phasorpy 0.1__cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

phasorpy/_typing.py

@@ -0,0 +1,77 @@
+"""Type annotations.
+
+This module should only be imported when type-checking, for example::
+
+    from __future__ import annotations
+
+    from typing import TYPE_CHECKING
+
+    if TYPE_CHECKING:
+        from ._typing import Any, ArrayLike, PathLike
+
+"""
+
+# flake8: noqa: F401
+# pylint: disable=unused-import
+# autoflake: skip_file
+
+from __future__ import annotations
+
+__all__ = [
+    'Any',
+    'ArrayLike',
+    'Callable',
+    'Collection',
+    'Container',
+    'DTypeLike',
+    'DataArray',
+    'EllipsisType',
+    'IO',
+    'ItemsView',
+    'Iterable',
+    'Iterator',
+    'KeysView',
+    'Literal',
+    'Mapping',
+    'NDArray',
+    'Optional',
+    'PathLike',
+    'Pooch',
+    'Sequence',
+    'TextIO',
+    'Union',
+    'ValuesView',
+    'cast',
+    'final',
+    'overload',
+]
+
+from collections.abc import (
+    Callable,
+    Collection,
+    Container,
+    ItemsView,
+    Iterable,
+    Iterator,
+    KeysView,
+    Mapping,
+    Sequence,
+    ValuesView,
+)
+from os import PathLike
+from types import EllipsisType
+from typing import (
+    IO,
+    Any,
+    Literal,
+    Optional,
+    TextIO,
+    Union,
+    cast,
+    final,
+    overload,
+)
+
+from numpy.typing import ArrayLike, DTypeLike, NDArray
+from pooch import Pooch
+from xarray import DataArray

phasorpy/_utils.py

@@ -0,0 +1,441 @@
+"""Private auxiliary and convenience functions.
+
+"""
+
+from __future__ import annotations
+
+__all__: list[str] = [
+    'chunk_iter',
+    'dilate_coordinates',
+    'kwargs_notnone',
+    'parse_harmonic',
+    'parse_kwargs',
+    'phasor_from_polar_scalar',
+    'phasor_to_polar_scalar',
+    'scale_matrix',
+    'sort_coordinates',
+    'update_kwargs',
+]
+
+import math
+import numbers
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from ._typing import Any, Sequence, ArrayLike, Literal, NDArray, Iterator
+
+import numpy
+
+
+def parse_kwargs(
+    kwargs: dict[str, Any],
+    /,
+    *keys: str,
+    _del: bool = True,
+    **keyvalues: Any,
+) -> dict[str, Any]:
+    """Return dict with keys from keys|keyvals and values from kwargs|keyvals.
+
+    If `_del` is true (default), existing keys are deleted from `kwargs`.
+
+    >>> kwargs = {'one': 1, 'two': 2, 'four': 4}
+    >>> kwargs2 = parse_kwargs(kwargs, 'two', 'three', four=None, five=5)
+    >>> kwargs == {'one': 1}
+    True
+    >>> kwargs2 == {'two': 2, 'four': 4, 'five': 5}
+    True
+
+    """
+    result = {}
+    for key in keys:
+        if key in kwargs:
+            result[key] = kwargs[key]
+            if _del:
+                del kwargs[key]
+    for key, value in keyvalues.items():
+        if key in kwargs:
+            result[key] = kwargs[key]
+            if _del:
+                del kwargs[key]
+        else:
+            result[key] = value
+    return result
+
+
+def update_kwargs(kwargs: dict[str, Any], /, **keyvalues: Any) -> None:
+    """Update dict with keys and values if keys do not already exist.
+
+    >>> kwargs = {'one': 1}
+    >>> update_kwargs(kwargs, one=None, two=2)
+    >>> kwargs == {'one': 1, 'two': 2}
+    True
+
+    """
+    for key, value in keyvalues.items():
+        if key not in kwargs:
+            kwargs[key] = value
+
+
+def kwargs_notnone(**kwargs: Any) -> dict[str, Any]:
+    """Return dict of kwargs which values are not None.
+
+    >>> kwargs_notnone(one=1, none=None)
+    {'one': 1}
+
+    """
+    return dict(item for item in kwargs.items() if item[1] is not None)
+
+
+def scale_matrix(factor: float, origin: Sequence[float]) -> NDArray[Any]:
+    """Return matrix to scale homogeneous coordinates by factor around origin.
+
+    Parameters
+    ----------
+    factor: float
+        Scale factor.
+    origin: (float, float)
+        Coordinates of point around which to scale.
