SCAN’R tm Snapshot Characterization and Analysis Version 1.6 Software Manual Copyright 2005-2009 Binary Acoustic Technology. All Rights Reserved.
This software and documentation are copyrighted by Binary Acoustic Technology, doing business under the trademark SCAN’Rtm. The software and documentation are licensed, not sold, and may be used or copied only in accordance with the SCAN’Rtm License Agreement accompanying the software and/or reprinted in this document. This software embodies valuable trade secrets proprietary to Binary Acoustic Technology. All trademarks referenced in this document are the property of their respective owners.
SCAN’Rtm LICENSE AGREEMENT This user license agreement (the "AGREEMENT") is an agreement between you (individual or single entity) and Binary Acoustic Technology LLC, for the SCAN’Rtm software (the "SOFTWARE") that is accompanying this AGREEMENT. USE OF THIS PRODUCT CONSTITUES YOUR ACCEPTANCE OF THESE TERMS AND CONDITIONS. The SOFTWARE is the property of Binary Acoustic Technology LLC and is protected by copyright laws and international copyright treaties. The SOFTWARE is not sold, it is licensed.
Chapter 1 : Installation 1.1 : What you should have received The SCAN’Rtm package includes one SCAN’Rtm CD-ROM and this manual. The CD-ROM contains the software distribution along with a setup function that uses the Microsoft Windows installer. 1.2 : New Installation Place the CD-ROM in the drive. After a short delay the CDROM window should open. If this does not happen, doubleclick the CD-ROM symbol in the My Computer folder. When the CD-ROM window appears double click the Setup icon.
Chapter 2 : SCAN’Rtm 2.1 : Introduction SCAN’Rtm is an automated snapshot characterization and analysis tool. It is designed to help address two main issues present in bat monitoring projects; namely 1) handling the high volume of data that is produced by modern Time Expanded (TE) and Full Bandwidth (FB) bat detectors, and 2) converting the recordings into meaningful measurements that can potentially be used to identify individual species and estimate populations.
Chapter 3 : Running SCAN’R 3.1 : Running from desktop A SCAN’Rtm desktop icon is created and placed on your desktop during the install. You can start SCAN’Rtm from the desktop by double clicking on the SCAN’Rtm icon illustrated by Figure 1. Figure 1: SCAN’Rtm Icon 3.2 : Running from Start Menu SCAN’Rtm can also be run from the Start menu. You can run it by selecting Start => All Programs => SCANR 3.3 : Exiting There are two ways to exit the program.
3.4 : The SCAN’R Main Window Upon startup the main window appears as shown in figure 2. The main window has two basic sections. The file selection section (left) allows the operator to select both input and output files. It can also be used to manually operate the scanner and select individual files to process. The sonogram “thumbnail” section (right) displays a sonogram for each detected bat call.
3.4.1 : Output File Selector The output file selector allows the operator to specify the file that will receive the parameter measurements . Clicking on the “Select Output…” button will bring up a standard windows file selection tool, Figure 3. This tool allows the operator to browse existing folders, create new folders and specify an output filename. Keep in mind that the output file is a parameter file.
3.4.2 : Input File Selector The input file selector operates much the same as the output file selection. Clicking on the “Select Input…” button will bring up a standard file selection window. However, rather than just selecting just a single file. The Input Selector will read in and display all of the files in the selected directory. All files will be listed and the original selected file will be highlighted as shown in figure 4.
3.4.3 : Sonogram “Thumbnail” Display The thumbnail is a sixteen pane sonographic display that is organized in four rows and four columns as illustrated in figure 5. The panes are updated with each new detection. Each pane holds a single call. The update order is left-to-right and top-to-bottom. The thumbnail display provides visual feedback of the scanner progression. It provides a mouse driven interface to allow the operator to select thumbnails of interest and inspect the results.
