pyfli-lib 0.1.0__tar.gz

pyfli_lib-0.1.0/LICENSE

@@ -0,0 +1,43 @@
+Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
+
+Copyright (c) 2026 Vikas Pandey
+
+This work is licensed under the Creative Commons
+Attribution-NonCommercial-NoDerivatives 4.0 International License.
+
+You are free to:
+  Share — copy and redistribute the material in any medium or format.
+
+Under the following terms:
+  Attribution — You must give appropriate credit, provide a link to the
+    license, and indicate if changes were made. You may do so in any
+    reasonable manner, but not in any way that suggests the licensor
+    endorses you or your use.
+
+  NonCommercial — You may not use the material for commercial purposes.
+
+  NoDerivatives — If you remix, transform, or build upon the material,
+    you may not distribute the modified material.
+
+  No additional restrictions — You may not apply legal terms or
+    technological measures that legally restrict others from doing
+    anything the license permits.
+
+Notices:
+  You do not have to comply with the license for elements of the material
+  in the public domain or where your use is permitted by an applicable
+  exception or limitation.
+
+  No warranties are given. The license may not give you all of the
+  permissions necessary for your intended use. For example, other rights
+  such as publicity, privacy, or moral rights may limit how you use the
+  material.
+
+To view a full copy of this license, visit:
+  https://creativecommons.org/licenses/by-nc-nd/4.0/
+
+Or send a letter to:
+  Creative Commons
+  PO Box 1866
+  Mountain View, CA 94042
+  USA

pyfli_lib-0.1.0/MANIFEST.in

@@ -0,0 +1,14 @@
+include LICENSE
+include README.md
+include pyproject.toml
+
+recursive-exclude data *
+recursive-exclude notebooks *
+recursive-exclude dist *
+recursive-exclude .vscode *
+recursive-exclude tests *
+global-exclude __pycache__
+global-exclude *.py[cod]
+global-exclude *.h5
+global-exclude *.sdt
+global-exclude *.tif

pyfli_lib-0.1.0/PKG-INFO

@@ -0,0 +1,118 @@
+Metadata-Version: 2.4
+Name: pyfli-lib
+Version: 0.1.0
+Summary: Unified Fluorescence Lifetime Imaging (FLI) data processing platform using analytical and deep learning methods.
+Author: Vikas Pandey
+License: CC BY-NC-ND 4.0
+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
+Keywords: fluorescence,lifetime,FLIM,FLI,TCSPC,phasor,microscopy,bioimaging,ICCD,SPAD,laguerre,deconvolution
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+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: imagecodecs
+Requires-Dist: joblib>=1.3.0
+Requires-Dist: scikit-image>=0.22.0
+Requires-Dist: opencv-python>=4.8.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Requires-Dist: seaborn
+Requires-Dist: pillow
+Requires-Dist: tabulate>=0.10.0
+Requires-Dist: torch>=2.0.0
+Provides-Extra: gpu
+Requires-Dist: tensorflow>=2.15.0; extra == "gpu"
+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: CC BY-NC-ND 4.0](https://img.shields.io/badge/License-CC%20BY--NC--ND%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc-nd/4.0/)
+[![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 Fitting (NLSF):** 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.
+* **Laguerre Method (LET):** Laguerre Expansion Technique for model-free IRF deconvolution followed by multi-exponential lifetime extraction on a per-pixel basis.
+
+---
+
+## Installation
+
+Install the stable version directly from PyPI:
+
+```bash
+pip install pyfli-lib
+```
+
+For users requiring GPU-based processing, install the optional tensor/AI dependencies:
+
+```bash
+pip install "pyfli-lib[gpu]"
+```
+
+## Quick Start
+
+Even though the package is installed as `pyfli-lib`, you import it as `pyfli` in your scripts:
+
+```python
+from pyfli import DataOperations
+
+loader = DataOperations(    
+    data_path = "experimental_data.sdt",
+    irf_path = "instrument_data.txt", 
+    bg_path = "background_data.tif",   
+    mask_path="background_data.png",
+    )
+decay_data = loader.load_data()
+irf_data = loader.load_irf()
+
+```
+
+## Repository & Issues
+
+The source code is hosted on GitHub. Please report any bugs or feature requests via the issues tracker.
+* **GitHub:** [https://github.com/vkp217/pyfli-pkg](https://github.com/vkp217/pyfli-pkg)
+

pyfli_lib-0.1.0/README.md

@@ -0,0 +1,73 @@
+# pyfli: A Unified Platform for FLI Data Processing
+
+[![License: CC BY-NC-ND 4.0](https://img.shields.io/badge/License-CC%20BY--NC--ND%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc-nd/4.0/)
+[![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 Fitting (NLSF):** 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.
+* **Laguerre Method (LET):** Laguerre Expansion Technique for model-free IRF deconvolution followed by multi-exponential lifetime extraction on a per-pixel basis.
+
+---
+
+## Installation
+
+Install the stable version directly from PyPI:
+
+```bash
+pip install pyfli-lib
+```
+
+For users requiring GPU-based processing, install the optional tensor/AI dependencies:
+
+```bash
+pip install "pyfli-lib[gpu]"
+```
+
+## Quick Start
+
+Even though the package is installed as `pyfli-lib`, you import it as `pyfli` in your scripts:
+
+```python
+from pyfli import DataOperations
+
+loader = DataOperations(    
+    data_path = "experimental_data.sdt",
+    irf_path = "instrument_data.txt", 
+    bg_path = "background_data.tif",   
+    mask_path="background_data.png",
+    )
+decay_data = loader.load_data()
+irf_data = loader.load_irf()
+
+```
+
+## Repository & Issues
+
+The source code is hosted on GitHub. Please report any bugs or feature requests via the issues tracker.
+* **GitHub:** [https://github.com/vkp217/pyfli-pkg](https://github.com/vkp217/pyfli-pkg)
+