+
+    Returns
+    -------
+    matrix: ndarray
+        A 3x3 homogeneous transformation matrix.
+
+    Examples
+    --------
+    >>> scale_matrix(1.1, (0.0, 0.5))
+    array([[1.1, 0, -0],
+           [0, 1.1, -0.05],
+           [0, 0, 1]])
+
+    """
+    mat = numpy.diag((factor, factor, 1.0))
+    mat[:2, 2] = origin[:2]
+    mat[:2, 2] *= 1.0 - factor
+    return mat
+
+
+def sort_coordinates(
+    real: ArrayLike,
+    imag: ArrayLike,
+    /,
+    origin: tuple[float, float] | None = None,
+) -> tuple[NDArray[Any], NDArray[Any], NDArray[Any]]:
+    """Return cartesian coordinates sorted counterclockwise around origin.
+
+    Parameters
+    ----------
+    real, imag : array_like
+        Coordinates to be sorted.
+    origin : (float, float)
+        Coordinates around which to sort by angle.
+
+    Returns
+    -------
+    real, imag : ndarray
+        Coordinates sorted by angle.
+    indices : ndarray
+        Indices used to reorder coordinates.
+
+    Examples
+    --------
+    >>> sort_coordinates([0, 1, 2, 3], [0, 1, -1, 0])
+    (array([2, 3, 1, 0]), array([-1,  0,  1,  0]), array([2, 3, 1, 0]...))
+
+    """
+    x, y = numpy.atleast_1d(real, imag)
+    if x.ndim != 1 or x.shape != y.shape:
+        raise ValueError(f'invalid {x.shape=} or {y.shape=}')
+    if x.size < 4:
+        return x, y, numpy.arange(x.size)
+    if origin is None:
+        origin = x.mean(), y.mean()
+    indices = numpy.argsort(numpy.arctan2(y - origin[1], x - origin[0]))
+    return x[indices], y[indices], indices
+
+
+def dilate_coordinates(
+    real: ArrayLike,
+    imag: ArrayLike,
+    offset: float,
+    /,
+) -> tuple[NDArray[Any], NDArray[Any]]:
+    """Return dilated coordinates.
+
+    Parameters
+    ----------
+    real, imag : array_like
+        Coordinates of convex hull, sorted by angle.
+    offset : float
+        Amount by which to dilate coordinates.
+
+    Returns
+    -------
+    real, imag : ndarray
+        Coordinates dilated by offset.
+
+    Examples
+    --------
+    >>> dilate_coordinates([2, 3, 1, 0], [-1, 0, 1, 0], 0.05)
+    (array([2.022, 3.05, 0.9776, -0.05]), array([-1.045, 0, 1.045, 0]))
+
+    """
+    x = numpy.asanyarray(real, dtype=numpy.float64)
+    y = numpy.asanyarray(imag, dtype=numpy.float64)
+    if x.ndim != 1 or x.shape != y.shape or x.size < 1:
+        raise ValueError(f'invalid {x.shape=} or {y.shape=}')
+    if x.size > 1:
+        dx = numpy.diff(numpy.diff(x, prepend=x[-1], append=x[0]))
+        dy = numpy.diff(numpy.diff(y, prepend=y[-1], append=y[0]))
+    else:
+        # TODO: this assumes coordinate on universal semicircle
+        dx = numpy.diff(x, append=0.5)
+        dy = numpy.diff(y, append=0.0)
+    s = numpy.hypot(dx, dy)
+    dx /= s
+    dx *= -offset
+    dx += x
+    dy /= s
+    dy *= -offset
+    dy += y
+    return dx, dy
+
+
+def phasor_to_polar_scalar(
+    real: float,
+    imag: float,
+    /,
+    *,
+    degree: bool = False,
+    percent: bool = False,
+) -> tuple[float, float]:
+    """Return polar from scalar phasor coordinates.
+
+    >>> phasor_to_polar_scalar(1.0, 0.0, degree=True, percent=True)
+    (0.0, 100.0)
+
+    """
+    phi = math.atan2(imag, real)
+    mod = math.hypot(imag, real)
+    if degree:
+        phi = math.degrees(phi)
+    if percent:
+        mod *= 100.0
+    return phi, mod
+
+
+def phasor_from_polar_scalar(
+    phase: float,
+    modulation: float,
+    /,
+    *,
+    degree: bool = False,
+    percent: bool = False,
+) -> tuple[float, float]:
+    """Return phasor from scalar polar coordinates.
