pyfli-lib 0.1.3__tar.gz

pyfli_lib-0.1.3/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Vikas Pandey
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyfli_lib-0.1.3/PKG-INFO

@@ -0,0 +1,70 @@
+Metadata-Version: 2.4
+Name: pyfli-lib
+Version: 0.1.3
+Summary: Unified Fluorescence Lifetime Imaging (FLI) data processing platform using analytical and deep learning methods.
+Author: Vikas Pandey
+Project-URL: Homepage, https://github.com/vkp217/pyfli-pkg
+Project-URL: Repository, https://github.com/vkp217/pyfli-pkg.git
+Project-URL: Issues, https://github.com/vkp217/pyfli-pkg/issues
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: h5py>=3.10.0
+Requires-Dist: sdtfile>=2025.0.0
+Requires-Dist: tifffile>=2025.0.0
+Requires-Dist: joblib>=1.3.0
+Requires-Dist: scikit-image>=0.22.0
+Requires-Dist: imagecodecs
+Requires-Dist: opencv-python>=4.8.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: matplotlib>=3.7.0
+Provides-Extra: ai
+Requires-Dist: tensorflow>=2.15.0; extra == "ai"
+Requires-Dist: torch>=2.0.0; extra == "ai"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ipykernel>=6.0.0; extra == "dev"
+Dynamic: license-file
+
+# pyfli: A Unified Platform for FLI Data Processing
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![PyPI version](https://img.shields.io/pypi/v/pyfli-lib.svg)](https://pypi.org/project/pyfli-lib/)
+
+`pyfli` is a comprehensive library designed for **Fluorescence Lifetime Imaging (FLI)** data processing. It streamlines the workflow for handling diverse file formats from various hardware manufacturers and provides a standardized pipeline for both traditional analytical and deep-learning-based inference.
+
+---
+
+## Key Features
+
+* **Universal Processing Pipeline:** Simplifies the handling of multiple FLI file types (ICCD, SPAD, TCSPC).
+* **Enhanced FLI Simulator:** A robust simulation engine adaptable to specific camera hardware parameters and noise models.
+* **Standardized Inference:** Unified interface for time-resolved microscopy and macroscopic FLI data (MFLI).
+
+## Supported Data Acquisition Methods
+
+The platform provides native support for several high-end imaging systems:
+
+1.  **ICCD:** Intensified Charge-Coupled Device cameras for fast-gated, wide-field imaging.
+2.  **SwissSPAD2 & SwissSPAD3:** High-speed SPAD (Single-Photon Avalanche Diode) architectures for high-resolution photon counting.
+3.  **SPCImage/TCSPC:** Standardized processing for Time-Correlated Single Photon Counting microscopy data.
+
+## Data Processing & Analysis
+
+`pyfli` implements industry-standard analytical methods to extract lifetime information:
+
+* **Non-linear Least Squares (NLLS) Fitting:** Robust mathematical approach for exponential decay modeling.
+* **Phasor Plot Analysis:** Graphical, model-free transformation of fluorescence decay into a 2D polar plot for easy species separation.
+* **Maximum Likelihood Estimation (MLE):** Statistical estimator optimized for low-photon regimes.
+* **Rapid Lifetime Determination (RLD):** Computationally efficient method for real-time applications and high-frame-rate data.
+
+---
+
+## Installation
+
+Install the stable version directly from PyPI:
+
+```bash
+pip install pyfli-lib

