changelog

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Release 0.8.0
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* major improvement in the clustering. No more max_clusters parameters
* much faster clustering (thanks to Ruben Herzog)
* added the statsmodels library as a required dependency
* enhancement of the smart search mode
* enhancement of the bicubic spline interpolation
* fix a typo when using dead times and the collect mode
* fix a minor bug when small amount of spikes are found during smart search
* fix a bug in the wrapper for BRW files

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Release 0.7.6
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* cosmetic changes in the GUI
* adding a deconverting method to switch back from phy to MATLAB
* support for the lags between templates in the MATLAB GUI
* warn user if data are corrupted because of interrupted filtering
* robust automatic selection of the centroids (thanks to Ruben Herzog)
* addition of the statsmodels dependency
* remove the max_cluster parameter
* reduction of the size for saved clusters
* display the file name in the header
* fix a nasty bug allowing spikes at the border of chunks to be fitted even during dead periods

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Release 0.7.5
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* fix a bug for MPICH when large dictionaries.
* fix a bug for numpy files when used with new numpy versions
* add the possibility to subtract one channel as a reference channel from others
* native support for blackrock files (only .ns5 tested so far)
* simplifications in the parameter file
* fix for display of progress bars with tqdm
* addition of a multi-folders mode for openephys
* hide GPU support for now, as this is not actively maintained and optimized
* fix in the MATLAB GUI for float32 data
* fix the broken log files
* default cpu number is now half the available cores

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Release 0.7.4
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* fix a regression with spline interpolation, more investigation needed

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Release 0.7.0
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* fix a possible rounding bug if triggers are given in ms
* artefacts are computed as medians and not means over the signal
* can turn off shared memory if needed
* a particular pattern can be specified for neuralynx files
* fix bugs with output_dir, as everything was not saved in the folder
* add a circus-folders script to process virtually files within several folders as a single recording
* add a circus-artefacts script to concatenate artefact files before using stream mode
* multi-files mode is now enabled for Neuralynx data
* fixes for conversion of old dataset with python GUI
* smooth exit if fitting with 0 templates (thanks to Alex Gonzalez)

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Release 0.6.7
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* optimizations for clusters (auto blosc and network bandwith)
* addition of a dead_channels option in the [detection] section, as requested
* prevent user to remove median with only 1 channel
* fix for parallel writes in HDF5 files
* hide h5py FutureWarning

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Release 0.6.6
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* fix for matplotlib 2.2.2
* fix a bug when loading merged data with phy GUI
* faster support for native MCD file with pyMCStream
* more robust whitening for large arrays with numerous overlaps
* add an experimental mode to refine coreset (isolated spikes)
* put merging units in Hz^2 in the merging GUI
* add a HDF5 compression mode to greatly reduce disk usage for very large probe
* add a Blosc compression mode to save bandwith for clusters
* fix a display bug in the merging GUI when performing multiple passes

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Release 0.6.5
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* reduce memory consumption for mixture removal with shared memory
* made an explicit parameter cc_mixtures for mixture removal in the [clustering] section
* Minor fixes in the MATLAB GUI
* fix in the exact times shown during preview if second is specified
* prevent errors if filter is False and overwrite is False

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Release 0.6.4
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* fix a bug in the BEER for windows platforms, enhancing robustness to mpi data types
* speed up the software when using ignore_dead_times
* ensure backward compatibility with hdf5 version for MATLAB
* fix a rare bug in clustering, when no spikes are found on electrodes
* fix a bug in the MATLAB GUI when reloading saved results, skipping overlap fixes

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Release 0.6.3
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* fix a bug if the parameter file have tabulations characters
* add a tab to edit parameters directly in the launcher GUI
* fix dtype offset for int32 and int64
* minor optimizations for computations of overlaps
* explicit message displayed on screen if filtering has already been performed
* can specify a distinct folder for output results with output_dir parameter
* fix a bug when launching phy GUI for datafiles without data_offset parameter (HDF5)
* fix a memory leak when using dead_times
* fix a bug for BRW and python3
* fix a bug in the BEER
* pin HDF5 to 1.8.18 versions, as MATLAB is not working well with 1.10
* fix a bug when relaunching code and overwrite is False
* make the multi-files more robust, also reading all files in a directory
* fix a bug when peak detection is set on both with only one channel

