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Create images from photon lists generated by a multiscaler.

Project description

Create images from photon lists generated by a multiscaler.

  • Free software: BSD license

Installation

Please refer to docs\installation.rst.

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.

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 IO.
  • Number of requested frames should actually matter now.
  • GUI improvements.

0.4.5 (2017-04-17)

  • Bug fixes and improvements to TAG lens interpolation.

0.4.6 (2017-05-XX)

  • Use Debug? to read a small portion of an .lst file.
  • Changed defaults in GUI.
  • Allows acquisition in bi-directional scanning mode. This is enabled with the Mirror phase and Flyback parameters in the GUI.
  • Backend changes for possible future support of binary files.
  • The code allows to dismiss unwanted input channels by specifying them as “Empty”.
    • If you mark a channel as containing data while it’s inactive, an error will terminate execution.
  • Massive refactoring of pipeline.

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