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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

* 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.

0.5.6 (2017-06-08)
------------------

* ML classification is functional.

0.5.7 (2017-06-08)
------------------

* More robust data generation.

* Added ``scikit-learn`` to ``requirements.txt`` and ``setup.py``.

* ``CensorCorrection().learn_histograms()`` now receives the power label as its input - must be an integer.

* Return of ``CensorCorrection().learn_histograms()`` is now ``data, labels``.

* Made ``__get_bincount_deque()`` private. To be accessed using ``learn_histograms()`` only.

0.5.8 (2017-06-08)
------------------

* Robustness upgrades.

* QOL changes to GUI.

* A "power" number is needed for ``learn_histograms()`` - the percent of power given to the Qubig. It's just for saving, labeling is done with the ``label`` keyword.

* A ``foldername`` to which the data will be saved to has also been added.

0.5.9 (2017-06-11)
------------------

* Much (MUCH) faster concatenation of the data.

* Fixed a bug with the number of empty histograms that were added to the learning dataset.

0.5.10 (2017-06-12)
-------------------

* Changes and optimizations for the file IO process.

* Fixed a bug with laser pulses verification.

* Added offset parameter for laser input.

0.5.11 (2017-06-22)
-------------------

* Added FLIM functionality with laser clock in the Multiscaler's clock.

0.5.12 (2017-06-22)
-------------------

* Fixed small bug with GUI.

* Possible fix to TAG lens interpolation.

0.5.13 (2017-06-26)
-------------------

* Added SciPy dependency.

* Added nanoFLIM histogramming.

0.5.14 (2017-06-26)
-------------------

* Bug fixes and performance improvements.

0.5.15 (2017-06-27)
-------------------

* Refactoring of output:

* Start of censor correction is integrated into the generation of the outputs.

* More efficient when required to output several types of data.

0.5.16 (2017-06-27)
-------------------

* Fixed small bug with censor correction.

0.5.17 (2017-06-29)
-------------------

* Fixed ``.tif`` generation.

* Refactoring of ``FileIO`` (tests still pass).

0.5.18 (2017-06-29)
-------------------

* Added metadata from ``.lst`` file to the saved ``.tif`` file. Variables saved:
* "fstchan"
* "holdafter"
* "periods"
* "rtpreset"
* "cycles"
* "sequences"
* "range"
* "sweepmode"
* "fdac"

0.5.19 (2017-06-29)
-------------------

* Fixed small bug with censoring.

* Added checks to see whether we need censor correction.

* Added tests for ``lst_tools`` - they should pass, much like ``file_io``'s tests.

0.5.20 (2017-07-01)
-------------------

* Refactored the output-generating script, while changing the possible outputs of PySight:
* Summed tif.
* Full stack as tif.
* In memory - both stack and tif accessed through the ``movie`` object.

0.5.21 (2017-07-07)
-------------------

* Added the acquisition delay and "hold-after" times to the calculation of the the absolute time of each event.

* Decreased package size dramatically by deleting unneeded test data.

* All 34 tests of code pass. I'll try to keep it that way :)

* Added an extrapolation method to create fake lines when the line data is too corrupt to work with. This is done using
the new "line frequency" and "frame delay" parmaeters in the GUI.

0.5.22 (2017-07-17)
-------------------

* Added an optional line frequency entry to the GUI.

* Refactoring of some parts of the validation tools.

* Small performance upgrade.

* Added an option to treat sweeps as lines.

0.5.23 (2017-07-20)
-------------------

* Supports generating images from pure sweeps, without a line signal.

* Supports generating images from combined sweep and line signals.

0.5.24 (2017-07-30)
-------------------

* Bugfixes for line validations.

* Added methods ``show_summed(channel)`` and ``show_stack(channel, iterable)``.

* More refactoring to decrease class absolute size.

* Small bug fix in the sweeps-as-lines implementation.

0.5.25 (2017-08-26)
-------------------

* Added the ``photons_per_pulse`` property to ``Movie()``.

* Introduced the ``run_batch(foldername)`` function to the ``main`` module, to run PySight with the same configs on multiple ``.lst`` files in a folder.

* Added the ``num_of_vols`` property to ``Movie()``.

0.6.0 (2017-08-27)
------------------

* Changed output file format to ``.hdf5`` due to compatibility issues of ``.tif``s.

0.6.1 (2017-08-28)
------------------

* Added gating to photons that arrive too early (or too late) after a laser pulse.

0.6.2 (2017-08-29)
------------------

* Fixed bug with ``movie.show_stack()``.

0.6.3 (2017-09-11)
------------------

* Better support for "early" photons.

* Allow for no outputs from PySight.

0.6.4 (2017-09-18)
------------------

* Fixed bug with two-channel output.

* Fixed bug with "early" photons.

0.6.5 (2017-09-18)
------------------

* Writing output ``.hdf5`` to disk is much faster now.

0.6.6 (2017-09-27)
------------------

* Now compressing HDF5 files.

* Fixed small bug in TAG implementation.

0.6.7 (2017-09-28)
------------------

* Faster I/O.

* Datasets are now ``uint8`` (full stack) and ``uint16`` (summed stack).

* Allowing outputs without the "In Memory" requirement.

* Added a progress bar.

* ``show_summed()`` works, ``show_stack()`` might not.

0.6.8 (2017-09-28)
------------------

* Small bug fix in progress bar.

0.6.9 (2017-09-29)
------------------

* Stacking the final array is now an order-of-magnitude faster - the first dimension is now considered `time`.

* Fixed a bug with singleton dimensions.

* Fixed a bug with no "In Memory" output.

0.6.10 (2017-10-03)
-------------------

* Fixed a bug occurring when TAG lens interpolation fails.

* Discovered another bug with the interpolation process which is currently unresolved.

* Fixed small issue with a TAG test function.

0.6.11 (2017-10-06)
-------------------

* Complete re-write of TAG lens processing module.

0.6.12 (2017-10-08)
-------------------

* Removed the experimental ``parallel`` feature from the Numba implementation.

* Fixed bidirectional image generation.

* Default fill fraction is now 75% to better suit ScanImage's defaults.

0.6.13 (2017-10-08)
-------------------

* The TAG phase is now between 0 and 1, generating non-cyclic volumes.

0.6.14 (2017-10-30)
-------------------

* Added a ``glob_str`` and ``recursive`` parameters to ``run_batch()``.

* Added a ``DEBUG`` suffix to files generated when debugging.

* Changed license to creative commons.

* Small bug fixes, somewhat decreased memory usage.

* Improved bidirectional scanning performance and robustness by reworking its mechanism.

0.6.15 (2017-11-05)
-------------------

* Better bidirectional support.

0.6.16 (2017-11-20)
-------------------

* Support for non-phase allocation of TAG pulses.

* Removal of old TAG module.

* ``run_batch()`` works without choosing a mock list file.

0.6.17 (2017-12-04)
-------------------

* Fixed a bug with the filename of the ``DEBUG``ged version.

0.6.18 (2017-12-05)
-------------------

* Fixed a bug with bidirectional scanning.

* Possible fix for data that don't have lines since the beginning of the experiment.


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