phasorpy 0.4__cp312-cp312-win_arm64.whl → 0.5__cp312-cp312-win_arm64.whl

phasorpy/color.py

@@ -19,13 +19,13 @@ def wavelength2rgb(
 ) -> tuple[float, float, float] | NDArray[Any]:
     """Return approximate sRGB color components of visible wavelength(s).
 
-    Wavelength values are clipped to 360..750, rounded, and used to index
-    the :py:attr:`SRGB_SPECTRUM` palette.
+    Wavelengths are clipped to range [360, 750] nm, rounded, and used to
+    index the :py:attr:`SRGB_SPECTRUM` palette.
 
     Parameters
     ----------
     wavelength : array_like
-        Scalar or array of wavelength(s) to convert.
+        Scalar or array of wavelengths in nm.
     dtype : data-type, optional
         Data-type of return value. The default is ``float32``.
 
@@ -33,8 +33,8 @@ def wavelength2rgb(
     -------
     ndarray or tuple
         Approximate sRGB color components of visible wavelength.
-        Floating-point types are in range 0.0 to 1.0.
-        Integer types are scaled to the dtype's maximum value.
+        Floating-point values are in range [0.0, 1.0].
+        Integer values are scaled to the dtype's maximum value.
 
     Examples
     --------
@@ -68,7 +68,7 @@ def float2int(
     /,
     dtype: DTypeLike = numpy.uint8,
 ) -> NDArray[Any]:
-    """Return normalized color components as integer type.
+    """Return normalized color components as integers.
 
     Parameters
     ----------
@@ -77,6 +77,11 @@ def float2int(
     dtype : data-type, optional
         Data type of return value. The default is ``uint8``.
 
+    Returns
+    -------
+    ndarray
+        Color components as integers scaled to dtype's range.
+
     Examples
     --------
     >>> float2int([0.0, 0.5, 1.0])
@@ -162,11 +167,11 @@ CATEGORICAL: NDArray[numpy.float32] = numpy.array([
     [0.523809, 0.888889, 0.460317],
     [0.285714, 0.0, 0.238095],
 ], dtype=numpy.float32)
-"""Categorical sRGB color palette inspired by C Glasbey.
+"""Categorical sRGB color palette inspired by C. Glasbey.
 
-The palette contains 64 maximally distinct colours.
+Contains 64 maximally distinct colours for visualization.
 
-Generated with the `glasbey <https://glasbey.readthedocs.io>`_ package::
+Generated using the `glasbey <https://glasbey.readthedocs.io>`_ package::
 
     import glasbey; numpy.array(glasbey.create_palette(64, as_hex=False))
 
@@ -568,11 +573,11 @@ SRGB_SPECTRUM: NDArray[numpy.float32] = numpy.array([
     [0.005006, 0.0, 0.0],
     [0.004664, 0.0, 0.0],
 ], dtype=numpy.float32)
-"""sRGB color components for visible light wavelengths 360-750 nm.
+"""sRGB color components for wavelengths of visible light (360-750 nm).
 
 Based on the CIE 1931 2° Standard Observer.
 
-Generated with the `colour <https://colour.readthedocs.io>`_ package::
+Generated using the `colour <https://colour.readthedocs.io>`_ package::
 
     import colour; colour.plotting.plot_visible_spectrum()
 

phasorpy/components.py

@@ -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.
+    components_real : array_like, shape (2,)
+        Real coordinates of first and second components.
+    components_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
@@ -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,)
+    components_real : array_like, shape (2,) or (3,)
         Real coordinates for two or three components.
-    components_imag: array_like, shape (2,) or (3,)
+    components_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
@@ -163,8 +163,8 @@ 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
     ------
@@ -172,7 +172,7 @@ def graphical_component_analysis(
         The array shapes of `real` and `imag`, or `components_real` and
         `components_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
     --------
@@ -216,7 +216,7 @@ def graphical_component_analysis(
     >>> graphical_component_analysis(
     ...     [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:
 
@@ -227,9 +227,9 @@ def graphical_component_analysis(
     ...     [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)
@@ -305,7 +305,7 @@ def graphical_component_analysis(
                         components_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))

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
         )

phasorpy/datasets.py

@@ -14,8 +14,11 @@ Datasets from the following repositories are available:
   <https://github.com/zoccoler/napari-flim-phasor-plotter/tree/0.0.6/src/napari_flim_phasor_plotter/data>`_
 - `Phasor-based multi-harmonic unmixing for in-vivo hyperspectral imaging
   <https://zenodo.org/records/13625087>`_
+  (`second record <https://zenodo.org/records/14860228>`_)
 - `Convallaria slice acquired with time-resolved 2-photon microscope
   <https://zenodo.org/records/14026720>`_
+- `Convallaria FLIM dataset in FLIM LABS JSON format
+  <https://zenodo.org/records/15007900>`_
 
