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Changelog

Latest version

0.12.2 (2020-12-20)

  • Enables FLIM with the "Laser" key in the input dictionary.
  • Removed Modin from the required packages list.

Previous Versions

0.12.1 (2020-11-20)

  • Fixed a bug with the API usage.

0.12.0 (2020-10-26)

  • Added FLIM capabilites (thanks to @berkodev). Check the correct boxes in the GUI and as long as your data was synched to the laser clock it should Just Work.
  • A few bug fixes and package updates.

0.11.4 (2020-01-19)

  • Better handling of full stack files with number of frames per chunk equals one.

0.11.3 (2020-01-18)

  • When a frame chunk contains fewer-than-expected lines, PySight should now warn and move on to the next chunk instead of crashing.

0.11.2 (2020-01-01)

  • Fixed a bug related to writing to disk using zarr.

0.11.1 (2019-12-30)

  • Fix the sdist tar.gz file.

0.11.0 (2019-12-30)

  • Output file format is now .zarr and not HDF5, due to repeated misbehaviors of the latter.
  • Initial support for FLIM.
  • General bug fixes.

0.10.1 (2019-08-18)

This is a critical bug fix release, which deals with list files containing multiple sweeps. Up untill the previous version (0.10.0), list files with more than one sweep weren't parsed correctly due to a bug in PySight. This issue is now considered resolved.

0.10.0 (2019-05-04)

This is a minor release containing new features and bug fixes.

  • Added support for FLIM and image deinterleaving. This allows the user utilize the time-of-arrival of each photon relative to the last laser pulse for various applications. For more information please refer to the docs.
  • Fixed several minor issues with the build process and installation.
  • Upgrades depenedencies, now supports Python 3.7.
  • Refactoring of code base structure for higher clarity.
  • The "memory" output of PySight is now a PySightOutput object with simpler handles to the data, both raw and processed.
  • Configuration files are now TOML. Please look at default.toml in the repo for reference.
  • Improvemnets to use less RAM during runtime.
  • Fixed a memory leak affecting mostly the processing of large .lst files.

0.9.8 (2018-12-13)

  • Fixed issues with the use of data not generated by a multiscaler.
  • Documentation updates, especially for Windows installations.
  • Re-introduced binary wheels.

0.9.7 (2018-10-07)

  • Added the ReadData class for easier testing of the data readout process.
  • Consequently, added tests.
  • Should now support Mac/Linux-generated list files.

0.9.6 (2018-10-02)

  • Removed numba caching as it was causing some bugs on remote clusters.
  • Added initial pyproject.toml.
  • Moved to the black codestyle.
  • No wheels are currently generated. This might change in a future version.

0.9.5 (2018-08-01)

  • ScanImage-generated stacks better fit the original fill fraction value.
  • Small fix with non-ordered line signals.
  • Dependency upgrades to support Python 3.7. Note - still not officially supported.

0.9.4 (2018-06-14)

  • Small bug fixes.

0.9.3 (2018-06-13)

  • More documentation work.
  • Lower memory usage in certain parts of the application.

0.9.2 (2018-06-12)

  • Many documentation updates, especially for the raw API.
  • Tweaks to memory usage when writing chunks.
  • PySight allows zero-events in binary files.
  • Fixed lex-sort issue with the Frames column.

0.9.1 (2018-06-05)

  • Fixed a bug with single-frame-chunks.
  • Smarter usage of memory using the psutil package.
  • Improvements to line extrapolation.

0.9.0 (2018-05-21)

  • Added binary list file support.

0.8.4 (2018-05-20)

  • Pinned versions of required libraries.
  • Fixed bidirectional TAG stack generation.

0.8.3 (2018-05-13)

  • Fixed bug in VolumeGenerator when having a single frame slice.

0.8.2 (2018-05-12)

  • Unified configuration file keyword to be cfg_file.
  • Dramatically increased performance to due faster I/O.
  • Refactored the Movie class, changing the Volume class with a FrameChunk class.
  • Added tests.
  • Updated docs.
  • Changed many internal file names.

0.8.1 (2018-03-19)

  • Bug fix in setup.py.

0.8.0 (2018-03-19)

  • Added recursive and n_proc keywords to mp_batch, and changed return type to None.
  • Changed source tree structure for better clarity.
  • Renamed run_batch to run_batch_lst.
  • More internal improvements.
  • Z-axis bins range is equal, i.e. each bin spans the same axial distance in microns.
  • Travis CI is back on.
  • Added option to run PySight with a predetermined config file: main.run(cfg_file='/path/to/file.json').
  • New integration tests.

0.7.3 (2018-01-01)

  • Bug fixes to run_batch.
  • New function mp_batch(foldername, glob_str) for parallel processing of a folder of list files.

0.7.2 (2018-01-01)

  • Minor bug fixes.

0.7.1 (2018-01-01)

  • GUI is now startable with "S" key and or "Enter".
  • More tests to new SignalValidator class.
  • Bug fix for the validation process.
  • Making progress on multiprocessing support.

0.7.0 (2018-01-01)

  • Refactoring and additions to GUI, including new choices between imaging systems.
  • Better UI and UX.
  • Not all tests pass.

0.6.34 (2017-12-27)

  • Changed output of run_batch to a DataFrame.
  • Refactored tabulation_tools.

0.6.33 (2017-12-26)

  • Hotfix to attrs problem in setup.py.

0.6.32 (2017-12-26)

  • Trial with Numba and setuptools.
  • Type annotations.
  • Documentation update.
  • Fixes for single-photon bug.

0.6.31 (2017-12-26)

  • Bug fix for empty volumes with multichannel support.

