phasorpy 0.5__cp313-cp313-win_arm64.whl → 0.7__cp313-cp313-win_arm64.whl

phasorpy/utils.py

@@ -1,315 +1,36 @@
 """Utility functions.
 
 The ``phasorpy.utils`` module provides auxiliary and convenience functions
-that do not naturally fit into other modules.
+that do not fit naturally into other modules.
 
 """
 
 from __future__ import annotations
 
 __all__ = [
-    'anscombe_transformation',
-    'anscombe_transformation_inverse',
+    'logger',
     'number_threads',
-    'spectral_vector_denoise',
+    'versions',
 ]
 
-import math
+import logging
 import os
-from typing import TYPE_CHECKING
 
-if TYPE_CHECKING:
-    from ._typing import Any, NDArray, ArrayLike, DTypeLike, Literal, Sequence
 
-import numpy
-
-from ._phasorpy import (
-    _anscombe,
-    _anscombe_inverse,
-    _anscombe_inverse_approx,
-    _phasor_from_signal_vector,
-    _signal_denoise_vector,
-)
-from ._utils import parse_harmonic
-
-
-def spectral_vector_denoise(
-    signal: ArrayLike,
-    /,
-    spectral_vector: ArrayLike | None = None,
-    *,
-    axis: int = -1,
-    harmonic: int | Sequence[int] | Literal['all'] | str | None = None,
-    sigma: float = 0.05,
-    vmin: float | None = None,
-    dtype: DTypeLike | None = None,
-    num_threads: int | None = None,
-) -> NDArray[Any]:
-    """Return spectral-vector-denoised signal.
-
-    The spectral vector denoising algorithm is based on a Gaussian weighted
-    average calculation, with weights obtained in n-dimensional Chebyshev or
-    Fourier space [4]_.
-
-    Parameters
-    ----------
-    signal : array_like
-        Hyperspectral data to be denoised.
-        A minimum of three samples are required along `axis`.
-        The samples must be uniformly spaced.
-    spectral_vector : array_like, optional
-        Spectral vector.
-        For example, phasor coordinates, PCA projected phasor coordinates,
-        or Chebyshev coefficients.
-        Must be of same shape as `signal` with `axis` removed and axis
-        containing spectral space appended.
-        If None (default), phasor coordinates are calculated at specified
-        `harmonic`.
-    axis : int, optional, default: -1
-        Axis over which `spectral_vector` is computed if not provided.
-        The default is the last axis (-1).
-    harmonic : int, sequence of int, or 'all', optional
-        Harmonics to include in calculating `spectral_vector`.
-        If `'all'`, include all harmonics for `signal` samples along `axis`.
-        Else, harmonics must be at least one and no larger than half the
-        number of `signal` samples along `axis`.
-        The default is the first harmonic (fundamental frequency).
-        A minimum of `harmonic * 2 + 1` samples are required along `axis`
-        to calculate correct phasor coordinates at `harmonic`.
-    sigma : float, default: 0.05
-        Width of Gaussian filter in spectral vector space.
-        Weighted averages are calculated using the spectra of signal items
-        within an spectral vector Euclidean distance of `3 * sigma` and
-        intensity above `vmin`.
-    vmin : float, optional
-        Signal intensity along `axis` below which not to include in denoising.
-    dtype : dtype_like, optional
-        Data type of output arrays. Either float32 or float64.
-        The default is float64 unless the `signal` is float32.
-    num_threads : int, optional
-        Number of OpenMP threads to use for parallelization.
-        By default, multi-threading is disabled.
-        If zero, up to half of logical CPUs are used.
-        OpenMP may not be available on all platforms.
+def logger() -> logging.Logger:
+    """Return PhasorPy logger instance.
 
     Returns
     -------
-    ndarray
-        Denoised signal of `dtype`.
-        Spectra with integrated intensity below `vmin` are unchanged.
-
-    References
-    ----------
-
-    .. [4] Harman RC, Lang RT, Kercher EM, Leven P, and Spring BQ.
-       `Denoising multiplexed microscopy images in n-dimensional spectral space
-       <https://doi.org/10.1364/BOE.463979>`_.
-       *Biomed Opt Express*, 13(8): 4298-4309 (2022)
+    logging.Logger
+        Logger instance for 'phasorpy' namespace.
 
