# File-System Toolbox for RAVE Project

## Documentation for package ‘raveio’ version 0.1.0

- DESCRIPTION file.

## Help Pages

A B C D E F G H I J L M N P R S T U V W

## -- A --

add_module_registry | 'RAVE' module registry
ants_coreg | Register 'CT' or 'MR' images via "ANTs"
ants_morph_electrode | Register 'CT' or 'MR' images via "ANTs"
ants_mri_to_template | Register 'CT' or 'MR' images via "ANTs"
as_rave_project | Convert character to 'RAVEProject' instance
as_rave_subject | Get 'RAVESubject' instance from character
as_rave_unit | Convert numeric number into print-friendly format
auto_process_blackrock | Monitors 'BlackRock' output folder and automatically import data into 'RAVE'

## -- B --

backup_file | Back up and rename the file or directory
BlackrockFile | Class definition to load data from 'BlackRock' 'Micro-systems' files

## -- C --

cache_path | Manipulate cached data on the file systems
cache_root | Manipulate cached data on the file systems
catgl | Print colored messages
clear_cached_files | Manipulate cached data on the file systems
cmd-external | External shell commands for 'RAVE'
cmd_afni_home | Find and execute external command-line tools
cmd_dcm2niix | Find and execute external command-line tools
cmd_execute | External shell commands for 'RAVE'
cmd_freesurfer_home | Find and execute external command-line tools
cmd_fsl_home | Find and execute external command-line tools
cmd_homebrew | Find and execute external command-line tools
cmd_run_3dAllineate | External shell commands for 'RAVE'
cmd_run_ants_coreg | Register 'CT' or 'MR' images via "ANTs"
cmd_run_ants_mri_to_template | Register 'CT' or 'MR' images via "ANTs"
cmd_run_dcm2niix | External shell commands for 'RAVE'
cmd_run_flirt | External shell commands for 'RAVE'
cmd_run_niftyreg_coreg | Register 'CT' to 'MR' images via "NiftyReg"
cmd_run_nipy_coreg | Register 'CT' to 'MR' images via "nipy" script
cmd_run_recon_all | External shell commands for 'RAVE'
collapse2 | Collapse high-dimensional tensor array
collapse2.array | Collapse high-dimensional tensor array
collapse2.FileArray | Collapse high-dimensional tensor array
collapse2.Tensor | Collapse high-dimensional tensor array
collapse_power | Collapse power array with given analysis cubes
collapse_power.array | Collapse power array with given analysis cubes
collapse_power.FileArray | Collapse power array with given analysis cubes
configure_knitr | Configure "rmarkdown" files to build 'RAVE' pipelines
convert-fst | Convert 'fst' files to other formats
convert_blackrock | Convert 'BlackRock' 'NEV/NSx' files
convert_fst_to_csv | Convert 'fst' files to other formats
convert_fst_to_hdf5 | Convert 'fst' files to other formats

## -- D --

dir_create2 | Force creating directory with checks

## -- E --

ECoGTensor | 'iEEG/ECoG' Tensor class inherit from 'Tensor'

## -- F --

find_path | Try to find path along the root directory

## -- G --

generate_reference | Generate common average reference signal for 'RAVE' subjects
get_modules_registries | 'RAVE' module registry
get_projects | Get all possible projects in 'RAVE' directory
get_val2 | Get value or return default if invalid

## -- H --

h5_names | Returns all names contained in 'HDF5' file
h5_valid | Check whether a 'HDF5' file can be opened for read/write

## -- I --

import_electrode_table | Import electrode table into subject meta folder
IMPORT_FORMATS | Validate raw files in 'rave' directory
install_modules | Install 'RAVE' modules
is.blank | Check If Input Has Blank String
is.zerolenth | Check If Input Has Zero Length
is_dry_run | Find and execute external command-line tools
is_valid_ish | Check if data is close to "valid"

