phasorpy 0.4__cp311-cp311-win_arm64.whl → 0.6__cp311-cp311-win_arm64.whl

phasorpy/components.py

@@ -3,31 +3,29 @@
 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`
+  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 three or four known components by using higher
-  harmonic information (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:`graphical_component_analysis`
+  graphically with histogram (:py:func:`phasor_component_graphical`)
 
-- blindly resolve fractions of `n` components by using harmonic
-  information (not implemented)
+- blindly resolve fractions of multiple components by using harmonic
+  information (:py:func:`phasor_component_blind`, not implemented)
 
 """
 
 from __future__ import annotations
 
 __all__ = [
-    'two_fractions_from_phasor',
-    'graphical_component_analysis',
+    # phasor_component_blind,
+    'phasor_component_fit',
+    'phasor_component_fraction',
+    'phasor_component_graphical',
 ]
 
 import numbers
@@ -39,18 +37,20 @@ if TYPE_CHECKING:
 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
 
 
-def two_fractions_from_phasor(
+def phasor_component_fraction(
     real: ArrayLike,
     imag: ArrayLike,
-    components_real: ArrayLike,
-    components_imag: ArrayLike,
+    component_real: ArrayLike,
+    component_imag: ArrayLike,
     /,
 ) -> NDArray[Any]:
     """Return fraction of first of two components from phasor coordinates.
@@ -65,10 +65,10 @@ def two_fractions_from_phasor(
         Real component of phasor coordinates.
     imag : array_like
         Imaginary component of phasor coordinates.
-    components_real: array_like, shape (2,)
-        Real coordinates of the first and second components.
-    components_imag: array_like, shape (2,)
-        Imaginary coordinates of the first and second components.
+    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
     -------
@@ -78,7 +78,7 @@ def two_fractions_from_phasor(
     Raises
     ------
     ValueError
-        If the real and/or imaginary coordinates of the known components are
+        If the real or imaginary coordinates of the known components are
         not of size 2.
 
     See Also
@@ -95,39 +95,39 @@ def two_fractions_from_phasor(
 
     Examples
     --------
-    >>> two_fractions_from_phasor(
+    >>> 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])
 
     """
-    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,)')
+    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 (
-        components_real[0] == components_real[1]
-        and components_imag[0] == components_imag[1]
+        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,
-        components_real[0],
-        components_imag[0],
-        components_real[1],
-        components_imag[1],
+        component_real[0],
+        component_imag[0],
+        component_real[1],
+        component_imag[1],
     )
 
 
-def graphical_component_analysis(
+def phasor_component_graphical(
     real: ArrayLike,
     imag: ArrayLike,
-    components_real: ArrayLike,
-    components_imag: ArrayLike,
+    component_real: ArrayLike,
+    component_imag: ArrayLike,
     /,
     *,
     radius: float = 0.05,
@@ -145,13 +145,13 @@ def graphical_component_analysis(
         Real component of phasor coordinates.
     imag : array_like
         Imaginary component of phasor coordinates.
-    components_real: array_like, shape (2,) or (3,)
+    component_real : array_like, shape (2,) or (3,)
         Real coordinates for two or three components.
-    components_imag: array_like, shape (2,) or (3,)
+    component_imag : array_like, shape (2,) or (3,)
         Imaginary coordinates for two or three components.
-    radius: float, optional, default: 0.05
-        Radius of the cursor in phasor coordinates.
-    fractions: array_like or int, optional
+    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
@@ -163,16 +163,16 @@ def graphical_component_analysis(
     Returns
     -------
     counts : tuple of ndarray
-        Counts along each line segment connecting the components, ordered
-        0-1 (2 components) or 0-1, 0-2, 1-2 (3 components).
+        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 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 not in range [0.0, 1.0].
+        Fraction values are out of range [0.0, 1.0].
 
