phasorpy 0.7__tar.gz → 0.8__tar.gz

{phasorpy-0.7 → phasorpy-0.8}/MANIFEST.in

@@ -1,13 +1,12 @@
 include LICENSE.txt
 include README.md
 
-include tests/*.py
-
 include docs/*.py
 include docs/*.rst
 include docs/api/*.rst
 include docs/_static/*.*
 
+recursive-include tests *.py
 recursive-include tutorials *.py
 recursive-include tutorials *.rst
 

{phasorpy-0.7/src/phasorpy.egg-info → phasorpy-0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.7
+Version: 0.8
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -18,20 +18,20 @@ Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy>=1.26.0
-Requires-Dist: matplotlib>=3.8.0
-Requires-Dist: scipy>=1.11.0
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: matplotlib>=3.9.0
+Requires-Dist: scipy>=1.13.0
 Requires-Dist: click
 Requires-Dist: pooch
 Requires-Dist: tqdm
 Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: xarray>=2023.4.0
+Requires-Dist: xarray>=2024.6.0
 Requires-Dist: tifffile>=2024.8.30
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
@@ -46,6 +46,7 @@ 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>=2025.2.10; extra == "all"
+Requires-Dist: fbdfile>=2025.9.18; extra == "all"
 Requires-Dist: pawflim; extra == "all"
 Dynamic: license-file
 

{phasorpy-0.7 → phasorpy-0.8}/docs/_static/switcher.json

@@ -1,23 +1,23 @@
 [
   {
     "name": "dev",
-    "version": "0.8",
+    "version": "0.9",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.7 (stable)",
-    "version": "0.7",
+    "name": "0.8 (stable)",
+    "version": "0.8",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
+  {
+    "name": "0.7",
+    "version": "0.7",
+    "url": "https://www.phasorpy.org/docs/v0.7/"
+  },
   {
     "name": "0.6",
     "version": "0.6",
     "url": "https://www.phasorpy.org/docs/v0.6/"
-  },
-  {
-    "name": "0.5",
-    "version": "0.5",
-    "url": "https://www.phasorpy.org/docs/v0.5/"
   }
 ]

phasorpy-0.8/docs/api/_phasorpy.rst

@@ -0,0 +1,8 @@
+phasorpy._phasorpy
+------------------
+
+.. automodule:: phasorpy._phasorpy
+    :members:
+    :undoc-members:
+    :private-members:
+    :special-members:

phasorpy-0.8/docs/api/_utils.rst

@@ -0,0 +1,5 @@
+phasorpy._utils
+---------------
+
+.. automodule:: phasorpy._utils
+    :members:

phasorpy-0.8/docs/api/filter.rst

@@ -0,0 +1,5 @@
+phasorpy.filter
+---------------
+
+.. automodule:: phasorpy.filter
+    :members:

{phasorpy-0.7 → phasorpy-0.8}/docs/api/index.rst

@@ -14,6 +14,7 @@ PhasorPy library version |version|.
     phasorpy
     phasor
     lifetime
+    filter
     component
     cluster
     cursor

{phasorpy-0.7 → phasorpy-0.8}/docs/conf.py

@@ -26,7 +26,7 @@ import phasorpy
 
 version = phasorpy.__version__
 release = phasorpy.__version__
-version_match = version.replace('.dev', '').replace('.rc', '')
+version_match = version.split('.dev')[0].split('.rc')[0]
 
 # general configuration
 
@@ -35,7 +35,8 @@ extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.doctest',
-    'sphinx.ext.viewcode',
+    # 'sphinx.ext.viewcode',  # include source code in documentation
+    'sphinx.ext.linkcode',  # link to source code on GitHub
     'sphinx.ext.todo',
     # don't enable intersphinx since tutorials are getting littered with links
     # 'sphinx.ext.intersphinx',
@@ -60,6 +61,7 @@ html_static_path = ['_static']
 html_js_files = ['custom-icons.js']
 html_show_sourcelink = False
 
+html_title = f'PhasorPy {version} documentation'
 html_logo = '_static/phasorpy_logo.svg'
 html_favicon = '_static/favicon.ico'
 
