938
|
+
]
|
939
|
+
else:
|
940
|
+
ax.add_patch(
|
941
|
+
Arc(
|
942
|
+
(phasor_reference[0] / 2, phasor_reference[1] / 2),
|
943
|
+
polar_reference[1],
|
944
|
+
polar_reference[1],
|
945
|
+
theta1=math.degrees(polar_reference[0]),
|
946
|
+
theta2=math.degrees(polar_reference[0]) + 180.0,
|
947
|
+
fill=False,
|
948
|
+
**kwargs,
|
949
|
+
)
|
950
|
+
)
|
951
|
+
|
952
|
+
if frequency is not None and polar_reference == (0.0, 1.0):
|
953
|
+
# draw ticks and labels
|
954
|
+
lifetime, labels = _semicircle_ticks(frequency, lifetime, labels)
|
955
|
+
self._semicircle_ticks = SemicircleTicks(labels=labels)
|
956
|
+
lines.extend(
|
957
|
+
ax.plot(
|
958
|
+
*phasor_transform(
|
959
|
+
*phasor_from_lifetime(frequency, lifetime),
|
960
|
+
*polar_reference,
|
961
|
+
),
|
962
|
+
path_effects=[self._semicircle_ticks],
|
963
|
+
**kwargs,
|
964
|
+
)
|
965
|
+
)
|
966
|
+
self._reset_limits()
|
967
|
+
return lines
|
968
|
+
|
969
|
+
def _on_format_coord(self, x: float, y: float) -> str:
|
970
|
+
"""Callback function to update coordinates displayed in toolbar."""
|
971
|
+
phi, mod = phasor_to_polar_scalar(x, y)
|
972
|
+
ret = [
|
973
|
+
f'[{x:4.2f}, {y:4.2f}]',
|
974
|
+
f'[{math.degrees(phi):.0f}°, {mod * 100:.0f}%]',
|
975
|
+
]
|
976
|
+
if x > 0.0 and y > 0.0 and self._frequency > 0.0:
|
977
|
+
tp, tm = phasor_to_apparent_lifetime(x, y, self._frequency)
|
978
|
+
ret.append(f'[{tp:.2f}, {tm:.2f} ns]')
|
979
|
+
return ' '.join(reversed(ret))
|
980
|
+
|
981
|
+
|
982
|
+
class SemicircleTicks(AbstractPathEffect):
|
983
|
+
"""Draw ticks on universal semicircle.
|
984
|
+
|
985
|
+
Parameters
|
986
|
+
----------
|
987
|
+
size : float, optional
|
988
|
+
Length of tick in dots.
|
989
|
+
The default is ``rcParams['xtick.major.size']``.
|
990
|
+
labels : sequence of str, optional
|
991
|
+
Tick labels for each vertex in path.
|
992
|
+
**kwargs
|
993
|
+
Extra keywords passed to matplotlib's
|
994
|
+
:py:meth:`matplotlib.patheffects.AbstractPathEffect._update_gc`.
|
995
|
+
|
996
|
+
"""
|
997
|
+
|
998
|
+
_size: float # tick length
|
999
|
+
_labels: tuple[str, ...] # tick labels
|
1000
|
+
_gc: dict[str, Any] # keywords passed to _update_gc
|
1001
|
+
|
1002
|
+
def __init__(
|
1003
|
+
self,
|
1004
|
+
size: float | None = None,
|
1005
|
+
labels: Sequence[str] | None = None,
|
1006
|
+
**kwargs: Any,
|
1007
|
+
) -> None:
|
1008
|
+
super().__init__((0.0, 0.0))
|
1009
|
+
|
1010
|
+
if size is None:
|
1011
|
+
self._size = pyplot.rcParams['xtick.major.size']
|
1012
|
+
else:
|
1013
|
+
self._size = size
|
1014
|
+
if labels is None or not labels:
|
1015
|
+
self._labels = ()
|
1016
|
+
else:
|
1017
|
+
self._labels = tuple(labels)
|
1018
|
+
self._gc = kwargs
|
1019
|
+
|
1020
|
+
@property
|
1021
|
+
def labels(self) -> tuple[str, ...]:
|
1022
|
+
"""Tick labels."""
|
1023
|
+
return self._labels
|
1024
|
+
|
1025
|
+
@labels.setter
|
1026
|
+
def labels(self, value: Sequence[str] | None, /) -> None:
|
1027
|
+
if value is None or not value:
|
1028
|
+
self._labels = ()
|
1029
|
+
else:
|
1030
|
+
self._labels = tuple(value)
|
1031
|
+
|
1032
|
+
def draw_path(
|
1033
|
+
self,
|
1034
|
+
renderer: Any,
|
1035
|
+
gc: Any,
|
1036
|
+
tpath: Any,
|
1037
|
+
affine: Any,
|
1038
|
+
rgbFace: Any = None,
|
1039
|
+
) -> None:
|
1040
|
+
"""Draw path with updated gc."""
