def update_single_md(fname, guano_md={}, project_md={}, site_md={}):
g = GuanoFile(fname)
parts = parse_nabat_fname(fname)
# content from the NABat filename
g['NABat', 'Grid Cell GRTS ID'] = parts['GrtsId']
g['NABat', 'Site Name'] = parts['SiteName']
#content from the site_md
if guano_md is None:
g['GUANO', 'time_to_time'] = str(parts['datetime'])
else:
for k, v in guano_md.items():
g['GUANO', k] = v
#content from the project_md
if project_md is not None:
for k, v in project_md.items():
g['NABat', k] = v
#content from the site_md
if site_md is not None:
for k, v in site_md.items():
g['NABat', k] = v
g.write(make_backup=False)
def sonobat2guano(fname):
"""Convert a file with Sonobat metadata to GUANO metadata"""
print '\n', fname
sb_md = extract_sonobat_metadata(fname)
if not sb_md:
print >> sys.stderr, 'Skipping non-Sonobat file: ' + fname
return False
pprint(sb_md)
gfile = GuanoFile(fname)
gfile['GUANO|Version'] = 1.0
if 'timestamp' in sb_md:
gfile['Timestamp'] = sb_md['timestamp']
if sb_md.get('te', 1) != 1:
gfile['TE'] = sb_md['te']
gfile['Length'] = sb_md['length']
gfile['Note'] = sb_md['note'].strip().replace('\r\n', '\\n').replace('\n', '\\n')
if sb_md.get('species', None):
gfile['Species Auto ID'] = sb_md['species']
if 'd500x' in sb_md:
for k, v in sb_md['d500x'].items():
gfile['PET', k] = v
if 'ar125' in sb_md:
for k, v in sb_md['ar125'].items():
gfile['BAT', k] = v
print gfile._as_string()
gfile.write()
def d500x2guano(fname):
"""Convert a file with raw D500X metadata to use GUANO metadata instead"""
print "\n", fname
md = extract_d500x_metadata(fname)
if not md:
print >> sys.stderr, "Skipping non-D500X file: " + fname
return False
pprint(md)
gfile = GuanoFile(fname)
gfile["GUANO|Version"] = 1.0
gfile["Make"] = "Pettersson"
gfile["Model"] = "D500X"
gfile["Timestamp"] = md.pop("File Time")
gfile["Samplerate"] = md.pop("Samplerate")
gfile["Length"] = md.pop("Length")
if md.get("Profile HP", None) == "Y":
gfile["Filter HP"] = 20
lat, lon = md.pop("LAT", None), md.pop("LON", None)
if lat and lon:
gfile["Loc Position"] = dms2decimal(lat), dms2decimal(lon)
for k, v in md.items():
gfile["PET", k] = v
print gfile._as_string()
gfile.wav_data = gfile.wav_data[D500X_DATA_SKIP_BYTES:] # throw out the metadata bytes from 'data' chunk
unlock(fname) # D500X "locks" files as unwriteable, we must unlock before we can modify
gfile.write()
def wamd2guano(fname):
"""Convert a Wildlife Acoustics WAMD metadata file to GUANO metadata format"""
wamd_md = wamd(fname)
pprint(wamd_md)
gfile = GuanoFile(fname)
gfile['GUANO|Version'] = 1.0
gfile['Timestamp'] = wamd_md.pop('timestamp')
gfile['Note'] = wamd_md.pop('notes', '')
gfile['Make'] = 'Wildlife Acoustics'
gfile['Model'] = wamd_md.pop('model', '')
gfile['Firmware Version'] = wamd_md.pop('firmware', '')
gfile['Species Auto ID'] = wamd_md.pop('auto_id', '')
gfile['Species Manual ID'] = wamd_md.pop('manual_id', '')
gfile['TE'] = wamd_md.pop('time_expansion', 1)
gfile['Samplerate'] = gfile.wav_params.framerate * gfile['TE']
gfile['Length'] = gfile.wav_params.nframes / float(gfile.wav_params.framerate) * gfile['TE']
if 'gpsfirst' in wamd_md:
