napari-phasors 0.0.1__tar.gz

napari_phasors-0.0.1/LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2024, Marcelo L. Zoccoler, Bruno Pannunzio, Bruno Schuty
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

napari_phasors-0.0.1/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

napari_phasors-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: napari-phasors
+Version: 0.0.1
+Summary: A simple plugin to use phasor analysis
+Home-page: https://github.com/napari-phasors/napari-phasors
+Author: Bruno Pannunzio, Marcelo L. Zoccoler, Bruno Schuty
+Author-email: bpannunzio@pasteur.edu.uy, marzoccoler@gmail.com, schutyb@schutyb.com
+License: BSD-3-Clause
+Project-URL: Bug Tracker, https://github.com/napari-phasors/napari-phasors/issues
+Project-URL: Documentation, https://github.com/napari-phasors/napari-phasors#README.md
+Project-URL: Source Code, https://github.com/napari-phasors/napari-phasors
+Project-URL: User Support, https://github.com/napari-phasors/napari-phasors/issues
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: phasorpy
+Requires-Dist: qtpy
+Requires-Dist: scikit-image
+Requires-Dist: biaplotter>=0.0.5a2
+Requires-Dist: lfdfiles
+Requires-Dist: sdtfile
+Requires-Dist: ptufile
+Requires-Dist: tifffile
+Requires-Dist: pandas
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: napari; extra == "testing"
+Requires-Dist: qtpy; extra == "testing"
+Requires-Dist: scikit-image; extra == "testing"
+Requires-Dist: biaplotter>=0.0.5a0; extra == "testing"
+Requires-Dist: PyQt5; extra == "testing"
+Requires-Dist: pandas; extra == "testing"
+Requires-Dist: black; extra == "testing"
+Requires-Dist: isort; extra == "testing"
+Requires-Dist: phasorpy; extra == "testing"
+Requires-Dist: tifffile; extra == "testing"
+Requires-Dist: lfdfiles; extra == "testing"
+Requires-Dist: sdtfile; extra == "testing"
+Requires-Dist: ptufile; extra == "testing"
+
+# napari-phasors
+
+[![License BSD-3](https://img.shields.io/pypi/l/napari-phasors.svg?color=green)](https://github.com/napari-phasors/napari-phasors/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-phasors.svg?color=green)](https://pypi.org/project/napari-phasors)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-phasors.svg?color=green)](https://python.org)
+[![tests](https://github.com/napari-phasors/napari-phasors/workflows/tests/badge.svg)](https://github.com/napari-phasors/napari-phasors/actions)
+[![codecov](https://codecov.io/gh/napari-phasors/napari-phasors/branch/main/graph/badge.svg)](https://codecov.io/gh/napari-phasors/napari-phasors)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-phasors)](https://napari-hub.org/plugins/napari-phasors)
+
+A simple plugin to do phasor analysis in napari. Based on the [phasorpy](https://www.phasorpy.org/) library.
+
+[Jump to Intallation](#installation)
+
+----------------------------------
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Usage
+
+napari-phasors is composed of a few widgets that allow reading a few specific FLIM and hyperspectral file formats, perform phasor analysis, and display and export the results of manual phasor selections.
+
+### Sample Data
+
+Two sample datasets for FLIM are provided, along with their corresponding calibration images. Additionally, a paramecium image is included as sample data for hyperspectral analysis.
+
+![sample_data](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/sample_data.gif)
+
+### Phasor Analysis
+
+#### Plot FLIM Data
+
+FLIM phasor data can be plotted as a 2D histogram or scatter plot. The colormap, the number of bins and the scale of the colors can be customized.
+Filtering and thresholding can also be applied to process phasor data and the mean intensity image. 
+
+![phasors_flim](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/phasors_flim.gif)
+
+#### Plot Hyperspectral Data
+
+Hyperspectral phasor data can also be plotted as a 2D histogram or scatter plot and visualized in the full universal circle.
+
+![phasors_hyperspectral](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/phasors_hyperspectral.gif)
+
+### Apparent Lifetime Display
+
+A FLIM image can be colormapped according to the phase or modulation apparent lifetime. A histogram is also created for visualization of the distribution of apparent lifetimes of the FLIM image.
+
+![lifetimes](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/lifetimes.gif)
+
+### Phasor Calibration
+
+FLIM images can be calibrated using a reference image acquired under the same experimental parameters. This reference image should consist of a homogeneous solution of a fluorophore with a known fluorescence lifetime and the laser frequency used in the experiment. This ensures accuracy and consistency in lifetime measurements.
+
+![calibration](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/calibration.gif)
+
+### Phasor Custom Import
+
+Supported file formats (`.tif`, `.ptu`, `.sdt`, `.fbd`, `.lsm`, `.ome.tif`) can be read and transformed to the phasor space. Additional options, such as the harmonics, channels and frames, can be specified depending on the file format to be read.
+
+![custom_import](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/custom_import.gif)
+
+### Phasor Export
+
+The average intensity image and the phasor coordinates can be exported as OME-TIF files that can be read by napari-phasors and PhasorPy. Alternatively, the phasor coordinates, as well as the selections (cursors) can be exported as a CSV file.
+
+![export_phasors](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/export_phasors.gif)
+
+## Installation
+
+You can install `napari-phasors` via [pip]. Follow these steps from a terminal.
+
+We recommend using `miniforge` whenever possible. Click [here](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge) to choose the right download option for your OS.
+**If you do not use `miniforge`, but rather Anaconda or Miniconda, replace the `mamba` term whenever you see it below with `conda`.**
+
+Create a conda environment with napari by typing :
+
+    mamba create -n napari-phasors-env napari pyqt python=3.10
+    
+Activate the environment :
+
+    mamba activate napari-phasors-env
+
+Install `napari-phasors` via [pip] :
+
+    pip install napari-phasors
+
+Alternatively, install latest development version with :
+
+    pip install git+https://github.com/napari-phasors/napari-phasors.git
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [BSD-3] license,
+"napari-phasors" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+
+[file an issue]: https://github.com/napari-phasors/napari-phasors/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_phasors-0.0.1/README.md