 The implementation is based on the `Pooch <https://www.fatiando.org/pooch>`_
 library.
@@ -266,14 +269,15 @@ ZENODO_13625087 = pooch.create(
     base_url=(
         'https://github.com/phasorpy/phasorpy-data/raw/main/zenodo_13625087'
         # if DATA_ON_GITHUB
-        # else 'doi:10.1088/2050-6120/ac9ae9'
+        # else 'doi:10.1088/2050-6120/ac9ae9'  # TODO: not working with Pooch
     ),
     env=ENV,
     registry={
-        '33_Hoechst_Golgi_Mito_Lyso_CellMAsk_404_488_561_633_SP.lsm': (
-            'sha256:'
-            '68fcefcad4e750e9ec7068820e455258c986f6a9b724e66744a28bbbb689f986'
-        ),
+        # part of ZENODO_14860228
+        # '33_Hoechst_Golgi_Mito_Lyso_CellMAsk_404_488_561_633_SP.lsm': (
+        #    'sha256:'
+        #    '68fcefcad4e750e9ec7068820e455258c986f6a9b724e66744a28bbbb689f986'
+        # ),
         '34_Hoechst_Golgi_Mito_Lyso_CellMAsk_404_488_561_633_SP.lsm': (
             'sha256:'
             '5c0b7d76c274fd64891fca2507013b7c8c9979d8131ce282fac55fd24fbb38bd'
@@ -289,9 +293,65 @@ ZENODO_13625087 = pooch.create(
     },
 )
 
+ZENODO_14860228 = pooch.create(
+    path=pooch.os_cache('phasorpy'),
+    base_url=(
+        'https://github.com/phasorpy/phasorpy-data/raw/main/zenodo_14860228'
+        if DATA_ON_GITHUB
+        else 'doi:10.5281/zenodo.14860228'
+    ),
+    env=ENV,
+    registry={
+        '38_Hoechst_Golgi_Mito_Lyso_CellMAsk_404_488_561_633_SP.lsm': (
+            'sha256:'
+            '092ac050edf55e26dcda8cba10122408c6f1b81d19accf07214385d6eebfcf3e'
+        ),
+        'spectral cell mask.lsm': (
+            'sha256:'
+            'c4c2c567bd99ef4930d7278794d4e3daebaad0375c0852a5ab86a2ea056f4fe3'
+        ),
+        'spectral golgi.lsm': (
+            'sha256:'
+            'd0a5079d9ed18b1248434f3f6d4b2b240fb034891121262cfe9dfec64d8429cd'
+        ),
+        'spectral hoehst.lsm': (
+            'sha256:'
+            '3ee44a7f9f125698bb5e34746d9723669f67c520ffbf21244757d7fc25dbbb88'
+        ),
+        'spectral lyso tracker green.lsm': (
+            'sha256:'
+            '0964448649e2c73a57f5ca0c705c86511fb4625c0a2af0d7850dfa39698fcbb9'
+        ),
+        'spectral mito tracker.lsm': (
+            'sha256:'
+            '99b9892b247256ebf8a9917c662bc7bb66a8daf3b5db950fbbb191de0cd35b37'
+        ),
+    },
+)
+
+ZENODO_14976703 = pooch.create(
+    path=pooch.os_cache('phasorpy'),
+    base_url=(
+        'https://github.com/phasorpy/phasorpy-data/raw/main/zenodo_14976703'
+        if DATA_ON_GITHUB
+        else 'doi:10.5281/zenodo.14976703'
+    ),
+    env=ENV,
+    registry={
+        'Convalaria_LambdaScan.lif': (
+            'sha256:'
+            '27f1282cf02f87e11f8c7d3064066a4517ad4c9c769c796b32e459774f18c62a'
+        ),
+    },
+)
+
 CONVALLARIA_FBD = pooch.create(
     path=pooch.os_cache('phasorpy'),
-    base_url='doi:10.5281/zenodo.14026719',
+    base_url=(
+        'https://github.com/phasorpy/phasorpy-data/raw/main/zenodo_14026720'
+        if DATA_ON_GITHUB
+        else 'doi:10.5281/zenodo.14026719'
+    ),
     env=ENV,
     registry={
         'Convallaria_$EI0S.fbd': (
@@ -307,80 +367,94 @@ CONVALLARIA_FBD = pooch.create(
 
