phasorpy 0.7__cp314-cp314t-win_amd64.whl

phasorpy/experimental.py

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+"""Experimental functions.
+
+The ``phasorpy.experimental`` module provides functions related to phasor
+analysis for evaluation.
+The functions may be removed or moved to other modules in future releases.
+
+"""
+
+from __future__ import annotations
+
+__all__ = [
+    'anscombe_transform',
+    'anscombe_transform_inverse',
+    'spectral_vector_denoise',
+]
+
+import math
+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
+from .utils import number_threads
+
+
+def anscombe_transform(
+    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_transform(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_transform_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
+          + 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_transform_inverse(anscombe_transform(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]
+
+
+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 the same shape as `signal` with `axis` removed and an 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 a spectral vector Euclidean distance of `3 * sigma` and
+        intensity above `vmin`.
+    vmin : float, optional
+        Signal intensity along `axis` below which spectra are excluded from
+        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.
+
+    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)
+
+    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([[[...]]])
+
+    """
+    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)  # type: ignore[assignment]
+    if axis != -1:
+        denoised = numpy.moveaxis(denoised, -1, axis)
+    return denoised

phasorpy/io/__init__.py

@@ -0,0 +1,138 @@
+"""Read and write time-resolved and hyperspectral image file formats.
+
+The ``phasorpy.io`` module provides functions to:
+
+- read time-resolved and hyperspectral signals, as well as metadata from
+  many file formats used in bio-imaging:
+
+  - :py:func:`signal_from_lif` - Leica LIF and XLEF
+  - :py:func:`signal_from_lsm` - Zeiss LSM
+  - :py:func:`signal_from_ptu` - PicoQuant PTU
+  - :py:func:`signal_from_pqbin` - PicoQuant BIN
+  - :py:func:`signal_from_sdt` - Becker & Hickl SDT
+  - :py:func:`signal_from_fbd` - FLIMbox FBD
+  - :py:func:`signal_from_flimlabs_json` - FLIM LABS JSON
+  - :py:func:`signal_from_imspector_tiff` - ImSpector FLIM TIFF
+  - :py:func:`signal_from_flif` - FlimFast FLIF
+  - :py:func:`signal_from_b64` - SimFCS B64
+  - :py:func:`signal_from_z64` - SimFCS Z64
+  - :py:func:`signal_from_bhz` - SimFCS BHZ
+  - :py:func:`signal_from_bh` - SimFCS B&H
+
+- read phasor coordinates, lifetime images, and metadata from
+  specialized file formats:
+
+  - :py:func:`phasor_from_ometiff` - PhasorPy OME-TIFF
+  - :py:func:`phasor_from_ifli` - ISS IFLI
+  - :py:func:`phasor_from_lif` - Leica LIF and XLEF
+  - :py:func:`phasor_from_flimlabs_json` - FLIM LABS JSON
+  - :py:func:`phasor_from_simfcs_referenced` - SimFCS REF and R64
+  - :py:func:`lifetime_from_lif` - Leica LIF and XLEF
+
+- write phasor coordinate images to OME-TIFF and SimFCS file formats:
+
+  - :py:func:`phasor_to_ometiff`
+  - :py:func:`phasor_to_simfcs_referenced`
+
+  Support for other file formats is being considered:
+
+  - OME-TIFF
+  - Zeiss CZI
+  - Nikon ND2
+  - Olympus OIB/OIF
+  - Olympus OIR
+
+The functions are implemented as minimal wrappers around specialized
+third-party file reader libraries, currently
+`tifffile <https://github.com/cgohlke/tifffile>`_,
+`ptufile <https://github.com/cgohlke/ptufile>`_,
+`liffile <https://github.com/cgohlke/liffile>`_,
+`sdtfile <https://github.com/cgohlke/sdtfile>`_, and
+`lfdfiles <https://github.com/cgohlke/lfdfiles>`_.
+For advanced or unsupported use cases, consider using these libraries directly.
+
+The signal-reading functions typically have the following signature::
+
+    signal_from_ext(
+        filename: str | PathLike,
+        /,
+        **kwargs
+    ): -> xarray.DataArray
+
+where ``ext`` indicates the file format and ``kwargs`` are optional arguments
+passed to the underlying file reader library or used to select which data is
+returned. The returned `xarray.DataArray
+<https://docs.xarray.dev/en/stable/user-guide/data-structures.html>`_
+contains an N-dimensional array with labeled coordinates, dimensions, and
+attributes:
+
+- ``data`` or ``values`` (*array_like*)
+
+  Numpy array or array-like holding the array's values.
+
+- ``dims`` (*tuple of str*)
+
+  :ref:`Axes character codes <axes>` for each dimension in ``data``.
+  For example, ``('T', 'C', 'Y', 'X')`` defines the dimension order in a
+  4-dimensional array of a time-series of multi-channel images.
+
+- ``coords`` (*dict_like[str, array_like]*)
+
+  Coordinate arrays labelling each point in the data array.
+  The keys are :ref:`axes character codes <axes>`.
+  Values are 1-dimensional arrays of numbers or strings.
+  For example, ``coords['C']`` could be an array of emission wavelengths.
+
+- ``attrs`` (*dict[str, Any]*)
+
+  Arbitrary metadata such as measurement or calibration parameters required to
+  interpret the data values.
+  For example, the laser repetition frequency of a time-resolved measurement.
+
+.. _axes:
+
+Axes character codes from the OME model and tifffile library are used as
+``dims`` items and ``coords`` keys:
+
+- ``'X'`` : width (OME)
+- ``'Y'`` : height (OME)
+- ``'Z'`` : depth (OME)
+- ``'S'`` : sample (color components or phasor coordinates)
+- ``'I'`` : sequence (of images, frames, or planes)
+- ``'T'`` : time (OME)
+- ``'C'`` : channel (OME. Acquisition path or emission wavelength)
+- ``'A'`` : angle (OME)
+- ``'P'`` : phase (OME. In LSM, ``'P'`` maps to position)
+- ``'R'`` : tile (OME. Region, position, or mosaic)
+- ``'H'`` : lifetime histogram (OME)
+- ``'E'`` : lambda (OME. Excitation wavelength)
+- ``'F'`` : frequency (ISS)
+- ``'Q'`` : other (OME. Harmonics in PhasorPy TIFF)
+- ``'L'`` : exposure (FluoView)
+- ``'V'`` : event (FluoView)
+- ``'M'`` : mosaic (LSM 6)
+- ``'J'`` : column (NDTiff)
+- ``'K'`` : row (NDTiff)
+
+"""
+
+from __future__ import annotations
+
+__all__: list[str] = []
+
+from .._utils import init_module
+from ._flimlabs import *
+from ._leica import *
+from ._ometiff import *
+from ._other import *
+from ._simfcs import *
+
+# The `init_module()` function dynamically populates the `__all__` list with
+# all public symbols imported from submodules or defined in this module.
+# Any name not starting with an underscore will be automatically exported
+# when using "from phasorpy.io import *"
+
+init_module(globals())
+del init_module
+
+# flake8: noqa: F401, F403