phasorpy 0.7__cp314-cp314t-macosx_11_0_arm64.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 +9 -0
- phasorpy/__main__.py +7 -0
- phasorpy/_phasorpy.cpython-314t-darwin.so +0 -0
- phasorpy/_phasorpy.pyx +2688 -0
- phasorpy/_typing.py +77 -0
- phasorpy/_utils.py +786 -0
- phasorpy/cli.py +160 -0
- phasorpy/cluster.py +200 -0
- phasorpy/color.py +589 -0
- phasorpy/component.py +707 -0
- phasorpy/conftest.py +38 -0
- phasorpy/cursor.py +500 -0
- phasorpy/datasets.py +722 -0
- phasorpy/experimental.py +310 -0
- phasorpy/io/__init__.py +138 -0
- phasorpy/io/_flimlabs.py +360 -0
- phasorpy/io/_leica.py +331 -0
- phasorpy/io/_ometiff.py +444 -0
- phasorpy/io/_other.py +890 -0
- phasorpy/io/_simfcs.py +652 -0
- phasorpy/lifetime.py +2058 -0
- phasorpy/phasor.py +2018 -0
- phasorpy/plot/__init__.py +27 -0
- phasorpy/plot/_functions.py +723 -0
- phasorpy/plot/_lifetime_plots.py +563 -0
- phasorpy/plot/_phasorplot.py +1507 -0
- phasorpy/plot/_phasorplot_fret.py +561 -0
- phasorpy/py.typed +0 -0
- phasorpy/utils.py +172 -0
- phasorpy-0.7.dist-info/METADATA +74 -0
- phasorpy-0.7.dist-info/RECORD +35 -0
- phasorpy-0.7.dist-info/WHEEL +6 -0
- phasorpy-0.7.dist-info/entry_points.txt +2 -0
- phasorpy-0.7.dist-info/licenses/LICENSE.txt +21 -0
- phasorpy-0.7.dist-info/top_level.txt +1 -0
phasorpy/color.py
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"""Color palettes and color manipulation utilities."""
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from __future__ import annotations
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__all__ = ['float2int', 'wavelength2rgb', 'CATEGORICAL', 'SRGB_SPECTRUM']
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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, DTypeLike, NDArray
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import numpy
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def wavelength2rgb(
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wavelength: ArrayLike,
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/,
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dtype: DTypeLike | None = None,
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) -> tuple[float, float, float] | NDArray[Any]:
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"""Return approximate sRGB color components of visible wavelength(s).
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Wavelengths are clipped to the range [360, 750] nm, rounded, and used to
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index the :py:attr:`SRGB_SPECTRUM` palette.
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Parameters
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----------
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wavelength : array_like
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Scalar or array of wavelengths in nm.
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dtype : dtype_like, optional
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Data-type of return value. The default is ``float32``.
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Returns
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-------
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ndarray or tuple of float
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Approximate sRGB color components of visible wavelength(s).
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If input is scalar, return tuple of three floats.
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If input is array, return ndarray with shape (..., 3).
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Floating-point values are in range [0.0, 1.0].
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Integer values are scaled to the dtype's maximum value.
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Examples
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--------
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>>> wavelength2rgb(517.2, 'uint8')
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(0, 191, 0)
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>>> wavelength2rgb([517, 566], 'uint8')
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array([[ 0, 191, 0],
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[133, 190, 0]], dtype=uint8)
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"""
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astuple = isinstance(wavelength, (float, int))
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indices = numpy.asarray(wavelength)
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indices = numpy.clip(indices, 360, 750)
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indices -= 360
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if indices.dtype.kind not in {'u', 'i'}:
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indices = numpy.round(indices).astype(numpy.uint32)
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rgb = SRGB_SPECTRUM.take(indices, axis=0)
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if dtype is not None:
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dtype = numpy.dtype(dtype)
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if dtype.kind in {'u', 'i'}:
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rgb = float2int(rgb)
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else:
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rgb = rgb.astype(dtype)
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if astuple:
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return tuple(rgb.tolist()[:3])
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return rgb
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def float2int(
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rgb: ArrayLike,
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/,
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dtype: DTypeLike = numpy.uint8,
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) -> NDArray[Any]:
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"""Return normalized color components as integers.
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Parameters
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----------
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rgb : array_like
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Scalar or array of normalized floating-point color components.
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dtype : dtype_like, optional
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Data type of return value. The default is ``uint8``.
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Returns
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-------
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ndarray
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Color components as integers scaled to dtype's range.
