What's new?

What's new on current master

Core

• Methods turned properties: Data.time_max, Data.time_min, Data.name
• Set corrections factors by assigning Data.leakage, Data.gamma, Data.dir_ex (properties)
• Deprecate Data.burst_search_t in favor of Data.burst_search
• Preliminary work toward python 3 support

Plotting

• Plots: hist_* plot function now use a common API and share code and are better documented.
• Use plot_alternation_hist() and loader.alex_apply_period() both for usALEX and nsALEX data
• Moved alex_jointplot from example notebook to burst_plot module
• Integrated seaborn plot styles: now you can enable inline plots with seaborn style with init_notebook()
• Added plot functions to the official docs

HDF5

• Add new field num_detectors and new groups /setup and /provenance to the Photon-HDF5 read/save functions
• Fixes in the Photon-HDF5 loader

Documentation

• Updated installation docs

0.4 release candidate 4

• Improve installation
• Improved documentation
• Use the new Photon-HDF5 (renamed and improved from HDF5-Ph-Data)

0.4 release candidate 3

• Integrate with Zenodo (to get a DOI) and Travis-CI (automated test run)
• load_fretbursts.py loads fretbursts from system installation by default. If fretbursts is not installed with pip it will be loaded from the source folder. To force-load from source folder use the --source flag.
• Improve installation (handle case of cython not installed)
• Fix ReadTheDoc docs building and version extraction
• Update installation notebook
• Update installation docs

0.4 release candidate 2

###Main

• Simplified Cython burst search making it ~30% faster.
• Plots improvements and cleanups
• Add example notebook showing different ALEX histogram plot styles
• Add correction formula for S in fretmath.py
• Add Data.burst_width property
• HDF5: various fixes and better support for save/load lifetime data (ns-ALEX and single laser excitation)

###Installation

• Standard package installation:

python setup.py build
python setup.py install

• Use versioneer for the version string
• Build and install cython extension during installation
• Hopefully working binary distribution

###Architecture

• Add iterator for per-bursts photon-data

0.4 release candidate 1

Many changes from previous release.

Briefly:

• A new fitting framework based on lmfit
• Rewritten many plot functions to have a more uniform API and to be more customizable
• AND-gate burst search
• Background analysis as a function of the threshold (see bext.calc_bg_cache())
• Choice of 2 error metrics (Kolgomorov-Smirnov and Cramer-von Mise) for background fit
• Shortcuts for per-channel fields to access channel 0 (d.nd_ is a shortcut for d.nd[0] and so on).
• Many changes described here #18

First pre-release

This is the first pre-release of FRETBursts.

###Closed Issues

• Improve definition of photon selections (issue #1)
• Add loader function for nsALEX (issue #2)
• Print git commit date on loading (issue #6)
• Generate docs for the fitting function (issue #9)
• Add loader.py to the docs (issue #11)