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cmddefs.cpp
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// --------------------------------------------------------------------
//
// This file is part of Luna.
//
// LUNA is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Luna is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Luna. If not, see <http://www.gnu.org/licenses/>.
//
// Please see LICENSE.txt for more details.
//
// --------------------------------------------------------------------
#include "luna.h"
#include "db/db.h"
#include <iomanip>
//#pragma GCC push_options
//#pragma GCC optimize ("O0")
#include "cmddefs.h"
extern globals global;
cmddefs_t::cmddefs_t()
{
//init();
}
void cmddefs_t::init()
{
//
// parameters
//
allz = false;
nonez = false;
/////////////////////////////////////////////////////////////////////////
//
// Document domains, commands, parameters, output tables and variables
//
/////////////////////////////////////////////////////////////////////////
//
// base URL
//
url_root = "http://zzz.bwh.harvard.edu/luna/ref/";
//
// Domains
//
add_domain( "summ" , "Summaries" , "Basic summary commands" );
add_domain( "annot" , "Annotations" , "Adding and displaying annotations" );
add_domain( "expr" , "Expressions" , "Evaluating more advanced annotation-based expressions" );
add_domain( "epoch" , "Epochs" , "Epoching signals and epoch-level annotations" );
add_domain( "mask" , "Masks" , "Masking epochs based on annotations and other criteria" );
add_domain( "freeze" , "Freezes & caches" , "EDF freezes and cache mechanisms" );
add_domain( "canon" , "Canonoical signals" , "Canonical signal mapping" );
add_domain( "manip" , "Manipulations" , "Manipulating signal data" );
add_domain( "align" , "Record alignment" , "Signal/annotation alignment" );
add_domain( "output" , "Outputs" , "Commands to output signals in different formats" );
add_domain( "filter" , "FIR filters" , "FIR filter design and application" );
add_domain( "artifact" , "Artifacts" , "Artifacts detection/correction routines" );
add_domain( "hypno" , "Hypnograms" , "Characterizations of hypnograms" );
add_domain( "stage" , "Staging" , "Automated staging/stage evaluation" );
add_domain( "power" , "Time/frequency analysis" , "TF including power spectral density estimation" );
add_domain( "trans" , "NREM transients (spindle/SO)" , "Spindles and slow oscillations" );
add_domain( "cc" , "Coupling/connectvitiy" , "Coherence and other topographical analyses" );
add_domain( "interval" , "Interval-based analysis" , "Analyses and summaries based on time-domain intervals" );
add_domain( "cfc" , "Cross-frequency" , "Phase-amplitude coupling" );
add_domain( "psc" , "Principal spectral components" , "PSC command" );
add_domain( "spatial" , "Topographical analysis" , "EEG channel locations, interpolation and surface Laplacian" );
add_domain( "multi" , "Multi-channel analysis" , "ICA and PCA" );
add_domain( "ms" , "EEG microstate analysis" , "Segmentation, backfitting and sequence analysis" );
add_domain( "cluster" , "Clustering" , "PDC-based epoch/channel clustering " );
add_domain( "assoc" , "Association" , "Association models" );
add_domain( "pred" , "Prediction" , "Prediction models" );
add_domain( "simul" , "Simulation" , "Basic signal simulation" );
add_domain( "helpers" , "Helper utilities" , "Misc. utility functions" );
add_domain( "exp" , "Experimental" , "Experimental features: under heavy development, for internal use only" );
/////////////////////////////////////////////////////////////////////////////////
//
// COMMAND-LINE OPTIONS
//
/////////////////////////////////////////////////////////////////////////////////
//
// -h (help)
//
add_cmd( "helpers" , "-h" , "Help functions" );
//
// --version
//
add_cmd( "helpers" , "--version" , "Show version (or -v)" );
//
// --build
//
add_cmd( "helpers" , "--build" , "Scan folders recursively to geneate a sample list" );
add_param( "--build" , "-nsrr" , "" , "Use NSRR annotation extension, i.e. `-ext=-nsrr.xml`" );
add_param( "--build" , "-edfid" , "" , "Use filename as ID, instead of looking in each EDF header" );
add_param( "--build" , "-nospan" , "" , "Do not match similarly-named files across folders" );
add_param( "--build" , "-ext" , "-ext=txt,eannot,annot" , "Consider these extensions as annotation files" );
//
// --validate
//
add_cmd( "helpers" , "--validate" , "Validate EDFs/annotation files in a sample list" );
add_param( "--validate" , "slist" , "slist=s.lst" , "Specficy the sample list" );
add_table( "--validate" , "" , "Primary VALIDATE output" );
add_var( "--validate" , "" , "EDF" , "Valid/invalid EDF (1=valid)" );
add_var( "--validate" , "" , "ANNOTS" , "Valid/invalid annotations (1=valid)" );
//
// --repath
//
add_cmd( "helpers" , "--repath" , "Swap out file paths in a sample list" );
