BAP Command Line - UVA-CAMA/NICUHDF5Viewer GitHub Wiki

I created a command line version of the Batch Algorithm Processor. It, admittedly, doesn't have great name. It is called Run All Tagging Algorithms cmd. This is only for advanced users. It is a command line version of run_all_tagging_algs.m that requires you to install the core script running the BAP with Matlab runtime. I don't anticipate many people will use this, so documentation is minimal.

• v2.2 Release Notes

• v2.0 Release Notes

• v1.1 Release Notes

• To make new versions of this

v2.2 Release Notes

Download RATA Cmd v2.2 Executable

This is equivalent to BAP 2.2

You will need to run the executable to install the code and matlab runtime. Then, you will be able to go to the command line and type in the following:

Command Line Input:

C:\Program Files\University of Virginia\run_all_tagging_algs\application>run_all_tagging_algs "path_to_file_to_convert" "[]" "[binary array of algorithms to run for the 67 algorithms listed below]"

Example Command Line Input:

C:\Program Files\University of Virginia\run_all_tagging_algs\application>run_all_tagging_algs "V:\Amanda\TestInputFiles\ConvertedUsing1_1_6\NU\20190413000000_PreVent_Prentice_2053_MC3_20190413.hdf5" "[]" "[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1]"

The results files will be saved in the same directory as the input file.

These are the algorithms (and their version numbers) which are available:

QRS Detection: ECG I v2
QRS Detection: ECG II v2
QRS Detection: ECG III v2
Brady Detection <100 v4
Brady Detection <90 v4
Brady Detection <80 v4
Brady Detection <70 v4
Apnea Detection v3
Periodic Breathing v3
Brady Detection Pete v4
Desat Detection Pete v4
Brady Desat v4
Brady Desat Pete v4
ABD v3
Data Available: Pulse v4
Data Available: HR v4
Data Available: SPO2_pct v4
Data Available: Resp v3
Data Available: ECG I v3
Data Available: ECG II v3
Data Available: ECG III v3
Desat Detection <75 v4
Desat Detection <80 v4
Desat Detection <85 v4
Desat Detection <90 v4
Desat Detection <95 v4
Hyperoxemia Detection >95 v1
Hyperoxemia Detection >98 v1
Flat Detection Resp >10s v1
HR Mean v3
Pulse Mean v3
SPO2_pct Mean v3
HR Std v3
Pulse Std v3
SPO2_pct Std v3
HR Skewness v3
Pulse Skewness v3
SPO2_pct Skewness v3
HR Kurtosis v3
Pulse Kurtosis v3
SPO2_pct Kurtosis v3
Max Cross Correlation HR SPO2_pct v3
Max Cross Correlation Pulse SPO2_pct v3
HCTSA FC_Surprise HR How Surprised v2
HCTSA SB_MotifTwo HR Prob Increases v2
HCTSA PH_Walker SPO2 Std Rand Walk v2
HCTSA EX_MovingThreshold HR Avg Thresh v2
HCTSA EX_MovingThreshold SPO2 Avg Thresh v2
HCTSA DN_cv HR Std Dist v2
HCTSA DN_Cumulants HR Skew Dist v2
HCTSA DN_Quantile HR Max Dist v2
HCTSA SB_TransitionMatrix3 HR Sym Autocorr v2
HCTSA SB_MotifThree HR Sym Entropy v2
HCTSA MF_arfit HR Wavelet Autoregress v2
HCTSA SB_MotifThree HR Sym Diffs v2
HCTSA SY_StdNthDer HR 17thDeriv v2
HCTSA DN_RemovePoints SPO2 Mean Dist v2
HCTSA SB_BinaryStats SPO2 Sym IQR v2
HCTSA MF_arfit SPO2 Wavelet Autoregress v2
HCTSA SB_TransitionMatrix2 SPO2 Sym Eigen v2
HCTSA CO_AutoCorr SPO2 v2
HCTSA SB_MotifThree SPO2 Sym Entropy v2
HCTSA SB_TransitionMatrix1 SPO2 Sym Bin v2
HCTSA ST_LocalExtrema SPO2 Stationarity Min v2
HCTSA ST_LocalExtrema HR Stationarity Min v2
HCTSA CO_tc3 HR Correlation Mean v2
HCTSA CO_tc3 SPO2 Correlation Mean v2

v2.0 Release Notes

Download RATA Cmd v2.0 Executable

This is equivalent to BAP 2.0

You will need to run the executable to install the code and matlab runtime. Then, you will be able to go to the command line and type in the following:

Command Line Input:

C:\Program Files\University of Virginia\run_all_tagging_algs\application>run_all_tagging_algs "path_to_file_to_convert" "[]" "[binary array of algorithms to run for the 53 algorithms listed below]"

Example Command Line Input:

C:\Program Files\University of Virginia\run_all_tagging_algs\application>run_all_tagging_algs "V:\Amanda\TestInputFiles\ConvertedUsing1_1_6\NU\20190413000000_PreVent_Prentice_2053_MC3_20190413.hdf5" "[]" "[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1]"

The results files will be saved in the same directory as the input file.

