def _get_string_annotation_constraint_dict_aux(
constraint_name, visited_constraint_names):
"""
Gets the specified string annotation value constraint from the
database, parses its YAML to produce a constraint dictionary, and
recursively substitutes similarly parsed constraint dictionaries for
constraint names in the `extends` value (if there is one) of the result.
This method detects cycles in constraint inheritance graphs, raising
a `ValueError` when one is found.
"""
if constraint_name in visited_constraint_names:
# constraint inheritance graph is cyclic
i = visited_constraint_names.index(constraint_name)
cycle = ' -> '.join(visited_constraint_names[i:] + [constraint_name])
raise ValueError(
('Cycle detected in constraint inheritance graph. '
'Cycle is: {}.').format(cycle))
constraint = AnnotationConstraint.objects.get(name=constraint_name)
constraint = yaml_utils.load(constraint.text)
constraint['parents'] = _get_string_annotation_constraint_parents(
constraint, visited_constraint_names)
return constraint
def _get_string_annotation_constraint_dict_aux(constraint_name,
visited_constraint_names):
"""
Gets the specified string annotation value constraint from the
database, parses its YAML to produce a constraint dictionary, and
recursively substitutes similarly parsed constraint dictionaries for
constraint names in the `extends` value (if there is one) of the result.
This method detects cycles in constraint inheritance graphs, raising
a `ValueError` when one is found.
"""
if constraint_name in visited_constraint_names:
# constraint inheritance graph is cyclic
i = visited_constraint_names.index(constraint_name)
cycle = ' -> '.join(visited_constraint_names[i:] + [constraint_name])
raise ValueError(('Cycle detected in constraint inheritance graph. '
'Cycle is: {}.').format(cycle))
constraint = AnnotationConstraint.objects.get(name=constraint_name)
constraint = yaml_utils.load(constraint.text)
constraint['parents'] = _get_string_annotation_constraint_parents(
constraint, visited_constraint_names)
return constraint
def __init__(self, name, data):
# Parse YAML into a Python data structure.
try:
data = yaml_utils.load(data)
except Exception as e:
raise ValueError(str(e))
super().__init__(name, data)
def compile_yaml(spec, lat=None, lon=None, time_zone=None):
try:
spec = yaml_utils.load(spec)
except Exception as e:
raise ValueError(
'Could not load schedule YAML. Error message was: {}'.format(
e.message))
return Schedule.compile_dict(spec, lat, lon, time_zone)
def read_yaml_file(path):
contents = read_file(path)
try:
return yaml_utils.load(contents)
except Exception as e:
raise OSError(
'Could not load YAML file "{:s}". Error message was: {:s}'.format(
path, str(e)))
def read_yaml_file(path):
contents = read_file(path)
try:
return yaml_utils.load(contents)
except Exception as e:
raise OSError(
'Could not load YAML file "{:s}". Error message was: {:s}'.format(
path, str(e)))
def test_sexagesimal_load(self):
"""
The PyYAML `load` function parses YAML 1.1, in which "12:34:56"
is the sexagesimal number 12 * 3600 + 34 * 60 + 56 = 45296. We
use `ruaml_yaml` rather than PyYAML because it can also parse
YAML 1.2, in which "12:34:56" is simply the string "12:34:56".
This test checks that `yaml_utils.load` parses its input as we
would like.
"""
x = yaml_utils.load('12:34:56')
self.assertEqual(x, '12:34:56')
def test_sexagesimal_load(self):
"""
The PyYAML `load` function parses YAML 1.1, in which "12:34:56"
is the sexagesimal number 12 * 3600 + 34 * 60 + 56 = 45296. We
use `ruaml_yaml` rather than PyYAML because it can also parse
YAML 1.2, in which "12:34:56" is simply the string "12:34:56".
This test checks that `yaml_utils.load` parses its input as we
would like.
