phasorpy 0.12__tar.gz → 0.13__tar.gz

{phasorpy-0.12/src/phasorpy.egg-info → phasorpy-0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.12
+Version: 0.13
 Summary: Analysis of luminescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -21,14 +21,15 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: numpy>=2.1.0
-Requires-Dist: matplotlib>=3.9.0
-Requires-Dist: pandas>=2.3.0
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: pandas>=2.3.2
 Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: scipy>=1.14.0
+Requires-Dist: scipy>=1.14.1
 Requires-Dist: tifffile>=2026.5.2
 Requires-Dist: xarray>=2024.6.0
 Requires-Dist: click
@@ -42,8 +43,7 @@ Requires-Dist: liffile>=2025.2.10; extra == "all"
 Requires-Dist: ptufile>=2024.9.14; extra == "all"
 Requires-Dist: sdtfile>=2024.5.24; extra == "all"
 Requires-Dist: pawflim>=1.0.4; extra == "all"
-Requires-Dist: brighteyes-mcs-reader>=0.1.0; extra == "all"
-Requires-Dist: imagecodecs==2026.6.6; (sys_platform == "darwin" and platform_machine == "x86_64") and extra == "all"
+Requires-Dist: brighteyes-mcs-reader>=0.1.0; python_version < "3.15" and extra == "all"
 Dynamic: license-file
 
 # <img src="https://www.phasorpy.org/_static/phasorpy_logo.svg" alt="&#x25CB;" width="48" height="48" align="left"/> PhasorPy

{phasorpy-0.12 → phasorpy-0.13}/docs/_static/switcher.json

@@ -1,15 +1,20 @@
 [
   {
     "name": "dev",
-    "version": "0.13",
+    "version": "0.14",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.12 (stable)",
-    "version": "0.12",
+    "name": "0.13 (stable)",
+    "version": "0.13",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
+  {
+    "name": "0.12",
+    "version": "0.12",
+    "url": "https://www.phasorpy.org/docs/v0.12/"
+  },
   {
     "name": "0.11",
     "version": "0.11",
@@ -19,10 +24,5 @@
     "name": "0.10",
     "version": "0.10",
     "url": "https://www.phasorpy.org/docs/v0.10/"
-  },
-  {
-    "name": "0.9",
-    "version": "0.9",
-    "url": "https://www.phasorpy.org/docs/v0.9/"
   }
 ]

{phasorpy-0.12 → phasorpy-0.13}/docs/conf.py

@@ -1,3 +1,7 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
 """Sphinx build configuration file.
 
 https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -13,6 +17,8 @@ sys.path.insert(0, os.path.dirname(__file__))
 
 # remove the examples header from HTML tutorials
 import sphinx_gallery.gen_rst
+from docutils import nodes
+from sphinx.application import Sphinx
 from sphinx_gallery.sorting import ExplicitOrder
 
 sphinx_gallery.gen_rst.EXAMPLE_HEADER = (
@@ -170,6 +176,7 @@ class TutorialOrder:
         'multi_harmonic',
         'phasorplot',
         'cursor',
+        'cluster',
         'component',
         'pca',
         # misc
@@ -206,6 +213,29 @@ intersphinx_mapping = {
 # do not show typehints
 autodoc_typehints = 'none'
 
+# redirect links to defunct websites, for example, to the Web Archive
+link_redirects = {
+    'https://www.lfd.uci.edu': (
+        'https://web.archive.org/web/20260926221331/https://www.lfd.uci.edu'
+    ),
+}
+
+
+def redirect_links(app: Sphinx, doctree: nodes.document) -> None:
+    """Replace URL prefixes in links according to link_redirects."""
+    del app
+    for node in doctree.findall(nodes.reference):
+        refuri = node.get('refuri', '')
+        for old, new in link_redirects.items():
+            if refuri.startswith(old):
+                node['refuri'] = new + refuri[len(old) :]
+                break
+
+
+def setup(app: Sphinx) -> None:
+    """Set up Sphinx app with link redirection."""
+    app.connect('doctree-read', redirect_links)
+
 
 def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
     """Return GitHub URL for Python object."""
@@ -231,8 +261,8 @@ def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
         except AttributeError:
             return None
 