add_param( "--repath" , "{1st arg}" , "/home/john/" , "First argument: match string" );
add_param( "--repath" , "{2nd arg}" , "/home/mary/" , "Second argument: replacement string" );
//
// --merge
//
add_cmd( "helpers" , "--merge" , "Merge two or more EDFS" );
add_param( "--merge" , "slist" , "slist=s.lst" , "Specficy the sample list" );
add_param( "--merge" , "id" , "id=id001" , "Specficy the ID in the new EDF header" );
add_param( "--merge" , "edf" , "edf=m.edf" , "Filename for the resulting EDF (instead of merged.edf)" );
add_param( "--merge" , "{edfs}" , "f1.edf f2.edf" , "Two or more EDFs" );
//
// --bind
//
add_cmd( "helpers" , "--bind" , "Combine two or more channels to a single EDF" );
add_param( "--bind" , "slist" , "slist=s.lst" , "Specficy the sample list" );
add_param( "--bind" , "id" , "id=id001" , "Specficy the ID in the new EDF header" );
add_param( "--bind" , "edf" , "edf=m.edf" , "Filename for the resulting EDF (instead of merged.edf)" );
//
// --xml
//
add_cmd( "helpers" , "--xml" , "Dump annotations from an XML annotation file (to console)" );
add_param( "--xml" , "{xml}" , "f1.xml" , "A single XML file" );
//
// --xml2
//
add_cmd( "helpers" , "--xml2" , "Dump entire XML tree (to console)" );
add_param( "--xml2" , "{xml}" , "f1.xml" , "A single XML file" );
//
// --otsu
//
add_cmd( "helpers" , "--otsu" , "Calculate thresholds based on Otsu's method (external data)" );
add_param( "--otsu" , "slist" , "slist=s.lst" , "Specficy the sample list" );
//
// --eval
//
add_cmd( "helpers" , "--eval" , "Evaluate expressions from stdin (or --eval-verbose)" );
add_param( "--eval" , "{expr}" , "2+2" , "Evaluate expression (via stdin)" );
//
// --fir
//
add_cmd( "helpers" , "--fir" , "Design FIR (--fir-design)" );
add_param( "--fir" , "fs" , "fs=256" , "Sampling rate" );
add_param( "--fir" , "bandpass", "bandpass=0.3,35", "Band-pass filter between 0.3 and 35 Hz" );
add_param( "--fir" , "lowpass" , "lowpass=35", "Low-pass filter with cutoff of 35 Hz" );
add_param( "--fir" , "highpass" , "highpass=0.3", "High-pass filter with cutoff of 0.3 Hz" );
add_param( "--fir" , "bandstop", "bandstop=55,65", "Band-stop filter between 0.3 and 35 Hz" );
add_param( "--fir" , "ripple", "0.01", "Ripple (proportion); can be two values for bandpass filters)" );
add_param( "--fir" , "tw" , "1" , "Transition width (in Hz)" );
add_param( "--fir" , "file" , "coef.txt" , "Read FIR coefficients from a file" );
add_param( "--fir" , "order" , "10" , "Fix FIR order" );
add_param( "--fir" , "rectangular" , "" , "Specify a rectangular window" );
add_param( "--fir" , "bartlett" , "" , "Specify a Bartlett window" );
add_param( "--fir" , "hann" , "" , "Specify a Hann window" );
add_param( "--fir" , "blackman" , "" , "Specify a Blackman window" );
add_table( "--fir" , "" , "FIR design parameters" );
add_var( "--fir" , "" , "FIR" , "Label for FIR filter (constructed from input parameters)" );
add_var( "--fir" , "" , "FS" , "Sampling rate (from fs input parameter)" );
add_var( "--fir" , "" , "NTAPS" , "Filter order (number of taps)" );
add_table( "--fir" , "F,FIR" , "Frequency response characteristics" );
add_var( "--fir" , "F,FIR" , "F" , "Frequency (Hz)" );
add_var( "--fir" , "F,FIR" , "FIR" , "FIR filter label" );
add_var( "--fir" , "F,FIR" , "MAG" , "Magnitude" );
add_var( "--fir" , "F,FIR" , "MAG_DB" , "Magnitude (dB)" );
add_var( "--fir" , "F,FIR" , "PHASE" , "Phase" );
add_table( "--fir" , "FIR,SEC" , "Impulse response" );
add_var( "--fir" , "FIR,SEC" , "SEC" , "Time (seconds)" );
add_var( "--fir" , "FIR,SEC" , "FIR" , "FIR filter label" );
add_var( "--fir" , "FIR,SEC" , "IR" , "Impulse response" );
//
// --cwt
//
add_cmd( "helpers" , "--cwt" , "Or --cwt-design" );
/////////////////////////////////////////////////////////////////////////////////
//
// SUMMARIES
//
/////////////////////////////////////////////////////////////////////////////////
// DESC Simple description of an EDF, sent to the console
// SUMMARY More verbose description, sent to the console
// HEADERS Tabulate (channel-specific) EDF header information
// CONTAINS Indicate whether certain signals/stages/annotations are present
// ALIASES Display aliases assigned for channels and annotations
// TYPES Display current channel types
// VARS Display current individual-level variables
// TAG Generic command to add a tag (level/factor) to the output
// STATS Basic signal statistics (min/max, mean, RMS, etc)
// SIGSTATS Hjorth parameters and other signal statistics
// TABULATE Tabulate discrete values in a signal
// DUPES Finds flat signals and digital duplicates
//
// DESC
//
add_cmd1( "summ" , "DESC" , "Simple description of an EDF, sent to the console" );
add_param1( "DESC" , "channels" , "" , "Only write channel names, one-per-line" );
//
// SUMMARY
//
add_cmd1( "summ" , "SUMMARY" , "More verbose description, sent to the console" );
//
// HEADERS
//
