"""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:`phasor_component_fraction`)
- calculate phasor coordinates of second component if only one is
known (not implemented)
- calculate fractions of multiple known components by using higher
harmonic information (:py:func:`phasor_component_fit`)
- calculate fractions of two or three known components by resolving
graphically with histogram (:py:func:`phasor_component_graphical`)
- blindly resolve fractions of multiple components by using harmonic
information (:py:func:`phasor_component_blind`, not implemented)
"""
from __future__ import annotations
__all__ = [
# phasor_component_blind,
'phasor_component_fit',
'phasor_component_fraction',
'phasor_component_graphical',
]
import numbers
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ._typing import Any, ArrayLike, NDArray
import numpy
from ._phasorpy import (
_blend_and,
_fraction_on_segment,
_is_inside_circle,
_is_inside_stadium,
_segment_direction_and_length,
)
from .phasor import phasor_threshold
[docs]
def phasor_component_fraction(
real: ArrayLike,
imag: ArrayLike,
component_real: ArrayLike,
component_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.
component_real : array_like, shape (2,)
Real coordinates of first and second components.
component_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
--------
>>> phasor_component_fraction(
... [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])
"""
component_real = numpy.asarray(component_real)
component_imag = numpy.asarray(component_imag)
if component_real.shape != (2,):
raise ValueError(f'{component_real.shape=} != (2,)')
if component_imag.shape != (2,):
raise ValueError(f'{component_imag.shape=} != (2,)')
if (
component_real[0] == component_real[1]
and component_imag[0] == component_imag[1]
):
raise ValueError('components must have different coordinates')
return _fraction_on_segment( # type: ignore[no-any-return]
real,
imag,
component_real[0],
component_imag[0],
component_real[1],
component_imag[1],
)
[docs]
def phasor_component_graphical(
real: ArrayLike,
imag: ArrayLike,
component_real: ArrayLike,
component_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.
component_real : array_like, shape (2,) or (3,)
Real coordinates for two or three components.
component_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 `component_real` and
`component_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:
>>> phasor_component_graphical(
... [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:
>>> phasor_component_graphical(
... [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)
component_real = numpy.asarray(component_real)
component_imag = numpy.asarray(component_imag)
if (
real.shape != imag.shape
or component_real.shape != component_imag.shape
):
raise ValueError('input array shapes must match')
if component_real.ndim != 1:
raise ValueError(
'component arrays are not one-dimensional: '
f'{component_real.ndim} dimensions found'
)
num_components = len(component_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 = component_real[i]
a_imag = component_imag[i]
for j in range(i + 1, num_components):
b_real = component_real[j]
b_imag = component_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 = component_real[i]
a_imag = component_imag[i]
for j in range(i + 1, num_components):
b_real = component_real[j]
b_imag = component_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
component_real[3 - i - j], # c_real
component_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)
[docs]
def phasor_component_fit(
mean: ArrayLike,
real: ArrayLike,
imag: ArrayLike,
component_real: ArrayLike,
component_imag: ArrayLike,
/,
**kwargs: Any,
) -> tuple[NDArray[Any], ...]:
"""Return fractions of multiple components from phasor coordinates.
Component fractions are obtained from the least-squares solution of a
linear matrix equation that relates phasor coordinates from one or
multiple harmonics to component fractions according to [2]_.
Up to ``2 * number harmonics + 1`` components can be fit to multi-harmonic
phasor coordinates, that is up to three components for single harmonic
phasor coordinates.
Parameters
----------
mean : array_like
Intensity of phasor coordinates.
real : array_like
Real component of phasor coordinates.
Harmonics, if any, must be in the first dimension.
imag : array_like
Imaginary component of phasor coordinates.
Harmonics, if any, must be in the first dimension.
component_real : array_like
Real coordinates of components.
Must be one or two-dimensional with harmonics in the first dimension.
component_imag : array_like
Imaginary coordinates of components.
Must be one or two-dimensional with harmonics in the first dimension.
**kwargs : optional
Additional arguments passed to :py:func:`scipy.linalg.lstsq()`.
Returns
-------
fractions : tuple of ndarray
Component fractions, one array per component.
Fractions may not exactly add up to 1.0.
Raises
------
ValueError
The array shapes of `real` and `imag` do not match.
The array shapes of `component_real` and `component_imag` do not match.
The number of harmonics in the components does not
match the ones in the phasor coordinates.
The system is underdetermined; the component matrix having more
columns than rows.
