phasorpy 0.3__cp313-cp313-win_amd64.whl → 0.4__cp313-cp313-win_amd64.whl

phasorpy/phasor.py

@@ -149,7 +149,7 @@ from ._phasorpy import (
     _polar_from_single_lifetime,
     _polar_to_apparent_lifetime,
 )
-from ._utils import parse_harmonic
+from ._utils import parse_harmonic, parse_signal_axis
 from .utils import number_threads
 
 
@@ -157,7 +157,7 @@ def phasor_from_signal(
     signal: ArrayLike,
     /,
     *,
-    axis: int = -1,
+    axis: int | str | None = None,
     harmonic: int | Sequence[int] | Literal['all'] | str | None = None,
     sample_phase: ArrayLike | None = None,
     use_fft: bool | None = None,
@@ -174,9 +174,10 @@ def phasor_from_signal(
         Frequency-domain, time-domain, or hyperspectral data.
         A minimum of three samples are required along `axis`.
         The samples must be uniformly spaced.
-    axis : int, optional
+    axis : int or str, optional
         Axis over which to compute phasor coordinates.
-        The default is the last axis (-1).
+        By default, the 'H' or 'C' axes if signal contains such dimension
+        names, else the last axis (-1).
     harmonic : int, sequence of int, or 'all', optional
         Harmonics to return.
         If `'all'`, return all harmonics for `signal` samples along `axis`.
@@ -287,6 +288,9 @@ def phasor_from_signal(
     """
     # TODO: C-order not required by rfft?
     # TODO: preserve array subtypes?
+
+    axis, _ = parse_signal_axis(signal, axis)
+
     signal = numpy.asarray(signal, order='C')
     if signal.dtype.kind not in 'uif':
         raise TypeError(f'signal must be real valued, not {signal.dtype=}')
@@ -1243,7 +1247,14 @@ def phasor_calibrate(
 
     has_harmonic_axis = reference_mean.ndim + 1 == reference_real.ndim
     harmonic, _ = parse_harmonic(
-        harmonic, reference_real.shape[0] if has_harmonic_axis else None
+        harmonic,
+        (
+            reference_real.shape[0]
+            if has_harmonic_axis
+            and isinstance(harmonic, str)
+            and harmonic == 'all'
+            else None
+        ),
     )
 
     if has_harmonic_axis:
@@ -1966,6 +1977,7 @@ def lifetime_fraction_from_amplitude(
     array([0.8, 0.2])
 
     """
+    t: NDArray[numpy.float64]
     t = numpy.multiply(amplitude, lifetime, dtype=numpy.float64)
     t /= numpy.sum(t, axis=axis, keepdims=True)
     return t