add_cmd1( "summ" , "HEADERS" , "Tabulate (channel-specific) EDF header information" );
add_table1( "HEADERS" , "" , "Basic EDF header information" );
add_var1( "HEADERS" , "" , "NR" , "Number of records" );
add_var1( "HEADERS" , "" , "NS" , "Number of signals/channels" );
add_var( "HEADERS" , "" , "EDF_ID" , "ID in the EDF header" );
add_var1( "HEADERS" , "" , "START_TIME" , "Start time in the EDF header" );
add_var1( "HEADERS" , "" , "STOP_TIME" , "Stop time" );
add_var1( "HEADERS" , "" , "START_DATE" , "Start date in the EDF header" );
add_var( "HEADERS" , "" , "REC_DUR" , "Duration of each record (seconds)" );
add_var( "HEADERS" , "" , "TOT_DUR_SEC" , "Current EDF duration (seconds)" );
add_var1( "HEADERS" , "" , "TOT_DUR_HMS" , "Current EDF duration (hh:mm:ss)" );
add_var1( "HEADERS" , "" , "EDF_TYPE" , "EDF, EDF+C or EDF+D" );
add_var( "HEADERS" , "" , "NS_ALL" , "Number of signals in original EDF" );
add_var( "HEADERS" , "" , "REC_DUR_HMS" , "Original recording duration (hh:mm:ss)" );
add_var( "HEADERS" , "" , "REC_DUR_SEC" , "Original recording duration (seconds)" );
add_table1( "HEADERS" , "CH" , "Per-channel header information" );
add_var( "HEADERS" , "CH" , "DMAX" , "Digital max" );
add_var( "HEADERS" , "CH" , "DMIN" , "Digital min" );
add_var1( "HEADERS" , "CH" , "PDIM", "Physical dimension" );
add_var1( "HEADERS" , "CH" , "PMAX", "Physical min" );
add_var1( "HEADERS" , "CH" , "PMIN", "Physical max" );
add_var1( "HEADERS" , "CH" , "SR", "Sample rate (Hz)" );
add_var( "HEADERS" , "CH" , "SENS", "Sensitivity (unit/bit)" );
add_var( "HEADERS" , "CH" , "TRANS", "Transducer type" );
add_var( "HEADERS" , "CH" , "POS", "Position in EDF" );
add_var( "HEADERS" , "CH" , "TYPE", "Channel type (from Luna TYPES)" );
//
// CONTAINS
//
add_cmd( "manip" , "CONTAINS" , "Tests for particular signals/annotations/staging being present" );
add_url( "CONTAINS" , "manipulatons/#contains" );
add_param( "CONTAINS" , "sig" , "EMG,ECG" , "Test for these signals" );
add_param( "CONTAINS" , "annots" , "apnea,hypopnea" , "Test for these annotations" );
add_param( "CONTAINS" , "stages" , "" , "Test for valid staging" );
add_param( "CONTAINS" , "skip" , "" , "Skip to next EDF on failure" );
add_table( "CONTAINS" , "" , "Base" );
add_var( "CONTAINS" , "" , "STAGE_COUNTS" , "Sleep stage counts" );
add_var( "CONTAINS" , "" , "UNIQ_STAGES" , "Number of unique stage labels" );
add_var( "CONTAINS" , "" , "NA_REQ" , "Number of required annots" );
add_var( "CONTAINS" , "" , "NA_OBS" , "Number of observed annots" );
add_var( "CONTAINS" , "" , "NS_OBS" , "Number of required channels" );
add_var( "CONTAINS" , "" , "NS_REQ" , "Number of observed channels" );
add_var( "CONTAINS" , "" , "NS_TOT" , "Tot number of channels" );
add_table( "CONTAINS" , "ANNOT" , "Annotation informationm" );
add_var( "CONTAINS" , "CH" , "PRESENT" , "Annotation resent" );
add_table( "CONTAINS" , "CH" , "Channel informationm" );
add_var( "CONTAINS" , "CH" , "PRESENT" , "Channel present" );
//
// ALIASES
//
add_cmd( "summ" , "ALIASES" , "Tabulate channel and annotation alias replacements" );
add_table( "ALIASES" , "CH" , "Channel aliasing" );
add_var( "ALIASES" , "CH" , "ORIG" , "Original channel label in EDF" );
add_table( "ALIASES" , "ANNOT" , "Annotation aliasing" );
add_var( "ALIASES" , "ANNOT" , "ORIG" , "Original annotation label" );
//
// TYPES
//
//
// VARS
//
//
// TAG
//
add_cmd( "summ" , "TAG" , "Generic command to add a tag (level/factor) to the output" );
add_param( "TAG" , "" , "RUN/L1" , "Add tag with level L1 to factor RUN in output" );
add_param( "TAG" , "tag" , "RUN/L1" , "Identical to the above, but explicitly using the tag option" );
//
// STATS
//
add_cmd( "summ" , "STATS" , "Basic signal statistics (min/max, mean, RMS, etc)" );
add_param( "STATS" , "sig" , "C3,C4" , "Restrict analysis to these channels" );
add_param( "STATS" , "epoch" , "" , "Calculate per-epoch statistics" );
add_table( "STATS" , "CH" , "Whole-night, per-channel statistics, based on all epochs" );
add_var( "STATS" , "CH" , "MIN" , "Signal minimum (from data, not EDF header)" );
add_var( "STATS" , "CH" , "MAX" , "Signal maximum (from data, not EDF header)" );
add_var( "STATS" , "CH" , "MEAN" , "Signal mean" );
add_var( "STATS" , "CH" , "MEDIAN" , "Signal median" );
add_var( "STATS" , "CH" , "RMS" , "Signal root mean square" );
add_var( "STATS" , "CH" , "P01" , "1st percentile" );
add_var( "STATS" , "CH" , "P02" , "2nd percentile" );
add_var( "STATS" , "CH" , "P05" , "5th percentile" );
add_var( "STATS" , "CH" , "P10" , "10th percentile" );
add_var( "STATS" , "CH" , "P20" , "20th percentile" );
add_var( "STATS" , "CH" , "P30" , "30th percentile" );
add_var( "STATS" , "CH" , "P40" , "40th percentile" );
add_var( "STATS" , "CH" , "P50" , "50th percentile" );
add_var( "STATS" , "CH" , "P60" , "60th percentile" );
add_var( "STATS" , "CH" , "P70" , "70th percentile" );
