def getAnnWavSec(wavFi,
annFi,
t0Label='startTime',
tfLabel='endTime',
label='label',
sr=None):
'''read annotated sections from a waveform
Parameters
----------
wavFi : string
path to wav file
annFi : string (*.txt)
path to annotations file, if None => the whole waveform is returned
Annotations are assumed to be in a list of dictionaries, see annT.parseAupFile
t0Label : string
name of the dictionary label for the start time (used by annT.parseAupFile)
tfLabel : string
name of the dictionary label for the end time (used by annT.parseAupFile)
label : string
name of the dictionary label with the annotation tag (used by annT.parseAupFile)
Returns
-------
sectionsLi : list of dictionaries
mapping label of the annotation section to the waveform
{ <label>, <waveFormSection (np.array)> }
[ { <label>, <waveFormSection> }, ... , { <label>, <waveFormSection> }]
'''
sr = loadWaveform(wavFi, 0, 0, sr=sr)[1]
#waveform, fs = sT.wav2waveform(wavFi) # read wav
if annFi is None: # no annotations given
return ([{
label: os.path.basename(wavFi),
'waveform': loadWaveform(wavFi, 0, None, sr=sr)[0]
}], sr)
else:
sectionsLi = []
annLi = annT.parseAupFile(annFi) # read annotations
for annDi in annLi:
t0 = annDi[t0Label]
tf = annDi[tfLabel]
l = annDi[label]
item = {label: l, 'waveform': loadWaveform(wavFi, t0, tf, sr=sr)[0]}
#getWavSec(waveform, fs, t0, tf)}
sectionsLi.append(item)
return sectionsLi, sr
def plotAnnotatedSpectro(wavFi, annFi, outDir, callAsTitle=True, figsize=None, dpi=None,
labelsHeight=10, cmapName='seismic', lw = 1, **kwargs):
'''
plots the spectrogram with it's annotations
Parameters
----------
wavAnnCollection : collection of paths to wavs and annotations files
outDir : dir where the plots will be saved
labelHeight : dictionary with the names of the labels and the height
dpi : size of the image
lw : line width for the annotated section
'''
## wav file
try:
waveForm, fs = sT.wav2waveform(wavFi)
except:
return False
M, ff, tf, _ = sT.spectralRep(waveForm, fs)#plt.specgram(waveForm, Fs=fs)
plt.ioff()
fig, ax = plt.subplots(figsize=figsize)
ax.imshow(M.T, aspect='auto', origin='bottom', #interpolation='nearest',
extent=[0, tf, 0, fs/2/1000.], **kwargs)
ax.set_xlabel('time (s)')
ax.set_ylabel('frequency (KHz)')
### read annotations
annD = annT.parseAupFile(annFi)
## custom ann clrs
idx2labs = list(set([item['label'] for item in annD]))
labs2idx = { idx2labs[i] : i for i in range(len(idx2labs)) }
cmap = plt.cm.get_cmap( cmapName, len(idx2labs))
annLabel=''
### annotate
for item in annD: # plot call segments - black line
ax.hlines(labelsHeight, float(item['startTime']), float(item['endTime']),
colors=cmap(labs2idx[item['label']]) , lw=lw)
annLabel += '{} '.format(item['label']) #read labels
if callAsTitle:
ax.set_title('{}'.format(annLabel))
#if callAsTitle: ax.set_title('{}'.format(fp.parseHeikesNameConv(wavFi)['call']))
outPl = os.path.join( outDir, os.path.basename(wavFi).replace('wav', 'png'))
plt.savefig(outPl, dpi=dpi)
del fig, ax
return outPl