-    if inspect.isfunction(obj):
-        obj = inspect.unwrap(obj)
+    if inspect.isfunction(obj):  # type: ignore[unreachable]
+        obj = inspect.unwrap(obj)  # type: ignore[unreachable]
     try:
         fn = inspect.getsourcefile(obj)
     except TypeError:

{phasorpy-0.12 → phasorpy-0.13}/docs/phasor_approach.rst

@@ -148,9 +148,9 @@ luminescence time-resolved or spectral images:
 
    * - **Library**
      - :ref:`PhasorPy <phasorpy>`,
-       :ref:`PyFLI <pyfli>`,
        :ref:`tttrlib <tttrlib>`,
        :ref:`FLIMLib <flimlib>`:sup:`2`,
+       :ref:`PyFLI <pyfli>`:sup:`2`,
        :ref:`BrightEyes <brighteyes>`:sup:`2`,
        :ref:`FLIM_tools <flim_tools>`:sup:`2,4`,
        :ref:`Cell-analysis-tools <cell_analysis_tools>`:sup:`2,4`
@@ -333,7 +333,7 @@ Details:
   is an open-source Python platform for Fluorescence Lifetime Imaging
   (FLI) data simulation, processing and visualization, including phasor
   analysis.
-  The library is distributed under the CC BY-NC-ND 4.0 license.
+  The library is distributed under the AGPL-3.0 license.
 
 -
   .. _flim_tools:

{phasorpy-0.12 → phasorpy-0.13}/pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 requires = [
-    "setuptools>=68",
+    "setuptools>=77",
     "numpy>=2.1.0",
-    "cython>=3.2.4",
+    "cython>=3.2.9",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -15,11 +15,11 @@ dependencies = [
     # sync with [dependency-groups.run]
     # https://scientific-python.org/specs/spec-0000/
     "numpy>=2.1.0",
-    "matplotlib>=3.9.0",
-    "pandas>=2.3.0",
+    "matplotlib>=3.10.3",
+    "pandas>=2.3.2",
     # "scikit-image>=0.24.0",
     "scikit-learn>=1.5.0",
-    "scipy>=1.14.0",
+    "scipy>=1.14.1",
     "tifffile>=2026.5.2",
     "xarray>=2024.6.0",
     "click",
@@ -39,6 +39,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
 ]
 authors = [{ name = "PhasorPy Contributors" }]
 license = "MIT"
@@ -65,8 +66,8 @@ all = [
     "ptufile>=2024.9.14",
     "sdtfile>=2024.5.24",
     "pawflim>=1.0.4",
-    "brighteyes-mcs-reader>=0.1.0",
-    "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
+    "brighteyes-mcs-reader>=0.1.0; python_version < '3.15'",
+    # "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
     # "mkl-fft>=2.1.1",
 ]
 
@@ -74,10 +75,10 @@ all = [
 run = [
     # runtime dependencies; sync with [project.dependencies]
     "numpy>=2.1.0",
-    "matplotlib>=3.10.0",
-    "pandas>=2.3.0",
+    "matplotlib>=3.10.3",
+    "pandas>=2.3.2",
     "scikit-learn>=1.5.0",
-    "scipy>=1.14.0",
+    "scipy>=1.14.1",
     "tifffile>=2026.5.2",
     "xarray>=2024.6.0",
     "click",
@@ -93,8 +94,8 @@ optional = [
     "ptufile>=2024.9.14",
     "sdtfile>=2024.5.24",
     "pawflim>=1.0.4",
-    "brighteyes-mcs-reader>=0.1.0",
-    "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
+    "brighteyes-mcs-reader>=0.1.0; python_version < '3.15'",
+    # "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
 ]
 minimal = [
     # minimal runtime versions for testing against oldest supported versions
@@ -117,7 +118,7 @@ minimal = [
 ]
 build = [
     # build requirements
-    "cython>=3.2.4",
+    "cython>=3.2.9",
     "numpy>=2.1.0",
     "abi3audit",
     "build",
@@ -150,7 +151,7 @@ docs = [
 lint = [
     # static code analysis requirements
     "autoflake",
-    "black",
+    "black>=26.10.1",
     "blackdoc",
     # "codespell",
     "cython_lint",
@@ -262,9 +263,9 @@ typing-modules = ["_typing"]
 "__init__.py" = ["F401", "F403"]
 "conftest.py" = ["ARG001"]
 "setup.py" = ["T201"]
-"tests/*" = ["INP001", "PT011", "SLF001", "TC001"]
+"tests/*" = ["INP001", "PT011", "SLF001", "TC001", "PLR0917"]
 "tools/*" = ["ANN", "INP001", "T201"]
-"tutorials/*" = ["ANN", "D", "E402", "INP001", "T201", "S101", "ERA001"]
+"tutorials/*" = ["ANN", "D", "E402", "INP001", "T201", "PLR0917"]
 "docs/conf.py" = ["A001", "ANN204", "D102", "E402", "INP001", "RUF012"]
 
