Processing mobile transect data in SonoBat

Scroll down for detailed guidance on assigning automated species IDs to recordings, scrubbing noise files, attributing metadata to recordings, and exporting metadata in the NABat bulk upload template. 

Processing mobile transect data in SonoBat

Attribute Files

  1. Open SonoBat Data Wizard.

  2. Click the folder icon in the top right corner of the window and navigate to the folder containing your .wav/.zc files.

    • NOTE: In order to embed and export metadata, mobile transects must be processed individually. Select a folder containing data for a single mobile transect.

  3. To add/update NABat metadata, select "NABat Attributer" from the dropdown menu in the top left of the window. For users with older versions of  SonoBat that do not feature the NABat attributer, select "Attribute Files." Check to ensure that the input folder is still correct and navigate back to the desired folder if necessary. Once the correct input folder is selected, specify an output directory location to save the final files (there is also an option to "rename and attribute in place"). Notice that the right panel of the application fills with a display of the existing GUANO metadata in the file. This will be augmented with NABat metadata fields. Required NABat fields and optional NABat fields are outlined here. Users with SonoBat versions that do not include the NABat Attributer can skip to step 9.​

    • Users with SonoBat versions that include the automatic NABat metadata attributer, click the "NABat Metadata" button. In the pop-up window, click the box to confirm that you are processing mobile transect data.

    • The SonoBat NABat attributer is somewhat out of date, and several fields can be ignored while others must be manually entered (outlined in step 9). However, this tool is useful for entering required fields.

    • If your mobile transect passes through > 1 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 to each call. Otherwise, calls recorded outside the primary cell will produce a Lat/Long-Grid Cell mismatch error.

    • If you are unable to provide the X,Y location where each file was recorded, 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 for the route prior to uploading 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.

  4. Complete the fields for Site Name, Monitoring Start Time, and Monitoring End Time, and click the arrow (bottom right) to proceed to the next page. These are required fields and must be completed before uploading data to NABat.

  5. Complete the fields for Surveyor and Habitat Type (not required) and ignore the remaining fields. Click the arrow to proceed to the next page.

  6. Complete fields for Detector Type, Detector Serial Number, and Microphone Type (not required) and ignore the remaining fields. Click the arrow to proceed to the next page.

  7. Click "Finish" in the bottom right.

  8. Software Type and Species List are required fields that must be entered manually. Microphone Serial Number, Microphone Placement, and weather covariates are not required, but must also be entered manually if you wish to include these data. Guidance for manually adding metadata fields is listed in step 9.

  9. For users with older versions of SonoBat that do not include the NABat attributer, you must manually add metadata fields for which you have data using the instructions below:   

    • To manually add a new metadata field, click on one of the yellow dropdown triangles and select "add new…"

    • In the pop-up menu, enter one of the NABat field names exactly as it appears here (include the NABat| as well).

    • Click the drop-down menu in the bottom left corner of the window and select "Create advanced metadata field" from the available options.

    • Input the value for that field and click "Accept."

    • Repeat the above steps for all NABat metadata fields for which you have data.

Rename Files

Users with software versions that include the automatic NABat attributor can skip to the next section (Scrub Noise Files). Software versions with the automatic NABat attributor will automatically rename files based on user-added metadata.

  1. If the detector model you're using automatically embeds a timestamp into call files, "Timestamp" should appear in the list of file metadata in the right half of the SonoBat Data Wizard. If so, you may skip the file renaming process. However, before uploading metadata to NABat, users should ensure that the "Audio Recording Time" column of the exported metadata CSV contains values. Otherwise, file names must adhere to the NABat naming format outlined below.

    • GRTS ID_LOCATION NAME_RECORDING DATE_TIMESTAMP.wav/zc ​

  2. If your files do not contain an embedded timestamp, select the "Filname Editor" option from the drop-down menu in the top left of the SonoBat Data Wizard window to add the Grid Cell GRTS ID and Site Name components as a prefix to filenames. This strips the text before the date timestamp and adds a new prefix. However, the system may separate the new prefix and the date stamp with a dash rather than an underscore. All fields MUST be separated by an underscore. This can be corrected using the "rename with wildcards" function, available from the drop-down menu above the prefix box.​

  3. Use the "rename with wildcards" option to perform a "find-and-replace" function to replace any characters that conflict with the NABat file naming format. Enter the text you wish to replace in the "search pattern" field and the text you wish to replace it with in the "replace search pattern with" field. A preview of the resulting file names is provided so you can tweak the formula before making final changes. Click "Edit Filenames" when you’re ready to update the filenames. You might need to make multiple file renaming runs to achieve the desired format.

Scrub Noise Files

  1. Click the folder icon in the top right corner of the Data Wizard window and navigate to the folder containing your .wav files.

  2. Click the drop-down menu in the top left and select "Batch File Scrubber."

  3. Select "medium" from the filter options and ensure the appropriate frequency filter is selected.

  4. Click "Scrub" in the bottom left of the window.

Assign Species IDs

  1. Open SonoBat Universal and click the "SonoBatch" button in the lower left corner.

  2. Click the folder icon in the top center of the window and navigate to the folder containing files you wish to process.

  3. Select the classifier most appropriate for your location using the drop-down menus on the left side of the window.

  4. Ensure "Append species codes to filenames?" is not selected.

  5. Select "autofilter" in areas without low-frequency bat species and "auto-low" in areas with low-frequency bats present.