phasorpy/plot.py

@@ -43,6 +43,7 @@ from ._phasorpy import _intersection_circle_circle, _intersection_circle_line
 from ._utils import (
     dilate_coordinates,
     parse_kwargs,
+    parse_signal_axis,
     phasor_from_polar_scalar,
     phasor_to_polar_scalar,
     sort_coordinates,
@@ -217,7 +218,7 @@ class PhasorPlot:
         /,
         fmt: str = 'o',
         *,
-        label: str | Sequence[str] | None = None,
+        label: Sequence[str] | None = None,
         **kwargs: Any,
     ) -> list[Line2D]:
         """Plot imag versus real coordinates as markers and/or lines.
@@ -232,7 +233,7 @@ class PhasorPlot:
             Must be of same shape as `real`.
         fmt : str, optional, default: 'o'
             Matplotlib style format string.
-        label : str or sequence of str, optional
+        label : sequence of str, optional
             Plot label.
             May be a sequence if phasor coordinates are two dimensional arrays.
         **kwargs
@@ -1858,7 +1859,7 @@ def plot_signal_image(
     signal: ArrayLike,
     /,
     *,
-    axis: int | None = None,
+    axis: int | str | None = None,
     percentile: float | Sequence[float] | None = None,
     title: str | None = None,
     show: bool = True,
@@ -1876,9 +1877,10 @@ def plot_signal_image(
     ----------
     signal : array_like
         Image stack. Must be three or more dimensional.
-    axis : int, optional, default: -1
+    axis : int or str, optional
         Axis over which phasor coordinates would be computed.
-        The default is the last axis (-1).
+        By default, the 'H' or 'C' axes if signal contains such dimension
+        names, else the last axis (-1).
     percentile : float or [float, float], optional
         The [q, 100-q] percentiles of image data are covered by colormaps.
         By default, the complete value range of `mean` is covered,
@@ -1899,13 +1901,22 @@ def plot_signal_image(
     """
     # TODO: add option to separate channels?
     # TODO: add option to plot non-images?
+
+    axis, axis_label = parse_signal_axis(signal, axis)
+    if (
+        axis_label
+        and hasattr(signal, 'coords')
+        and axis_label in signal.coords
+    ):
+        axis_coords = signal.coords[axis_label]
+    else:
+        axis_coords = None
+
     update_kwargs(kwargs, interpolation='nearest')
     signal = numpy.asarray(signal)
     if signal.ndim < 3:
         raise ValueError(f'not an image stack {signal.ndim=} < 3')
 
-    if axis is None:
-        axis = -1
     axis %= signal.ndim
 
     # for MyPy
@@ -1922,8 +1933,13 @@ def plot_signal_image(
     axes = list(range(signal.ndim))
     del axes[axis]
     ax = fig.add_subplot(gs[0, 1])
-    ax.set_title(f'mean, axis {axis}')
-    ax.plot(numpy.nanmean(signal, axis=tuple(axes)))
+
+    if axis_coords is not None:
+        ax.set_title(f'{axis=} {axis_label!r}')
+        ax.plot(axis_coords, numpy.nanmean(signal, axis=tuple(axes)))
+    else:
+        ax.set_title(f'{axis=}')
+        ax.plot(numpy.nanmean(signal, axis=tuple(axes)))
 
     # image
     axes = list(sorted(axes[:-2] + [axis]))

phasorpy/version.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-__version__ = '0.3'
+__version__ = '0.4'
 
 
 def versions(
@@ -44,6 +44,7 @@ def versions(
         'lfdfiles',
         'sdtfile',
         'ptufile',
+        'liffile',
         'matplotlib',
         'scipy',
         'skimage',

{phasorpy-0.3.dist-info → phasorpy-0.4.dist-info}/LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2024 PhasorPy Contributors
+Copyright (c) 2022-2025 PhasorPy Contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{phasorpy-0.3.dist-info → phasorpy-0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: phasorpy
-Version: 0.3
+Version: 0.4
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License: MIT
@@ -52,6 +52,7 @@ Provides-Extra: all
 Requires-Dist: lfdfiles>=2024.5.24; extra == "all"
 Requires-Dist: sdtfile>=2024.5.24; extra == "all"
 Requires-Dist: ptufile>=2024.9.14; extra == "all"
+Requires-Dist: liffile>=2025.1.30; extra == "all"
 
 # PhasorPy
 
@@ -61,7 +62,7 @@ lifetime and hyperspectral images using the phasor approach.
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)
-- [Download releases](https://pypi.org/project/phasorpy/#files)
+- [Install with pip](https://pypi.org/project/phasorpy/) or [conda](https://anaconda.org/conda-forge/phasorpy).
 - [Data files](https://zenodo.org/communities/phasorpy/)
 - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 

phasorpy-0.4.dist-info/RECORD

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+phasorpy-0.4.dist-info/RECORD,,

{phasorpy-0.3.dist-info → phasorpy-0.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: false
 Tag: cp313-cp313-win_amd64
 

phasorpy-0.3.dist-info/RECORD

@@ -1,24 +0,0 @@
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