add_var( "STATS" , "CH" , "P80" , "80th percentile" );
add_var( "STATS" , "CH" , "P90" , "90th percentile" );
add_var( "STATS" , "CH" , "P95" , "95th percentile" );
add_var( "STATS" , "CH" , "P98" , "98th percentile" );
add_var( "STATS" , "CH" , "P99" , "99th percentile" );
add_var( "STATS" , "CH" , "MAX_ENCODING" , "Possible # of unique values" );
add_var( "STATS" , "CH" , "OBS_ENCODING" , "Observed # of unique values" );
add_var( "STATS" , "CH" , "PCT_ENCODING" , "Obs/possible unique values" );
add_table( "STATS" , "CH,VAL" , "Encoding value distribution [encoding]" );
add_var( "STATS" , "CH,VAL" , "CNT" , "Number of observations" );
add_var( "STATS" , "CH" , "NE" , "Total number of epochs in record [epoch]" );
add_var( "STATS" , "CH" , "NE1" , "Number of unmasked epochs actually used in calculations [epoch]" );
add_var( "STATS" , "CH" , "MEDIAN_MEAN" , "Median of all per-epoch means [epoch]" );
add_var( "STATS" , "CH" , "MEDIAN_MEDIAN" , "Median of all per-epoch medians [epoch]" );
add_var( "STATS" , "CH" , "MEDIAN_RMS" , "Median of all per-epoch RMS [epoch]" );
add_table( "STATS" , "CH,E" , "Per-epoch, per-channel statistics for unmasked epochs only" );
add_var( "STATS" , "CH,E" , "MIN" , "Signal minimum (from data, not EDF header)" );
add_var( "STATS" , "CH,E" , "MAX" , "Signal maximum (from data, not EDF header)" );
add_var( "STATS" , "CH,E" , "MEAN" , "Signal mean" );
add_var( "STATS" , "CH,E" , "MEDIAN" , "Signal median" );
add_var( "STATS" , "CH,E" , "RMS" , "Signal root mean square" );
add_var( "STATS" , "CH,E" , "P01" , "1st percentile" );
add_var( "STATS" , "CH,E" , "P02" , "2nd percentile" );
add_var( "STATS" , "CH,E" , "P05" , "5th percentile" );
add_var( "STATS" , "CH,E" , "P10" , "10th percentile" );
add_var( "STATS" , "CH,E" , "P20" , "20th percentile" );
add_var( "STATS" , "CH,E" , "P30" , "30th percentile" );
add_var( "STATS" , "CH,E" , "P40" , "40th percentile" );
add_var( "STATS" , "CH,E" , "P50" , "50th percentile" );
add_var( "STATS" , "CH,E" , "P60" , "60th percentile" );
add_var( "STATS" , "CH,E" , "P70" , "70th percentile" );
add_var( "STATS" , "CH,E" , "P80" , "80th percentile" );
add_var( "STATS" , "CH,E" , "P90" , "90th percentile" );
add_var( "STATS" , "CH,E" , "P95" , "95th percentile" );
add_var( "STATS" , "CH,E" , "P98" , "98th percentile" );
add_var( "STATS" , "CH,E" , "P99" , "99th percentile" );
//
// SIGSTATS
//
// SIGSTATS
add_cmd( "artifact" , "SIGSTATS" , "Per-epoch outlier detection (RMS, Hjorth parameters, clipped signals)" );
add_url( "SIGSTATS" , "artifacts/#sigstats" );
add_param( "SIGSTATS" , "sig" , "C3,C4" , "Restrict analysis to these channels" );
add_param( "SIGSTATS" , "verbose" , "" , "Report epoch-level statistics" );
add_param( "SIGSTATS" , "epoch" , "" , "Report epoch-level statistics (same as verbose)" );
add_param( "SIGSTATS" , "chep" , "" , "Set CHEP mask for outlier epochs" );
add_param( "SIGSTATS" , "astats" , "3,3" , "Between-epoch, betwee-channel filtering" );
add_param( "SIGSTATS" , "cstats" , "2" , "Within-epoch, between-channel filtering" );
add_param( "SIGSTATS" , "rms" , "" , "Calculate/mask on RMS" );
add_param( "SIGSTATS" , "clipped" , "0.05" , "Calculate/mask on signal clipping" );
add_param( "SIGSTATS" , "flat" , "0.05" , "Calculate/mask on signal clipping" );
add_param( "SIGSTATS" , "max" , "0.05" , "Calculate/mask on signal clipping" );
add_param( "SIGSTATS" , "threshold" , "2,2" , "Set eppoch masks based on SD unit (iterative) outlier detection" );
add_param( "SIGSTATS" , "th" , "2,2" , "Same as 'threshold'" );
add_param( "SIGSTATS" , "cstats" , "2" , "Run channel-comparisons, with threshold in SD units" );
add_param( "SIGSTATS" , "cstats-unmasked-only" , "" , "Channel-comparisons only for unmasked epochs" );
add_table( "SIGSTATS" , "CH" , "Per-channel whole-signal statistics" );
add_var( "SIGSTATS" , "CH" , "CLIP" , "Proportion of clipped sample points" );
add_var( "SIGSTATS" , "CH" , "FLAT" , "Proportion of flat sample points" );
add_var( "SIGSTATS" , "CH" , "MAX" , "Proportion of max sample points" );
add_var( "SIGSTATS" , "CH" , "H1" , "First Hjorth parameter (activity)" );
add_var( "SIGSTATS" , "CH" , "H2" , "Second Hjorth parameter (mobility)" );
add_var( "SIGSTATS" , "CH" , "H3" , "Third Hjorth parameter (complexity)" );
add_var( "SIGSTATS" , "CH" , "RMS" , "Signal root mean square" );
add_var( "SIGSTATS" , "CH" , "P_H1" , "Proportion flagged epochs for H1 [cstats]" );
add_var( "SIGSTATS" , "CH" , "P_H2" , "Proportion flagged epochs for H2 [cstats]" );
add_var( "SIGSTATS" , "CH" , "P_H3" , "Proportion flagged epochs for H3 [cstats]" );
add_var( "SIGSTATS" , "CH" , "P_OUT" , "Proportion flagged epochs for H1, H2 or H3 [cstats]" );
add_var( "SIGSTATS" , "CH" , "Z_H1" , "Z score for H1 [cstats]" );
add_var( "SIGSTATS" , "CH" , "Z_H2" , "Z score for H2 [cstats]" );
add_var( "SIGSTATS" , "CH" , "Z_H3" , "Z score for H3 [cstats]" );