3.4.4 : Zooming the “Thumbnail” Display Double click the left mouse button to zoom , on any of the sixteen thumbnails, to get a closer look. When zoomed, the resolution of the display is increased and the display is updated with the automated parameter estimates for that call. As shown in figure 6, the zoomed thumbnail is enlarged by nearly a factor of four. To un-zoom, click the right mouse button. The zoomed thumbnail now includes parameter measurements in the upper right corner .
3.4.5 : Selecting the Range of Thumbnails SCAN’R displays only sixteen (16) thumbnails at a time. As of version 1.2, SCAN’R includes a scrolling feature that allows the operator to select the range of 16 thumbnails to display. The scroll bar is located at the right side of the thumbnail display group. As each file is scanned, SCAN’R creates a thumbnail for each bat call that is detected.
3.4.6 : Operating Brightness and Contrast Controls Simply stated, the Brightness and Contrast controls allow the operator to adjust the screen appearance. Moving either slider left reduces the screen brightness/contrast, while moving the slider right increase the screen brightness/contrast. To be more precise, the Brightness and Contrast controls actually control how the underlying sonographic data maps to the screen color and/or intensity.
3.5 : SCAN’R Menu Operation 3.5.1 : File Menu The File menu provides 1) an alternate method to select the Input and Output files and 2) it provides the main mechanism to exit SCAN’R. Clicking on either Select Input… will bring up a standard windows file selection utility and update the input file list as described in selection 3.4.2. Clicking on or Select Output... will again bring up a standard selection utility and then update the output file as described in section 3.4.1. Figure 7: File Menu 3.5.
3.5.3 : Action Menu The Action menu provides options to start and stop file scanning operations. Action=>Scan initiates a scan of the currently selected file (file list box). Action=>Scan All initiates scanning of all files in the file list box. This effectively scans an entire directory. Action=>Stop terminates the current scanning operation. Please note that the Stop operation is primarily intended to give the operator a mechanism to abort the current scanning operation.
3.5.5 : Configuration Menu The configuration menu is a special menu that appears only in the extended license version of SCAN’R. The configuration menu provides a mechanism for the operator to select default settings for reading generic wave files. As of version 1.3.6, the configuration menu allows the operator to supply the default time expansion factor that will be used to interpret the sample rate of the file. Two time expansion factors are supported 1X and 10X.
3.6 : SCAN’R Setup and Operation Windows 3.6.1 : Output Format Window The Output format window controls the format of the output parameter file. SCAN’Rtm supports two output format options, an Analooktm and a SonoBattm compatible base format. It also allows the base format to be augmented with additional parameters. Click on the Setup=>Output Format… menu entry. This will bring up the Output Format window as illustrated in figure 11.
3.6.2 : Scan Setup Window The Scan Setup Window is a control panel which allows the operator to setup the scanner and configure the call selection criteria. The control parameters are separated into two function groups as show in figure 12. The upper section controls the initial call detection criteria, while the lower section controls the final call filtering.
Figure 12 : Scan Setup Window
The peak power filter is used to reject detections that don’t reach a required peak sound pressure level during the duration of the call. Like the trigger level , this setting is referenced to the current value of the noise floor. It should be higher than the trigger level by at least 3 dB (default is set 6dB greater). The minimum duration filter is used to reject detections that don’t last long enough. Many of the false detections due to insects can be considered “pop” noise.
3.6.3 : Scan Results Window The Scan Results Windows presents the final results of the scan processing. The Scan Results Window is illustrated in figure 13. At the very top of the window is the selection criteria filter. This is the final filter in the selection process. SCAN’Rtm counts up the total number of detections in each file and compares this to the selection criteria.
3.6.3.1 : Maintaining Call Archives The Scan Results window provides flexible options to help maintain call archives and minimize disk storage by weeding out bad files. The operator is given the option to delete, move, or archive select files or groups of files. The Scan Results window groups files into two lists, “passed” files and “Failed” files. The passed file list includes all files that meet the file selection criteria specified in the Scan Setup window.