+
+    >>> phasor_from_polar_scalar(0.0, 100.0, degree=True, percent=True)
+    (1.0, 0.0)
+
+    """
+    if degree:
+        phase = math.radians(phase)
+    if percent:
+        modulation /= 100.0
+    real = modulation * math.cos(phase)
+    imag = modulation * math.sin(phase)
+    return real, imag
+
+
+def parse_harmonic(
+    harmonic: int | Sequence[int] | Literal['all'] | str | None,
+    samples: int,
+    /,
+) -> tuple[list[int], bool]:
+    """Return parsed harmonic parameter.
+
+    Parameters
+    ----------
+    harmonic : int, list of int, 'all', or None
+        Harmonic parameter to parse.
+    samples : int
+        Number of samples in signal.
+        Used to verify harmonic values and set maximum harmonic value.
+
+    Returns
+    -------
+    harmonic : list of int
+        Parsed list of harmonics.
+    has_harmonic_axis : bool
+        If true, `harmonic` input parameter is an integer, else a list.
+
+    Raises
+    ------
+    IndexError
+        Any element is out of range [1..samples // 2].
+    ValueError
+        Elements are not unique.
+        Harmonic is empty.
+        String input is not 'all'.
+    TypeError
+        Any element is not an integer.
+
+    """
+    if samples < 3:
+        raise ValueError(f'{samples=} < 3')
+
+    if harmonic is None:
+        return [1], False
+
+    harmonic_max = samples // 2
+    if isinstance(harmonic, (int, numbers.Integral)):
+        if harmonic < 1 or harmonic > harmonic_max:
+            raise IndexError(f'{harmonic=} out of range [1..{harmonic_max}]')
+        return [int(harmonic)], False
+
+    if isinstance(harmonic, str):
+        if harmonic == 'all':
+            return list(range(1, harmonic_max + 1)), True
+        raise ValueError(f'{harmonic=!r} is not a valid harmonic')
+
+    h = numpy.atleast_1d(numpy.asarray(harmonic))
+    if h.size == 0:
+        raise ValueError(f'{harmonic=} is empty')
+    if h.dtype.kind not in 'iu' or h.ndim != 1:
+        raise TypeError(f'{harmonic=} element not an integer')
+    if numpy.any(h < 1) or numpy.any(h > harmonic_max):
+        raise IndexError(
+            f'{harmonic=} element out of range [1..{harmonic_max}]'
+        )
+    if numpy.unique(h).size != h.size:
+        raise ValueError(f'{harmonic=} elements must be unique')
+    return h.tolist(), True
+
+
+def chunk_iter(
+    shape: tuple[int, ...],
+    chunk_shape: tuple[int, ...],
+    /,
+    axes: str | Sequence[str] | None = None,
+    *,
+    pattern: str | None = None,
+    squeeze: bool = False,
+    use_index: bool = False,
+) -> Iterator[tuple[tuple[int | slice, ...], str, bool]]:
+    """Yield indices and labels of chunks from ndarray's shape.
+
+    Parameters
+    ----------
+    shape : tuple of int
+        Shape of C-order ndarray to chunk.
+    chunk_shape : tuple of int
+        Shape of chunks in the most significant dimensions.
+    axes : str or sequence of str, optional
+        Labels for each axis in shape if `pattern` is None.
+    pattern : str, optional
+        String to format chunk indices.
+        If None, use ``_[{axes[index]}{chunk_index[index]}]`` for each axis.
+    squeeze : bool
+        If true, do not include length-1 chunked dimensions in label
+        unless dimensions are part of `chunk_shape`.
+        Applies only if `pattern` is None.
+    use_index : bool
+        If true, use indices of chunks in `shape` instead of chunk indices to
+        format pattern.
+
+    Yields
+    ------
+    index : tuple of int or slice
+        Indices of chunk in ndarray.
+    label : str
+        Pattern formatted with chunk indices.
+    cropped : bool
+        True if chunk exceeds any border of ndarray.
+        Indexing ndarray with `index` will yield a slice smaller than
+        `chunk_shape`.
+
+    Examples
+    --------
+
+    >>> list(chunk_iter((2, 2), (2,), pattern='Y{}'))
+    [((0, slice(0, 2, 1)), 'Y0', False), ((1, slice(0, 2, 1)), 'Y1', False)]
+
+    Chunk a four-dimensional image stack into 2x2 sized image tiles:
+
+    >>> stack = numpy.zeros((2, 3, 4, 5))
+    >>> for index, label, cropped in chunk_iter(stack.shape, (2, 2)):
+    ...     chunk = stack[index]
+    ...