add_var( "SIGSTATS" , "CH" , "CNT_ACT" , "Number of epochs flagged based on H1 [mask]" );
add_var( "SIGSTATS" , "CH" , "CNT_MOB" , "Number of epochs flagged based on H2 [mask]" );
add_var( "SIGSTATS" , "CH" , "CNT_CMP" , "Number of epochs flagged based on H3 [mask]" );
add_var( "SIGSTATS" , "CH" , "CNT_CLP" , "Number of epochs flagged based on clipping metric" );
add_var( "SIGSTATS" , "CH" , "CNT_RMS" , "Number of epochs flagged based on RMS" );
add_var( "SIGSTATS" , "CH" , "FLAGGED_EPOCHS" , "Number of epochs flagged as outliers [mask]" );
add_var( "SIGSTATS" , "CH" , "ALTERED_EPOCHS" , "Number of epochs whose mask was altered [mask]" );
add_var( "SIGSTATS" , "CH" , "TOTAL_EPOCHS" , "Total number of masked epochs [mask]" );
add_table( "SIGSTATS" , "CH,E" , "Per-channel per-epoch statistics [epoch]" );
add_var( "SIGSTATS" , "CH,E" , "H1" , "First Hjorth parameter (activity)" );
add_var( "SIGSTATS" , "CH,E" , "H2" , "Second Hjorth parameter (mobility)" );
add_var( "SIGSTATS" , "CH,E" , "H3" , "Third Hjorth parameter (complexity)" );
hidden_var( "SIGSTATS" , "CH,E" , "CLIP" , "Proportion of clipped sample points" );
hidden_var( "SIGSTATS" , "CH,E" , "FLAT" , "Proportion of flat sample points" );
hidden_var( "SIGSTATS" , "CH,E" , "MAX" , "Proportion of max sample points" );
hidden_var( "SIGSTATS" , "CH,E" , "RMS" , "Signal root mean square" );
//
// TABULATE
//
//
// DUPES
//
/////////////////////////////////////////////////////////////////////////////////
//
// ANNOTATIONS
//
/////////////////////////////////////////////////////////////////////////////////
// --xml, --xml2 View NSRR XML annotation files
// REMAP Apply annotation remappings after loading
// ANNOTS Tabulate all annotations
// MAKE-ANNOTS Make new annotations
// WRITE-ANNOTS Write annotations as .annot or .xml
// META Add meta-data to annotations
// SPANNING Report on coverage of annotations
// ESPAN Epoch-based annotation coverage
// A2S Add a 0/1 signal based on an annotation
// S2A Add an annotation based on ranged values of a signal
// AXA
//
// ANNOTS
//
add_cmd( "annot" , "ANNOTS" , "Tabulate all annotations" );
add_url( "ANNOTS" , "annotations/#annots" );
// add_note( "ANNOTS" , "Any formatted free text goes here,\n shown at end of verbose help link\n");
add_param( "ANNOTS" , "epoch" , "" , "Show epoch-level summaries" );
add_param( "ANNOTS" , "show-masked" , "" , "Show masked annotations (default is not to do so)" );
add_param( "ANNOTS" , "any" , "" , "Keep annotations that have any overlap with one or more unmasked epochs (default)" );
add_param( "ANNOTS" , "all" , "" , "Only keep annotations that are completely within unmasked epochs" );
add_param( "ANNOTS" , "start" , "" , "Keep annotations that start in an unmasked epoch" );
add_table( "ANNOTS" , "ANNOT" , "Class-level annotation summary" );
add_var( "ANNOTS" , "ANNOT" , "COUNT" , "Number of instances of that annotation class" );
add_var( "ANNOTS" , "ANNOT" , "DUR" , "Combined duration (seconds) of all instances of that annotation class" );
add_table( "ANNOTS" , "ANNOT,INST" , "Instance-level annotation summary" );
add_var( "ANNOTS" , "ANNOT,INST" , "COUNT" , "Number of instances of that annotation class and instance ID" );
add_var( "ANNOTS" , "ANNOT,INST" , "DUR" , "Combined duration (seconds) of all instances of that annotation class and instance ID" );
add_table( "ANNOTS" , "ANNOT,INST,T" , "Instance-level annotation tabulation" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "START" , "Start time (secs) of this instance" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "STOP" , "Stop time (secs) of this instance" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "DUR" , "Annotation duration (secs)" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "VAL" , "The meta-data for this instance, if any exists (otherwise missing NA)" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "ALL_MASKED" , "? [show-masked]" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "ALL_UNMASKED" , "? [show-masked]" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "SOME_MASKED" , "? [show-masked]" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "SOME_UNMASKED" , "? [show-masked]" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "START_MASKED" , "? [show-masked]" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "CH" , "Any associated channel(s)" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "START_ELAPSED_HMS" , "Annotation start (elapsed hh:mm:ss)" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "START_HMS" , "Annotation start" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "STOP_ELAPSED_HMS" , "Annotation stop (elapsed hh:mm:ss)" );
add_var( "ANNOTS" , "ANNOT,INST,T" , "STOP_HMS" , "Annotation stop" );
add_table( "ANNOTS" , "E,INTERVAL,INST" , "Per-epoch instance-level annotation tabulation" );