pyfli_lib-0.1.3/README.md

@@ -0,0 +1,41 @@
+# pyfli: A Unified Platform for FLI Data Processing
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![PyPI version](https://img.shields.io/pypi/v/pyfli-lib.svg)](https://pypi.org/project/pyfli-lib/)
+
+`pyfli` is a comprehensive library designed for **Fluorescence Lifetime Imaging (FLI)** data processing. It streamlines the workflow for handling diverse file formats from various hardware manufacturers and provides a standardized pipeline for both traditional analytical and deep-learning-based inference.
+
+---
+
+## Key Features
+
+* **Universal Processing Pipeline:** Simplifies the handling of multiple FLI file types (ICCD, SPAD, TCSPC).
+* **Enhanced FLI Simulator:** A robust simulation engine adaptable to specific camera hardware parameters and noise models.
+* **Standardized Inference:** Unified interface for time-resolved microscopy and macroscopic FLI data (MFLI).
+
+## Supported Data Acquisition Methods
+
+The platform provides native support for several high-end imaging systems:
+
+1.  **ICCD:** Intensified Charge-Coupled Device cameras for fast-gated, wide-field imaging.
+2.  **SwissSPAD2 & SwissSPAD3:** High-speed SPAD (Single-Photon Avalanche Diode) architectures for high-resolution photon counting.
+3.  **SPCImage/TCSPC:** Standardized processing for Time-Correlated Single Photon Counting microscopy data.
+
+## Data Processing & Analysis
+
+`pyfli` implements industry-standard analytical methods to extract lifetime information:
+
+* **Non-linear Least Squares (NLLS) Fitting:** Robust mathematical approach for exponential decay modeling.
+* **Phasor Plot Analysis:** Graphical, model-free transformation of fluorescence decay into a 2D polar plot for easy species separation.
+* **Maximum Likelihood Estimation (MLE):** Statistical estimator optimized for low-photon regimes.
+* **Rapid Lifetime Determination (RLD):** Computationally efficient method for real-time applications and high-frame-rate data.
+
+---
+
+## Installation
+
+Install the stable version directly from PyPI:
+
+```bash
+pip install pyfli-lib

pyfli_lib-0.1.3/pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyfli-lib"
+version = "0.1.3"
+description = "Unified Fluorescence Lifetime Imaging (FLI) data processing platform using analytical and deep learning methods."
+readme = "README.md"
+requires-python = ">=3.11"
+authors = [
+    {name = "Vikas Pandey"}
+]
+# Core dependencies for the analytical methods
+dependencies = [
+    "h5py>=3.10.0",
+    "sdtfile>=2025.0.0",
+    "tifffile>=2025.0.0",
+    "joblib>=1.3.0",
+    "scikit-image>=0.22.0",
+    "imagecodecs",
+    "opencv-python>=4.8.0",
+    "numpy>=1.24.0",
+    "matplotlib>=3.7.0"
+]
+
+[project.optional-dependencies]
+# Deep learning specific tools
+ai = [
+    "tensorflow>=2.15.0",
+    "torch>=2.0.0",
+]
+dev = [
+    "pytest",
+    "black",
+    "ipykernel>=6.0.0",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["pyfli*"]
+exclude = ["notebooks*", "config*", "data*"]
+
+[project.urls]
+Homepage = "https://github.com/vkp217/pyfli-pkg"
+Repository = "https://github.com/vkp217/pyfli-pkg.git"
+Issues = "https://github.com/vkp217/pyfli-pkg/issues"