These are the algorithms (and their version numbers) which are available:

QRS Detection: ECG I v2
QRS Detection: ECG II v2
QRS Detection: ECG III v2
Brady Detection <100 v2
Apnea Detection v3
Periodic Breathing v2
Brady Detection Pete v2
Desat Detection Pete v2
Brady Desat v2
Brady Desat Pete v2
ABD v1
Data Available: Pulse v3
Data Available: HR v3
Data Available: SPO2_pct v3
Data Available: Resp v3
Data Available: ECG I v3
Data Available: ECG II v3
Data Available: ECG III v3
Desat Detection <75 v1
Desat Detection <76 v1
Desat Detection <77 v1
Desat Detection <78 v1
Desat Detection <79 v1
Desat Detection <80 v2
Desat Detection <81 v1
Desat Detection <82 v1
Desat Detection <83 v1
Desat Detection <84 v1
Desat Detection <85 v1
Desat Detection <86 v1
Desat Detection <87 v1
Desat Detection <88 v1
Desat Detection <89 v1
Desat Detection <90 v1
Desat Detection <91 v1
Desat Detection <92 v1
Desat Detection <93 v1
Desat Detection <94 v1
Desat Detection <95 v1
Hourly HR Mean v1
Hourly Pulse Mean v1
Hourly SPO2_pct Mean v1
Hourly HR Std v1
Hourly Pulse Std v1
Hourly SPO2_pct Std v1
Hourly HR Skewness v1
Hourly Pulse Skewness v1
Hourly SPO2_pct Skewness v1
Hourly HR Kurtosis v1
Hourly Pulse Kurtosis v1
Hourly SPO2_pct Kurtosis v1
Max Cross Correlation HR SPO2_pct v1
Max Cross Correlation Pulse SPO2_pct v1

v1.1 Release Notes

Download RATA Cmd v1.1 Executable

This is equivalent to BAP 1.4

You will need to run the executable to install the code and matlab runtime. Then, you will be able to go to the command line and type in the following:

Command Line Input:

C:\Program Files\University of Virginia\run_all_tagging_algs\application>run_all_tagging_algs path_to_file_to_convert "[]" "[binary array of algorithms to run]"

Example Command Line Input:

C:\Program Files\University of Virginia\run_all_tagging_algs\application>run_all_tagging_algs V:\Amanda\TestInputFiles\ConvertedUsing1_1_6\NU\20190413000000_PreVent_Prentice_2053_MC3_20190413.hdf5 "[]" "[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1]"

The results files will be saved in the same directory as the input file.

These are the algorithms (and their version numbers) which are available:

    'QRS Detection: ECG I',1
    'QRS Detection: ECG II',1
    'QRS Detection: ECG III',1
    'CU Artifact',1
    'WUSTL Artifact',1
    'Brady Detection',1
    'Desat Detection',1
    'Apnea Detection with ECG Lead I',1
    'Apnea Detection with ECG Lead II',1
    'Apnea Detection with ECG Lead III',1
    'Apnea Detection with No ECG Lead',1
    'Periodic Breathing with ECG Lead I',1
    'Periodic Breathing with ECG Lead II',1
    'Periodic Breathing with ECG Lead III',1
    'Periodic Breathing with No ECG Lead',1
    'Brady Detection Pete',1
    'Desat Detection Pete',1
    'Brady Desat',1
    'Brady Desat Pete',1
    'ABD Pete No ECG',2
    'Save HR in Results',1
    'Data Available: Pulse',1
    'Data Available: HR',1
    'Data Available: SPO2_pct',1
    'Data Available: Resp',1
    'Data Available: ECG I',1
    'Data Available: ECG II',1
    'Data Available: ECG III',1

To make new versions of this

At UVA: Check out the project file in CAMA\Amanda\NICUHDF5Viewer called run_all_tagging_algs_v2_0.prj and package that up for release.

Not at UVA: Use the matlab application compiler app and make the following selections:

/images/BAPCommandLine/ProjectFileScreenshot1.png /images/BAPCommandLine/ProjectFileScreenshot2.png