3.6.3.1.2 : Failed File Options For failed files, the operator has two primary options. First, the operator can choose to delete the file. Note that the deleted files are actually moved to Window’s Recycle bin and won’t actually be deleted until the recycle bin in emptied. This allows files to be recovered if deleted accidentally. Second, the operator can choose to move the file. In this case, the file is actually moved from the original directory and placed in another directory.
3.6.4 : Operation Timer Window SCAN’R includes an operation timer that can be used to perform periodic or daily automated batch processing. This is a new powerful feature that is included in version 1.5 and above. Because it is fully automated, the operation timer enables SCAN’R to be employed in remote field collection and used in conjunction with SPECT’R or SPECT’R Mobile.
3.6.4.1 : Time and Status Indicator The time and status indicator section displays both the current time and the current status of the operation timer. The time is displayed in ether UTC (universal coordinated time) or the local time. An indicator is also displayed showing which time is currently being displayed. The indicator with either be UTC or Local. The status indicator displays the current status of the operation timer.
3.6.4.3 : Program operation section Figure 18: Program operation section The program operation section allows the operator to select up to four operations to run each time the operation timer triggers. The four programs are provided to allow SCAN’R to process the snapshots from up to four AR125 ultrasonic receivers. This is the maximum number of receivers that can be run using a single computer. The program operation section, figure 18, is composed of four rows of control entries.
The output file selection allows the operatory to select a directory and file name to store all of the scan parameter results. To select an output directory click on the Output… button and this will bring up a windows file selection GUI. Use the GUI to select an output directory and then type in the desired file name. The file name specified in the output selection field is actually just a base file name, the beginning of a file name.
3.7 : Trace Window In addition to the Sonogram, SCAN’R includes a Trace Window that allows the operator to see a time versus frequency plot of the call sequence. The time is plotted horizontally with increasing time going from left to right. The frequency is plotted vertically with increasing frequency going from bottom to the top. The Trace Window is somewhat analogous to the bat call display of the Anabattm system (www.titley.com).
To bring up the Trace Window, select Window=>Trace… using the menu options at the top of the main window. The trace window will initially be blank, but it will update with call detections each time SCAN’R scans a file. Operating the Trace Window is fairly simple: 1) To select a call, simply point to the call using the mouse and double click the left mouse button. This will bring up a marker to highlight the selected call and update the main display with the corresponding sonogram.
3.8 : SCAN’R Output file If an output file is specified, SCAN’R writes the measured parameters to the output file. The output file is a tab-delimited file that conforms to the format selected by the Output Format window (section 3.6.1). The ability to provides detection parameter sets provides SCAN’R with two important applications: 1) it can be used to generate call parameters that can be used for bat species identification.
3.8.
3.8.2 : SonoBattm compatible format The SonoBattm base parameter set consists of twenty two (22) parameters which are tab-delimited and written in the following order: File Name Time Duration prev Fmax Fmin Bandwidth Dom.
3.8.3 : Optional Parameters Either base parameter set can be enhanced with up to three (3) additional parameters. These are also tab-delimited and are appended to the base parameter set in the following order: SPL Curv Fit : : : Peak Sound Pressure Level (SPL dB) Curvature measurement Curvature fit error (RMS error in Hz) The SPL parameter is valid only when using calibrated detectors like the BAT AR125.
Finally, the curve fit error parameter is a measurement of how much error exists between the curvature model and the actual shape of the call. The measurement is the Root Mean Squared (RMS) value calculated as the difference between the frequency calculated as a function of the model compared against the frequency measurements of the data. The units are RMS Hertz. Low values of curve fit error mean that the data is a closer match to the model. Higher values mean that the data is NOT fitting the model.
4.0 : Further Information For further information or trouble shooting, please contact us or visit our web site. Web: www.binaryacoustictech.com E-Mail : info@binaryacoustictech.