pyfli_lib-0.1.3/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

pyfli_lib-0.1.3/src/pyfli/__init__.py

@@ -0,0 +1,22 @@
+#### inside "pyfli.__init__.py"
+__version__ = "0.1.0"
+
+# Pulling everything from the scripts gatekeeper
+from .scripts import (DataOperations, IRFAligner, DataViewer, 
+                        AlliGprocessedImport, BHprocessedImport, PyFliprocessedImport, 
+                        HardSimulator, HardestSimulator, DatasetPlotter,
+                        PhasorAnalyzer, FLIFitter, PoissonLikelihoodFitter, FLIAnalysisSuite,
+                        Plotter, DLModelComparator, DataPreprocessing,
+                        BaseFLIFitter, Fli_CPUProcessor, Fli_GPUProcessor, MLEFLIFitter, 
+                        GlobalFLIFitter, ROIMaker, AnalyticalHelpers, DataIO_utils, Colorprocess)
+
+__all__ = ['DataOperations', 'IRFAligner', 'DataViewer', 
+        'AlliGprocessedImport', 'BHprocessedImport', 'PyFliprocessedImport', 
+        'HardSimulator', 'HardestSimulator', 'DatasetPlotter',
+        'PhasorAnalyzer', 'FLIFitter', 'PoissonLikelihoodFitter', 'FLIAnalysisSuite'
+        'Plotter', 'DLModelComparator', 'DataPreprocessing',
+        'MultiScaleRNNSummaryNet', 'BaseFLIFitter', 'Fli_CPUProcessor', 'Fli_GPUProcessor', 
+        'MLEFLIFitter', 'GlobalFLIFitter', 'ROIMaker', 'AnalyticalHelpers', 'DataIO_utils',
+        'Colorprocess'
+        ]
+

pyfli_lib-0.1.3/src/pyfli/scripts/__init__.py

@@ -0,0 +1,19 @@
+#### inside "scripts.__init__.py"
+from .dataIO import (DataOperations, AlliGprocessedImport, 
+                        BHprocessedImport, PyFliprocessedImport, DatasetPlotter, DataIO_utils )
+from .analytical_methods import (PhasorAnalyzer, FLIFitter, PoissonLikelihoodFitter, FLIAnalysisSuite, AnalyticalHelpers)
+from .dataCC import IRFAligner, DataPreprocessing
+from .dataVnP import DataViewer, Plotter, DLModelComparator, Colorprocess
+from .roiMaker import ROIMaker
+from .solver import (BaseFLIFitter, Fli_CPUProcessor, Fli_GPUProcessor, MLEFLIFitter, GlobalFLIFitter)
+
+from .simulatorPhysics import HardSimulator, HardestSimulator
+# This allows: from pyfli.scripts import DataViewer
+__all__ = ["DataOperations", "IRFAligner", "DataViewer", "AlliGprocessedImport", 
+    "BHprocessedImport", "PyFliprocessedImport", "DatasetPlotter", "HardSimulator",
+    "HardestSimulator", "FLIFitter", "PoissonLikelihoodFitter", "FLIAnalysisSuite", 
+    "PhasorAnalyzer", "Plotter", "DLModelComparator", "DataPreprocessing",
+    "BaseFLIFitter", "Fli_CPUProcessor", "Fli_GPUProcessor", "MLEFLIFitter", "GlobalFLIFitter",
+    "ROIMaker", "AnalyticalHelpers", "DataIO_utils", "Colorprocess"
+]
+    

pyfli_lib-0.1.3/src/pyfli/scripts/analytical_methods/__init__.py

@@ -0,0 +1,4 @@
+### inside analytical_methods
+from .phasor import PhasorAnalyzer
+from .nlsf import FLIFitter, PoissonLikelihoodFitter, FLIAnalysisSuite 
+from .am_utils import AnalyticalHelpers

pyfli_lib-0.1.3/src/pyfli/scripts/analytical_methods/am_utils.py

@@ -0,0 +1,15 @@
+import numpy as np
+
+class AnalyticalHelpers:
+    def __init__(self, laser_period = 12.5, gate_delay=None, num_gate = None):
+        self.laser_period = laser_period
+        self.gate_delay = gate_delay
+        self.num_gate = num_gate
+
+    def freq_computation(self):
+        freq = 1000.0/self.laser_period # laser_period in ns; freq in Hz
+        if  self.gate_delay is None or self.num_gate is None:
+            effective_freq = freq
+        else:
+            effective_freq = 1000.0/(self.num_gate*self.gate_delay) # frequency is computed in the MHz if the gate delays are in ns
+        return [freq, effective_freq]

pyfli_lib-0.1.3/src/pyfli/scripts/analytical_methods/laguerre_deconvolution.py

@@ -0,0 +1,2 @@
+import numpy as np
+import matplotlib.pyplot as plt