@@ -125,6 +127,11 @@ sphinx_gallery_conf = {
     'reference_url': {'phasorpy': None},
     'matplotlib_animations': True,
     'within_subsection_order': 'conf.TutorialOrder',
+    'show_memory': False,
+    'show_api_usage': False,
+    'remove_config_comments': True,
+    # 'min_reported_time': 0.5,
+    # 'backreferences_dir': None,
 }
 
 
@@ -176,7 +183,69 @@ intersphinx_mapping = {
     'skimage': ('https://scikit-image.org/docs/stable/', None),
 }
 
-intersphinx_disabled_reftypes = ['*']
+# limit intersphinx linking to avoid "littering" tutorials
+# disable doc links but allow function links
+# intersphinx_disabled_reftypes = ['std:doc']
 
 # do not show typehints
 autodoc_typehints = 'none'
+
+
+def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
+    """Return GitHub URL for Python object."""
+    # adapted from
+    # https://github.com/matplotlib/matplotlib/blob/main/doc/conf.py
+    import inspect
+    from pathlib import Path
+
+    if domain != 'py':
+        return None
+
+    modname = info['module']
+    fullname = info['fullname']
+
+    submod = sys.modules.get(modname)
+    if submod is None:
+        return None
+
+    obj = submod
+    for part in fullname.split('.'):
+        try:
+            obj = getattr(obj, part)
+        except AttributeError:
+            return None
+
+    if inspect.isfunction(obj):
+        obj = inspect.unwrap(obj)
+    try:
+        fn = inspect.getsourcefile(obj)
+    except TypeError:
+        fn = None
+    if not fn or fn.endswith('__init__.py'):
+        try:
+            fn = inspect.getsourcefile(sys.modules[obj.__module__])
+        except (TypeError, AttributeError, KeyError):
+            fn = None
+    if not fn:
+        return None
+
+    try:
+        source, lineno = inspect.getsourcelines(obj)
+    except (OSError, TypeError):
+        lineno = None
+
+    linespec = f"#L{lineno:d}-L{lineno + len(source) - 1:d}" if lineno else ''
+
+    startdir = Path(phasorpy.__file__).parent.parent
+    try:
+        fn = os.path.relpath(fn, start=startdir).replace(os.path.sep, '/')
+    except ValueError:
+        return None
+
+    if '.dev' in version or '.rc' in version:
+        tag = 'main'
+    else:
+        tag = f'v{version}'
+    return (
+        f'https://github.com/phasorpy/phasorpy/blob/{tag}/src/{fn}{linespec}'
+    )

{phasorpy-0.7 → phasorpy-0.8}/docs/phasor_approach.rst

@@ -166,12 +166,20 @@ approach to analyze fluorescence time-resolved or spectral images:
   images using the phasor approach. The software is distributed under an
   unknown license and was last updated in 2013.
 
+-
+  .. _napari_phasors:
+
+  `Napari-phasors <https://github.com/napari-phasors/napari-phasors>`_
+  is a napari plugin for phasor analysis based on PhasorPy.
+  The plugin is distributed under the BSD-3-Clause license.
+
 -
   .. _napari_flim_phasor_plotter:
 
   `Napari-flim-phasor-plotter <https://github.com/zoccoler/napari-flim-phasor-plotter>`_
   is a napari plugin to interactively load and show raw FLIM single images
   and series and generate phasor plots.
+  The plugin is distributed under the BSD-3-Clause license.
 
 -
   .. _napari_live_flim:
@@ -263,6 +271,13 @@ approach to analyze fluorescence time-resolved or spectral images:
   "instant FLIM" system. It supports image segmentation based on phasor plot
   regions of interest and K-means clustering.
 
+  .. _cell_analysis_tools:
+
+- `Cell-analysis-tools <https://github.com/skalalab/cell-analysis-tools>`_
+  is an open-source Python library for the analysis of single cell imaging
+  data, including phasor analysis of FLIM data.
+  The library is distributed under the GPL v3.
+
 -
   .. _flim_studio:
 

{phasorpy-0.7 → phasorpy-0.8}/docs/release.rst

@@ -9,8 +9,47 @@ documentation and maintenance changes.
     The PhasorPy library is still under construction. Backwards-incompatible
     changes may occur between revisions.
 