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+# napari-phasors
+
+[![License BSD-3](https://img.shields.io/pypi/l/napari-phasors.svg?color=green)](https://github.com/napari-phasors/napari-phasors/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-phasors.svg?color=green)](https://pypi.org/project/napari-phasors)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-phasors.svg?color=green)](https://python.org)
+[![tests](https://github.com/napari-phasors/napari-phasors/workflows/tests/badge.svg)](https://github.com/napari-phasors/napari-phasors/actions)
+[![codecov](https://codecov.io/gh/napari-phasors/napari-phasors/branch/main/graph/badge.svg)](https://codecov.io/gh/napari-phasors/napari-phasors)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-phasors)](https://napari-hub.org/plugins/napari-phasors)
+
+A simple plugin to do phasor analysis in napari. Based on the [phasorpy](https://www.phasorpy.org/) library.
+
+[Jump to Intallation](#installation)
+
+----------------------------------
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Usage
+
+napari-phasors is composed of a few widgets that allow reading a few specific FLIM and hyperspectral file formats, perform phasor analysis, and display and export the results of manual phasor selections.
+
+### Sample Data
+
+Two sample datasets for FLIM are provided, along with their corresponding calibration images. Additionally, a paramecium image is included as sample data for hyperspectral analysis.
+
+![sample_data](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/sample_data.gif)
+
+### Phasor Analysis
+
+#### Plot FLIM Data
+
+FLIM phasor data can be plotted as a 2D histogram or scatter plot. The colormap, the number of bins and the scale of the colors can be customized.
+Filtering and thresholding can also be applied to process phasor data and the mean intensity image. 
+
+![phasors_flim](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/phasors_flim.gif)
+
+#### Plot Hyperspectral Data
+
+Hyperspectral phasor data can also be plotted as a 2D histogram or scatter plot and visualized in the full universal circle.
+
+![phasors_hyperspectral](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/phasors_hyperspectral.gif)
+
+### Apparent Lifetime Display
+
+A FLIM image can be colormapped according to the phase or modulation apparent lifetime. A histogram is also created for visualization of the distribution of apparent lifetimes of the FLIM image.
+
+![lifetimes](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/lifetimes.gif)
+
+### Phasor Calibration
+
+FLIM images can be calibrated using a reference image acquired under the same experimental parameters. This reference image should consist of a homogeneous solution of a fluorophore with a known fluorescence lifetime and the laser frequency used in the experiment. This ensures accuracy and consistency in lifetime measurements.
+
+![calibration](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/calibration.gif)
+
+### Phasor Custom Import
+
+Supported file formats (`.tif`, `.ptu`, `.sdt`, `.fbd`, `.lsm`, `.ome.tif`) can be read and transformed to the phasor space. Additional options, such as the harmonics, channels and frames, can be specified depending on the file format to be read.
+
+![custom_import](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/custom_import.gif)
+
+### Phasor Export
+
+The average intensity image and the phasor coordinates can be exported as OME-TIF files that can be read by napari-phasors and PhasorPy. Alternatively, the phasor coordinates, as well as the selections (cursors) can be exported as a CSV file.
+
+![export_phasors](https://github.com/napari-phasors/napari-phasors/raw/main/gifs/export_phasors.gif)
+
+## Installation
+
+You can install `napari-phasors` via [pip]. Follow these steps from a terminal.
+
+We recommend using `miniforge` whenever possible. Click [here](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge) to choose the right download option for your OS.
+**If you do not use `miniforge`, but rather Anaconda or Miniconda, replace the `mamba` term whenever you see it below with `conda`.**
+
+Create a conda environment with napari by typing :
+
+    mamba create -n napari-phasors-env napari pyqt python=3.10
+    
+Activate the environment :
+
+    mamba activate napari-phasors-env
+
+Install `napari-phasors` via [pip] :
+
+    pip install napari-phasors
+
+Alternatively, install latest development version with :
+
+    pip install git+https://github.com/napari-phasors/napari-phasors.git
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [BSD-3] license,
+"napari-phasors" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+
+[file an issue]: https://github.com/napari-phasors/napari-phasors/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_phasors-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=42.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.black]
+line-length = 79
+target-version = ["py310"]
+skip-string-normalization = true
+
+[tool.isort]
+profile = "black"
+line_length = 79
+
+
+[tool.ruff]
+line-length = 79
+lint.select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+lint.ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py38"
+fix = true