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Release 0.6.2
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* fix for openephys and new python syntax
* fix in the handling of parameters 
* fix a bug on windows with unclosed hdf5 files
* fix a bug during converting with multi CPU on windows
* minor optimization in the fitting procedure
* support for qt5 (and backward compatibility with qt4 as long as phy is using Qt4)

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Release 0.6.1
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* fix for similarities and merged output from the GUIs
* fix for Python 3 and HDF5
* fix for Python 3 and launcher GUI
* fix for maxlag in the merging GUI
* optimization in the merging GUI for pairs suggestion
* addition of an auto_mode for meta merging, to suppress manual curation
* various fixes in the docs
* fix a bug when closing temporary files on windows
* allow spaces in names of probe files
* collect_all should take dead times into account
* patch to read INTAN 2.0 files
* fix in the MATLAB GUI when splitting neurons
* fix in the MATLAB GUI when selecting individual amplitudes

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Release 0.6.0
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* fix an IMPORTANT BUG in the similarities exported for phy/MATLAB, affect the suggestions in the GUI
* improvements in the neuralynx wrapper
* add the possibility to exclude some portions of the recordings from the analysis (see documentation)
* fix a small bug in MS-MPI (Windows only) when shared memory is activated and emtpy arrays are present

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Release 0.5.9
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* The validating step can now accept custom spikes as inputs
* Change the default frequency for filtering to 300Hz instead of 500Hz

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Release 0.5.8
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* fix a bug for int indices in some file wrappers (python 3.xx) (thanks to Ben Acland)
* fix a bug in the preview gui to write threshold
* fix a bug for some paths in Windows (thanks to Albert Miklos)
* add a wrapper for NeuraLynx (.ncs) file format
* fix a bug in the installation of the MATLAB GUI
* fix a bug to see results in MATLAB GUI with only 1 channel
* fix a bug to convert data to phy with only positive peaks
* add builds for python 3.6
* optimizations in file wrappers
* fix a bug for MCS headers in multifiles, if not all with same sizes
* add the possibility (with a flag) to turn off parallel HDF5 if needed
* fix a bug with latest version of HDF5, related to flush issues during clustering

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Release 0.5.7
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* Change the strsplit name in the MATLAB GUI
* Fix a bug in the numpy wrapper
* Fix a bug in the artefact removal (numpy 1.12), thanks to Chris Wilson
* Fixes in the matlab GUI to ease a refitting procedure, thanks to Chris Wilson
* Overlaps are recomputed if size of templates has changed (for refitting)
* Addition of a "second" argument for a better control of the preview mode
* Fix when using the phy GUI and the multi-file mode.
* Add a file wrapper for INTAN (RHD) file format

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Release 0.5.6
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* Fix in the smart_search when only few spikes are found
* Fix a bug in density estimation when only few spikes are found

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Release 0.5.5
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* Improvement in the smart_select option given various datasets
* Fix a regression for the clustering introduced in 0.5.2

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Release 0.5.2
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* fix for the MATLAB GUI
* smart_select can now be used [experimental]
* fix for non 0: DISPLAY
* cosmetic changes in the clustering plots
* ordering of the channels in the openephys wrapper
* fix for rates in the MATLAB GUI
* artefacts can now be given in ms or in timesteps with the trig_unit parameter

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Release 0.5rc
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* fix a bug when exporting for phy in dense mode
* compatibility with numpy 1.12
* fix a regression with artefact removal
* fix a display bug in the thresholds while previewing with a non unitary gain
* fix a bug when filtering in multi-files mode (overwrite False, various t_starts)
* fix a bug when filtering in multi-files mode (overwrite True)
* fix a bug if matlab gui (overwrite False)
* fix the gathering method, not working anymore
* smarter selection of the centroids, leading to more clusters with the smart_select option
* addition of a How to cite section, with listed publications

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Release 0.5b9
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* switch from progressbar2 to tqdm, for speed and practical issues
* optimization of the ressources by preventing numpy to use multithreading with BLAS
* fix MPI issues appearing sometimes during the fitting procedure
* fix a bug in the preview mode for OpenEphys files
* slightly more robust handling of openephys files, thanks to Ben Acland
* remove the dependency to mpi4py channel on osx, as it was crashing
* fix a bug in circus-multi when using extensions