"""
x = yaml_utils.load('12:34:56')
self.assertEqual(x, '12:34:56')
def create_from_yaml(s):
"""Creates a settings object from a YAML string."""
try:
d = yaml_utils.load(s)
except Exception as e:
raise ValueError(
'YAML parse failed. Error message was:\n{}'.format(str(e)))
if d is None:
d = dict()
elif not isinstance(d, dict):
raise ValueError('Settings must be a YAML mapping.')
return Settings.create_from_dict(d)
def _load_preferences(dir_path):
path = os.path.join(dir_path, _PREFERENCE_FILE_NAME)
defaults_message = 'Will use default preference values.'
if not os.path.exists(path):
logging.warning((
'Could not find preferences file "{}". {}').format(
path, defaults_message))
return {}
try:
with open(path, 'r') as file_:
contents = file_.read()
except Exception as e:
logging.error(
'Read failed for preferences file "{}". {}'.format(
path, defaults_message))
return {}
try:
preferences = yaml_utils.load(contents)
except Exception as e:
logging.error((
'YAML load failed for preferences file "{}". {} YAML load error '
'message was:\n{}').format(path, defaults_message, str(e)))
return {}
if preferences is None:
# preferences file contains no data
return {}
elif not isinstance(preferences, dict):
logging.error(
'Preferences file "{}" does not contain a YAML map. {}'.format(
path, defaults_message))
return {}
return _Preferences(preferences)
def _load_preferences(file_path):
defaults_message = 'Will use default preference values.'
if not os.path.exists(file_path):
logging.warning(
f'Preference file "{file_path}" does not exist. '
f'{defaults_message}')
return _Preferences()
try:
with open(file_path, 'r') as file_:
contents = file_.read()
except Exception as e:
logging.warning(
f'Read failed for preference file "{file_path}". '
f'{defaults_message}')
return _Preferences()
try:
preferences = yaml_utils.load(contents)
except Exception as e:
logging.warning(
f'YAML load failed for preference file "{file_path}". '
f'{defaults_message} YAML load error message was:\n{str(e)}')
return _Preferences()
if preferences is None:
# preference file contains no data
return _Preferences()
elif not isinstance(preferences, dict):
logging.warning(
f'Preference file "{file_path}" does not contain a YAML mapping. '
f'{defaults_message}')
return _Preferences()
return _Preferences(preferences)
import pyaudio
import vesper.util.yaml_utils as yaml_utils
_CONFIG = yaml_utils.load('''
channel_signals:
- signal_type: Chirp
signal_config:
amplitude: 10000
start_freq: 0
end_freq: 10000
duration: 5.1
- signal_type: Chirp
signal_config:
amplitude: 10000
start_freq: 5000
end_freq: 1000
duration: 3.1
sample_rate: 22050
buffer_size: .1
''')
_SAMPLE_DTYPE = '<i2'
_SAMPLE_SIZE = 16 # bits
_BUFFER_SIZE = .2 # seconds
_TOTAL_BUFFER_SIZE = 10 # seconds
def test_create_from_dict(self):
contents = os_utils.read_file(_SETTINGS_FILE_PATH)
d = yaml_utils.load(contents)
settings = Settings.create_from_dict(d)
self._check_settings(settings)
def _load_settings(self):
path = classifier_utils.get_settings_file_path(self._clip_type)
text = path.read_text()
d = yaml_utils.load(text)
return Settings.create_from_dict(d)
def clean_metadata(self):
try:
return yaml_utils.load(self.cleaned_data['metadata'])
except Exception:
raise ValidationError('Could not parse metadata YAML.')
def _load_extensions_if_needed(self):
if self._extensions is None:
spec = yaml_utils.load(self._extensions_spec)
self._extensions = dict(
(type_name, _load_extension_classes(module_class_names))
for type_name, module_class_names in spec.items())
def _load_settings(self):
path = classifier_utils.get_settings_file_path(self.clip_type)
logging.info('Loading classifier settings from "{}"...'.format(path))
text = path.read_text()
d = yaml_utils.load(text)
return Settings.create_from_dict(d)
def clean_archive_data(self):
try:
return yaml_utils.load(self.cleaned_data['archive_data'])
except Exception:
raise ValidationError('Could not parse specified YAML.')
