phasorpy 0.5__cp311-cp311-win_amd64.whl → 0.7__cp311-cp311-win_amd64.whl

phasorpy/components.py

@@ -1,313 +0,0 @@
-"""Component analysis of phasor coordinates.
-
-The ``phasorpy.components`` module provides functions to:
-
-- calculate fractions of two known components by projecting onto the
-  line between the components:
-
-  - :py:func:`two_fractions_from_phasor`
-
-- calculate phasor coordinates of second component if only one is
-  known (not implemented)
-
-- calculate fractions of three or four known components by using higher
-  harmonic information (not implemented)
-
-- calculate fractions of two or three known components by resolving
-  graphically with histogram:
-
-  - :py:func:`graphical_component_analysis`
-
-- blindly resolve fractions of `n` components by using harmonic
-  information (not implemented)
-
-"""
-
-from __future__ import annotations
-
-__all__ = [
-    'two_fractions_from_phasor',
-    'graphical_component_analysis',
-]
-
-import numbers
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from ._typing import Any, ArrayLike, NDArray
-
-import numpy
-
-from ._phasorpy import (
-    _fraction_on_segment,
-    _is_inside_circle,
-    _is_inside_stadium,
-    _segment_direction_and_length,
-)
-
-
-def two_fractions_from_phasor(
-    real: ArrayLike,
-    imag: ArrayLike,
-    components_real: ArrayLike,
-    components_imag: ArrayLike,
-    /,
-) -> NDArray[Any]:
-    """Return fraction of first of two components from phasor coordinates.
-
-    Return the relative distance (normalized by the distance between the two
-    components) to the second component for each phasor coordinate projected
-    onto the line between two components.
-
-    Parameters
-    ----------
-    real : array_like
-        Real component of phasor coordinates.
-    imag : array_like
-        Imaginary component of phasor coordinates.
-    components_real : array_like, shape (2,)
-        Real coordinates of first and second components.
-    components_imag : array_like, shape (2,)
-        Imaginary coordinates of first and second components.
-
-    Returns
-    -------
-    fraction : ndarray
-        Fractions of first component.
-
-    Raises
-    ------
-    ValueError
-        If the real or imaginary coordinates of the known components are
-        not of size 2.
-
-    See Also
-    --------
-    :ref:`sphx_glr_tutorials_api_phasorpy_components.py`
-
-    Notes
-    -----
-    The fraction of the second component is ``1.0 - fraction``.
-
-    For now, calculation of fraction of components from different
-    channels or frequencies is not supported. Only one pair of components can
-    be analyzed and will be broadcast to all channels/frequencies.
-
-    Examples
-    --------
-    >>> two_fractions_from_phasor(
-    ...     [0.6, 0.5, 0.4], [0.4, 0.3, 0.2], [0.2, 0.9], [0.4, 0.3]
-    ... )  # doctest: +NUMBER
-    array([0.44, 0.56, 0.68])
-
-    """
-    components_real = numpy.asarray(components_real)
-    components_imag = numpy.asarray(components_imag)
-    if components_real.shape != (2,):
-        raise ValueError(f'{components_real.shape=} != (2,)')
-    if components_imag.shape != (2,):
-        raise ValueError(f'{components_imag.shape=} != (2,)')
-    if (
-        components_real[0] == components_real[1]
-        and components_imag[0] == components_imag[1]
-    ):
-        raise ValueError('components must have different coordinates')
-
-    return _fraction_on_segment(  # type: ignore[no-any-return]
-        real,
-        imag,
-        components_real[0],
-        components_imag[0],
-        components_real[1],
-        components_imag[1],
-    )
-
-
-def graphical_component_analysis(
-    real: ArrayLike,
-    imag: ArrayLike,
-    components_real: ArrayLike,
-    components_imag: ArrayLike,
-    /,
-    *,
-    radius: float = 0.05,
-    fractions: ArrayLike | None = None,
-) -> tuple[NDArray[Any], ...]:
-    r"""Return fractions of two or three components from phasor coordinates.
-
-    The graphical method is based on moving circular cursors along the line
-    between pairs of components and quantifying the phasors for each
-    fraction.
-
-    Parameters
-    ----------
-    real : array_like
-        Real component of phasor coordinates.
-    imag : array_like
-        Imaginary component of phasor coordinates.
-    components_real : array_like, shape (2,) or (3,)
-        Real coordinates for two or three components.
-    components_imag : array_like, shape (2,) or (3,)
-        Imaginary coordinates for two or three components.
-    radius : float, optional, default: 0.05
-        Radius of cursor.
-    fractions : array_like or int, optional
-        Number of equidistant fractions, or 1D array of fraction values.
-        Fraction values must be in range [0.0, 1.0].
-        If an integer, ``numpy.linspace(0.0, 1.0, fractions)`` fraction values
-        are used.
-        If None (default), the number of fractions is determined from the
-        longest distance between any pair of components and the radius of
-        the cursor (see Notes below).
-
-    Returns
-    -------
-    counts : tuple of ndarray
-        Counts along each line segment connecting components.
-        Ordered 0-1 (2 components) or 0-1, 0-2, 1-2 (3 components).
-
-    Raises
-    ------
-    ValueError
-        The array shapes of `real` and `imag`, or `components_real` and
-        `components_imag` do not match.