     See Also
     --------
@@ -213,51 +213,51 @@ def graphical_component_analysis(
     --------
     Count the number of phasors between two components:
 
-    >>> graphical_component_analysis(
+    >>> 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]),)
+    (array([0, 0, 1, 0, 1, 0], dtype=uint64),)
 
     Count the number of phasors between the combinations of three components:
 
-    >>> graphical_component_analysis(
+    >>> 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]),
-     array([0, 1, 0, 0, 0, 0]),
-     array([0, 1, 2, 0, 0, 0]))
+    (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)
+    component_real = numpy.asarray(component_real)
+    component_imag = numpy.asarray(component_imag)
     if (
         real.shape != imag.shape
-        or components_real.shape != components_imag.shape
+        or component_real.shape != component_imag.shape
     ):
         raise ValueError('input array shapes must match')
-    if components_real.ndim != 1:
+    if component_real.ndim != 1:
         raise ValueError(
             'component arrays are not one-dimensional: '
-            f'{components_real.ndim} dimensions found'
+            f'{component_real.ndim} dimensions found'
         )
-    num_components = len(components_real)
+    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 = components_real[i]
-            a_imag = components_imag[i]
+            a_real = component_real[i]
+            a_imag = component_imag[i]
             for j in range(i + 1, num_components):
-                b_real = components_real[j]
-                b_imag = components_imag[j]
+                b_real = component_real[j]
+                b_imag = component_imag[j]
                 _, _, length = _segment_direction_and_length(
                     a_real, a_imag, b_real, b_imag
                 )
@@ -274,11 +274,11 @@ def graphical_component_analysis(
 
     counts = []
     for i in range(num_components):
-        a_real = components_real[i]
-        a_imag = components_imag[i]
+        a_real = component_real[i]
+        a_imag = component_imag[i]
         for j in range(i + 1, num_components):
-            b_real = components_real[j]
-            b_imag = components_imag[j]
+            b_real = component_real[j]
+            b_imag = component_imag[j]
             ab_real = a_real - b_real
             ab_imag = a_imag - b_imag
 
@@ -301,13 +301,184 @@ def graphical_component_analysis(
                         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
+                        component_real[3 - i - j],  # c_real
+                        component_imag[3 - i - j],  # c_imag
                         radius,
                     )
-                fraction_counts = numpy.sum(mask)
+                fraction_counts = numpy.sum(mask, dtype=numpy.uint64)
                 component_counts.append(fraction_counts)
 
             counts.append(numpy.asarray(component_counts))
 
     return tuple(counts)
+
+
+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)

phasorpy/conftest.py

@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+__all__: list[str] = []
+
 import math
 from typing import TYPE_CHECKING
 

phasorpy/cursors.py

@@ -291,15 +291,15 @@ def mask_from_polar_cursor(
     imag : array_like
         Imaginary component of phasor coordinates.
     phase_min : array_like, shape (n,)
-        Minimum of angular range of cursors in radians.
-        Values should be between -pi and pi.
+        Lower bound of angular range of cursors in radians.
+        Values should be in range [-pi, pi].
     phase_max : array_like, shape (n,)
-        Maximum of angular range of cursors in radians.
-        Values should be between -pi and pi.
+        Upper bound of angular range of cursors in radians.
+        Values should be in range [-pi, pi].
     modulation_min : array_like, shape (n,)
-        Minimum of radial range of cursors.
+        Lower bound of radial range of cursors.
     modulation_max : array_like, shape (n,)
-        Maximum of radial range of cursors.
+        Upper bound of radial range of cursors.
 
     Returns
     -------
@@ -362,7 +362,7 @@ def mask_from_polar_cursor(
             f'{phase_min.ndim=}, {phase_max.ndim=}, '
             f'{modulation_min.ndim=}, or {modulation_max.ndim=} > 1'
         )
-    # TODO: check if angles are between -pi and pi
+    # TODO: check if angles are in range [-pi and pi]
 
     moveaxis = False
     if real.ndim > 0 and (
@@ -406,7 +406,7 @@ def pseudo_color(
         Maximum value to normalize `intensity`.
         If None, the maximum value of `intensity` is used.
     colors : array_like, optional, shape (N, 3)
-        Colors assigned to each cursor.
+        RGB colors assigned to each cursor.
         The last dimension contains the normalized RGB floating point values.
         The default is :py:data:`phasorpy.color.CATEGORICAL`.
 
@@ -463,7 +463,7 @@ def pseudo_color(
     shape = numpy.asarray(masks[0]).shape
 
     if intensity is not None:
-        # normalize intensity to range 0..1
+        # normalize intensity to range [0, 1]
         intensity = numpy.array(
             intensity, dtype=numpy.float32, ndmin=1, copy=True
         )