     Examples
     --------
-    Denoise a hyperspectral image with a Gaussian filter width of 0.1 in
-    spectral vector space using first and second harmonic:
-
-    >>> signal = numpy.random.randint(0, 255, (8, 16, 16))
-    >>> spectral_vector_denoise(signal, axis=0, sigma=0.1, harmonic=[1, 2])
-    array([[[...]]])
+    >>> logger().info('This is a log message')
 
     """
-    num_threads = number_threads(num_threads)
-
-    signal = numpy.asarray(signal)
-    if axis == -1 or axis == signal.ndim - 1:
-        axis = -1
-    else:
-        signal = numpy.moveaxis(signal, axis, -1)
-    shape = signal.shape
-    samples = shape[-1]
-
-    if harmonic is None:
-        harmonic = 1
-    harmonic, _ = parse_harmonic(harmonic, samples // 2)
-    num_harmonics = len(harmonic)
-
-    if vmin is None or vmin < 0.0:
-        vmin = 0.0
-
-    sincos = numpy.empty((num_harmonics, samples, 2))
-    for i, h in enumerate(harmonic):
-        phase = numpy.linspace(
-            0,
-            h * math.pi * 2.0,
-            samples,
-            endpoint=False,
-            dtype=numpy.float64,
-        )
-        sincos[i, :, 0] = numpy.cos(phase)
-        sincos[i, :, 1] = numpy.sin(phase)
-
-    signal = numpy.ascontiguousarray(signal).reshape(-1, samples)
-    size = signal.shape[0]
-
-    if dtype is None:
-        if signal.dtype.char == 'f':
-            dtype = signal.dtype
-        else:
-            dtype = numpy.float64
-    dtype = numpy.dtype(dtype)
-    if dtype.char not in {'d', 'f'}:
-        raise ValueError('dtype is not floating point')
-
-    if spectral_vector is None:
-        spectral_vector = numpy.zeros((size, num_harmonics * 2), dtype=dtype)
-        _phasor_from_signal_vector(
-            spectral_vector, signal, sincos, num_threads
-        )
-    else:
-        spectral_vector = numpy.ascontiguousarray(spectral_vector, dtype=dtype)
-        if spectral_vector.shape[:-1] != shape[:-1]:
-            raise ValueError('signal and spectral_vector shape mismatch')
-        spectral_vector = spectral_vector.reshape(
-            -1, spectral_vector.shape[-1]
-        )
-
-    if dtype == signal.dtype:
-        denoised = signal.copy()
-    else:
-        denoised = numpy.zeros(signal.shape, dtype=dtype)
-        denoised[:] = signal
-    integrated = numpy.zeros(size, dtype=dtype)
-    _signal_denoise_vector(
-        denoised, integrated, signal, spectral_vector, sigma, vmin, num_threads
-    )
-
-    denoised = denoised.reshape(shape)
-    if axis != -1:
-        denoised = numpy.moveaxis(denoised, -1, axis)
-    return denoised
-
-
-def anscombe_transformation(
-    data: ArrayLike,
-    /,
-    **kwargs: Any,
-) -> NDArray[Any]:
-    r"""Return Anscombe variance-stabilizing transformation.
-
-    The Anscombe transformation normalizes the standard deviation of noisy,
-    Poisson-distributed data.
-    It can be used to transform un-normalized phasor coordinates to
-    approximate standard Gaussian distributions.
-
-    Parameters
-    ----------
-    data : array_like
-        Noisy Poisson-distributed data to be transformed.
-    **kwargs
-        Optional `arguments passed to numpy universal functions
-        <https://numpy.org/doc/stable/reference/ufuncs.html#ufuncs-kwargs>`_.
-
-    Returns
-    -------
-    ndarray
-        Anscombe-transformed data with variance of approximately 1.
-
-    Notes
-    -----
-    The Anscombe transformation according to [1]_:
-
-    .. math::
-
-        z = 2 \cdot \sqrt{x + 3 / 8}
-
-    References
-    ----------
-
-    .. [1] Anscombe FJ.
-       `The transformation of Poisson, binomial and negative-binomial data
-       <https://doi.org/10.2307/2332343>`_.
-       *Biometrika*, 35(3-4): 246-254 (1948)
-
-    Examples
-    --------
-
-    >>> z = anscombe_transformation(numpy.random.poisson(10, 10000))
-    >>> numpy.allclose(numpy.std(z), 1.0, atol=0.1)
-    True
-
-    """
-    return _anscombe(data, **kwargs)  # type: ignore[no-any-return]
-
-
-def anscombe_transformation_inverse(
-    data: ArrayLike,
-    /,
-    *,
-    approx: bool = False,
-    **kwargs: Any,
-) -> NDArray[Any]:
-    r"""Return inverse Anscombe transformation.
-
-    Parameters
-    ----------
-    data : array_like
-        Anscombe-transformed data.
-    approx : bool, default: False
-        If true, return approximation of exact unbiased inverse.
-    **kwargs
-        Optional `arguments passed to numpy universal functions
-        <https://numpy.org/doc/stable/reference/ufuncs.html#ufuncs-kwargs>`_.
-
-    Returns
-    -------
-    ndarray
-        Inverse Anscombe-transformed data.
-
-    Notes
-    -----
-    The inverse Anscombe transformation according to [1]_:
-
-    .. math::
-
-        x = (z / 2.0)^2 - 3 / 8
-
-    The approximate inverse Anscombe transformation according to [2]_ and [3]_:
-
-    .. math::
-
-        x = 1/4 \cdot z^2{2}
-          + 1/4 \cdot \sqrt{3/2} \cdot z^{-1}
-          - 11/8 \cdot z^{-2}
-          + 5/8 \cdot \sqrt(3/2) \cdot z^{-3}
-          - 1/8
-
-    References
-    ----------
-
-    .. [2] Makitalo M, and Foi A.
-       `A closed-form approximation of the exact unbiased inverse of the
-       Anscombe variance-stabilizing transformation
-       <https://doi.org/10.1109/TIP.2011.2121085>`_.
-       *IEEE Trans Image Process*, 20(9): 2697-8 (2011).
-
-    .. [3] Makitalo M, and Foi A
-       `Optimal inversion of the generalized Anscombe transformation for
-       Poisson-Gaussian noise
-       <https://doi.org/10.1109/TIP.2012.2202675>`_,
-       *IEEE Trans Image Process*, 22(1): 91-103 (2013)
-
-    Examples
-    --------
-
-    >>> x = numpy.random.poisson(10, 100)
-    >>> x2 = anscombe_transformation_inverse(anscombe_transformation(x))
-    >>> numpy.allclose(x, x2, atol=1e-3)
-    True
-
-    """
-    if approx:
-        return _anscombe_inverse_approx(  # type: ignore[no-any-return]
-            data, **kwargs
-        )
-    return _anscombe_inverse(data, **kwargs)  # type: ignore[no-any-return]
+    return logging.getLogger('phasorpy')
 