def test_dump_and_load(self):
x = {'x': 1, 'y': [1, 2, 3], 'z': {'one': 1}}
s = yaml_utils.dump(x)
y = yaml_utils.load(s)
self.assertEqual(x, y)
_TABLE_FORMAT = yaml_utils.load('''
columns:
- name: season
measurement: Night
format: Bird Migration Season
- name: year
measurement: Night
format:
name: Time
parameters:
format: "%Y"
- name: detector
measurement: Detector
format: Lower Case
- name: species
measurement: Clip Class
format:
name: Call Clip Class
parameters:
mapping:
DoubleUp: dbup
Other: othe
Unknown: unkn
- name: site
measurement: Station
format:
name: Mapping
parameters:
mapping:
Baldy: baldy
Floodplain: flood
Ridge: ridge
Sheep Camp: sheep
- name: date
measurement: Night
format:
name: Time
parameters:
format: "%m/%d/%y"
- name: recording_start
measurement: Recording Start Time
format: Time
- name: recording_length
measurement: Recording Duration
format: Duration
- name: detection_time
measurement: Elapsed Start Time
format: Duration
- name: real_detection_time
measurement: Start Time
format:
name: Time
parameters:
format: "%H:%M:%S"
- name: real_detection_time
measurement: Start Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: rounded_to_half_hour
measurement: Rounded Start Time
format: Time
- name: duplicate
measurement:
name: Duplicate Call
parameters:
min_intercall_interval: 60
ignored_classes: [Other, Unknown, Weak]
format:
name: Boolean
parameters:
values:
true: 'yes'
false: 'no'
- name: sunset
measurement: Sunset Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: civil_dusk
measurement: Civil Dusk Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: nautical_dusk
measurement: Nautical Dusk Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: astronomical_dusk
measurement: Astronomical Dusk Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: astronomical_dawn
measurement: Astronomical Dawn Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: nautical_dawn
measurement: Nautical Dawn Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: civil_dawn
measurement: Civil Dawn Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: sunrise
measurement: Sunrise Time
format:
name: Time
parameters:
format: "%m/%d/%y %H:%M:%S"
- name: moon_altitude
measurement: Moon Altitude
format:
name: Decimal
parameters:
detail: ".1"
- name: moon_illumination
measurement: Moon Illumination
format:
name: Decimal
parameters:
detail: ".1"
''')
def test_dump_and_load_with_non_default_flow_style(self):
x = {'x': 1, 'y': [1, 2, 3], 'z': {'one': 1}}
s = yaml_utils.dump(x, default_flow_style=False)
y = yaml_utils.load(s)
self.assertEqual(x, y)
def __init__(self, name, data):
data = yaml_utils.load(data)
super().__init__(name, data)
def _populate_database_from_yaml(s):
d = yaml_utils.load(s)
num_stations = d.get('num_stations', 1)
stations = []
for i in range(num_stations):
name = 'Station {}'.format(i + 1)
station = Station.objects.create(name=name, time_zone='US/Eastern')
stations.append(station)
model = DeviceModel.objects.create(name='Recorder Model',
type='Recorder',
manufacturer='Nagra',
model='X')
device = Device.objects.create(name='Recorder',
model=model,
serial_number='0')
clips = d['clips']
num_clips = len(clips)
clip_length = _CLIP_DURATION * _SAMPLE_RATE
recording_length = num_clips * clip_length
recording_duration = recording_length / _SAMPLE_RATE
recording_end_time = \
_RECORDING_START_TIME + datetime.timedelta(seconds=recording_duration)
station_recorder = StationDevice.objects.create(
station=station,
device=device,
start_time=_RECORDING_START_TIME,
end_time=recording_end_time)
creation_time = _RECORDING_START_TIME
recording = Recording.objects.create(station_recorder=station_recorder,
num_channels=_NUM_CHANNELS,
length=recording_length,
sample_rate=_SAMPLE_RATE,
start_time=_RECORDING_START_TIME,
end_time=recording_end_time,
creation_time=creation_time)
annotation_names = _get_annotation_names(clips)
annotation_infos = dict(
(name, _create_annotation_info(name, creation_time))
for name in annotation_names)
for i, clip_d in enumerate(clips):
clip_start_index = i * clip_length
offset = clip_start_index / _SAMPLE_RATE
clip_start_time = \
_RECORDING_START_TIME + datetime.timedelta(seconds=offset)
clip_duration = clip_length / _SAMPLE_RATE
clip_end_time = \
clip_start_time + datetime.timedelta(seconds=clip_duration)
clip = Clip.objects.create(recording=recording,
channel_num=0,
start_index=clip_start_index,