 FLIMLABS = pooch.create(
     path=pooch.os_cache('phasorpy'),
-    base_url='https://github.com/phasorpy/phasorpy-data/raw/main/flimlabs',
+    base_url=(
+        'https://github.com/phasorpy/phasorpy-data/raw/main/flimlabs'
+        if DATA_ON_GITHUB
+        else 'doi:10.5281/zenodo.15007900'
+    ),
     env=ENV,
     registry={
-        'calibrator_2_5_1737112045_imaging.json': (
-            'sha256:'
-            'a34c7077e88d1e7272953a46b2bb4e3ab8adf5a2f61c824dfc27032d952b920e'
-        ),
-        'calibrator_2_5_1737112045_imaging.json.zip': (
+        'Convallaria_m2_1740751781_phasor_ch1.json': (
             'sha256:'
-            'fea791b28afd8365152018810cbbaaac1177cb72827578073587a1050d1af329'
+            'a8bf0179f352ab2c6c78d0bd399545ab1fb6d5537f23dc06e5f12a7ef5af6615'
         ),
-        'calibrator_2_5_1737112045_imaging_calibration.json': (
+        'Convallaria_m2_1740751781_phasor_ch1.json.zip': (
             'sha256:'
-            '8f2ebe9b544fae9524dc13221c1a5ab1b57d9dfd40ec2eb06a7b1475fcd63057'
+            '9c5691f55e85778717ace13607d573bcd00c29e357e063c8db4f173340f72984'
         ),
-        'calibrator_2_5_bis_1737112494_imaging.json': (
+        'Fluorescein_Calibration_m2_1740751189_imaging.json': (
             'sha256:'
-            '0509c5aba066419b03f83264eba58acbf4aae470aa1057c52f45e60225e033a4'
+            'aeebb074dbea6bff7578f409c7622b2f7f173bb23e5475d1436adedca7fc2eed'
         ),
-        'calibrator_2_5_bis_1737112494_imaging.json.zip': (
+        'Fluorescein_Calibration_m2_1740751189_imaging.json.zip': (
             'sha256:'
-            'bdc5df2a3f08a64ec7b7bb57b36e21546de142e67c59c052318252dbb66d8abf'
+            '32960bc1dec85fd16ffc7dd74a3cd63041fb3b69054ee6582f913129b0847086'
         ),
-        'calibrator_2_5_bis_1737112494_imaging_calibration.json': (
+        'Fluorescein_Calibration_m2_1740751189_imaging_calibration.json': (
             'sha256:'
-            '9bb0e21b1e7c04add672aa8a78048b09908c860fcaf907ca33c0c87d161f6ebf'
+            '7fd1b9749789bd139c132602a771a127ea0c76f403d1750e9636cd657cce017a'
         ),
-        'convallaria_1_1737112980_phasor_ch1.json': (
-            'sha256:'
-            '4a296a0d7898dc660a388e1bba5cf98b43c35fe12d94b7aba48d00245e37242d'
-        ),
-        'convallaria_1_1737112980_phasor_ch1.json.zip': (
+    },
+)
+
+FIGSHARE_22336594 = pooch.create(
+    path=pooch.os_cache('phasorpy'),
+    base_url=(
+        'https://github.com/phasorpy/phasorpy-data/raw/main/figshare_22336594'
+        if DATA_ON_GITHUB
+        else 'doi:10.6084/m9.figshare.22336594.v1'
+    ),
+    env=ENV,
+    registry={
+        'FLIM_testdata.lif': (
             'sha256:'
-            '79c416b9099c9f58d2092fe5b26ea6d0f695977b877784cf564d3ead896d9354'
+            '902d8fa6cd39da7cf062b32d43aab518fa2a851eab72b4bd8b8eca1bad591850'
         ),
-        'convallaria_2_1737113097_phasor_ch1.json': (
+    },
+)
+
+FIGSHARE_22336594_EXPORTED = pooch.create(
+    path=pooch.os_cache('phasorpy'),
+    base_url=(
+        'https://github.com/phasorpy/phasorpy-data/raw/main/figshare_22336594'
+    ),
+    env=ENV,
+    registry={
+        'FLIM_testdata.lif.ptu': (
             'sha256:'
-            'da549645ffd898238c26f7a1eac3aca4ffccec86653c0d241a6ece674dfce90d'
+            'c85792b25d0b274f1484e490c99aa19052ab8e48e4e5022aabb1f218cd1123b6'
         ),
-        'convallaria_2_1737113097_phasor_ch1.json.zip': (
+        'FLIM_testdata.lif.ptu.zip': (
             'sha256:'
-            '8801bb14b457dceaef42e8b3bf6af770a2e14264cd2b282ba7e3d70b91ea954c'
+            'c5134c470f6a3e5cb21eabd538cbd5061d9911dad96d58e3a4040cfddadaef33'
         ),
-        'data_2_calibrator_2_5_1737112409_phasor_ch1.json': (
+        'FLIM_testdata.xlef': (
             'sha256:'
-            'ea8683892eb76f52231e5d6ceab64a3737454aa95fe73185366de8f758fd9b70'
+            '7860ef0847dc9f5534895a9c11b979bb446f67382b577fe63fb166e281e5dc5e'
         ),
-        'data_2_calibrator_2_5_1737112409_phasor_ch1.json.zip': (
+        'FLIM_testdata.xlef.zip': (
             'sha256:'
-            '40d2aa90b95fd8864a2392337c83a1a4f4931d7359cb30a486f65173f208de0a'
+            'ad0ad6389f38dcba6f9809b54934ef3f19da975d9dabeb4c3a248692b959b9cf'
         ),
-        'data_calibrator_2_5_1737112133_phasor_ch1.json': (
+        'FLIM_testdata.lif.filtered.ptu': (
             'sha256:'
-            '6a8790212bc62014d597402ec5feb0e50ec6ae2aa62d63fae8cb62c6c5656268'
+            'a00b84f626a39e79263322c60ae50b64163b36bb977ecc4dc54619097ba7f5b7'
         ),
-        'data_calibrator_2_5_1737112133_phasor_ch1.json.zip': (
+        'FLIM_testdata.lif.filtered.ptu.zip': (
             'sha256:'
-            'c9ef343bdbd7a51d23fdf4082e379dcdb1ce9f3e2ba065289bf2925d68ef55ba'
+            '717366b231213bfd6e295c3efb7bf1bcd90e720eb28aab3223376087172e93e5'
         ),
     },
 )
 
