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Create images from photon lists generated by a multiscaler.

Project description

========
Overview
========



Create images from photon lists generated by a multiscaler.

* Free software: BSD license

Installation
============

.. include:: ./docs/installation.rst

Documentation
=============

https://python-pysight.readthedocs.io/

Development
===========

To run the all tests run::

tox

Note, to combine the coverage data from all the tox environments run:

.. list-table::
:widths: 10 90
:stub-columns: 1

- - Windows
- ::

set PYTEST_ADDOPTS=--cov-append
tox

- - Other
- ::

PYTEST_ADDOPTS=--cov-append tox


Changelog
=========

0.1.0 (2017-02-27)
------------------

* First release on PyPI.

0.1.1 (2017-02-27)
------------------

* Bug fixes during installation of Numba.

* Added the ``run()`` method for ``main_multiscaler_readout``.

0.1.2 (2017-02-27)
------------------

* Includes ``tifffile`` and minor improvements.

0.1.3 (2017-02-28)
------------------

* Changed IO from ``.read()`` to ``.readlines()`` for better Linux compatibility.

* ``.tif`` is now saved frame-by-frame to save memory, and the method was renamed to ``create_tif()``.

0.1.4 (2017-02-28)
------------------

* Frames are now generated with a generator.
* Fix to installation problems of previous version.

0.1.5 (2017-02-28)
------------------

* Single-lined frames are now supported.

0.1.6 (2017-02-28)
------------------

* More tests coverage.

* Enforced a few types checks.

0.1.7 (2017-03-01)
------------------

* Potential fix to ``pip install`` issues.

* Start of TAG lens interpolation support.

0.2.0 (2017-03-05)
------------------

* Support for TAG lens added - phase interpolation and image display. Note: The algorithm currently assumes that the pulse is triggered at the zero-phase of the TAG lens.

* ``pip`` installation fixed by requiring Numba as a prerequisite.

* Number of pixels in the "Frame" direction (x) supersedes the number of frames as listed by the user.

* Due to massive changes, one test is currently broken.

0.3.0 (2017-03-07)
------------------

* Added method ``create_array`` to Movie() that returns a deque containing the raw data generated by the ``np.histogram`` function, for visualization and analysis purposes.

* Added method ``create_single_volume`` to Movie() that sums all stacks into a single array.

* Fixed bugs in ``tag_tools``, mainly in ``verify_periodicity()``.

* Allows for more elaborate user inputs, requiring to choose which type of output you wish for.

* Basic FLIM support.

0.3.1 (2017-03-07)
------------------

* Tiffs are now saved untiled. Depth axis is x-axis.

* Installation should run smoothly if following the instructions.

0.3.2 (2017-03-07)
------------------

* Added verifications on the FLIM input.

* Bug fixes in FLIM implementation.

0.3.3 (2017-03-08)
------------------

* Code can take care of the the infamous [-1, ..., -1] index list.

* Added ``debug`` mode in which the algorithm reads only a limited amount of lines from a file.

* Fixed minor bug in ``__create_hist``.

* Decreased size of package by removing excess lines of data for tests.

0.3.4 (2017-03-09)
------------------

* More fixes to the [-1] vector problem.

* Added a ``sort`` function before handling the data, because of irregularities.


0.3.5 (2017-03-11)
------------------

* Added sinusoidal interpolation to TAG phase.

* Sorting is now only done for TAG lens input.

* Added ``fileIO_tools.py`` module for increased simplicity.

* Added more verifications to user inputs from GUI that pop up sooner, before heavy computation is made.

* Increased file IO speed with a new ``np.fromfile`` method.


0.3.6 (2017-03-14)
------------------

* Basic support for TAG bits - no actual interpolation yet.

* GUI additions and changes.

* Minor performance upgrades.


0.4.0 (2017-03-16)
------------------

* Changes file IO completely. Performance should be higher.

* TAG lens bug fixes.

* Updated docs.

* Updated tests.

0.4.1 (2017-03-30)
------------------

* Updates to setup.py to allow docs to build successfully.

* Small updates to docs.

* GUI improvements.

0.4.2 (2017-03-30)
------------------

* Added Dask ``delayed`` interface.

0.4.3 (2017-04-02)
------------------

* Removed Dask.

* Refactored class structure, remove the ``Frame`` class.

* Refactored GUI code.

0.4.4 (2017-04-08)
------------------

* Changes to file I\O.

* Number of requested frames should actually matter now.

* GUI improvements.

* This version is the last one supporting ASCII list files. Next one will only use binary files as input.


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