-0.7 (2025.8.22)
----------------
+0.8 (2025-10-10)
+----------------
+
+This is the eighth alpha release of the PhasorPy library.
+It contains several improvements and breaking changes.
+
+Filter-related functions have moved from the ``phasor`` module to the new
+``filter`` module.
+A new ``signal_filter_ncpca`` function has been added that filters signals
+using noise-corrected principal component analysis.
+The ``experimental.spectral_vector_denoise`` function has been renamed to
+``filter.signal_filter_svd``.
+
+The ``signal_from_fbd`` function has been updated to use the ``fbdfile``
+package.
+
+This release supports Python 3.12 to 3.14. Python 3.11 is no longer supported.
+
+What's Changed
+..............
+
+* Bump version by @cgohlke in https://github.com/phasorpy/phasorpy/pull/287
+* Fix sdist does not contain all tests by @cgohlke in https://github.com/phasorpy/phasorpy/pull/288
+* Improve documentation by @cgohlke in https://github.com/phasorpy/phasorpy/pull/295
+* Mention cell-analysis-tools library by @cgohlke in https://github.com/phasorpy/phasorpy/pull/296
+* Add filter module by @cgohlke in https://github.com/phasorpy/phasorpy/pull/290
+* Document how to calibrate LIF Fast FLIM lifetimes by @cgohlke in https://github.com/phasorpy/phasorpy/pull/289
+* Add signal_filter_ncpca function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/297
+* Raise minimum version requirements by @cgohlke in https://github.com/phasorpy/phasorpy/pull/298
+* Mention napari-phasors software by @cgohlke in https://github.com/phasorpy/phasorpy/pull/301
+* Add phasor_combine function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/300
+* Bump the github-actions group with 2 updates by @dependabot[bot] in https://github.com/phasorpy/phasorpy/pull/299
+* Update to mkl_fft 2.0 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/302
+* Use fbdfile package to read FBD files by @cgohlke in https://github.com/phasorpy/phasorpy/pull/303
+* Support Python 3.14 and drop Python 3.11 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/304
+* Release v0.8 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/306
+
+**Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.7...v0.8
+
+0.7 (2025-08-22)
+----------------
 
 This is the seventh alpha release of the PhasorPy library.
 It contains several bug fixes, improvements, and breaking changes.
@@ -77,8 +116,8 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.6...v0.7
 
-0.6 (2025.6.22)
----------------
+0.6 (2025-06-22)
+----------------
 
 This is the sixth alpha release of the PhasorPy library.
 It contains several bug fixes, improvements, and breaking changes.
@@ -141,8 +180,8 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.5...v0.6
 
-0.5 (2025.4.11)
----------------
+0.5 (2025-04-11)
+----------------
 
 This is the fifth alpha release of the PhasorPy library.
 It contains several bug fixes and improvements.
@@ -193,8 +232,8 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.4...v0.5
 
-0.4 (2025.1.30)
----------------
+0.4 (2025-01-30)
+----------------
 
 This is the fourth alpha release of the PhasorPy library.
 It contains several bug fixes and many improvements, mostly to the
@@ -226,7 +265,7 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.3...v0.4
 
-0.3 (2024.12.16)
+0.3 (2024-12-16)
 ----------------
 
 This is the third alpha release of the PhasorPy library.
@@ -251,7 +290,7 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.2...v0.3
 
-0.2 (2024.11.30)
+0.2 (2024-11-30)
 ----------------
 
 This is the second alpha release of the PhasorPy library.
@@ -285,8 +324,8 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.1...v0.2
 
-0.1 (2024.9.30)
----------------
+0.1 (2024-09-30)
+----------------
 
 This is the first alpha release of the PhasorPy library.
 It contains over 70 documented and tested functions and class methods to