## -- J --

join_tensors | Join Multiple Tensors into One Tensor

## -- L --

LazyFST | R6 Class to Load 'fst' Files
LazyH5 | Lazy 'HDF5' file loader
LFP_electrode | Definitions of reference with 'LFP' signal type
LFP_reference | Definitions of reference with 'LFP' signal type
load_bids_ieeg_header | Read in description files from 'BIDS-iEEG' format
load_fst | Read a 'fst' file
load_fst_or_h5 | Function try to load 'fst' arrays, if not found, read 'HDF5' arrays
load_h5 | Lazy Load 'HDF5' File via 'hdf5r-package'
load_json | Save or load R object in 'JSON' format
load_meta2 | Load 'RAVE' subject meta data
load_snippet | 'RAVE' code snippets
load_targets | 'RAVE' pipeline functions
load_yaml | A port to 'read_yaml'
LOCATION_TYPES | The constant variables

## -- M --

mgh_to_nii | Convert 'FreeSurfer' "mgh" to 'Nifti'
MNI305_to_MNI152 | The constant variables
module_add | Add new 'RAVE' (2.0) module to current project
module_registry | 'RAVE' module registry
module_registry2 | 'RAVE' module registry

## -- N --

new_electrode | Create new electrode channel instance or a reference signal instance
new_reference | Create new electrode channel instance or a reference signal instance
niftyreg_coreg | Register 'CT' to 'MR' images via "NiftyReg"
normalize_commandline_path | Find and execute external command-line tools

## -- P --

pipeline | Creates 'RAVE' pipeline instance
pipeline-knitr-markdown | Configure "rmarkdown" files to build 'RAVE' pipelines
PipelineResult | Pipeline result object
PipelineTools | Class definition for pipeline tools
pipeline_attach | 'RAVE' pipeline functions
pipeline_build | 'RAVE' pipeline functions
pipeline_clean | 'RAVE' pipeline functions
pipeline_create_subject_pipeline | 'RAVE' pipeline functions
pipeline_create_template | 'RAVE' pipeline functions
pipeline_debug | 'RAVE' pipeline functions
pipeline_description | 'RAVE' pipeline functions
pipeline_eval | 'RAVE' pipeline functions
pipeline_find | 'RAVE' pipeline functions
pipeline_fork | 'RAVE' pipeline functions
pipeline_hasname | 'RAVE' pipeline functions
pipeline_install | Install 'RAVE' pipelines
pipeline_install_github | Install 'RAVE' pipelines
pipeline_install_local | Install 'RAVE' pipelines
pipeline_list | 'RAVE' pipeline functions
pipeline_load_extdata | 'RAVE' pipeline functions
pipeline_progress | 'RAVE' pipeline functions
pipeline_read | 'RAVE' pipeline functions
pipeline_root | 'RAVE' pipeline functions
pipeline_run | 'RAVE' pipeline functions
pipeline_run_bare | 'RAVE' pipeline functions
pipeline_save_extdata | 'RAVE' pipeline functions
pipeline_settings_get | Get or change pipeline input parameter settings
pipeline_settings_get_set | Get or change pipeline input parameter settings
pipeline_settings_set | Get or change pipeline input parameter settings
pipeline_setup_rmd | Configure "rmarkdown" files to build 'RAVE' pipelines
pipeline_target_names | 'RAVE' pipeline functions
pipeline_vartable | 'RAVE' pipeline functions
pipeline_visualize | 'RAVE' pipeline functions
pipeline_watch | 'RAVE' pipeline functions
power_baseline | Calculate power baseline
power_baseline.array | Calculate power baseline
power_baseline.ECoGTensor | Calculate power baseline
power_baseline.FileArray | Calculate power baseline
power_baseline.rave_prepare_power | Calculate power baseline
prepare_subject_bare | Prepare 'RAVE' single-subject data
prepare_subject_bare0 | Prepare 'RAVE' single-subject data
prepare_subject_power | Prepare 'RAVE' single-subject data
prepare_subject_raw_voltage_with_epoch | Prepare 'RAVE' single-subject data
prepare_subject_voltage_with_epoch | Prepare 'RAVE' single-subject data
prepare_subject_with_blocks | Prepare 'RAVE' single-subject data
prepare_subject_with_epoch | Prepare 'RAVE' single-subject data
progress_with_logger | Enhanced progress with logger message
py_nipy_coreg | Register 'CT' to 'MR' images via "nipy" script