  6. Set "acceptable call quality" to 0.80.

  7. Set "sqnc decision threshold" to 0.90.

  8. Set "max number of calls to consider" to 16.

  9. Click "Process" in the bottom center of the window.

Export Metadata into the NABat Bulk Upload Template

The following steps can be used to export metadata from all processed transects simultaneously, resulting in a single CSV with metadata from numerous routes. Simply select the parent folder that contains all of your processed transects 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.

  1. Open SonoBat universal and click the "SonoVet" button in the lower left corner.

  2. Click the "Add to Project" button in the Project Vetter window and navigate to the folder containing .wav files that have been processed, renamed, and which contain all required metadata.

    • NABat requests that users provide metadata for scrubbed NOISE files. However, SonoBat automatically ignores any folder labeled "Noise Files," "Deleted Files," or "Scrubbed Files." To ensure scrubbed files load in the SonoVet table, rename folders containing scrubbed files as "NOTBAT" before loading folders in SonoVet.

  3. Click the "Settings" tab on the top menu bar and click the "Load Layout" button to load the NABat metadata form. Be sure to select the appropriate SonoBat form for the software version and survey type. Project forms are available for download here

  4. ​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.​

  5. If everything is correct, click the "Export" tab from the top menu bar. Select a destination folder to save the metadata file and select "Output null as """  or "Output null as an empty cell" from the dropdown menu in the bottom center of the window.

  6. Click "Save to File."

  7. The resulting .txt file must be converted to a .csv file. To convert the file in Excel, open a new workbook, click the Data tab, then "Get Data," "From File," and finally "From Text/CSV." Note: depending on your version of Excel, the process may vary slightly.

  8. In the pop-up window, navigate to the SonoBat text file and click "Import." Select "Tab" as the "Delimiter" and click "Load" in the bottom right of the window. Your data will now open in an Excel spreadsheet.

  9. Users who saved latitude and longitude of recordings with an external GPS unit must manually add X,Y locations to the bulk metadata spreadsheet. To begin, download the locations file from your GPS unit. This is typically in the form of a text file with columns for filename, latitude, and longitude. Users with GPS enabled detectors that embed X,Y locations into call files (the latitude/longitude columns of your CSV will already contain data) can skip to step 16.

  10. Import the GPS text file into Excel:

    • Open a new spreadsheet. Click the "Data" tab and select "Get Data," "From File," "From Text/CSV."

    • Navigate to your GPS text file and click "Open."

    • A dialogue box will appear with a preview of the data to be imported. The GPS text files are typically tab delimited. If your data are properly sorted into columns, click "Load." If not, use the "Delimiter" drop-down menu to select the appropriate delimiter and click "Load."​

  11. When your data are loaded into an Excel spreadsheet, click the "Sort and Filter" button (under the Home tab) and select "Custom Sort."​

  12. In the dialogue box, select the column containing your filenames to "Sort by."

  13. Next, open the CSV containing your transect metadata. Follow steps 11-12 to sort the metadata document by the Audio Recording Name column.

  14. The two Excel documents (metadata CSV and GPS spreadsheet) should now be sorted by filename. Double check to ensure that the filename columns match.

  15. If the documents are sorted properly, you can now copy and paste the latitude and longitude columns from the GPS file into the metadata CSV. Select the latitude and longitude columns of the GPS document. Highlight the latitude and longitude columns, right click, and select "Copy." Next, select the Latitude cell of the first call for the deployment, right click, and select "Paste." The Latitude and Longitude columns should now be filled with the corresponding values.

  16. In order for the NABat system to read your metadata, the column headers created by SonoBat must be replaced with the metadata field names from the NABat template. To do so:

    • Select and copy all the comma-separated column headers from the table below. 

    • Select cell A1 of your spreadsheet, and paste in the new column headers.

    • Click the "Data" tab in Excel. 

    • Select the "Text to Columns" button. 

    • In the dialogue box, select "Delimited" as the file type and click "Next."

    • Select "Comma" as the "Delimiters" and click "Finish." 

    • The headers should now be distributed into the appropriate columns. 

  17. The specific software version must now be manually added. Highlight the "Software Type" column, and using the find/replace function, replace "SonoBat" with "SonoBat 3.x," "SonoBat 4.2," or "SonoBat 4.x," depending on your specific software version.

  18. Click File, then Save As, and select the folder where you wish to save the metadata spreadsheet. Give the file a unique and descriptive name and then select "CSV (Comma delimited)" from the "Save as type" dropdown.

  19. Your metadata is now ready for upload to the NABat Partner Portal.

Table 1. NABat metadata column headers for stationary acoustic surveys.

| GRTS Cell Id, Location Name, Survey Start Time, Survey End Time, Detector, Detector Serial Number, Microphone, Microphone Serial Number, Microphone Placement, Contact, Comments, Unusual Occurrences, Event Low Temperature, Event High Temperature, Event Low Relative Humidity, Event High Relative Humidity, Event Low Weather Event, Event High Weather Event, Event Low Wind Speed, Event High Wind Speed, Event Low Cloud Cover, Event High Cloud Cover, Audio Recording Name, Audio Recording Time, Latitude, Longitude, Software Type, Auto ID, Manual Id, Species List