 [tool.ruff.format]
@@ -273,6 +274,9 @@ quote-style = "single"
 [tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"
 
+[tool.ruff.lint.flake8-copyright]
+notice-rgx = "(#\\s*Copyright\\s*\\(c\\)\\s*PhasorPy\\s*Contributors)"
+
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
@@ -307,7 +311,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py312", "py313", "py314"]
+target-version = ["py312", "py313", "py314", "py315"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -345,6 +349,8 @@ warn_unreachable = true
 module = [
     "_conftest",
     "phasorpy._phasorpy",
+    "setuptools.*",
+    "sphinx_gallery.*",
     "pooch.*",
     "scipy.*",
     "mkl_fft.*",
@@ -353,6 +359,12 @@ module = [
 ]
 ignore_missing_imports = true
 
+[[tool.mypy.overrides]]
+# PyQt6 6.12 stubs contain syntax errors that block mypy
+module = ["PyQt6.*"]
+follow_imports = "skip"
+follow_imports_for_stubs = true
+
 [tool.coverage.run]
 plugins = ["Cython.Coverage"]
 omit = ["conftest.py", "__main__.py"]
@@ -392,7 +404,6 @@ norecursedirs = [
     ".pytest_cache",
     ".ruff_cache",
     ".vscode",
-    "htmlcov",
     "adhoc",
     "build",
     "docs/_build",
@@ -406,30 +417,20 @@ norecursedirs = [
 ]
 
 [tool.cibuildwheel]
-skip = [
-    "cp39*",
-    "cp310*",
-    "cp311*",
-    "cp313*",
-    "cp314-*",
-    "cp315*",
-    "*musllinux*",
-    "*i686*",
-    "*ppc64le*",
-    "*s390x*",
-]
+build = ["cp312-*", "cp314t-*", "cp315t-*"]
+skip = ["*musllinux*", "*i686*", "*ppc64le*", "*s390x*"]
 test-command = "pytest {project}/tests"
-test-skip = ["cp314t*", "cp315t*"]
+test-skip = ["cp3*t*"]
 test-requires = [
     # sync with [dependency-groups.optional]
-    "brighteyes-mcs-reader",
+    "brighteyes-mcs-reader>=0.1.0; python_version < '3.15'",
     "czifile>=2026.4.11",
-    "fbdfile",
-    "lfdfiles",
-    "liffile",
-    "ptufile",
-    "sdtfile",
-    "pawflim",
+    "fbdfile>=2025.9.18",
+    "lfdfiles>=2026.6.24",
+    "liffile>=2025.2.10",
+    "ptufile>=2024.9.14",
+    "sdtfile>=2024.5.24",
+    "pawflim>=1.0.4",
     # sync with [dependency-groups.test]
     "coverage",
     "cython",  # for Cython.Coverage plugin
@@ -439,10 +440,10 @@ test-requires = [
     "pytest-runner",
 ]
 
-[[tool.cibuildwheel.overrides]]
-select = "*-macosx_x86_64"
-inherit.test-requires = "append"
-test-requires = ["imagecodecs==2026.6.6"]
+# [[tool.cibuildwheel.overrides]]
+# select = "*-macosx_x86_64"
+# inherit.test-requires = "append"
+# test-requires = ["imagecodecs==2026.6.6"]
 
 [tool.cibuildwheel.test-environment]
 PHASORPY_DATA_ON_GITHUB = "1"

{phasorpy-0.12 → phasorpy-0.13}/setup.py

@@ -1,3 +1,7 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
 """PhasorPy package Setuptools script."""
 
