pysight 0.4.0

Create images from photon lists generated by a multiscaler.

Create images from photon lists generated by a multiscaler.

• Free software: BSD license

Installation

At the command line:

conda install numba
conda install tifffile -c conda-forge
pip install pysight

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:

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.