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Release 0.5b8
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* fix a bug in the MATLAB GUI in the BestElec while saving
* more consistency with "both" peak detection mode. Twice more waveforms are always collect during whitening/clustering
* sparse export for phy is now available
* addition of a dir_path parameter to be compatible with new phy
* fix a bug in the meta merging GUI when only one template left

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Release 0.5b7
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* fix a bug while converting data to phy with a non unitary gain
* fix a bug in the merging gui with some version of numpy, forcing ucast
* fix a bug if no spikes are detected while constructing the basis
* Optimization if both positive and negative peaks are detected
* fix a bug with the preview mode, while displaying non float32 data

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Release 0.5b6
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* fix a bug while launching the MATLAB GUI

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Release 0.5b3
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* code is now hosted on GitHub
* various cosmetic changes in the terminal
* addition of a garbage collector mode, to collect also all unfitted spikes, per channel
* complete restructuration of the I/O such that the code can now handle multiple file formats
* internal refactoring to ease interaction with new file formats and readibility
* because of the file format, slight restructuration of the parameter files
* N_t and radius have been moved to the [detection] section, more consistent
* addition of an explicit file_format parameter in the [data] section
* every file format may have its own parameters, see documentation for details (or --info)
* can now work natively with open ephys data files (.openephys)
* can now work natively with MCD data files (.mcd) [using neuroshare]
* can now work natively with Kwik (KWD) data files (.kwd)
* can now work natively with NeuroDataWithoutBorders files (.nwb)
* can now work natively with NiX files (.nix)
* can now work natively with any HDF5-like structure data files (.h5)
* can now work natively with Arf data files (.arf)
* can now work natively with 3Brain data files (.brw)
* can now work natively with Numpy arrays (.npy)
* can now work natively with all file format supported by NeuroShare (plexon, blackrock, mcd, ...)
* can still work natively with raw binary files with/without headers :)
* faster IO for raw binary files
* refactoring of the exports during multi-file/preview/benchmark: everything is now handled in raw binary
* fix a bug with the size of the safety time parameter during whitening and clustering
* all the interactions with the parameters are now done in the circus/shared/parser.py file
* all the interactions with the probe are now done in the circus/shared/probes.py file
* all the messages are now handled in circus/shared/messages.py
* more robust and explicit logging system
* more robust checking of the parameters
* display the electrode number in the preview/result GUI
* setting up a continuous integration workflow to test all conda packages with appveyor and travis automatically
* cuda support is now turned off by default, for smoother install procedures (GPU yet do not bring much)
* file format can be streamed. Over several files (former multi-file mode), but also within the same file
* several cosmetic changes in the default parameter file
* clustering:smart_search and merging:correct_lag are now True by default
* fix a minor bug in the smart search, biasing the estimation of densities
* fix a bug with the masks and the smart-search: improving results
* addition of an overwrite parameter. Note that any t_start/t_stop infos are lost
* if using streams, or internal t_start, output times are on the same time axis than the datafile
* more robust parameter checking

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Release 0.4.3
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* cosmetic changes in the terminal
* suggest to reduce chunk sizes for high density probes (N_e > 500) to save memory
* fix a once-in-a-while bug in the smart-search

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Release 0.4.2
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* fix a bug in the test suite
* fix a bug in python GUI for non integer thresholds
* fix a bug with output strings in python3
* fix a bug to kill processes in windows from the launcher
* fix graphical issues in the launcher and python3
* colors are now present also in python3
* finer control of the amplitudes with the dispersion parameter
* finer control of the cut off frequencies during the filtering
* the smart search mode is now back, with a simple True/False flag. Use it for long or noisy recordings
* optimizations in the smart search mode, now implementing a rejection method based on amplitudes
* show the mean amplitude over time in the MATLAB GUI
* MATLAB is automatically closed when closing the MATLAB GUI
* mean rate is now displayed in the MATLAB GUI, for new datasets only
* spike times are now saved as uint32, for new datasets only
* various fixes in the docs
* improvements when peak detection is set on "both"
* message about cc_merge for low density probes
* message about smart search for long recordings
* various cosmetic changes
* add a conda app for anaconda navigator

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Release 0.4.1
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* fix a bug for converting millions of PCs to phy, getting rid of MPI limitation to int32
* fix bugs with install on Windows 10, forcing int64 while default is int32 even on 64bits platforms
* improved errors messages if wrong MCS headers are used
* Various cosmetic changes

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Release 0.4
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First realease of the software