Merge pull request #3 from zoccoler/add_reader_and_plotter

Add reader and plotter

LICENSE

@@ -1,5 +1,5 @@
 
-Copyright (c) 2022, Napari Developer
+Copyright (c) 2022, Marcelo L. Zoccoler
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -7,33 +7,32 @@
 [![codecov](https://codecov.io/gh/zoccoler/napari-flim-phasor-calculator/branch/main/graph/badge.svg)](https://codecov.io/gh/zoccoler/napari-flim-phasor-calculator)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-flim-phasor-calculator)](https://napari-hub.org/plugins/napari-flim-phasor-calculator)
 
-A simple plugin to use FooBar segmentation within napari
+A napari plugin to generate a phasor plot for TCSPC FLIM data. 
 
 ----------------------------------
 
-This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
+## Usage
 
-<!--
-Don't miss the full getting started guide to set up your new package:
-https://github.com/napari/cookiecutter-napari-plugin#getting-started
+Open a raw TCSPC FLIM image in napari and call the plugin from the Plugins menu. Specify the laser frequency, which harmonic and a threshold for the phasor plot. Optionally, apply median filters. Below is a demonstration:
 
-and review the napari docs for plugin developers:
-https://napari.org/stable/plugins/index.html
--->
+<img src="https://github.com/zoccoler/napari-flim-phasor-calculator/raw/main/figures/napari_FLIM_phasor_calculator_Demo.gif" width="700"/>
 
-## Installation
+Manually draw curves on the plot to get the corresponding pixels highlighted in a new labels layer. Hold 'SHIFT' while drawing to add more than two colors.
 
-You can install `napari-flim-phasor-calculator` via [pip]:
+This plugin integrates with [napari-clusters-plotter plugin](https://github.com/BiAPoL/napari-clusters-plotter).
 
-    pip install napari-flim-phasor-calculator
+This plugin can read the following FLIM file types:
+  - ".ptu"
 
+This plugin works with the following data shapes:
+  - 2D timelapse, where time is the first dimension.
 
+## Installation
 
-To install latest development version :
+You can install `napari-flim-phasor-calculator` via [pip]. Currently, only the development version is available:
 
     pip install git+https://github.com/zoccoler/napari-flim-phasor-calculator.git
 
-
 ## Contributing
 
 Contributions are very welcome. Tests can be run with [tox], please ensure

setup.cfg

@@ -1,12 +1,12 @@
 [metadata]
 name = napari-flim-phasor-calculator
 version = 0.0.1
-description = A simple plugin to use FooBar segmentation within napari
+description = A plugin that performs phasor plot from TCSPC FLIM data.
 long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/zoccoler/napari-flim-phasor-calculator
-author = Napari Developer
-author_email = yourname@example.com
+author = Marcelo L. Zoccoler and Cornelia Wetzker
+author_email = marzoccoler@gmail.com
 license = BSD-3-Clause
 license_files = LICENSE
 classifiers =

src/napari_flim_phasor_calculator/__init__.py

@@ -2,9 +2,15 @@
 
 from ._reader import napari_get_reader
 from ._sample_data import make_sample_data
+from ._io.readPTU_FLIM import PTUreader
+from . import phasor, filters, _plotting
 
 
 __all__ = (
     "napari_get_reader",
     "make_sample_data",
+    "PTUreader",
+    "phasor",
+    "filters",
+    "_plotting"
 )