pyfli_lib-0.1.0/pyproject.toml

@@ -0,0 +1,76 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyfli-lib"
+version = "0.1.0"
+description = "Unified Fluorescence Lifetime Imaging (FLI) data processing platform using analytical and deep learning methods."
+readme = "README.md"
+requires-python = ">=3.11"
+license = {text = "CC BY-NC-ND 4.0"}
+authors = [
+    {name = "Vikas Pandey"}
+]
+keywords = [
+    "fluorescence", "lifetime", "FLIM", "FLI", "TCSPC", "phasor",
+    "microscopy", "bioimaging", "ICCD", "SPAD", "laguerre", "deconvolution"
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "License :: Other/Proprietary License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: OS Independent",
+]
+# Core dependencies for the analytical methods
+dependencies = [
+    "h5py>=3.10.0",
+    "sdtfile>=2025.0.0",
+    "tifffile>=2025.0.0",
+    "imagecodecs",
+    "joblib>=1.3.0",
+    "scikit-image>=0.22.0",
+    "opencv-python>=4.8.0",
+    "numpy>=1.24.0",
+    "matplotlib>=3.7.0",
+    "scipy",
+    "tqdm",
+    "seaborn",
+    "pillow",
+    "tabulate>=0.10.0",
+    "torch>=2.0.0"
+]
+
+
+[project.optional-dependencies]
+gpu = [
+    "tensorflow>=2.15.0",
+]
+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"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-v --tb=short"
+filterwarnings = [
+    "ignore::DeprecationWarning",
+    "ignore::RuntimeWarning",
+]

pyfli_lib-0.1.0/setup.cfg

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

pyfli_lib-0.1.0/src/pyfli/__init__.py

@@ -0,0 +1,39 @@
+#### inside "pyfli.__init__.py"
+__version__ = "0.1.17"
+
+# 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,
+                        Macro_sim, TCSPC_sim, FLIImageGenerator, FLICalibrator, FLIValidator,Normalization,
+                        recovery_plot, random_true_pixel, data_masking, save_plot,
+                        Msg_display, FittingComparator, Detector,
+                        BinnedFliFitter, FliBinner, ROIoperations, Batch_sim, DataSaver,
+                        load_flim_data, collapse_to_xyt, plot_xyt,
+                        LaguerreFLI)
+
+from .spAnalysis import (BasisPatterns, MeasurementSimulator, Reconstructor)
+
+__all__ = ['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', 'Macro_sim', 'TCSPC_sim', 'FLIImageGenerator', 
+        'recovery_plot', 'random_true_pixel', 'save_plot',
+        'FLICalibrator', 'FLIValidator', 'Normalization',
+        'Msg_display', 'FittingComparator',
+        'data_masking', 'Detector', 'BinnedFliFitter', 'FliBinner',
+        'ROIoperations', 'Batch_sim', 'DataSaver', 'LaguerreFLI',
+        # this is for SPAnalysis
+        'BasisPatterns', 'MeasurementSimulator', 'Reconstructor',
+        'load_flim_data', 'collapse_to_xyt', 'plot_xyt'
+        ]
+

pyfli_lib-0.1.0/src/pyfli/scripts/__init__.py

@@ -0,0 +1,34 @@
+#### inside "scripts.__init__.py"
+from .dataIO import (DataOperations, AlliGprocessedImport, 
+                        BHprocessedImport, PyFliprocessedImport, DatasetPlotter, DataIO_utils,
+                         Detector, load_flim_data, collapse_to_xyt, plot_xyt )
+from .analytical_methods import (PhasorAnalyzer, FLIFitter, PoissonLikelihoodFitter, 
+                                 FLIAnalysisSuite, AnalyticalHelpers,
+                                 LaguerreFLI)
+from .dataCC import IRFAligner, DataPreprocessing, Normalization, ROIoperations
+from .dataVnP import DataViewer, Plotter, DLModelComparator, Colorprocess
+from .roiMaker import ROIMaker
+from .solver import (BaseFLIFitter, Fli_CPUProcessor, Fli_GPUProcessor, 
+                     MLEFLIFitter, GlobalFLIFitter, FittingComparator,
+                     BinnedFliFitter, FliBinner)
+from .simulator import (Macro_sim, TCSPC_sim, FLIImageGenerator, FLICalibrator, FLIValidator, Batch_sim)
+from .data_text import Msg_display
+
+from .simulatorPhysics import HardSimulator, HardestSimulator
+from .utils_common import recovery_plot, random_true_pixel, data_masking, save_plot
+from .data_saving import DataSaver
+
+# 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",
+    "Macro_sim", "TCSPC_sim", "FLIImageGenerator", "recovery_plot", "random_true_pixel", "save_plot",
+    "FLICalibrator", "FLIValidator", "Normalization", "Msg_display", "FittingComparator",
+    "data_masking", "Detector", "BinnedFliFitter", "FliBinner", "ROIoperations",
+    "Batch_sim", "DataSaver", "load_flim_data", "collapse_to_xyt", "plot_xyt",
+    "LaguerreFLI"
+]
+    

pyfli_lib-0.1.0/src/pyfli/scripts/analytical_methods/__init__.py

@@ -0,0 +1,5 @@
+### inside analytical_methods
+from .phasor_simple import PhasorAnalyzer
+from .nlsf import FLIFitter, PoissonLikelihoodFitter, FLIAnalysisSuite 
+from .am_utils import AnalyticalHelpers
+from .laguerre_deconvolution import LaguerreFLI

pyfli_lib-0.1.0/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]