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Changelog

Source: NEWS.md

raveio 0.9.0

CRAN release: 2023-07-16

We are close to a major release.

Major changes:

  • Pipeline supports Python now! (I think this deserves the first place)

  • Referencing electrodes does not require users to run wavelet anymore (this one wins the second as it allows for more flexible data processing pipelines)

  • Added PipelineCollections, allowing users to build and run multiple pipelines

  • run_wavelet will trigger caching existing references

  • The pipeline errors is properly handled

  • Pipeline error messages also print out the expressions causing the issues

  • Clears pipeline object directory when related errors are raised; in this case pipeline is rescheduled automatically

  • Pipeline also reports warning messages

  • Allow pipelines to fork

  • Added external data path (extdata) to pipeline to store large temporary data

  • Added prepare_subject_phase and prepare_subject_wavelet to support loading phase and time-frequency data (besides amplitude)

  • Pipeline shared scripts uses script directory as working directory

  • Added lapply_async that can run in parallel standalone while is compatible with with_future_parallel; this function replaces dipsaus::lapply_async2

  • Added a new subject class RAVEMetaSubject for meta-analysis

  • Added support for FreeSurfer recon-all-clinical.sh, allowing users to apply super-resolution to their clinical MRI before surface reconstruction

  • Supports when one NSx block data contains multiple recordings (discontinued/paused recording in one block)

  • rave_export exports summary in Matlab format as well (thanks @Kaitlyn)

  • Added cmd_run_r to generate reproducible shell scripts that run code

  • Added pipeline$visualize to view the target relationships and schedule graphs

  • Added pipeline$shared_env to obtain shared environment

Minor changes:

  • Default pipeline repository user name has been changed to rave-ieeg
  • Updated Github action configurations
  • Copy MRI to derivative folder when importing images from NIfTI format (before imaging segmentation and CT to MRI registration)
  • Updated pipeline template to display the latest pipeline dependency
  • Pipeline dependency are installed at the same directory as ravemanager
  • Removed improper S3generics in validate_raw_file_lfp
  • Pipeline root searching path can be set with temporary values
  • Added is_on_cran, allowing certain examples and tests to be suppressed during CRAN check, while these code are enabled in the local tests - this helps me to keep examples up-to-date

Bug fixes:

  • Fixed template module UI having extra padding on bottom
  • Fixed Blackrock NEV-3.0 specification configurations
  • Fixed errors when subject set_default and get_default raise errors when configuration files are corrupted
  • Fixed a potential code injection issue
  • Fixed parallel code not closing socket connections correctly

raveio 0.1.0

CRAN release: 2023-03-15

Major changes:

  • Added pipeline target format interface; an example for rave-subject has been implemented
  • rewrote as_rave_subject such that the subject information will be updated when called
  • Revised error handlers in pipeline generating engine, so that when errors occur, the enclosing target expressions and back-trace will be printed
  • Supported brain viewer to be loaded without electrodes via include_electrodes argument
  • Added coregistration via ANTs
  • Supports MRI registering to templates via non-linear transforms

Minor changes:

  • When importing electrodes from other formats, the subject used to be required. However, this is totally unnecessary; removed such requirement
  • Fixed a small typo that may cause inconsistent electrode labels (Nolabel to NoLabel)

Bug fixes:

  • When executing pipeline shared script, it is possible to leak some variables to the global environment; fixed
  • Fixing a bug where shared scripts might not be loaded properly in pipeline_run

raveio 0.0.9

CRAN release: 2022-10-14

Major changes:

  • Added run_wavelet to isolate wavelet kernels for each subject, requires to update ravetools
  • Avoid override ravetools options when loading the package
  • Added clean method to pipeline to clean the data objects
  • Allowed pipelines to save and load customized data to avoid polluting the settings.yaml
  • Allowed pipelines to eval instead of run
  • Added new data type raw-voltage to method load_blocks (class LFP_electrode) to load the raw voltage data
  • Added prepare_subject_bare0 to load subject that with only voltage data imported (before Notch filters)
  • Added repository type for voltage signals
  • Added .nev converter to export BlackRock format to Matlab or HDF5 formats
  • Backup pipeline files when updating
  • Added baseline method for voltage signals

Minor changes:

  • Changed FLIRT script to perform less search to speed up
  • Exported MNI305_to_MNI152 matrix
  • Added quiet option when loading electrodes to suppress warnings
  • Try to use ravetools whenever possible
  • Added an option to avoid reading BlackRock.nev headers to shorten loading time
  • Allow electrodes to be loaded without warnings