0.6.30 (2017-12-25)

  • Fixed another bug with the line handling.
  • Fixed a bug with a missing PMT channel.

0.6.29 (2017-12-25)

  • Code cleanups.
  • More adjustments to line handling in bidirectional mode.

0.6.28 (2017-12-25)

  • Better handling of line signal.

0.6.27 (2017-12-24)

  • Separated handling of unidir and bidir corrupt line signals.
  • Refactored line signal handling module.
  • Added multiple tests to line signal handling.

0.6.26 (2017-12-21)

  • Missing line signals take mirror phase into account.
  • Fixes for MScan system.

0.6.25 (2017-12-20)

  • Even more edge-case handling.

0.6.24 (2017-12-20)

  • Deals with more edge-cases in missing line signals.

0.6.23 (2017-12-20)

  • Fixed bugs with interpolations and TAG signals.

0.6.22 (2017-12-19)

  • Added interpolation for missing line signals.

0.6.21 (2017-12-19)

  • More work on TAG interpolation.

0.6.20 (2017-12-17)

  • Fixed a bug with TAG lens interpolation.

0.6.19 (2017-12-06)

  • Bug with lines allocation in the Volume object following an API change in pandas.
  • Allows for single frame experiments.

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.

0.6.17 (2017-12-04)

  • Fixed a bug with the filename of the DEBUG-ged version.

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.

0.6.15 (2017-11-05)

  • Better bidirectional support.

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.

0.6.13 (2017-10-08)

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

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.

0.6.11 (2017-10-06)

  • Complete re-write of TAG lens processing module.

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.

0.6.9 (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.

0.6.8 (2017-09-28)

  • Small bug fix in progress bar.

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.

0.6.6 (2017-09-27)

  • Now compressing HDF5 files.
  • Fixed small bug in TAG implementation.

0.6.5 (2017-09-18)

  • Writing output .hdf5 to disk is much faster now.

0.6.4 (2017-09-18)

  • Fixed bug with two-channel output.
  • Fixed bug with "early" photons.

0.6.3 (2017-09-11)

  • Better support for "early" photons.
  • Allow for no outputs from PySight.

0.6.2 (2017-08-29)

  • Fixed bug with movie.show_stack().

0.6.1 (2017-08-28)

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

0.6.0 (2017-08-27)

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

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().

0.5.24 (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.

0.5.23 (2017-07-20)

  • Supports generating images from pure sweeps, without a line signal.
  • Supports generating images from combined sweep and line signals.

0.5.22 (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.

0.5.21 (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.

0.5.20 (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.

0.5.19 (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.

0.5.18 (2017-06-29)

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

0.5.17 (2017-06-29)

  • Fixed .tif generation.
  • Refactoring of FileIO (tests still pass).

0.5.16 (2017-06-27)

  • Fixed small bug with censor correction.

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.

0.5.14 (2017-06-26)

  • Bug fixes and performance improvements.

0.5.13 (2017-06-26)

  • Added SciPy dependency.
  • Added nanoFLIM histogramming.

0.5.12 (2017-06-22)

  • Fixed small bug with GUI.
  • Possible fix to TAG lens interpolation.

0.5.11 (2017-06-22)

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

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.

0.5.9 (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.

0.5.8 (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.

0.5.7 (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.

0.5.6 (2017-06-08)

  • ML classification is functional.

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.

0.5.4 (2017-06-06)

  • Fixed untested typo.

0.5.3 (2017-06-06)

  • Bug fixes, including support for single-pixel images.
  • Script should require less memory while running.

0.5.2 (2017-06-06)

  • Added basic support for "Censor Correction".

0.5.1 (2017-06-04)

  • Another go at Linux namespace conflicts.

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.

0.4.8 (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.

0.4.7 (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.

0.4.6 (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.

0.4.5 (2017-04-17)

  • Bug fixes and improvements to TAG lens interpolation.

0.4.4 (2017-04-08)

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

0.4.3 (2017-04-02)

  • Removed Dask.
  • Refactored class structure, remove the Frame class.
  • Refactored GUI code.

0.4.2 (2017-03-30)

  • Added Dask delayed interface.

0.4.1 (2017-03-30)

  • Updates to setup.py to allow docs to build successfully.
  • Small updates to docs.
  • GUI improvements.

0.4.0 (2017-03-16)

  • Changes file IO completely. Performance should be higher.
  • TAG lens bug fixes.
  • Updated docs.
  • Updated tests.

0.3.6 (2017-03-14)

  • Basic support for TAG bits - no actual interpolation yet.
  • GUI additions and changes.
  • Minor performance upgrades.

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.

0.3.4 (2017-03-09)

  • More fixes to the [-1] vector problem.
  • Added a sort function before handling the data, because of irregularities.

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.

0.3.2 (2017-03-07)

  • Added verifications on the FLIM input.
  • Bug fixes in FLIM implementation.

0.3.1 (2017-03-07)

  • Tiffs are now saved untiled. Depth axis is x-axis.
  • Installation should run smoothly if following the instructions.

0.3.0 (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.

0.2.0 (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.

0.1.7 (2017-03-01)

  • Potential fix to pip install issues.
  • Start of TAG lens interpolation support.

0.1.6 (2017-02-28)

  • More tests coverage.
  • Enforced a few types checks.

0.1.5 (2017-02-28)

  • Single-lined frames are now supported.

0.1.4 (2017-02-28)

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

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().

0.1.2 (2017-02-27)

  • Includes tifffile and minor improvements.

0.1.1 (2017-02-27)

  • Bug fixes during installation of Numba.
  • Added the run() method for main_multiscaler_readout.

0.1.0 (2017-02-27)

  • First release on PyPI.