add_var( "ANNOTS" , "E,INTERVAL,INST" , "AMASK" , "Annotation instance mask status (1=masked/excluded) [epoch]" );
add_var( "ANNOTS" , "E,INTERVAL,INST" , "EMASK" , "Epoch mask status (1=masked/excluded) [epoch]" );
//
// AXA
//
add_cmd( "annot" , "AXA" , "Pairwise annotation cross-tabs" );
add_url( "AXA" , "annotations/#axa" );
add_param( "AXA" , "annot" , "N2,N3,arousal,apnea" , "Annotations to query" );
add_param( "AXA" , "by-instance" , "" , "Define distinct annotations using class/instance ID" );
add_table( "AXA" , "SEED,ANNOT" , "AXA pairwise metrics" );
add_var( "AXA" , "SEED,ANNOT" , "P" , "Mean proportion of each seed spanned by annotation" );
//add_var( "AXA" , "SEED,ANNOT" , "P_MD" , "Median proportion of each seed spanned by annotation" );
add_var( "AXA" , "SEED,ANNOT" , "T" , "Mean time (secs) spanned by annotation per seed event" );
//add_var( "AXA" , "SEED,ANNOT" , "T_MD" , "Median time (secs) spanned by annotation per seed event" );
add_var( "AXA" , "SEED,ANNOT" , "N" , "Mean number of spanning annotations per seed event" );
//add_var( "AXA" , "SEED,ANNOT" , "N_MD" , "Median number of spanning annotations per seed event" );
add_var( "AXA" , "SEED,ANNOT" , "A" , "Proportion of seeds with any spanning annotation" );
add_var( "AXA" , "SEED,ANNOT" , "D" , "Time (distance) to nearest" );
add_var( "AXA" , "SEED,ANNOT" , "D_N" , "Number of seeds with a nearest event" );
add_var( "AXA" , "SEED,ANNOT" , "TOT_N" , "Total number of (flattened) annotations spanning all seeds" );
add_var( "AXA" , "SEED,ANNOT" , "TOT_T" , "Total duration (secs) of (flattened) annotations spanning all seeds" );
add_table( "AXA" , "CH,SEED,ANNOT" , "AXA pairwise metrics, within-channel" );
add_var( "AXA" , "CH,SEED,ANNOT" , "P" , "Mean proportion of each seed spanned by annotation" );
//add_var( "AXA" , "CH,SEED,ANNOT" , "P_MD" , "Median proportion of each seed spanned by annotation" );
add_var( "AXA" , "CH,SEED,ANNOT" , "T" , "Mean time (secs) spanned by annotation per seed event" );
//add_var( "AXA" , "CH,SEED,ANNOT" , "T_MD" , "Median time (secs) spanned by annotation per seed event" );
add_var( "AXA" , "CH,SEED,ANNOT" , "N" , "Mean number of spanning annotations per seed event" );
//add_var( "AXA" , "CH,SEED,ANNOT" , "N_MD" , "Median number of spanning annotations per seed event" );
add_var( "AXA" , "CH,SEED,ANNOT" , "A" , "Proportion of seeds with any spanning annotation" );
add_var( "AXA" , "CH,SEED,ANNOT" , "D" , "Time (distance) to nearest" );
add_var( "AXA" , "CH,SEED,ANNOT" , "D_N" , "Number of seeds with a nearest event" );
add_var( "AXA" , "CH,SEED,ANNOT" , "TOT_N" , "Total number of (flattened) annotations spanning all seeds" );
add_var( "AXA" , "CH,SEED,ANNOT" , "TOT_T" , "Total duration (secs) of (flattened) annotations spanning all seeds" );
//
// SPANNING
//
add_cmd( "annot" , "SPANNING" , "Report duration spanned or not by group of annotations" );
add_url( "SPANNING" , "annotations/#spanning" );
add_param( "SPANNING" , "annot" , "N1,N2,N3,R,W" , "Spanning annotation group" );
add_table( "SPANNING" , "N" , "Invalid annotations" );
add_var( "SPANNING" , "N" , "ANNOT" , "Annotation class" );
add_var( "SPANNING" , "N" , "INST" , "Annotation instance" );
add_var( "SPANNING" , "N" , "START" , "Start (seconds)" );
add_var( "SPANNING" , "N" , "STOP" , "Stop (seconds)" );
add_table( "SPANNING" , "" , "Spanning summary report" );
add_var( "SPANNING" , "" , "REC_SEC" , "EDF recording duration (seconds)" );
add_var( "SPANNING" , "" , "REC_HMS" , "EDF recording duration (hh:mm:ss)" );
add_var( "SPANNING" , "" , "ANNOT_N" , "Number of annotations in group" );
add_var( "SPANNING" , "" , "ANNOT_SEC" , "Total (potentially overlapping) annotation duration (secs)" );
add_var( "SPANNING" , "" , "ANNOT_HMS" , "Total (potentially overlapping) annotation duration (hh:mm:ss)" );
add_var( "SPANNING" , "" , "ANNOT_OVERLAP" , "Do any annotations in group overlap w/ one another (0/1)?" );
add_var( "SPANNING" , "" , "INVALID_N" , "Number of annotations that over-extend EDF duration" );
add_var( "SPANNING" , "" , "VALID_N" , "Number of valid annotations, ANNOT_N - INVALID_N" );
add_var( "SPANNING" , "" , "INVALID_SEC" , "Total duration of all annotation beyond EDF end" );
add_var( "SPANNING" , "" , "SPANNED_PCT" , "% of EDF spanned by 1+ of these annotations" );
add_var( "SPANNING" , "" , "SPANNED_SEC" , "Duration of EDF spanned by 1+ of these annotations (secs)" );
add_var( "SPANNING" , "" , "SPANNED_HMS" , "Duration of EDF spanned by 1+ of these annotations (hh:mm:ss)" );
add_var( "SPANNING" , "" , "UNSPANNED_PCT" , "% of EDF unspanned by 1+ of these annotations" );
add_var( "SPANNING" , "" , "UNSPANNED_SEC" , "Duration of EDF unspanned by 1+ of these annotations (secs)" );
add_var( "SPANNING" , "" , "UNSPANNED_HMS" , "Duration of EDF unspanned by 1+ of these annotations (hh:mm:ss)" );
//
// REMAP
//
//
// MAKE-ANNOTS