 # project metadata are defined in pyproject.toml
@@ -8,17 +12,38 @@ import sysconfig
 import numpy
 from setuptools import Extension, setup
 
-DEBUG = bool(os.environ.get('PHASORPY_DEBUG', ''))
+DEBUG = os.environ.get('PHASORPY_DEBUG', '').strip().lower() in {
+    '1',
+    'true',
+    'yes',
+    'on',
+}
 LIMITED_API = not sysconfig.get_config_var('Py_GIL_DISABLED')
 
 print()
 print(f'Building with numpy-{numpy.__version__}')
 print()
 
-if sys.platform == 'win32':
+extra_compile_args: list[str] = []
+extra_link_args: list[str] = []
+
+if 'PYODIDE' in os.environ or 'PYODIDE_ROOT' in os.environ:
+    # OpenMP/threads not available in Pyodide
+    pass
+elif sys.platform == 'darwin':
+    # OpenMP not available in Xcode
+    # https://mac.r-project.org/openmp/
+    # extra_compile_args = ['-Xclang', '-fopenmp']
+    # extra_link_args = ['-lomp']
+    pass
+elif sys.platform == 'win32':
     extra_compile_args = ['/openmp']
-    extra_link_args: list[str] = []
-    if DEBUG:
+else:
+    extra_compile_args = ['-fopenmp']
+    extra_link_args = ['-fopenmp']
+
+if DEBUG:
+    if sys.platform == 'win32':
         extra_compile_args += [
             '/Zi',
             '/Od',
@@ -26,14 +51,9 @@ if sys.platform == 'win32':
             # '/DCYTHON_TRACE_NOGIL=1',  # too slow
         ]
         extra_link_args += ['-debug:full']
-elif sys.platform == 'darwin':
-    # OpenMP not available in Xcode
-    # https://mac.r-project.org/openmp/
-    extra_compile_args = []  # ['-Xclang', '-fopenmp']
-    extra_link_args = []  # ['-lomp']
-else:
-    extra_compile_args = ['-fopenmp']
-    extra_link_args = ['-fopenmp']
+    else:
+        extra_compile_args += ['-g', '-O0', '-DCYTHON_TRACE=1']
+        extra_link_args += ['-g']
 
 ext_modules = [
     Extension(
@@ -44,7 +64,7 @@ ext_modules = [
         extra_link_args=extra_link_args,
         define_macros=[
             # ('CYTHON_TRACE_NOGIL', '1'),
-            ('NPY_NO_DEPRECATED_API', 'NPY_2_0_API_VERSION'),
+            ('NPY_NO_DEPRECATED_API', 'NPY_2_1_API_VERSION'),
         ]
         + (
             [('Py_LIMITED_API', 0x030C0000), ('CYTHON_LIMITED_API', '1')]
@@ -55,6 +75,13 @@ ext_modules = [
     )
 ]
 
+if DEBUG:
+    from Cython.Build import cythonize
+
+    ext_modules = cythonize(
+        ext_modules, compiler_directives={'linetrace': True}
+    )  # type: ignore[no-untyped-call]
+
 
 setup(
     ext_modules=ext_modules,

phasorpy-0.13/src/phasorpy/__init__.py

@@ -0,0 +1,13 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
+"""PhasorPy package."""
+
+from __future__ import annotations
+
+__all__ = ['__version__']
+
+
+__version__ = '0.13'
+"""PhasorPy version string."""

{phasorpy-0.12 → phasorpy-0.13}/src/phasorpy/__main__.py

@@ -1,3 +1,7 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
 """PhasorPy package command-line interface."""
 
 import sys

{phasorpy-0.12 → phasorpy-0.13}/src/phasorpy/_phasorpy.pyx

@@ -1,3 +1,7 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
 # distutils: language = c
 # cython: boundscheck = False
 # cython: wraparound = False
@@ -31,6 +35,7 @@ from libc.math cimport (
     fmax,
     fmin,
     hypot,
+    isinf,
     isnan,
     sin,
     sqrt,
@@ -132,6 +137,8 @@ def _phasor_from_signal(
     # TODO: use NumPy iterator API?
     # https://numpy.org/devdocs/reference/c-api/iterator.html
 
