Metadata-Version: 2.1
Name: lfdfiles
Version: 2019.7.2
Summary: Laboratory for Fluorescence Dynamics (LFD) file formats
Home-page: https://www.lfd.uci.edu/~gohlke/
Author: Christoph Gohlke
Author-email: cgohlke@uci.edu
License: BSD
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=2.7
Requires-Dist: numpy (>=1.11.3)
Requires-Dist: tifffile (>=2019.7.2)
Requires-Dist: click
Provides-Extra: all
Requires-Dist: matplotlib (>=2.2) ; extra == 'all'

Laboratory for Fluorescence Dynamics (LFD) file formats
=======================================================

Lfdfiles is a Python library and console script for reading, writing,
converting, and viewing many of the proprietary file formats used to store
experimental data and metadata at the `Laboratory for Fluorescence Dynamics
<https://www.lfd.uci.edu/>`_. For example:

* SimFCS VPL, VPP, JRN, BIN, INT, CYL REF, BH, BHZ FBF, FBD, B64, I64, Z64, R64
* GLOBALS LIF, ASCII
* CCP4 MAP
* Vaa3D RAW
* Bio-Rad(r) PIC
* Vista IFLI
* FlimFast FLIF

For command line usage run ``python -m lfdfiles --help``

:Author:
  `Christoph Gohlke <https://www.lfd.uci.edu/~gohlke/>`_

:Organization:
  Laboratory for Fluorescence Dynamics. University of California, Irvine

:License: 3-clause BSD

:Version: 2019.7.2

Requirements
------------
* `CPython 2.7 or 3.5+ <https://www.python.org>`_
* `Numpy 1.11.3 <https://www.numpy.org>`_
* `Tifffile 2019.7.2 <https://pypi.org/project/tifffile/>`_
* `Matplotlib 2.2 <https://pypi.org/project/matplotlib/>`_
  (optional for plotting)
* `Click 7.0 <https://pypi.python.org/pypi/click>`_
  (optional for command line usage)

Revisions
---------
2019.7.2
   Require tifffile 2019.7.2.
   Remove some utility functions.
2019.5.22
    Read and write Bio-Rad(tm) PIC files.
    Read and write Voxx MAP palette files.
    Rename SimfcsMap to Ccp4Map and SimfcsV3draw to Vaa3dRaw.
    Rename save functions.
2019.4.22
    Fix setup requirements.
2019.1.24
    Add plots for GlobalsLif, SimfcsV3draw, and VistaIfli.
    Support Python 3.7 and numpy 1.15.
    Move modules into lfdfiles package.
2018.5.21
    Update SimfcsB64 to handle carpets and streams.
    Command line interface for plotting and converting to TIFF.
    Registry of LfdFile classes.
    Write image and metadata to TIFF.
    Read TIFF files.
2016.3.29
    Write R64 files.
2016.3.14
    Read and write Vaa3D RAW volume files.
2015.3.02
    Initial support for plotting.
2015.2.19
    Initial support for new FBD files containing headers.
2014.12.2
    Read B64, R64, I64 and Z64 files (SimFCS version 4).
2014.10.10
    Read SimFCS FIT files.
2014.4.8
    Read and write CCP4 MAP volume files.
2013.8.10
    Read second harmonics FlimBox data.

Notes
-----
Lfdfiles is currently developed, built, and tested on Windows only.

The API is not stable yet and might change between revisions.

The `Microsoft Visual C++ Redistributable Packages
<https://support.microsoft.com/en-us/help/2977003/
the-latest-supported-visual-c-downloads>`_ are required on Windows.

Many of the LFD's file formats are not documented and might change arbitrarily.
This implementation is mostly based on reverse engineering existing files.
No guarantee can be made as to the correctness of code and documentation.

Experimental data are often stored in plain binary files with metadata
available in separate, human readable journal files (.jrn).

Unless specified otherwise, data are stored in little-endian, C contiguous
order.

References
----------
The following software is referenced in this module:

(1)  `SimFCS <https://www.lfd.uci.edu/globals/>`_, a.k.a. Globals for
     Images, is software for fluorescence image acquisition, analysis, and
     simulation, developed by Enrico Gratton at UCI.
(2)  `Globals <https://www.lfd.uci.edu/globals/>`_, a.k.a. Globals for
     Spectroscopy, is software for the analysis of multiple files from
     fluorescence spectroscopy, developed by Enrico Gratton at UIUC and UCI.
(3)  ImObj is software for image analysis, developed by LFD at UIUC.
     Implemented on Win16.
(4)  `FlimFast <https://www.lfd.uci.edu/~gohlke/flimfast/>`_ is software for
     frequency-domain, full-field, fluorescence lifetime imaging at video
     rate, developed by Christoph Gohlke at UIUC.
(5)  FLImage is software for frequency-domain, full-field, fluorescence
     lifetime imaging, developed by Christoph Gohlke at UIUC.
     Implemented in LabVIEW.
(6)  FLIez is software for frequency-domain, full-field, fluorescence
     lifetime imaging, developed by Glen Redford at UIUC.
(7)  Flie is software for frequency-domain, full-field, fluorescence
     lifetime imaging, developed by Peter Schneider at MPIBPC.
     Implemented on a Sun UltraSPARC.
(8)  FLOP is software for frequency-domain, cuvette, fluorescence lifetime
     measurements, developed by Christoph Gohlke at MPIBPC.
     Implemented in LabVIEW.
(9)  `VistaVision <http://www.iss.com/microscopy/software/vistavision.html>`_
     is commercial software for instrument control, data acquisition and data
     processing by ISS Inc (Champaign, IL).
(10) `Vaa3D <https://github.com/Vaa3D>`_ is software for multi-dimensional
     data visualization and analysis, developed by the Hanchuan Peng group at
     the Allen Institute.
(11) `Voxx <http://www.indiana.edu/~voxx/>`_ is a volume rendering program
     for 3D microscopy, developed by Jeff Clendenon et al. at the Indiana
     University.
(12) `CCP4 <https://www.ccp4.ac.uk/>`_, the Collaborative Computational Project
     No. 4, is software for macromolecular X-Ray crystallography.


