Metadata-Version: 1.1
Name: pysight
Version: 0.5.5
Summary: Create images from photon lists generated by a multiscaler.
Home-page: https://github.com/HagaiHargil/python-pysight
Author: Hagai Hargil
Author-email: hagaihargil@gmail.com
License: BSD
Description: ========
        Overview
        ========
        
        
        
        Create images from photon lists generated by a multiscaler.
        
        * Free software: BSD license
        
        * Created by `Pablo Blinder's Lab`_.
        
        .. _Pablo Blinder's Lab: http://pblab.tau.ac.il/en/
        
        Installation
        ============
        
        .. include:: docs/installation.rst
        
        Please refer to ``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.
        
        0.4.5 (2017-04-17)
        ------------------
        
        * Bug fixes and improvements to TAG lens interpolation.
        
        0.4.6 (2017-05-16)
        ------------------
        
        * 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.
        
        0.4.7 (2017-05-25)
        ------------------
        
        * Fixed some of the tests.
        
        * Added option to save or discard photons arriving during the returning phase of a unidirectional scan. This is the default option now.
        
        * Introduced ``Fill Fraction`` parameter that determines the amount of `time` the mirrors spend "inside" the image.
        
        * Some tests are working again.
        
        * Many other bugfixes.
        
        0.4.8 (2017-05-31)
        ------------------
        
        * Added type hinting. As a result, disabled support for Python version 3.5. Code is now entirely 3.6-dependent.
        
        * Added ``.json`` configuration files to the GUI. It also automatically loads the last modified configuration file.
        
        * Updated docs.
        
        0.5.0 (2017-06-04)
        ------------------
        
        * Added the ``CensorCorrection`` class for processing generated data using the censor correction method. Current available methods are:
            * ``censored.gen_bincount_deque()``: Bin the photons into their relative laser pulses, and count how many photons arrived due to each pulse.
            * ``censored.find_temp_structure_deque()``: Generate a summed histogram of the temporal structure of detected photons.
        
        * Fixed linux bug with ``Deque`` import.
        
        * Added tests.
        
        0.5.1 (2017-06-04)
        ------------------
        
        * Another go at Linux namespace conflicts.
        
        0.5.2 (2017-06-06)
        ------------------
        
        * Added basic support for "Censor Correction".
        
        0.5.3 (2017-06-06)
        ------------------
        
        * Bug fixes, including support for single-pixel images.
        
        * Script should require less memory while running.
        
        0.5.4 (2017-06-06)
        ------------------
        
        * Fixed untested typo.
        
        0.5.5 (2017-06-07)
        ------------------
        
        * Bug fixes for single-pixel frames
        
        * Bug fixes for defining amount of frames manually in script.
        
        * Censor correction shouldn't require as much memory as it did. It's still not as fast as it can be.
        
        * Loading a configuration file will make it the "last used" file, reloading it when re-running PySight.
        
Keywords: multiscaler,photon counting
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Utilities