Bug fixes:

  • Fixed watchdog when electrode table is unavailable
  • Fixed rand_string not random when running with multicore future parallel
  • Fixed preprocess_file path in class LFP_electrode
  • Baseline window is no longer needed when mean and standard deviation is provided
  • Fixed .nev converter bugs causing index overflows in some cases

raveio 0.0.8

CRAN release: 2022-08-25

Major changes:

  • Added bundled validation functions to check data integrity: this function supports both RAVE 1.0 and 2.0 formats
  • Added backward support to convert 2.0 data format to 1.0
  • Added file support for BlackRock (NEV, NSx) formats with specification number (>=2.2)
  • Allowed pipelines to execute without targets to avoid serializing large objects
  • Added a repository type that requires no epoch information. This is useful when users want to analyze blocks of data
  • Added monitoring class RAVEWatchDog that can automatically monitor NEV and NSx files, import & process data
  • Added merge_subjects to merge multiple subjects from the same project but different blocks
  • Added support for recon-all, dcm2niix, 3dAllineate, and flirt shell-commands (requires external programs to be installed)
  • Added finalizing installation function to allow installing built-in processing pipelines

Minor changes:

  • Allow only one signal type to be loaded in each repository
  • Allowed electrodes to be text instead of vector of integers when creating repository

Bug fixes:

  • Fixed generate_reference set array to read-only mode before saving headers
  • Actively clear cache whenever a new reference is generated

raveio 0.0.7

CRAN release: 2022-06-20

Major changes:

  • Added PipelineTools class and wrapped constructor raveio::pipeline to load common utility tools needed to run the pipeline
  • Added module templates for RAVE-2.0
  • Allow import_electrode_table to import table without replacing existing electrode files with dry_run option

raveio 0.0.6

CRAN release: 2022-05-30

Major changes:

  • Added read_mat2 to allow reading Matlab files stored in HDF5 formats
  • Allow subject instances to store and retrieve default key-value pairs via set_default and get_default methods
  • Disable multicore by default, so users can use their own plan provided by the future package
  • Added location and signal types to electrodes
  • Added function to perform baseline via power_baseline directly from repository
  • Added multiple repository types for RAVE subjects with identical key as signature
  • Added with_future_parallel to enable multicore features in the expressions
  • Added reference signal class
  • Use ravedash log system provided if the package is installed
  • Speed-up raveio_getopt and raveio_setopt
  • Added validate_time_window to return intervals of time windows
  • Added save_json and load_json to handle JSON format using jsonlite package
  • Allow to set threeBrain template brain
  • Added import_electrode_table to import electrode table with coordinates in T1 or MNI space to tkrRAS
  • Electrodes can load corresponding block data
  • Added normalize_commandline_path and cmd_* functions to search for external system commands such as FreeSurfer, FSL-FLIRT, dcm2niix
  • Added backup_file to back up existing files instead of overwriting
  • Allow to download and install rave-server as services (currently only works on OSX)

Changes to pipeline framework:

  • Implemented and matured reproducible pipeline framework
  • Added R-markdown template to build pipelines
  • Allow pipelines to run in another process and can kill the process anytime
  • Pipelines run in async mode works in shiny applications
  • Created an R6 class for pipeline results in promises way
  • Allow to clear cache files at subject level
  • Async pipelines can have callback functions at each check, useful for monitoring the progress

Enhancements:

  • save_yaml can write to connections
  • rave_imports runs in parallel in native2 format
  • Added an option to disable fork-clusters (enabled by default on OSX and Linux)
  • Allows EDF files to be partially read
  • Added data format entry to the preprocess instance, allowing following modules to be aware of the raw data format
  • ravetools respects tensor_temp_path as its temporary path

raveio 0.0.5

CRAN release: 2021-10-13

Major changes:

  • Rewind back to hdf5r as it passes the CRAN checks now
  • Fixed HDF5 bugs
  • Added pipeline functions to self-expand RAVE
  • Added pipeline templates

raveio 0.0.4

CRAN release: 2021-08-05

Major changes:

  • removed lazyarray, pryr
  • fixed get_ram errors when system command not found
  • disabled support on Solaris
  • changed hdf5r to rhdf5

raveio 0.0.3

CRAN release: 2020-08-14

Initial CRAN submission.