See Also
--------
:ref:`sphx_glr_tutorials_api_phasorpy_components.py`
:ref:`sphx_glr_tutorials_applications_phasorpy_component_fit.py`
Notes
-----
For now, calculation of fractions of components from different channels
or frequencies is not supported. Only one set of components can be
analyzed and is broadcast to all channels/frequencies.
The method builds a linear matrix equation,
:math:`A\\mathbf{x} = \\mathbf{b}`, where :math:`A` consists of the
phasor coordinates of individual components, :math:`\\mathbf{x}` are
the unknown fractions, and :math:`\\mathbf{b}` represents the measured
phasor coordinates in the mixture. The least-squares solution of this
linear matrix equation yields the fractions.
References
----------
.. [2] Vallmitjana A, Lepanto P, Irigoin F, and Malacrida L.
`Phasor-based multi-harmonic unmixing for in-vivo hyperspectral
imaging <https://doi.org/10.1088/2050-6120/ac9ae9>`_.
*Methods Appl Fluoresc*, 11(1): 014001 (2022)
Example
-------
>>> phasor_component_fit(
... [1, 1, 1], [0.6, 0.5, 0.4], [0.4, 0.3, 0.2], [0.2, 0.9], [0.4, 0.3]
... ) # doctest: +NUMBER
(array([0.4644, 0.5356, 0.6068]), array([0.5559, 0.4441, 0.3322]))
"""
from scipy.linalg import lstsq
mean = numpy.atleast_1d(mean)
real = numpy.atleast_1d(real)
imag = numpy.atleast_1d(imag)
component_real = numpy.atleast_1d(component_real)
component_imag = numpy.atleast_1d(component_imag)
if real.shape != imag.shape:
raise ValueError(f'{real.shape=} != {imag.shape=}')
if mean.shape != real.shape[-mean.ndim :]:
raise ValueError(f'{mean.shape=} does not match {real.shape=}')
if component_real.shape != component_imag.shape:
raise ValueError(f'{component_real.shape=} != {component_imag.shape=}')
if numpy.isnan(component_real).any() or numpy.isnan(component_imag).any():
raise ValueError(
'component phasor coordinates must not contain NaN values'
)
if numpy.isinf(component_real).any() or numpy.isinf(component_imag).any():
raise ValueError(
'component phasor coordinates must not contain infinite values'
)
if component_real.ndim == 1:
component_real = component_real.reshape(1, -1)
component_imag = component_imag.reshape(1, -1)
elif component_real.ndim > 2:
raise ValueError(f'{component_real.ndim=} > 2')
num_harmonics, num_components = component_real.shape
# create component matrix for least squares solving:
# [real coordinates of components (for each harmonic)] +
# [imaginary coordinates of components (for each harmonic)] +
# [ones for intensity constraint]
component_matrix = numpy.ones((2 * num_harmonics + 1, num_components))
component_matrix[:num_harmonics] = component_real
component_matrix[num_harmonics : 2 * num_harmonics] = component_imag
if component_matrix.shape[0] < component_matrix.shape[1]:
raise ValueError(
'the system is undetermined '
f'({num_components=} > {num_harmonics * 2 + 1=})'
)
has_harmonic_axis = mean.ndim + 1 == real.ndim
if not has_harmonic_axis:
real = numpy.expand_dims(real, axis=0)
imag = numpy.expand_dims(imag, axis=0)
elif real.shape[0] != num_harmonics:
raise ValueError(f'{real.shape[0]=} != {component_real.shape[0]=}')
# TODO: replace Inf with NaN values?
mean, real, imag = phasor_threshold(mean, real, imag)
# replace NaN values with 0.0 for least squares solving
real = numpy.nan_to_num(real, nan=0.0, copy=False)
imag = numpy.nan_to_num(imag, nan=0.0, copy=False)
# create coordinates matrix for least squares solving:
# [real coordinates (for each harmonic)] +
# [imaginary coordinates (for each harmonic)] +
# [ones for intensity constraint]
coords = numpy.ones((2 * num_harmonics + 1,) + real.shape[1:])
coords[:num_harmonics] = real
coords[num_harmonics : 2 * num_harmonics] = imag
fractions = lstsq(
component_matrix, coords.reshape(coords.shape[0], -1), **kwargs
)[0]
# reshape to match input dimensions
fractions = fractions.reshape((num_components,) + coords.shape[1:])
# TODO: normalize fractions to sum up to 1.0?
# fractions /= numpy.sum(fractions, axis=0, keepdims=True)
# restore NaN values in fractions from mean
_blend_and(mean, fractions, out=fractions)
return tuple(fractions)