+
+    """
+    ndim = len(shape)
+
+    sep = '_'
+    if axes is None:
+        axes = sep * ndim
+        sep = ''
+    elif ndim != len(axes):
+        raise ValueError(f'{len(shape)=} != {len(axes)=}')
+
+    if pattern is not None:
+        try:
+            pattern.format(*shape)
+        except Exception as exc:
+            raise ValueError('pattern cannot be formatted') from exc
+
+    # number of high dimensions not included in chaunk_shape
+    hdim = ndim - len(chunk_shape)
+    if hdim < 0:
+        raise ValueError(f'{len(shape)=} < {len(chunk_shape)=}')
+    if hdim > 0:
+        # prepend length-1 dimensions
+        chunk_shape = ((1,) * hdim) + chunk_shape
+
+    chunked_shape = []
+    pattern_list = []
+    for i, (size, chunk_size, ax) in enumerate(zip(shape, chunk_shape, axes)):
+        if size <= 0:
+            raise ValueError('shape must contain positive sizes')
+        if chunk_size <= 0:
+            raise ValueError('chunk_shape must contain positive sizes')
+        div, mod = divmod(size, chunk_size)
+        chunked_shape.append(div + 1 if mod else div)
+
+        if not squeeze or chunked_shape[-1] > 1:
+            if use_index:
+                digits = int(math.log10(size)) + 1
+            else:
+                digits = int(math.log10(chunked_shape[-1])) + 1
+            pattern_list.append(f'{sep}{ax}{{{i}:0{digits}d}}')
+
+    if pattern is None:
+        pattern = ''.join(pattern_list)
+
+    chunk_index: tuple[int, ...]
+    for chunk_index in numpy.ndindex(tuple(chunked_shape)):
+        index: tuple[int | slice, ...] = tuple(
+            (
+                chunk_index[i]
+                if i < hdim
+                else slice(
+                    chunk_index[i] * chunk_shape[i],
+                    (chunk_index[i] + 1) * chunk_shape[i],
+                    1,
+                )
+            )
+            for i in range(ndim)
+        )
+        if use_index:
+            format_index = tuple(
+                chunk_index[i] * chunk_shape[i] for i in range(ndim)
+            )
+        else:
+            format_index = chunk_index
+        yield (
+            index,
+            pattern.format(*format_index),
+            any(
+                (chunk_index[i] + 1) * chunk_shape[i] > shape[i]
+                for i in range(ndim)
+            ),
+        )

phasorpy/cli.py

@@ -0,0 +1,87 @@
+"""PhasorPy package command line interface.
+
+Invoke the command line application with::
+
+    $ python -m phasorpy --help
+
+"""
+
+from __future__ import annotations
+
+import os
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from ._typing import Iterable
+
+import click
+
+from . import version
+
+
+@click.group(help='PhasorPy package command line interface.')
+@click.version_option(version=version.__version__)
+def main() -> int:
+    """PhasorPy command line interface."""
+    return 0
+
+
+@main.command(help='Show runtime versions.')
+@click.option(
+    '--verbose',
+    default=False,
+    is_flag=True,
+    type=click.BOOL,
+    help='Show module paths.',
+)
+def versions(verbose: bool) -> None:
+    """Versions command group."""
+    click.echo(version.versions(verbose=verbose))
+
+
+@main.command(help='Fetch sample files from remote repositories.')
+@click.argument('files', nargs=-1)
+@click.option(
+    '--hideprogress',
+    default=False,
+    is_flag=True,
+    type=click.BOOL,
+    help='Hide progressbar.',
+)
+def fetch(files: Iterable[str], hideprogress: bool) -> None:
+    """Fetch command group."""
+    from . import datasets
+
+    files = datasets.fetch(
+        *files, return_scalar=False, progressbar=not hideprogress
+    )
+    click.echo(f'Cached at {os.path.commonpath(files)}')
+
+
+@main.command(help='Start interactive FRET phasor plot.')
+@click.option(
+    '--hide',
+    default=False,
+    is_flag=True,
+    type=click.BOOL,
+    help='Do not show interactive plot.',
+)
+def fret(hide: bool) -> None:
+    """FRET command group."""
+    from .plot import PhasorPlotFret
+
+    plot = PhasorPlotFret(
+        frequency=60.0,
+        donor_lifetime=4.2,
+        acceptor_lifetime=3.0,
+        fret_efficiency=0.5,
+        interactive=True,
+    )
+    if not hide:
+        plot.show()
+
+
+if __name__ == '__main__':
+    import sys
+
+    sys.exit(main())  # pylint: disable=no-value-for-parameter