 
 def number_threads(
@@ -342,7 +63,7 @@ def number_threads(
     >>> number_threads()
     1
     >>> number_threads(0)  # doctest: +SKIP
-    8
+    8  # actual value depends on system
 
     """
     if num_threads is None or num_threads < 0:
@@ -371,3 +92,81 @@ def number_threads(
     if max_threads is None:
         return num_threads
     return min(num_threads, max(max_threads, 1))
+
+
+def versions(
+    *, sep: str = '\n', dash: str = '-', verbose: bool = False
+) -> str:
+    """Return version information for PhasorPy and its dependencies.
+
+    Parameters
+    ----------
+    sep : str, optional
+        Separator between version items. Defaults to newline.
+    dash : str, optional
+        Separator between module name and version. Defaults to dash.
+    verbose : bool, optional
+        Include paths to Python interpreter and modules.
+
+    Returns
+    -------
+    str
+        Formatted string containing version information.
+        Format: ``"<package><dash><version>[<space>(<path>)]<sep>"``
+
+    Examples
+    --------
+    >>> print(versions())  # doctest: +SKIP
+    Python-3.13.5
+    phasorpy-0.6
+    numpy-2.3.1
+    ...
+
+    """
+    import importlib.metadata
+    import os
+    import sys
+
+    if verbose:
+        version_strings = [f'Python{dash}{sys.version}  ({sys.executable})']
+    else:
+        version_strings = [f'Python{dash}{sys.version.split()[0]}']
+
+    for module in (
+        'phasorpy',
+        'numpy',
+        'tifffile',
+        'imagecodecs',
+        'lfdfiles',
+        'sdtfile',
+        'ptufile',
+        'liffile',
+        'matplotlib',
+        'scipy',
+        'skimage',
+        'sklearn',
+        'pandas',
+        'xarray',
+        'click',
+        'pooch',
+    ):
+        try:
+            __import__(module)
+        except ModuleNotFoundError:
+            version_strings.append(f'{module.lower()}{dash}n/a')
+            continue
+        lib = sys.modules[module]
+        try:
+            ver = importlib.metadata.version(module)
+        except importlib.metadata.PackageNotFoundError:
+            ver = getattr(lib, '__version__', 'unknown')
+        ver = f'{module.lower()}{dash}{ver}'
+        if verbose:
+            try:
+                path = getattr(lib, '__file__')
+            except NameError:
+                pass
+            else:
+                ver += f'  ({os.path.dirname(path)})'
+        version_strings.append(ver)
+    return sep.join(version_strings)

{phasorpy-0.5.dist-info → phasorpy-0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.5
+Version: 0.7
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -24,7 +24,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy>=1.25.0
+Requires-Dist: numpy>=1.26.0
 Requires-Dist: matplotlib>=3.8.0
 Requires-Dist: scipy>=1.11.0
 Requires-Dist: click
@@ -66,7 +66,7 @@ PhasorPy is a community-maintained project.
 in the form of bug reports, bug fixes, feature implementations, documentation,
 datasets, and enhancement proposals are welcome.
 
-This software project is supported in part by the
+This software project was supported in part by the
 [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
 program at
 [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).

phasorpy-0.7.dist-info/RECORD

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{phasorpy-0.5.dist-info → phasorpy-0.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: false
 Tag: cp313-cp313-win_arm64