-        The number of components is not 2 or 3.
-        Fraction values are out of range [0.0, 1.0].
-
-    See Also
-    --------
-    :ref:`sphx_glr_tutorials_api_phasorpy_components.py`
-
-    Notes
-    -----
-    For now, calculation of fraction of components from different
-    channels or frequencies is not supported. Only one set of components can
-    be analyzed and will be broadcast to all channels/frequencies.
-
-    The graphical method was first introduced in [1]_.
-
-    If no `fractions` are provided, the number of fractions (:math:`N`) used
-    is determined from the longest distance between any pair of components
-    (:math:`D`) and the radius of the cursor (:math:`R`):
-
-    .. math::
-
-        N = \frac{2 \cdot D}{R} + 1
-
-    The fractions can be retrieved by:
-
-    .. code-block:: python
-
-        fractions = numpy.linspace(0.0, 1.0, len(counts[0]))
-
-    References
-    ----------
-
-    .. [1] Ranjit S, Datta R, Dvornikov A, and Gratton E.
-      `Multicomponent analysis of phasor plot in a single pixel to
-      calculate changes of metabolic trajectory in biological systems
-      <https://doi.org/10.1021/acs.jpca.9b07880>`_.
-      *J Phys Chem A*, 123(45): 9865-9873 (2019)
-
-    Examples
-    --------
-    Count the number of phasors between two components:
-
-    >>> graphical_component_analysis(
-    ...     [0.6, 0.3], [0.35, 0.38], [0.2, 0.9], [0.4, 0.3], fractions=6
-    ... )  # doctest: +NUMBER
-    (array([0, 0, 1, 0, 1, 0], dtype=uint64),)
-
-    Count the number of phasors between the combinations of three components:
-
-    >>> graphical_component_analysis(
-    ...     [0.4, 0.5],
-    ...     [0.2, 0.3],
-    ...     [0.0, 0.2, 0.9],
-    ...     [0.0, 0.4, 0.3],
-    ...     fractions=6,
-    ... )  # doctest: +NUMBER +NORMALIZE_WHITESPACE
-    (array([0, 1, 1, 1, 1, 0], dtype=uint64),
-     array([0, 1, 0, 0, 0, 0], dtype=uint64),
-     array([0, 1, 2, 0, 0, 0], dtype=uint64))
-
-    """
-    real = numpy.asarray(real)
-    imag = numpy.asarray(imag)
-    components_real = numpy.asarray(components_real)
-    components_imag = numpy.asarray(components_imag)
-    if (
-        real.shape != imag.shape
-        or components_real.shape != components_imag.shape
-    ):
-        raise ValueError('input array shapes must match')
-    if components_real.ndim != 1:
-        raise ValueError(
-            'component arrays are not one-dimensional: '
-            f'{components_real.ndim} dimensions found'
-        )
-    num_components = len(components_real)
-    if num_components not in {2, 3}:
-        raise ValueError('number of components must be 2 or 3')
-
-    if fractions is None:
-        longest_distance = 0
-        for i in range(num_components):
-            a_real = components_real[i]
-            a_imag = components_imag[i]
-            for j in range(i + 1, num_components):
-                b_real = components_real[j]
-                b_imag = components_imag[j]
-                _, _, length = _segment_direction_and_length(
-                    a_real, a_imag, b_real, b_imag
-                )
-                longest_distance = max(longest_distance, length)
-        fractions = numpy.linspace(
-            0.0, 1.0, int(round(longest_distance / (radius / 2) + 1))
-        )
-    elif isinstance(fractions, (int, numbers.Integral)):
-        fractions = numpy.linspace(0.0, 1.0, fractions)
-    else:
-        fractions = numpy.asarray(fractions)
-        if fractions.ndim != 1:
-            raise ValueError('fractions is not a one-dimensional array')
-
-    counts = []
-    for i in range(num_components):
-        a_real = components_real[i]
-        a_imag = components_imag[i]
-        for j in range(i + 1, num_components):
-            b_real = components_real[j]
-            b_imag = components_imag[j]
-            ab_real = a_real - b_real
-            ab_imag = a_imag - b_imag
-
-            component_counts = []
-            for f in fractions:
-                if f < 0.0 or f > 1.0:
-                    raise ValueError(f'fraction {f} out of bounds [0.0, 1.0]')
-                if num_components == 2:
-                    mask = _is_inside_circle(
-                        real,
-                        imag,
-                        b_real + f * ab_real,  # cursor_real
-                        b_imag + f * ab_imag,  # cursor_imag
-                        radius,
-                    )
-                else:
-                    # num_components == 3
-                    mask = _is_inside_stadium(
-                        real,
-                        imag,
-                        b_real + f * ab_real,  # cursor_real
-                        b_imag + f * ab_imag,  # cursor_imag
-                        components_real[3 - i - j],  # c_real
-                        components_imag[3 - i - j],  # c_imag
-                        radius,
-                    )
-                fraction_counts = numpy.sum(mask, dtype=numpy.uint64)
-                component_counts.append(fraction_counts)
-
-            counts.append(numpy.asarray(component_counts))
-
-    return tuple(counts)

phasorpy/io.py

@@ -1,9 +0,0 @@
-# phasorpy.io proxy module
-# The VSCode debugger cannot to step into or break inside modules named io.py
-
-from ._io import *
-from ._io import __all__, __doc__
-from ._utils import set_module
-
-set_module(globals())
-del set_module