-FIGSHARE_22336594 = pooch.create(
+MISC = pooch.create(
     path=pooch.os_cache('phasorpy'),
-    base_url=(
-        'https://github.com/phasorpy/phasorpy-data/raw/main/figshare_22336594'
-        if DATA_ON_GITHUB
-        else 'doi:10.6084/m9.figshare.22336594.v1'
-    ),
+    base_url='https://github.com/phasorpy/phasorpy-data/raw/main/misc',
     env=ENV,
     registry={
-        'FLIM_testdata.lif': (
+        'NADHandSHG.ifli': (
             'sha256:'
-            '902d8fa6cd39da7cf062b32d43aab518fa2a851eab72b4bd8b8eca1bad591850'
+            'dfa65952850b8a222258776a8a14eb1ab7e70ff5f62b58aa2214797c5921b4a3'
         ),
     },
 )
@@ -391,9 +465,13 @@ REPOSITORIES: dict[str, pooch.Pooch] = {
     'flute': FLUTE,
     'napari-flim-phasor-plotter': NAPARI_FLIM_PHASOR_PLOTTER,
     'zenodo-13625087': ZENODO_13625087,
+    'zenodo-14860228': ZENODO_14860228,
+    'zenodo-14976703': ZENODO_14976703,
     'convallaria-fbd': CONVALLARIA_FBD,
     'flimlabs': FLIMLABS,
     'figshare_22336594': FIGSHARE_22336594,
+    'figshare_22336594_exported': FIGSHARE_22336594_EXPORTED,
+    'misc': MISC,
 }
 """Pooch repositories."""
 
@@ -406,19 +484,19 @@ def fetch(
 ) -> Any:  # str | tuple[str, ...]
     """Return absolute path(s) to sample file(s) in local storage.
 
-    The files are downloaded from a remote repository if they do not already
-    exist in the local storage.
+    The files are downloaded from a remote repository if not present in local
+    storage.
 
     Parameters
     ----------
-    *args: str or iterable of str, optional
+    *args : str or iterable of str, optional
         Name(s) of file(s) or repositories to fetch from local storage.
         If omitted, return files in all repositories.
     extract_dir : str or None, optional
         Path, relative to cache location, where ZIP files will be unpacked.
     return_scalar : bool, optional
         If true (default), return single path as string, else tuple of string.
-    **kwargs : optional
+    **kwargs
         Additional arguments passed to ``pooch.fetch()``.
         For example, ``progressbar=True``.
 

phasorpy/io.py

@@ -3,3 +3,7 @@
 
 from ._io import *
 from ._io import __all__, __doc__
+from ._utils import set_module
+
+set_module(globals())
+del set_module