blob_detection {bioacoustics} | R Documentation |
Blob detection of a region of interest into a spectrographic representation of the recording
Description
This function is a modified version of the Bat classify software developed by Christopher Scott (2014). It combines several algorithms for detection, filtering and audio feature extraction.
Usage
blob_detection(
wave,
channel = "left",
time_exp = 1,
min_dur = 1.5,
max_dur = 80,
min_area = 40,
min_TBE = 20,
max_TBE = 1000,
EDG = 0.9,
LPF,
HPF = 16000,
FFT_size = 256,
FFT_overlap = 0.875,
blur = 2,
bg_substract = 20,
contrast_boost = 20,
settings = FALSE,
acoustic_feat = TRUE,
metadata = FALSE,
spectro_dir = NULL,
time_scale = 0.1,
ticks = TRUE
)
Arguments
wave |
either a path to a file, or a Wave object. Audio files will be automatically decoded internally using the function read_audio. |
channel |
character. Channel to keep for analysis in a stereo recording: 'left' or 'right'. Do not need to be specified for mono recordings, recordings with more than two channels are not yet supported. Default setting is 'left'. |
time_exp |
integer. Time expansion factor of the recording. Set to 1 for real-time recording or above for time expanded recording. Default setting is 1. |
min_dur |
numeric. Minimum duration threshold in milliseconds (ms). Extracted audio events shorter than this threshold are ignored. Default setting is 1.5 ms. |
max_dur |
numeric. Maximum duration threshold in milliseconds (ms). Extracted audio events longer than this threshold are ignored. The default setting is 80 ms. |
min_area |
integer. Minimum area threshold in number of pixels. Extracted segments with an area shorter than this threshold are discarded. Default setting is 40 pixels. |
min_TBE |
numeric. Minimum time window between two audio events in milliseconds (ms). If the time interval between two successive audio events is shorter than this window, they are ignored. The default setting is 20 ms. |
max_TBE |
numeric. Maximum time window between two audio events in milliseconds (ms). If the time interval between two successive audio events is longer than this window, they are ignored. The default setting is 1000 ms. |
EDG |
numeric. Exponential Decay Gain from 0 to 1. Sets the degree of temporal masking at the end of each audio event. This filter avoids extracting noise or echoes at the end of the audio event. The default setting is 0.996. |
LPF |
integer. Low-Pass Filter (Hz). Frequencies above the cutoff are greatly attenuated. Default is set internally at the Nyquist frequency of the recording. |
HPF |
integer. High-Pass Filter (Hz). Frequencies below the cutoff are greatly attenuated. Default setting is 16000 Hz. A default of 1000 Hz is recommended for most bird vocalizations. |
FFT_size |
integer. Size of the Fast Fourrier Transform (FFT) window. Default setting is 256. |
FFT_overlap |
numeric. Percentage of overlap between two FFT windows (from 0 to 1). Default setting is 0.875. |
blur |
integer. Gaussian smoothing function for blurring the spectrogram of the audio event to reduce image noise. Default setting is 2. |
bg_substract |
integer. Foreground extraction with a mean filter applied on the spectrogram of the audio even for image denoising. Default setting is 20. |
contrast_boost |
integer. Edge contrast enhancement filter of the spectrogram of the audio event to improve its apparent sharpness. Default setting is 20. |
settings |
logical. |
acoustic_feat |
logical. |
metadata |
logical. |
spectro_dir |
character (path) or |
time_scale |
numeric. Time resolution of the spectrogram in milliseconds (ms) per pixel (px). Default setting is 0.1 ms for bat echolocation calls. A default of 2 ms/px is recommended for most bird vocalizations. |
ticks |
either logical or numeric. If |
Examples
data(myotis)
Output <- blob_detection(myotis, time_exp = 10, contrast_boost = 30, bg_substract = 30)
Output$data