lat, lon, alt = wamd_md.pop('gpsfirst')
gfile['Loc Position'] = lat, lon
gfile['Loc Elevation'] = alt
for k, v in wamd_md.items():
gfile['WA', k] = v
print(gfile.to_string())
gfile.write()
def d500x2guano(fname):
"""Convert a file with raw D500X metadata to use GUANO metadata instead"""
print('\n', fname)
md = extract_d500x_metadata(fname)
if not md:
print('Skipping non-D500X file: ' + fname, file=sys.stderr)
return False
pprint(md)
gfile = GuanoFile(fname)
gfile['GUANO|Version'] = 1.0
gfile['Make'] = 'Pettersson'
gfile['Model'] = 'D500X'
gfile['Timestamp'] = md.pop('File Time')
gfile['Original Filename'] = md.pop('File Name')
gfile['Samplerate'] = md.pop('Samplerate')
gfile['Length'] = md.pop('Length')
if md.get('Profile HP', None) == 'Y':
gfile['Filter HP'] = 20
lat, lon = md.pop('LAT', None), md.pop('LON', None)
if lat and lon:
gfile['Loc Position'] = dms2decimal(lat), dms2decimal(lon)
for k, v in md.items():
gfile['PET', k] = v
print(gfile.to_string())
gfile.wav_data = gfile.wav_data[D500X_DATA_SKIP_BYTES:] # throw out the metadata bytes from 'data' chunk
unlock(fname) # D500X "locks" files as unwriteable, we must unlock before we can modify
gfile.write()
def batlogger2guano(fname):
"""Convert an Elekon BatLogger .WAV with sidecar .XML to GUANO metadata"""
xmlfname = os.path.splitext(fname)[0] + '.xml'
if not os.path.exists(xmlfname):
raise ValueError('Unable to find XML metadata file for %s' % fname)
g = GuanoFile(fname)
with open(xmlfname, 'rt') as f:
xml = ElementTree.parse(f)
g['Timestamp'] = get(xml, 'DateTime', lambda x: datetime.strptime(x, '%d.%m.%Y %H:%M:%S'))
g['Firmware Version'] = get(xml, 'Firmware')
g['Make'] = 'Elekon'
g['Model'] = 'BatLogger'
g['Serial'] = get(xml, 'SN')
g['Samplerate'] = get(xml, 'Samplerate', lambda x: int(x.split()[0]))
g['Length'] = get(xml, 'Duration', lambda x: float(x.split()[0]))
g['Original Filename'] = get(xml, 'Filename')
g['Temperature Ext'] = get(xml, 'Temperature', lambda x: float(x.split()[0]))
g['Loc Position'] = get(xml, 'GPS/Position', lambda x: tuple(map(float, x.split())))
g['Loc Elevation'] = get(xml, 'GPS/Altitude', lambda x: float(x.split()[0]))
g['Elekon|BattVoltage'] = get(xml, 'BattVoltage')
for node in xml.find('Trigger'):
g['Elekon|Trigger|%s' % node.tag] = node.text
for node in xml.find('GPS'):
g['Elekon|GPS|%s' % node.tag] = node.text
# for k, v in g.items():
# print('%s:\t%s' % (k, v))
print(g.to_string())
g.write()
os.remove(xmlfname)
return g
def wamd2guano(fname):
"""Convert a Wildlife Acoustics WAMD metadata file to GUANO metadata format"""
wamd_md = wamd(fname)
pprint(wamd_md)
gfile = GuanoFile(fname)
gfile['GUANO|Version'] = 1.0
gfile['Timestamp'] = wamd_md.pop('timestamp')
gfile['Note'] = wamd_md.pop('notes', '')
gfile['Make'] = 'Wildlife Acoustics'
gfile['Model'] = wamd_md.pop('model', '')
gfile['Firmware Version'] = wamd_md.pop('firmware', '')
gfile['Species Auto ID'] = wamd_md.pop('auto_id', '')
gfile['Species Manual ID'] = wamd_md.pop('manual_id', '')
gfile['TE'] = wamd_md.pop('time_expansion', 1)
gfile['Samplerate'] = gfile.wav_params.framerate * gfile['TE']
