Processing

Access to all Processing options is gained through the Processes dropdown menu in the Sequences and Calls views.

A selected process can then either be run on all filtered sequences, or only on the filtered sequences that are also selected.

Processing Sequences

To successfully process a sequence, the Cut, Inspect and Classify stages need to be run in order.

The available processes are:

• CUT - identify and extract individual animal calls from a sequence

  • Peak Search Cutter - calls are identified by spectral amplitude peaks

  • Period Cutter - calls are identified by sinusoidal, tonal regions in the sequence. This method is better able to differentiate and ignore calls from unrelated species such as insects.

• INSPECT - measure and numerically record the identifying parameters of a sequence’s calls

  • Bat Inspector

• CLASSIFY - classify a sequence’s calls using one or more machine learning algorithms, or clear a previous classification

  • KNN (R Classifier) - K Nearest Neighbors

  • QDA (R Classifier) - Quadratic Discriminant Analysis

  • RF (R Classifier) - Random Forest

  • rSVM (R Classifier) - Support Vector Machine

  • KKNN (R Classifier) - Weighted K Nearest Neighbors

  • NN (R Classifier) - Feedforward Neural Network

  • SVM (SVM based Classifier) - Support Vector Machine

Tip

both SVMs perform identical but SVM is considerably faster than rSVM.

• VERIFY - definitive, user-specified assignment of sequences to a taxon

  • Delete Auto-Verifications - remove verifications from sequences that were added in batch by a process

  • Delete Verifications - remove all verifications from sequences

  • Reverify Sequences - revalidate verifications outdated by changing the Status of the sequence’s calls or rerunning an earlier stage

  • Verify As - add a verification for the specified taxon at the specified rank

  • Verify First - accept the first classification from the Classify stage

  • Verify First and Second - accept the first two classifications from the Classify stage

  • Verify First, Location Pass - accept the first classification from the Classify stage for which the recording location is within the species’ distribution range (according to the selected range base)

  • Verify Top N - accept the first N classifications from the Classify stage

• SHARE - upload verified sequences to a server

  • WSL Bat - Full - upload all data associated with a sequence to the WSL server, including its WAV file

  • WSL Bat - Full (anonymous) - as WSL Bat - Full, but in an anonymized form that excludes any identifying fields such as names, notes, locations and dates

  • WSL Bat - Light - as WSL Bat - Full, but without its WAV file, for use with slow internet connections

  • WSL Bat - Light (anonymous) - as WSL Bat - Light, but in the anonymized form

• STATUS - edit the Status of sequences

  • Disable Sequences - disable the Status of the sequences

  • Enable Sequences - enable the Status of the sequences

• CATEGORY - edit the categories assigned to sequences

  • Add Category - add an existing category

  • Delete Categories - remove all categories

• OTHER

  • Delete Sequences - delete the sequence and all related data, including its WAV file

  • Open in Editor - open first sequence in the audio editor helper application

  • Set Notes - set the notes associated with the sequence (single quotes must inserted as double quotes)

Processing Calls

There are only few processes for calls, namely:

• Delete Calls - delete the call and all related data

• Disable Calls - disable the Status of the call, such that it will not be included in its sequence’s classification

• Enable Calls - enable the Status of the call

• Open in Editor - open all selected calls in a single window in the audio editor helper application

Batch Processes

With BatScope 4 a predefined sequence of processes can be saved and executed. To create a custom batch process, open the Processes dialog from the Edit menu.

To create a new batch process, select New, enter a name and press Enter to confirm.

Next, select Add Sequence Stage to run sequence processes, Add Call Process to run a call process or Add Batch Process to call another batch process from this one.

Warning

Make sure not to introduce cycles when calling other batch processes from a process, as these would then run forever!

Set the filter to be used to determine which records to run the processes on. Previously saved filters can also be loaded here.

Finally, add processes to the stage, which will be run in order on the filtered records.

Note

These processes will be saved with the species-set in your user settings directory.

Use the Show Species-Sets Configs button from the About BatScope 4 dialog to access these files directly.

You can exchange saved processes with other BatScope 4 users by copying the corresponding XML file from the processes in your species-set directory into theirs.