//
//
// WRITE-ANNOTS
//
add_cmd( "output" , "WRITE-ANNOTS" , "Write all annotations to file" );
add_url( "WRITE-ANNOTS" , "outputs/#write-annots" );
add_param( "WRITE-ANNOTS" , "file" , "f1.xml" , "Required filename for output" );
add_param( "WRITE-ANNOTS" , "luna" , "" , "Output in Luna .annot format instead of XML" );
//
// META
//
//
// ESPAN
//
//
// A2S
//
//
// S2A
//
// ALIGN-ANNOTS
/////////////////////////////////////////////////////////////////////////////////
//
// EXPRESSIONS
//
/////////////////////////////////////////////////////////////////////////////////
// EVAL Evaluate annotation-based general expressions
// TRANS Arbitrary transformations of signal data
// DERIVE Derive summary statistics based on annotation meta-data
/////////////////////////////////////////////////////////////////////////////////
//
// EPOCHS
//
/////////////////////////////////////////////////////////////////////////////////
// EPOCH Specify epochs
// EPOCH-ANNOT Load epoch-wise annotations from a .eannot-format file
/////////////////////////////////////////////////////////////////////////////////
//
// MASKS
//
/////////////////////////////////////////////////////////////////////////////////
// MASK Mask epochs based on annotations and other features (standard mask)
// DUMP-MASK Output epoch-level mask information (standard mask)
// RESTRUCTURE, RE Remove masked out epochs (and channels) based on the standard mask
// CHEP Process CHannel/EPoch CHEP masks and modify the standard mask based on them
/////////////////////////////////////////////////////////////////////////////////
//
// FREEZES/CACHES
//
/////////////////////////////////////////////////////////////////////////////////
// FREEZE Make a named freeze of the current datatset
// THAW Revert to a previous data freeze
// CLEAN-FREEZER Empty the freezer
// CACHE Cache operations
/////////////////////////////////////////////////////////////////////////////////
//
// CANONICAL SIGNALS
//
/////////////////////////////////////////////////////////////////////////////////
// CANONICAL Generate canonical signals
/////////////////////////////////////////////////////////////////////////////////
//
// MANIPULATIONS
//
/////////////////////////////////////////////////////////////////////////////////
// SIGNALS Retain/remove specific EDF channels
// RENAME Rename channels
// COPY Duplicate one or more EDF channels
// RESAMPLE Resample signal(s)
// ENFORCE-SR Require a particular sample rate
// REFERENCE Re-reference signals
// DEREFERENCE De-reference signals
// MINMAX Set digital/physical min/max across channels
// uV Rescale units to uV
// mV Rescale units to mV
// FLIP Flip polarity of signal
// ZC Mean-center signal
// ROBUST-NORM Robust normalisation
// COMBINE Combine two or more channels into a new channel (e.g. sum/mean)
// SCALE Rescale a channel (min/max scaling)
// SHIFT Shift a signal
// SCRAMBLE Scramble a signal
// TIME-TRACK Add a time-track to an EDF
// RECORD-SIZE Change EDF record size
// EDF-MINUS Realign EDF records, annotations and epochs
// ANON Strip ID information from EDF header
// SET-HEADERS Directly specify certain EDF headers
// SET-VAR Directly specify Luna variables
// SET-TIMESTAMPS Directly specify EDF record time-stamps
// RECTIFY Rectify a signal
// REVERSE Reverse a signal
// MOVING-AVERAGE Moving average (or median) of a signal
/////////////////////////////////////////////////////////////////////////////////
//
// ALIGNMENT
//
/////////////////////////////////////////////////////////////////////////////////
// EDF-MINUS
// ALIGN-EPOCHS Align epochs between files
// ALIGN-ANNOTS Realign annotations given an ALIGN-EPOCHS solution
// INSERT Insert new channels, allowing for varying sample rates
//
// EDF-MINUS
//
//
// ALIGN-EPOCHS
//
//
// ALIGN-ANNOTS
//
//
// INSERT
//
/////////////////////////////////////////////////////////////////////////////////
//
// OUTPUTS
//
/////////////////////////////////////////////////////////////////////////////////
// WRITE Write a new EDF file
// MATRIX Dump signals (and annotations) to a file
// HEAD Show a small interval of signal data
// DUMP-RECORDS Dump annotations and signals, by EDF record
// RECS Dump basic information on EDF record structure
// SEGMENTS Dump (discontinuous EDF+) intervals
// SEDF Generate a "summary EDF"
/////////////////////////////////////////////////////////////////////////////////
//
// FILTERS
//
/////////////////////////////////////////////////////////////////////////////////
// FILTER Apply a FIR filter to one or more signals
// FILTER-DESIGN Display filter properties
/////////////////////////////////////////////////////////////////////////////////
//
// ARTIFACTS
//
/////////////////////////////////////////////////////////////////////////////////
// CHEP-MASK CHannel/EPoch (CHEP) outlier detection
// ARTIFACTS Per-epoch Buckelmueller et al. (2006) artifact detection