+    # allow samples=2: the calculation is mathematically defined, but
+    # the imaginary component is always zero and phase information is lost
     if (
         samples < 2
         or harmonics > samples // 2
@@ -295,6 +302,11 @@ def _phasor_from_lifetime(
 
     if nfreq == 1 and ntau == 1 and nfrac == 1 and ncomp == 1:
         # scalar
+        frac = fraction[0, 0]
+        if isnan(frac) or fabs(frac) < 1e-15:
+            phasor[0, 0, 0] = <float_t> NAN
+            phasor[1, 0, 0] = <float_t> NAN
+            return
         tau = lifetime[0, 0] * frequency[0] * twopi  # omega_tau
         gs = 1.0 / (1.0 + tau * tau)
         phasor[0, 0, 0] = <float_t> gs
@@ -440,14 +452,14 @@ def _gaussian_signal(
     if samples < 1:
         return
 
-    if folds < 0:
-        folds = <ssize_t> (-floor(-6.0 * stdev / <double> samples))
-
     with nogil:
-        if isnan(mean) or isnan(stdev) or stdev <= 0.0:
+        if isnan(mean) or isnan(stdev) or isinf(stdev) or stdev <= 0.0:
             for i in range(samples):
                 signal[i] = <float_t> NAN
         else:
+            if folds < 0:
+                folds = <ssize_t> (-floor(-6.0 * stdev / <double> samples))
+
             c = 1.0 / (sqrt(2.0 * M_PI) * stdev)
 
             for i in range(-folds * samples, (folds + 1) * samples):
@@ -766,7 +778,7 @@ cdef (float_t, float_t) _phasor_to_apparent_lifetime(
         double taumod = INFINITY
         double t
 
-    if isnan(real) or isnan(imag):
+    if isnan(real) or isnan(imag) or isnan(omega):
         return <float_t> NAN, <float_t> NAN
 
     t = real * real + imag * imag
@@ -816,7 +828,7 @@ cdef float_t _phasor_to_normal_lifetime(
         double taunorm = INFINITY
         double t
 
-    if isnan(real) or isnan(imag):
+    if isnan(real) or isnan(imag) or isnan(omega):
         return <float_t> NAN
 
     omega *= omega
@@ -1162,6 +1174,7 @@ cdef unsigned char _is_inside_polar_rectangle(
     """Return whether point is inside polar rectangle.
 
     Angles should be in the range [-pi, pi]. Otherwise performance is degraded.
+    If angle_min > angle_max, the angular range wraps around +/- pi.
 
     """
     cdef:
@@ -1180,10 +1193,11 @@ cdef unsigned char _is_inside_polar_rectangle(
         angle_min = <float_t> atan2(sin(angle_min), cos(angle_min))
     if angle_max < -M_PI or angle_max > M_PI:
         angle_max = <float_t> atan2(sin(angle_max), cos(angle_max))
-    if angle_min > angle_max:
-        angle_min, angle_max = angle_max, angle_min
     t = <float_t> atan2(y, x)
-    if t < angle_min or t > angle_max:
+    if angle_min <= angle_max:
+        if t < angle_min or t > angle_max:
+            return False
+    elif t < angle_min and t > angle_max:
         return False
 
     return True
@@ -1504,7 +1518,7 @@ cdef float_t _fraction_on_segment(
     # square of line length
     t = x0 * x0 + y0 * y0
     if t <= 0.0:
-        # not a line segment, return start
+        # degenerate segment, return fraction at (x1, y1)
         return 0.0
     # projection of point on line
     t = (x * x0 + y * y0) / t
@@ -1549,8 +1563,8 @@ cdef float_t _fraction_on_line(
     # square of line length
     t = x0 * x0 + y0 * y0
     if t <= 0.0:
-        # not a line, return end
-        return 1.0
+        # degenerate line, return fraction at (x1, y1)
+        return 0.0
     # projection of point on line
     t = (x * x0 + y * y0) / t
     return t
@@ -1891,7 +1905,7 @@ def _lifetime_search_2(
         raise ValueError('invalid lifetime shape')
     if fraction.shape[0] != 2 or fraction.shape[1] != real.shape[1]:
         raise ValueError('invalid fraction shape')
-    if real.shape[0] != imag.shape[0] != 2:
+    if real.shape[0] != 2 or imag.shape[0] != 2:
         raise ValueError('invalid phasor harmonics')
     if real.shape[1] != imag.shape[1]:
         raise ValueError('invalid phasor size')
@@ -2103,7 +2117,7 @@ def _mean_value_coordinates(
     """
     cdef:
         ssize_t i, j, k, p, nv
-        double x, y, alpha, weight, weight_sum
+        double x, y, alpha, weight, weight_sum, weight_abs_sum
         double* weights = NULL
         double* sigma = NULL
         double* length = NULL
@@ -2147,6 +2161,7 @@ def _mean_value_coordinates(
                 length[i] = hypot(vx[i] - x, vy[i] - y)
 
