ISHMAEL 3.O User Guide - Bioa before and wish to learn more about them, I recommend Principles of Animal

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  • ISHMAEL 3.O User Guide

    David K. Mellinger, Sharon L. Nieukirk and Sara L. Heimlich

    CIMRS, Oregon State University and NOAA PMEL Hatfield Marine Science Center

    Newport, OR

    November 2017

  • Development Team

    Cooperative Institute for Marine Resources Studies (CIMRS), Oregon State University, and

    NOAA Pacific Marine Environmental Laboratory

    David K. Mellinger David.Mellinger@oregonstate.edu

    Sharon L. Nieukirk Sharon.Nieukirk@oregonstate.edu

    Curtis Lending Curtis.Lending@oregonstate.edu

    Sara Heimlich Sara.Heimlich@oregonstate.edu

    Bio-Waves, Inc.

    Elizabeth Ferguson eferguson@bio-waves.net

    Julie Oswald julie.oswald@bio-waves.net

    Michael Oswald mike.oswald@bio-waves.net

    San Diego State University

    Chris Marsh chmarsh76@gmail.com

    Ishmael and ROCCA have been principally supported by the Living Marine Resources (LMR)

    program, U.S. Navy, and the Office of Naval Research (ONR), U.S. Navy

    Contribution XXXX from NOAA/Pacific Marine Environmental Laboratory

    file://///BIOAC3/analysis/LMRIsh/workshop/12Jan17REVISIONS/David.Mellinger@oregonstate.edu mailto:Sharon.Nieukirk@oregonstate.edu mailto:Curtis.Lending@oregonstate.edu mailto:Sara.Heimlich@oregonstate.edu mailto:eferguson@bio-waves.net file:///C:/Users/heimlich/Music/julie.oswald@bio-waves.net mailto:mike.oswald@bio-waves.net mailto:chmarsh76@gmail.com

  • Table of Contents 1. Introduction ...............................................................................................................................6

    1.1 What is Ishmael? ................................................................................................................6

    1.2 What Ishmael Isn’t..............................................................................................................6

    1.3 Companion tutorial.............................................................................................................6

    2. Obtaining and Installing Ishmael ................................................................................................6

    3. Getting Started...........................................................................................................................7

    3.1 Opening and viewing a sound file .......................................................................................7

    3.1.1 The basics tab..............................................................................................................8

    3.1.2 Time Stamps................................................................................................................8

    3.1.3 Advanced ....................................................................................................................9

    3.2 Display Options ................................................................................................................ 10

    3.2.1 Signal waveform and spectrogram............................................................................. 10

    3.2.2 Brightness and contrast ......................................................................................... 11

    3.2.3 Time and frequency display ....................................................................................... 12

    3.2.4 Time and frequency scaling ....................................................................................... 12

    3.2.5 Spectrogram parameters ........................................................................................... 13

    3.2.6 Equalization............................................................................................................... 16

    4. Loading and Saving Settings ..................................................................................................... 18

    4.1 The Ishmael Preferences File (*.ipf) .................................................................................. 18

    5. Playing Back a Sound................................................................................................................ 20

    6. Opening a Multi-Channel File ................................................................................................... 22

    7. Opening unknown file formats ................................................................................................. 23

    8. Monitor a real-time sound signal ............................................................................................. 24

    9. Record a real-time sound signal ............................................................................................... 25

    10. Convert sound file formats ................................................................................................... 26

    10.1 The basics ......................................................................................................................... 26

    10.2 Converting many files at once (batch processing) ............................................................. 29

    10.3 Using a default IPF for file conversion ............................................................................... 29

    10.4 Subsampling your data ..................................................................................................... 29

    11. Filtering ................................................................................................................................ 29

    11.1 Important Filtering Parameters......................................................................................... 31

    11.2 Filter response stability .................................................................................................... 31

    12. Acoustic measurement in Ishmael ........................................................................................ 32

    13. Logging Comments ............................................................................................................... 34

  • 14. Detection ............................................................................................................................. 34

    14.1 Detection methods ........................................................................................................... 34

    14.1.1 Energy summation..................................................................................................... 34

    14.1.2 Spectrogram correlation ............................................................................................ 36

    14.1.3 Matched filtering....................................................................................................... 36

    14.1.4 Repetitive calls .......................................................................................................... 37

    14.1.5 Whistle and moan detection: tonal sounds................................................................ 38

    14.1.6 Downloading detectors from the Ishmael detector archive........................................ 38

    14.2 Condition the spectrogram ............................................................................................... 40

    14.3 Examine the detection function ........................................................................................ 41

    14.4 Smooth the detection function ......................................................................................... 41

    14.5 Set a threshold ................................................................................................................. 41

    14.6 Set a neighborhood .......................................................................................................... 41

    14.7 Set up regular sequence detection .................................................................................... 42

    14.8 Specify what to do with detection events ......................................................................... 42

    14.9 Specify file names of saved calls ....................................................................................... 42

    14.10 Specify the log file ......................................................................................................... 43

    14.11 Run it ............................................................................................................................ 43

    14.12 Automatic Detection Summary ..................................................................................... 43

    14.13 Manual verification of detections.................................................................................. 44

    14.14 Evaluating the performance of detectors via Matlab ..................................................... 46

    14.15 Grouping detections...................................................................................................... 48

    15. Time stamps in Ishmael ........................................................................................................ 49

    16. Advanced detection using the MATLAB interface ................................................................. 51

    16.1 Example: Generalized Power Law (GPL) detector .............................................................. 51

    17. Advanced detection using ROCCA ......................................................................................... 52

    17.1