// LINE-DENOISE Line denoising via spectrum interpolation
// SUPPRESS-ECG Correct cardiac artifact based on ECG
// ALTER Reference-channel regression-based artifact correction
// EDGER Utility to flag likely artifactual leading/trailing intervals
/////////////////////////////////////////////////////////////////////////////////
//
// HYPNOGRAMS
//
/////////////////////////////////////////////////////////////////////////////////
// HYPNO Sleep macro-architecture summaries
// STAGE Output sleep stages per epoch
// DYNAM Summarize epoch-level outputs by NREM cycles
/////////////////////////////////////////////////////////////////////////////////
//
// STAGING TOOLS (SOAP/POPS)
//
/////////////////////////////////////////////////////////////////////////////////
// RUN-POPS A high-level convenience wrapper around POPS
// POPS Apply automated sleep stage prediction
// EVAL-STAGES Apply POPS evaluation metrics to external predictions
// --eval-stages Similar to above, but without an attached EDF
// POPS train training mode Create level 1 feature matrices for training
// --pops training mode Combine trainers for level 2 features and train POPS models
/////////////////////////////////////////////////////////////////////////////////
//
// T/F ANALYSIS
//
/////////////////////////////////////////////////////////////////////////////////
// PSD Welch's method for power spectral density estimation
// MTM Multi-taper method for power spectral density estimation
// FFT Basic discrete Fourier transform of a signal
// IRASA Irregular-resampling auto-spectral analysis
// HILBERT Hilbert transform
// CWT Continuous wavelet transform
// CWT-DESIGN Complex Morlet wavelet properties
// PCOUPL Generic phase coupling
// EMD Empirical mode decomposition
// MSE Multi-scale entropy statistics
// LZW LZW compression (information content) index
// 1FNORM Remove the 1/f trend from a signal
// TV Total variation denoiser
// ACF Autocorrelation function
/////////////////////////////////////////////////////////////////////////////////
//
// NREM TRANSIENTS
//
/////////////////////////////////////////////////////////////////////////////////
// SPINDLES Wavelet-based spindle detection
// SO Slow oscillation detection
/////////////////////////////////////////////////////////////////////////////////
//
// COUPLING/CONNECTIVITY
//
/////////////////////////////////////////////////////////////////////////////////
// COH Pairwise channel coherence
// CORREL Pairwise channel correlation
// CC Coupling (dPAC) and connectivity (wPLI)
// PSI Phase slope index (PSI) connectivity metric
// XCORR Cross-correlation
// MI Mutual information
// TSYNC Cross-correlation and phase delay (alternate implementation)
// GP Granger prediction
/////////////////////////////////////////////////////////////////////////////////
//
// INTERVALS
//
/////////////////////////////////////////////////////////////////////////////////
// OVERLAP Annotation overlap/enrichment (single-sample)
// --overlap Annotation overlap/enrichment (multi-sample)
// MEANS Signal means by annotation
// PEAKS Detect and cache signal peaks
// Z-PEAKS Detect and cache signal peaks, alternative method
// TLOCK Time-locked (e.g. peak-locked) signal averaging
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//
// PSC
//
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// --psc Estimate PSCs from samples of spectral/connectivity metrics
// PSC Project new samples into an existing PSC space
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//
// SPATIAL
//
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// CLOCS Specify EEG channel locations
// SL Surface Laplacian spatial filtering
// INTERPOLATE Epoch-wise interpolation of bad channels
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//
// MULTI-CHANNEL
//
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// ICA Fit ICA model to signal data
// ADJUST Adjust original signals given one or more ICs
// SVD Apply time-series PCA to multiple channels
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//
// MICROSTATS
//
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// MS EEG microstate analysis
// --kmer (Group-level) permutation-based analysis of state sequences
// --cmp-maps Group/individual map spatial analysis
// --label-maps Label maps given a template
// --correl-maps Spatial correlations between maps
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//
// CLUSTERING
//
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// EXE Epoch-by-epoch or channel-by-channel time-series clustering
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//
// ASSOCIATION
//
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// GPA General permutation-based association analysis for one or more sets of metrics
// CPT Cluster-based permutation to one or more sets of metrics