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Examples
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--------
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>>> float2int([0.0, 0.5, 1.0])
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array([ 0, 128, 255], dtype=uint8)
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"""
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dtype = numpy.dtype(dtype)
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if dtype.kind not in {'u', 'i'}:
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raise ValueError('not an integer dtype')
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arr: NDArray[Any] = numpy.asarray(rgb)
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if not arr.dtype.kind == 'f':
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raise ValueError('not a floating-point array')
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iinfo = numpy.iinfo(dtype)
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arr = numpy.round(arr * iinfo.max)
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numpy.clip(arr, iinfo.min, iinfo.max, out=arr)
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return arr.astype(dtype)
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# fmt: off
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CATEGORICAL: NDArray[numpy.float32] = numpy.array([
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[0.825397, 0.095238, 0.126984],
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[0.095239, 0.412698, 1.0],
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[0.000001, 0.539682, 0.0],
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[0.952381, 0.428571, 1.0],
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[0.444444, 0.0, 0.476191],
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[0.666667, 0.984127, 0.0],
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[0.0, 0.746032, 0.761905],
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[1.0, 0.634921, 0.206349],
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[0.365079, 0.238095, 0.015873],
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[0.031746, 0.0, 0.539683],
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[0.0, 0.365079, 0.365079],
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[0.603175, 0.492064, 0.507937],
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[0.634921, 0.68254, 1.0],
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[0.587302, 0.714286, 0.460317],
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[0.619048, 0.15873, 1.0],
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[0.301587, 0.0, 0.079365],
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[1.0, 0.68254, 0.746032],
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[0.809524, 0.0, 0.571429],
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[0.000001, 1.0, 0.714286],
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[0.0, 0.174603, 0.0],
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[0.619048, 0.460317, 0.0],
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[0.238095, 0.206349, 0.253968],
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[0.952381, 0.920635, 0.571429],
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[0.396825, 0.380952, 0.539683],
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[0.539683, 0.238095, 0.301587],
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[0.349206, 0.015873, 0.730159],
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[0.333333, 0.539683, 0.444444],
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[0.698413, 0.746032, 0.761905],
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[1.0, 0.365079, 0.507936],
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[0.111113, 0.777778, 0.0],
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[0.571429, 0.968254, 1.0],
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[0.174603, 0.52381, 0.650794],
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[0.222222, 0.365079, 0.15873],
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[0.920635, 0.809524, 1.0],
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[1.0, 0.365079, 0.0],
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[0.650794, 0.380952, 0.666667],
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[0.52381, 0.0, 0.0],
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[0.206349, 0.0, 0.349206],
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[0.0, 0.31746, 0.555556],
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[0.619048, 0.285714, 0.063492],
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[0.809524, 0.746032, 0.0],
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[0.0, 0.15873, 0.15873],
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[0.000001, 0.698413, 1.0],
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[0.793651, 0.650794, 0.52381],
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[0.746032, 0.603175, 0.761905],
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[0.174603, 0.126984, 0.047619],
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[0.460317, 0.396825, 0.269841],
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[0.507937, 0.47619, 0.873016],
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[0.0, 0.761905, 0.539682],
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[0.730159, 0.904762, 0.761905],
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[0.52381, 0.555556, 0.650794],
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[0.793651, 0.444444, 0.349206],
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[0.507937, 0.603175, 0.0],
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[0.174603, 0.0, 1.0],
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[0.825397, 0.015873, 0.968254],
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[1.0, 0.84127, 0.746032],
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[0.571429, 0.809524, 0.968254],
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[0.730159, 0.365079, 0.492063],
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[1.0, 0.253968, 0.761905],
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[0.746032, 0.523809, 1.0],
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[0.571429, 0.555556, 0.396825],
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[0.650794, 0.015874, 0.666667],
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[0.523809, 0.888889, 0.460317],
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[0.285714, 0.0, 0.238095],
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], dtype=numpy.float32)
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"""Categorical sRGB color palette inspired by C. Glasbey.
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Contains 64 maximally distinct colors for visualization.
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Generated using the `glasbey <https://glasbey.readthedocs.io>`_ package::
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import glasbey; numpy.array(glasbey.create_palette(64, as_hex=False))
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"""
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# numpy.set_printoptions(6, suppress=True, threshold=512)
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# fmt: on
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# fmt: off
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SRGB_SPECTRUM: NDArray[numpy.float32] = numpy.array([
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[0.000637, 0.0, 0.003852],
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[0.000715, 0.0, 0.004328],
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[0.000802, 0.0, 0.004863],
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[0.000899, 0.0, 0.005466],
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[0.001009, 0.0, 0.006144],
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[0.001131, 0.0, 0.006903],
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[0.001269, 0.0, 0.007758],
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[0.001425, 0.0, 0.008725],