## -- R --

rave-pipeline | 'RAVE' pipeline functions
rave-prepare | Prepare 'RAVE' single-subject data
rave-raw-validation | Validate raw files in 'rave' directory
rave-server | Install and configure 'RAVE' server as background service using shiny-server
rave-snippet | 'RAVE' code snippets
RAVEAbstarctElectrode | Abstract definition of electrode class in RAVE
RAVEEpoch | Definition for epoch class
raveio-constants | The constant variables
raveio-option | Set/Get 'raveio' option
raveio_confpath | Set/Get 'raveio' option
raveio_getopt | Set/Get 'raveio' option
raveio_resetopt | Set/Get 'raveio' option
raveio_setopt | Set/Get 'raveio' option
RAVEPreprocessSettings | Defines preprocess configurations
RAVEProject | Definition for 'RAVE' project class
RAVESubject | Defines 'RAVE' subject class
rave_brain | Load 'FreeSurfer' or 'AFNI/SUMA' brain from 'RAVE'
rave_command_line_path | Find and execute external command-line tools
rave_directories | Returns a list of 'RAVE' directories
rave_export | Export 'RAVE' data
rave_export.default | Export 'RAVE' data
rave_export.rave_prepare_power | Export 'RAVE' data
rave_export.rave_prepare_subject_raw_voltage_with_epoch | Export 'RAVE' data
rave_export.rave_prepare_subject_voltage_with_epoch | Export 'RAVE' data
rave_import | Import data into 'rave' projects
rave_server_configure | Install and configure 'RAVE' server as background service using shiny-server
rave_server_install | Install and configure 'RAVE' server as background service using shiny-server
rave_subject_format_conversion | Compatibility support for 'RAVE' 1.0 format
read-brainvision-eeg | Load from 'BrainVision' file
read-write-fst | Read a 'fst' file
read_csv_ieeg | Read comma separated value file and ignore headers
read_edf_header | Read 'EDF(+)' or 'BDF(+)' file headers
read_edf_signal | Read 'EDF(+)' or 'BDF(+)' file signals
read_eeg_data | Load from 'BrainVision' file
read_eeg_header | Load from 'BrainVision' file
read_mat | Read 'Matlab' files
read_mat2 | Read 'Matlab' files
read_nsx_nev | Read 'BlackRock' event and signal files

## -- S --

safe_read_csv | Read comma separated value files with given column classes
safe_write_csv | Save data to comma separated value files with backups
save_fst | Read a 'fst' file
save_h5 | Save objects to 'HDF5' file without trivial checks
save_json | Save or load R object in 'JSON' format
save_meta2 | Function to save meta data to 'RAVE' subject
save_yaml | Write named list to file
SIGNAL_TYPES | The constant variables

## -- T --

Tensor | R6 Class for large Tensor (Array) in Hybrid Mode
test_hdspeed | Simple hard disk speed test
time_diff2 | Calculate time difference in seconds

## -- U --

update_local_snippet | 'RAVE' code snippets
url_neurosynth | Get 'Neurosynth' website address using 'MNI152' coordinates

## -- V --

validate_raw_file | Validate raw files in 'rave' directory
validate_subject | Validate subject data integrity
validate_time_window | Validate time windows to be used
voltage_baseline | Calculate voltage baseline
voltage_baseline.array | Calculate voltage baseline
voltage_baseline.FileArray | Calculate voltage baseline
voltage_baseline.rave_prepare_subject_raw_voltage_with_epoch | Calculate voltage baseline
voltage_baseline.rave_prepare_subject_voltage_with_epoch | Calculate voltage baseline

## -- W --

with_future_parallel | Enable parallel computing provided by 'future' package within the context