{phasorpy-0.7 → phasorpy-0.8}/pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=68",
     "numpy",
-    "cython>=3.1.0",
+    "cython>=3.1.4",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -14,19 +14,19 @@ dynamic = ["version"]
 dependencies = [
     # sync with requirements_min.txt
     # https://scientific-python.org/specs/spec-0000/
-    "numpy>=1.26.0",
-    "matplotlib>=3.8.0",
-    "scipy>=1.11.0",
+    "numpy>=2.0.0",
+    "matplotlib>=3.9.0",
+    "scipy>=1.13.0",
     "click",
     "pooch",
     "tqdm",
     "scikit-learn>=1.5.0",
-    # "scikit-image>=0.21.0",
-    # "pandas>=2.1.0",
-    "xarray>=2023.4.0",
+    # "scikit-image>=0.23.0",
+    # "pandas>=2.2.0",
+    "xarray>=2024.6.0",
     "tifffile>=2024.8.30",
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Developers",
@@ -36,9 +36,9 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
 ]
 authors = [{ name = "PhasorPy Contributors" }]
 license = "MIT"
@@ -70,6 +70,7 @@ all = [
     "sdtfile>=2024.5.24",
     "ptufile>=2024.9.14",
     "liffile>=2025.2.10",
+    "fbdfile>=2025.9.18",
     "pawflim",
 ]
 
@@ -113,7 +114,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py311", "py312", "py313"]
+target-version = ["py312", "py313"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -178,7 +179,7 @@ norecursedirs = [
 ]
 
 [tool.cibuildwheel]
-skip = "cp38* cp39* cp310* *musllinux* *i686 *ppc64le *s390x"
-test-requires = ["scikit-learn", "lfdfiles", "sdtfile", "ptufile", "liffile", "pawflim", "pytest", "pytest-cov", "pytest-runner", "pytest-doctestplus", "coverage"]
+skip = "cp38* cp39* cp310* cp311* *musllinux* *i686 *ppc64le *s390x"
+test-requires = ["scikit-learn", "lfdfiles", "fbdfile", "sdtfile", "ptufile", "liffile", "pawflim", "pytest", "pytest-cov", "pytest-runner", "pytest-doctestplus", "coverage"]
 test-command = "pytest {project}/tests"
 test-environment = "SKIP_FETCH=1"

{phasorpy-0.7 → phasorpy-0.8}/src/phasorpy/__init__.py

@@ -5,5 +5,5 @@ from __future__ import annotations
 __all__ = ['__version__']
 
 
-__version__ = '0.7'
+__version__ = '0.8'
 """PhasorPy version string."""

{phasorpy-0.7 → phasorpy-0.8}/src/phasorpy/_phasorpy.pyx

@@ -6,7 +6,13 @@
 # cython: nonecheck = False
 # cython: freethreading_compatible = True
 
-"""Cython implementation of low-level functions for the PhasorPy library."""
+"""Private functions implemented in Cython for performance.
+
+.. note::
+    This module and its functions are not part of the public interface.
+    They are intended to facilitate the development of the PhasorPy library.
+
+"""
 
 cimport cython
 
@@ -1005,6 +1011,38 @@ cdef (float_t, float_t) _phasor_divide(
     )
 
 
+@cython.ufunc
+cdef (float_t, float_t, float_t) _phasor_combine(
+    float_t int0,
+    float_t real0,
+    float_t imag0,
+    float_t int1,
+    float_t real1,
+    float_t imag1,
+    float_t fraction0,
+    float_t fraction1,
+) noexcept nogil:
+    """Return linear combination of two phasor coordinates."""
+    cdef:
+        float_t intensity
+
+    fraction1 += fraction0
+    if fraction1 == 0.0:
+        return <float_t> 0.0, <float_t> NAN, <float_t> NAN
+    fraction0 /= fraction1
+
+    int0 *= fraction0
+    int1 *= <float_t> 1.0 - fraction0
+    intensity = int0 + int1
+
+    if intensity == 0.0:
+        return <float_t> 0.0, <float_t> NAN, <float_t> NAN
+
+    int0 /= intensity
+    int1 /= intensity
+    return intensity, int0 * real0 + int1 * real1, int0 * imag0 + int1 * imag1
+
+
 ###############################################################################
 # Geometry ufuncs
 

{phasorpy-0.7 → phasorpy-0.8}/src/phasorpy/_utils.py

@@ -1,4 +1,10 @@
-"""Private auxiliary and convenience functions."""
+"""Private auxiliary and convenience functions.
+
+.. note::
+    This module and its functions are not part of the public interface.
+    They are intended to facilitate the development of the PhasorPy library.
+
+"""
 
 from __future__ import annotations
 
@@ -667,7 +673,7 @@ def chunk_iter(
 
 
 def init_module(globs: dict[str, Any], /) -> None:
-    """Add names in module to ``__all__`` and set ``__module__`` attributes.
+    """Add names in module to ``__all__`` attribute.
 