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[0.0016, 0.0, 0.009811],
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[0.001794, 0.0, 0.011023],
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[0.00201, 0.0, 0.012369],
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[0.002247, 0.0, 0.013842],
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[0.00251, 0.0, 0.015481],
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[0.002811, 0.0, 0.017364],
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[0.003162, 0.0, 0.019563],
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[0.003575, 0.0, 0.022156],
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[0.004067, 0.0, 0.025266],
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[0.004636, 0.0, 0.028861],
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[0.005257, 0.0, 0.032785],
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[0.005906, 0.0, 0.036882],
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[0.006558, 0.0, 0.040984],
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[0.007197, 0.0, 0.044803],
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[0.007867, 0.0, 0.04859],
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[0.00863, 0.0, 0.052687],
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[0.009552, 0.0, 0.057365],
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[0.010697, 0.0, 0.062824],
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[0.012123, 0.0, 0.069172],
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[0.013823, 0.0, 0.076199],
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[0.015764, 0.0, 0.083636],
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[0.017911, 0.0, 0.091277],
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[0.020232, 0.0, 0.098967],
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[0.022687, 0.0, 0.106577],
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[0.025366, 0.0, 0.114362],
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[0.028425, 0.0, 0.122688],
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[0.032022, 0.0, 0.131827],
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[0.036313, 0.0, 0.141965],
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[0.04149, 0.0, 0.153349],
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[0.047101, 0.0, 0.165553],
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[0.052759, 0.0, 0.177868],
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[0.058222, 0.0, 0.189771],
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[0.063308, 0.0, 0.200873],
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[0.067943, 0.0, 0.211017],
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[0.07248, 0.0, 0.220985],
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[0.077342, 0.0, 0.231705],
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[0.082871, 0.0, 0.243915],
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[0.089323, 0.0, 0.258172],
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[0.096763, 0.0, 0.274629],
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[0.104948, 0.0, 0.292759],
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[0.113649, 0.0, 0.312047],
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[0.122685, 0.0, 0.332089],
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[0.131916, 0.0, 0.352572],
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[0.141263, 0.0, 0.373353],
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[0.150829, 0.0, 0.394689],
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[0.160741, 0.0, 0.416865],
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[0.171093, 0.0, 0.440085],
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[0.181952, 0.0, 0.464491],
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[0.193196, 0.0, 0.4898],
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[0.20469, 0.0, 0.515787],
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[0.216461, 0.0, 0.542603],
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[0.228524, 0.0, 0.570357],
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[0.240891, 0.0, 0.599121],
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[0.253574, 0.0, 0.628923],
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[0.266254, 0.0, 0.659006],
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[0.278515, 0.0, 0.688434],
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[0.290023, 0.0, 0.716465],
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[0.300501, 0.0, 0.742501],
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[0.309873, 0.0, 0.766385],
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[0.318252, 0.0, 0.788388],
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[0.325666, 0.0, 0.808609],
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[0.332132, 0.0, 0.827124],
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[0.337655, 0.0, 0.843989],
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[0.34221, 0.0, 0.859194],
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[0.345826, 0.0, 0.872791],
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[0.348574, 0.0, 0.884896],
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[0.350514, 0.0, 0.895609],
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[0.351698, 0.0, 0.905015],
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[0.35214, 0.0, 0.913161],
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[0.351844, 0.0, 0.920111],
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[0.350835, 0.0, 0.925957],
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[0.349134, 0.0, 0.930785],
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[0.346758, 0.0, 0.934672],
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[0.343711, 0.0, 0.937667],
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[0.339997, 0.0, 0.939848],
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[0.335622, 0.0, 0.941331],
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[0.330587, 0.0, 0.94223],
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[0.324891, 0.0, 0.942656],
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[0.318511, 0.0, 0.942657],
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[0.311425, 0.0, 0.942271],
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[0.303629, 0.0, 0.941593],
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[0.29511, 0.0, 0.940715],
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[0.285853, 0.0, 0.939732],
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[0.275831, 0.0, 0.938721],
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[0.264929, 0.0, 0.937617],
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[0.252956, 0.0, 0.936302],
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[0.239668, 0.0, 0.934652],
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[0.224736, 0.0, 0.932547],
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[0.207739, 0.0, 0.929913],
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|
+
[0.013036, 0.0, 0.0],
|
563
|
+
[0.012105, 0.0, 0.0],
|
564
|
+
[0.011239, 0.0, 0.0],
|
565
|
+
[0.010434, 0.0, 0.0],
|
566
|
+
[0.009686, 0.0, 0.0],
|
567
|
+
[0.00899, 0.0, 0.0],
|
568
|
+
[0.008344, 0.0, 0.0],
|
569
|
+
[0.007746, 0.0, 0.0],
|
570
|
+
[0.007192, 0.0, 0.0],
|
571
|
+
[0.006681, 0.0, 0.0],
|
572
|
+
[0.00621, 0.0, 0.0],
|
573
|
+
[0.005776, 0.0, 0.0],
|
574
|
+
[0.005375, 0.0, 0.0],
|
575
|
+
[0.005006, 0.0, 0.0],
|
576
|
+
[0.004664, 0.0, 0.0],
|
577
|
+
], dtype=numpy.float32)
|
578
|
+
"""sRGB color components for wavelengths of visible light (360-750 nm).
|
579
|
+
|
580
|
+
Array of shape (391, 3) containing normalized sRGB color components
|
581
|
+
for wavelengths from 360 to 750 nm in 1 nm increments.
|
582
|
+
Based on the CIE 1931 2° Standard Observer.
|
583
|
+
|
584
|
+
Generated using the `colour <https://colour.readthedocs.io>`_ package::
|
585
|
+
|
586
|
+
import colour; colour.plotting.plot_visible_spectrum()
|
587
|
+
|
588
|
+
"""
|
589
|
+
# fmt: on
|