napari_phasors-0.0.1/setup.cfg

@@ -0,0 +1,81 @@
+[metadata]
+name = napari-phasors
+version = attr: napari_phasors.__version__
+description = A simple plugin to use phasor analysis
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/napari-phasors/napari-phasors
+author = Bruno Pannunzio, Marcelo L. Zoccoler, Bruno Schuty
+author_email = bpannunzio@pasteur.edu.uy, marzoccoler@gmail.com, schutyb@schutyb.com
+license = BSD-3-Clause
+license_files = LICENSE
+classifiers = 
+	Development Status :: 2 - Pre-Alpha
+	Framework :: napari
+	Intended Audience :: Developers
+	License :: OSI Approved :: BSD License
+	Operating System :: OS Independent
+	Programming Language :: Python
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3 :: Only
+	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
+	Topic :: Scientific/Engineering :: Image Processing
+project_urls = 
+	Bug Tracker = https://github.com/napari-phasors/napari-phasors/issues
+	Documentation = https://github.com/napari-phasors/napari-phasors#README.md
+	Source Code = https://github.com/napari-phasors/napari-phasors
+	User Support = https://github.com/napari-phasors/napari-phasors/issues
+
+[options]
+packages = find:
+install_requires = 
+	phasorpy
+	qtpy
+	scikit-image
+	biaplotter>=0.0.5a2
+	lfdfiles
+	sdtfile
+	ptufile
+	tifffile
+	pandas
+python_requires = >=3.10
+include_package_data = True
+package_dir = 
+	=src
+
+[options.packages.find]
+where = src
+
+[options.entry_points]
+napari.manifest = 
+	napari-phasors = napari_phasors:napari.yaml
+
+[options.extras_require]
+testing = 
+	tox
+	pytest  # https://docs.pytest.org/en/latest/contents.html
+	pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+	pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
+	napari
+	qtpy
+	scikit-image
+	biaplotter>=0.0.5a0
+	PyQt5
+	pandas
+	black
+	isort
+	phasorpy
+	tifffile
+	lfdfiles
+	sdtfile
+	ptufile
+
+[options.package_data]
+* = *.yaml
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

napari_phasors-0.0.1/src/napari_phasors/__init__.py

@@ -0,0 +1,29 @@
+__version__ = "0.0.1"
+
+from ._reader import napari_get_reader
+from ._sample_data import (
+    convallaria_FLIM_sample_data,
+    embryo_FLIM_sample_data,
+    paramecium_HSI_sample_data,
+)
+from ._widget import (
+    CalibrationWidget,
+    LifetimeWidget,
+    PhasorTransform,
+    WriterWidget,
+)
+from ._writer import write_ome_tiff
+from .plotter import PlotterWidget
+
+__all__ = (
+    "napari_get_reader",
+    "write_ome_tiff",
+    "convallaria_FLIM_sample_data",
+    "embryo_FLIM_sample_data",
+    "paramecium_HSI_sample_data",
+    "PhasorTransform",
+    "PlotterWidget",
+    "CalibrationWidget",
+    "WriterWidget",
+    "LifetimeWidget",
+)