     Parameters
     ----------
@@ -690,9 +696,11 @@ def init_module(globs: dict[str, Any], /) -> None:
         }:
             continue
         names.append(name)
-        obj = getattr(module, name)
-        if hasattr(obj, '__module__'):
-            obj.__module__ = module_name
+        # do not change __module__ attributes because that may interfere
+        # with introspection and pickling
+        # obj = getattr(module, name)
+        # if hasattr(obj, '__module__'):
+        #     obj.__module__ = module_name
     globs['__all__'] = sorted(set(names))
 
 

{phasorpy-0.7 → phasorpy-0.8}/src/phasorpy/cluster.py

@@ -1,6 +1,6 @@
 """Cluster phasor coordinates.
 
-The `phasorpy.cluster` module provides functions to:
+The ``phasorpy.cluster`` module provides functions to:
 
 - fit elliptic clusters to phasor coordinates using a
   Gaussian Mixture Model (GMM):
@@ -66,7 +66,7 @@ def phasor_cluster_gmm(
         - 'area': Sort by inverse area of ellipse (-major * minor).
 
     **kwargs
-        Additional keyword arguments passed to
+        Optional arguments passed to
         :py:class:`sklearn.mixture.GaussianMixture`.
 
         Common options include:

{phasorpy-0.7 → phasorpy-0.8}/src/phasorpy/component.py

@@ -1,4 +1,4 @@
-"""Component analysis of phasor coordinates.
+"""Analyze components in phasor coordinates.
 
 The ``phasorpy.component`` module provides functions to:
 
@@ -53,7 +53,7 @@ from ._phasorpy import (
     _segment_direction_and_length,
 )
 from ._utils import sort_coordinates
-from .phasor import phasor_threshold
+from .filter import phasor_threshold
 from .utils import number_threads
 
 
@@ -95,6 +95,10 @@ def phasor_from_component(
     imag : ndarray
         Imaginary component of phasor coordinates.
 
+    See Also
+    --------
+    phasorpy.phasor.phasor_combine
+
     Examples
     --------
     Calculate phasor coordinates from two components and their fractional
@@ -110,7 +114,7 @@ def phasor_from_component(
     if dtype.char not in {'f', 'd'}:
         raise ValueError(f'{dtype=} is not a floating point type')
 
-    fraction = numpy.array(fraction, dtype=dtype, copy=True)
+    fraction = numpy.asarray(fraction, dtype=dtype, copy=True)
     if fraction.ndim < 1:
         raise ValueError(f'{fraction.ndim=} < 1')
     if fraction.shape[axis] < 2:
@@ -362,7 +366,7 @@ def phasor_component_graphical(
 
     dtype = numpy.min_scalar_type(real.size)
     counts = numpy.empty(
-        (1 if num_components == 2 else 3, fractions.size), dtype
+        (1 if num_components == 2 else 3, fractions.size), dtype=dtype
     )
 
     c = 0
@@ -438,8 +442,8 @@ def phasor_component_fit(
     component_imag : array_like
         Imaginary coordinates of components.
         Must be one or two-dimensional with harmonics in the first dimension.
-    **kwargs : optional
-        Additional arguments passed to :py:func:`scipy.linalg.lstsq()`.
+    **kwargs
+        Optional arguments passed to :py:func:`scipy.linalg.lstsq`.
 
     Returns
     -------

{phasorpy-0.7 → phasorpy-0.8}/src/phasorpy/datasets.py

@@ -600,7 +600,7 @@ def fetch(
     return_scalar : bool, optional
         If true (default), return single path as string, else tuple of string.
     **kwargs
-        Additional arguments passed to ``pooch.fetch()``.
+        Optional arguments passed to :py:func:`pooch.fetch`.
         For example, ``progressbar=True``.
 
     Returns