gfile['Length'] = gfile.wav_params.nframes / float(gfile.wav_params.framerate) * gfile['TE']
if 'gpsfirst' in wamd_md:
lat, lon, alt = wamd_md.pop('gpsfirst')
gfile['Loc Position'] = lat, lon
gfile['Loc Elevation'] = alt
for k, v in wamd_md.items():
gfile['WAC', k] = v
print gfile._as_string()
gfile.write()
def sonobat2guano(fname):
"""Convert a file with Sonobat metadata to GUANO metadata"""
print('\n', fname)
sb_md = extract_sonobat_metadata(fname)
if not sb_md:
print('Skipping non-Sonobat file: ' + fname, file=sys.stderr)
return False
pprint(sb_md)
gfile = GuanoFile(fname)
gfile['GUANO|Version'] = 1.0
if 'timestamp' in sb_md:
gfile['Timestamp'] = sb_md['timestamp']
if sb_md.get('te', 1) != 1:
gfile['TE'] = sb_md['te']
gfile['Length'] = sb_md['length']
gfile['Note'] = sb_md['note'].strip().replace('\r\n',
'\\n').replace('\n', '\\n')
if sb_md.get('species', None):
gfile['Species Auto ID'] = sb_md['species']
if 'd500x' in sb_md:
for k, v in sb_md['d500x'].items():
gfile['PET', k] = v
if 'ar125' in sb_md:
for k, v in sb_md['ar125'].items():
gfile['BAT', k] = v
print(gfile.to_string())
gfile.write()
def save(self):
fname = self.ui.file_name.text()
try:
g = GuanoFile(fname)
except:
msg = f"There was a problem loading the Guano MD from:\n{fname}\n\nPlease verify that it is a valid wav file"
QMessageBox.warning(self, "File Error", msg)
return None
for namespace_name, namespace_group in self.namespaces.items():
print(namespace_name)
namespace_data = namespace_group.get_data()
if namespace_name == 'guano_base':
namespace_name = ''
for k, v in namespace_data.items():
if v == '':
try:
del g[f"{namespace_name}|{k}"]
except KeyError:
pass
else:
g[f"{namespace_name}|{k}"] = v
g.write(make_backup=False)
def save(self):
d = Path(self.ui.directory_name.text())
wavs = list(d.glob('**\*.wav'))
wavs += list(d.glob('**\*.zc'))
self.ui.progressBar.setVisible(True)
self.ui.progressBar.setMinimum(1)
self.ui.progressBar.setMaximum(len(wavs))
self.ui.progressBar.setVisible(1)
if self.ui.directory_name_output.text():
if not Path(self.ui.directory_name_output.text()).exists():
msq = r"The output directory specified does not exist! Please point to an existing directory."
QMessageBox.warning(self, "Output directory does not exist",
msg)
return None
out_dir = Path(self.ui.directory_name_output.text())
make_copy = True
else:
out_dir = Path(self.ui.directory_name.text())
make_copy = False
for f in wavs:
original_fname = f.name
new_fname = self.change_fname_function(original_fname, f=f)
full_name = f.parent.joinpath(new_fname)
full_name = str(full_name).replace(str(Path(self.ui.directory_name.text())), \
str(out_dir))
if not Path(full_name).exists():
Path(full_name).parent.mkdir(parents=True, exist_ok=True)
if make_copy:
shutil.copy(str(f), full_name)
else:
f.rename(full_name)
if original_fname != new_fname:
try:
g = GuanoFile(full_name)
g['Original Filename'] = original_fname
g.write(make_backup=False)
except:
pass
self.ui.progressBar.setValue(self.ui.progressBar.value() + 1)
msg = f"Finished renaming files in directory:\n\n{out_dir}"
QMessageBox.information(self, "Renaming Process Complete", msg)
self.ui.progressBar.setVisible(False)
