Processing mobile transect data in SonoBat 4
See below for detailed guidance on attributing metadata to recordings, scrubbing noise files, assigning automated species IDs to recordings, and exporting metadata in the NABat bulk upload template.
Updates to SonoBat 4 are no longer supported by software manufacturer, therefore NABat will no longer provide updates to the guidance listed below.
Attribute Files:
1. Open the SonoBat Data Wizard and select NABat Attributer from the drop-down menu in the top left of the window. Click the folder icon in the top right of the window and navigate to the folder containing the .wav files you intend to attribute (this should be a folder for a single deployment). Next, determine if you would like to Copy and Attribute to Output Folder or Rename and Attribute in place using the dropdown option. Specify an output directory in the Output Folder section where attributed files will be saved. The right panel of the application displays the GUANO metadata present in your selected acoustic files. This will be updated as NABat metadata fields are assigned in the Data Wizard.
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NOTE: the NABat Attributer metadata fields available in SonoBat 4 do not reflect the current metadata fields required and accepted by NABat as of Fall 2024. Only fill out the fields on the Location/Time (required) dropdown in the NABat Metadata pop-up window as the other metadata drop-down fields are outdated.
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2. Click the NABat Metadata button. In the pop-up window, select True to confirm that you are processing mobile transect data.
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NOTE: The NABat system will estimate the location based on user-provided spatial information for the route, timestamps of each file, and the start/end times of the survey. In this case, it is critical that users provide a spatial object (a KML or GEOJSON) for the route prior to uploading NABat metadata, ensure timestamps are provided for each file, provide start and end times of the route, and leave the GRTS Cell Id column of the metadata upload blank. Instructions on uploading or drawing a spatial object for mobile transect routes is available here.​
​If transects pass through > 1 grid cell and you have a record of the X,Y location where each call was recorded (using an external GPS or a GPS enabled detector), leave the Start/End GPS and NABat Grid Cell Id fields blank. The NABat system will use the X,Y locations to auto-assign the correct grid cell id to each call. Otherwise, calls recorded outside the primary cell will produce a lat/long-grid cell mismatch error.​​​​
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3. Click Finish in the bottom right.​
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4. Once you have added only the NABat Location/Time (required) fields, select Attribute Files button in the bottom center of the window.
Processing Mobile Transect Data in SonoBat 4
Scrub Noise Files:
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5. Click the folder icon in the top right corner of the Data Wizard window and navigate to the folder containing your .wav files.
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6. Click the drop-down menu in the top left and select Batch File Scrubber.
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7. Select medium from the filter options and ensure the appropriate frequency filter is selected.
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8. Click Scrub in the bottom left of the window.
Assign Species IDs:
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9. Open SonoBat 4 western [or eastern] North America and click the SonoBatch button in the lower left corner.
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​10. Click the folder icon in the top center of the window and navigate to the folder containing the files you intend to process.
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11. Select the classifier most appropriate for your location using the drop-down menus on the left side of the window.
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12. Ensure Append species codes to filenames? is NOT selected.
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13. Select autofilter in areas without low-frequency bat species and auto-low in areas with low-frequency bats present.
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14. Set acceptable call quality to 0.80.
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15. Set sqnc decision threshold to 0.90.
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16. Set max number of calls to consider to 16.
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17. Click Process in the bottom center of the window.
Export Metadata into the NABat Bulk Upload Template:
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The following steps can be used to export metadata from all processed deployments simultaneously, resulting in a single CSV with metadata from numerous sites. Simply select the parent folder that contains all of your processed deployments and follow the steps outlined below. The presence of non .wav files in the folder will not interfere with this process. SonoBat will ignore non .wav files.​
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1. Open SonoBat 4.x.x North America, select the regional and subregional classifier appropriate for your survey location. Click the I understand button to access the applications primary user interface.
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2. Click the SonoVet button in the lower left corner to access the Project Vetter pop-up window.
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3. Click the Add to Project button and navigate to the folder containing .wav files that have been attributed and processed in the above steps.
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4. Click the Settings tab on the top menu bar and then click the Load Layout button to load the NABat metadata form. Be sure to select the appropriate SonoBat form for your software version. SonoBat project forms are available for download here.
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​5. Click the Vetting Table tab from the top menu bar. Ensure all required fields have values and that all fields for which you have entered data are filled.​
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6. If everything is correct, click the Export tab from the top menu bar. Select a destination folder to save the metadata file and select Use current layout – and Output null as or Output null as an empty cell from the dropdown menu in the bottom center of the window. DO NOT select NABat Summary for export – this summary format does not reflect the NABat metadata updates.
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7. Click Save to File.
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8. The resulting .txt file must be converted to a .csv file. To convert the file in Excel, open a new workbook, drag and drop your .txt file directly into your new workbook.​
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10. The specific software version must now be manually added. Highlight the Software Type column, and using the find/replace function, replace SonoBat with SonoBat 4.x, depending on your specific software version.​
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11. Click File, Save As, and select the folder where you intend to save the metadata spreadsheet. Give the file a unique and descriptive name and select CSV (Comma delimited) from the Save As type dropdown.​​
Formatting the NABat Template​:
NABat mobile acoustic metadata fields were updated Fall of 2024. Because updates to SonoBat 4 are no longer supported by the software manufacturer, the SonoBat 4 NABat Attributer does not reflects the most up to date NABat metadata. Therefore, a scripted solution to format data from SonoBat 4 for NABat upload is provided below.
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1. Click the R Script button below to download a .pdf version of the script. Open R studio and copy and paste the script into the upper left window. Adapt the code to your computer path and file names. Click Run until you reach the end of the code. A new CSV file should now be written and saved to your local working directory with a unique filename.
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2. You must manually enter information for all required NABat metadata fields into your newly created .csv. You can review the mobile acoustic required metadata fields by downloading the bulk upload template here.
3. Once all required fields are populated, your metadata are now ready for upload to the NABat Partner Portal.
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