             weight_sum = 0.0
+            weight_abs_sum = 0.0
             for i in range(nv):
                 j = (i + 1) % nv  # next vertex, wrapped around
                 k = (i - 1 + nv) % nv  # previous vertex, wrapped around
@@ -2162,9 +2177,11 @@ def _mean_value_coordinates(
                     if j != k and j != i:
                         weight = weight * length[j] * sin(fabs(sigma[j]) * 0.5)
                 weight_sum = weight_sum + weight
+                weight_abs_sum = weight_abs_sum + fabs(weight)
                 weights[i] = weight
 
-            if fabs(weight_sum) > 1e-12:
+            # weights scale with polygon size. use relative threshold
+            if fabs(weight_sum) > 1e-12 * weight_abs_sum:
                 for i in range(nv):
                     fraction[order[i], p] = <float_t> (weights[i] / weight_sum)
             else:
@@ -2323,11 +2340,13 @@ cdef (float_t, float_t, float_t) _phasor_threshold_open(
     if not isnan(imag_max) and imag >= imag_max:
         return <float_t> NAN, <float_t> NAN, <float_t> NAN
 
-    if not isnan(modulation_min):
+    if not isnan(modulation_min) and modulation_min >= 0.0:
         mod = real * real + imag * imag
         if mod <= modulation_min * modulation_min:
             return <float_t> NAN, <float_t> NAN, <float_t> NAN
     if not isnan(modulation_max):
+        if modulation_max <= 0.0:
+            return <float_t> NAN, <float_t> NAN, <float_t> NAN
         if isnan(mod):
             mod = real * real + imag * imag
         if mod >= modulation_max * modulation_max:
@@ -2385,11 +2404,13 @@ cdef (float_t, float_t, float_t) _phasor_threshold_closed(
     if not isnan(imag_max) and imag > imag_max:
         return <float_t> NAN, <float_t> NAN, <float_t> NAN
 
-    if not isnan(modulation_min):
+    if not isnan(modulation_min) and modulation_min > 0.0:
         mod = real * real + imag * imag
         if mod < modulation_min * modulation_min:
             return <float_t> NAN, <float_t> NAN, <float_t> NAN
     if not isnan(modulation_max):
+        if modulation_max < 0.0:
+            return <float_t> NAN, <float_t> NAN, <float_t> NAN
         if isnan(mod):
             mod = real * real + imag * imag
         if mod > modulation_max * modulation_max:
@@ -2832,6 +2853,8 @@ def _flimlabs_signal(
             for pixels in channels:
                 signal_ = signal[c, i]
                 for h, count in pixels:
+                    if count < 0 or <ssize_t> <uint_t> count != count:
+                        raise ValueError(f'{count=} overflows signal dtype')
                     signal_[h] = <uint_t> count
                 i += 1
             c += 1
@@ -2840,6 +2863,8 @@ def _flimlabs_signal(
         for pixels in data[channel]:
             signal_ = signal[0, i]
             for h, count in pixels:
+                if count < 0 or <ssize_t> <uint_t> count != count:
+                    raise ValueError(f'{count=} overflows signal dtype')
                 signal_[h] = <uint_t> count
             i += 1
 

{phasorpy-0.12 → phasorpy-0.13}/src/phasorpy/_typing.py

@@ -1,3 +1,7 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
 """Type annotations.
 
 This module should only be imported when type-checking, for example::