|
1041
|
+
gc0 = renderer.new_gc()
|
1042
|
+
gc0.copy_properties(gc)
|
1043
|
+
|
1044
|
+
# TODO: this uses private methods of the base class
|
1045
|
+
gc0 = self._update_gc(gc0, self._gc) # type: ignore[attr-defined]
|
1046
|
+
trans = affine
|
1047
|
+
trans += self._offset_transform(renderer) # type: ignore[attr-defined]
|
1048
|
+
|
1049
|
+
font = FontProperties()
|
1050
|
+
# approximate half size of 'x'
|
1051
|
+
fontsize = renderer.points_to_pixels(font.get_size_in_points()) / 4
|
1052
|
+
size = renderer.points_to_pixels(self._size)
|
1053
|
+
origin = affine.transform([[0.5, 0.0]])
|
1054
|
+
|
1055
|
+
transpath = affine.transform_path(tpath)
|
1056
|
+
polys = transpath.to_polygons(closed_only=False)
|
1057
|
+
|
1058
|
+
for p in polys:
|
1059
|
+
# coordinates of tick ends
|
1060
|
+
t = p - origin
|
1061
|
+
t /= numpy.hypot(t[:, 0], t[:, 1])[:, numpy.newaxis]
|
1062
|
+
d = t.copy()
|
1063
|
+
t *= size
|
1064
|
+
t += p
|
1065
|
+
|
1066
|
+
xyt = numpy.empty((2 * p.shape[0], 2))
|
1067
|
+
xyt[0::2] = p
|
1068
|
+
xyt[1::2] = t
|
1069
|
+
|
1070
|
+
renderer.draw_path(
|
1071
|
+
gc0,
|
1072
|
+
Path(xyt, numpy.tile([Path.MOVETO, Path.LINETO], p.shape[0])),
|
1073
|
+
affine.inverted() + trans,
|
1074
|
+
rgbFace,
|
1075
|
+
)
|
1076
|
+
if not self._labels:
|
1077
|
+
continue
|
1078
|
+
# coordinates of labels
|
1079
|
+
t = d * size * 2.5
|
1080
|
+
t += p
|
1081
|
+
|
1082
|
+
if renderer.flipy():
|
1083
|
+
h = renderer.get_canvas_width_height()[1]
|
1084
|
+
else:
|
1085
|
+
h = 0.0
|
1086
|
+
|
1087
|
+
for s, (x, y), (dx, _) in zip(self._labels, t, d):
|
1088
|
+
# TODO: get rendered text size from matplotlib.text.Text?
|
1089
|
+
# this did not work:
|
1090
|
+
# Text(d[i,0], h - d[i,1], label, ha='center', va='center')
|
1091
|
+
x = x + fontsize * len(s.split()[0]) * (dx - 1.0)
|
1092
|
+
y = h - y + fontsize
|
1093
|
+
renderer.draw_text(gc0, x, y, s, font, 0.0)
|
1094
|
+
|
1095
|
+
gc0.restore()
|
1096
|
+
|
1097
|
+
|
1098
|
+
def _semicircle_ticks(
|
1099
|
+
frequency: float,
|
1100
|
+
lifetime: Sequence[float] | None = None,
|
1101
|
+
labels: Sequence[str] | None = None,
|
1102
|
+
) -> tuple[tuple[float, ...], tuple[str, ...]]:
|
1103
|
+
"""Return semicircle tick lifetimes and labels at frequency."""
|
1104
|
+
if lifetime is None:
|
1105
|
+
lifetime = [0.0] + [
|
1106
|
+
2**t
|
1107
|
+
for t in range(-8, 32)
|
1108
|
+
if phasor_from_lifetime(frequency, 2**t)[1] >= 0.18
|
1109
|
+
]
|
1110
|
+
unit = 'ns'
|
1111
|
+
else:
|
1112
|
+
unit = ''
|
1113
|
+
if labels is None:
|
1114
|
+
labels = [f'{tau:g}' for tau in lifetime]
|
1115
|
+
try:
|
1116
|
+
labels[2] = f'{labels[2]} {unit}'
|
1117
|
+
except IndexError:
|
1118
|
+
pass
|
1119
|
+
return tuple(lifetime), tuple(labels)
|