length=clip_length,
start_time=clip_start_time,
end_time=clip_end_time,
creation_time=creation_time)
for name, value in clip_d['annotations'].items():
info = annotation_infos[name]
model_utils.annotate_clip(clip, info, value, creation_time)
def _load_settings(self):
path = classifier_utils.get_settings_file_path(self.clip_type)
logging.info('Loading classifier settings from "{}"...'.format(path))
text = path.read_text()
d = yaml_utils.load(text)
return Settings.create_from_dict(d)
def test_dump_and_load(self):
x = {'x': 1, 'y': [1, 2, 3], 'z': {'one': 1}}
s = yaml_utils.dump(x)
y = yaml_utils.load(s)
self.assertEqual(x, y)
DATASET_CONFIGS = yaml_utils.load('''
- dataset_name_prefix: Thrush 20K
detector_name: Thrush
train_dataset_size: [6000, 6000]
val_dataset_size: [2000, 2000]
test_dataset_size: [2000, 2000]
- dataset_name_prefix: Thrush 100K
detector_name: Tseep
train_dataset_size: [36000, 36000]
val_dataset_size: [2000, 2000]
test_dataset_size: [2000, 2000]
- dataset_name_prefix: Thrush 1M
detector_name: Thrush
train_dataset_size: [496000, 496000]
val_dataset_size: [2000, 2000]
test_dataset_size: [2000, 2000]
- dataset_name_prefix: Tseep 3K
detector_name: Tseep
train_dataset_size: [2000, 2000]
val_dataset_size: [500, 500]
test_dataset_size: [500, 500]
- dataset_name_prefix: Tseep 20K
detector_name: Tseep
train_dataset_size: [6000, 6000]
val_dataset_size: [2000, 2000]
test_dataset_size: [2000, 2000]
- dataset_name_prefix: Tseep 100K
detector_name: Tseep
train_dataset_size: [40000, 40000]
val_dataset_size: [5000, 5000]
test_dataset_size: [5000, 5000]
- dataset_name_prefix: Tseep 340K
detector_name: Tseep
train_dataset_size: [158579, 158579]
val_dataset_size: [5000, 5000]
test_dataset_size: [5000, 5000]
- dataset_name_prefix: Tseep 1M
detector_name: Tseep
train_dataset_size: [480000, 480000]
val_dataset_size: [10000, 10000]
test_dataset_size: [10000, 10000]
''')
Schedule complementation.
See Simplenote entry "Recording Schedules, Take 2" for more information
about schedules.
'''
_INTERVAL_SCHEMA = yaml_utils.load('''
type: object
properties:
interval:
type: object
properties:
start: {}
end: {}
duration: {type: string}
additionalProperties: false
required: [interval]
additionalProperties: false
''')
_INTERVALS_SCHEMA = yaml_utils.load('''
type: object
properties:
intervals:
type: array
items:
type: object
def _populate_database_from_yaml(s):
d = yaml_utils.load(s)
num_stations = d.get('num_stations', 1)
stations = []
for i in range(num_stations):
name = 'Station {}'.format(i + 1)
station = Station.objects.create(name=name, time_zone='US/Eastern')
stations.append(station)
model = DeviceModel.objects.create(
name='Recorder Model', type='Recorder', manufacturer='Nagra',
model='X')
device = Device.objects.create(
name='Recorder', model=model, serial_number='0')
clips = d['clips']
num_clips = len(clips)
clip_length = _CLIP_DURATION * _SAMPLE_RATE
recording_length = num_clips * clip_length
recording_duration = recording_length / _SAMPLE_RATE
recording_end_time = \
_RECORDING_START_TIME + datetime.timedelta(seconds=recording_duration)
station_recorder = StationDevice.objects.create(
station=station, device=device, start_time=_RECORDING_START_TIME,
end_time=recording_end_time)
creation_time = _RECORDING_START_TIME
recording = Recording.objects.create(
station_recorder=station_recorder, num_channels=_NUM_CHANNELS,
length=recording_length, sample_rate=_SAMPLE_RATE,
start_time=_RECORDING_START_TIME, end_time=recording_end_time,
creation_time=creation_time)
annotation_names = _get_annotation_names(clips)
annotation_infos = dict(
(name, _create_annotation_info(name, creation_time))
for name in annotation_names)
for i, clip_d in enumerate(clips):
clip_start_index = i * clip_length
offset = clip_start_index / _SAMPLE_RATE
clip_start_time = \
_RECORDING_START_TIME + datetime.timedelta(seconds=offset)
clip_duration = clip_length / _SAMPLE_RATE
clip_end_time = \
clip_start_time + datetime.timedelta(seconds=clip_duration)
clip = Clip.objects.create(
recording=recording, channel_num=0,
start_index=clip_start_index, length=clip_length,
start_time=clip_start_time, end_time=clip_end_time,
creation_time=creation_time)
for name, value in clip_d['annotations'].items():
info = annotation_infos[name]
model_utils.annotate_clip(clip, info, value, creation_time)
def test_dump_and_load_with_non_default_flow_style(self):
x = {'x': 1, 'y': [1, 2, 3], 'z': {'one': 1}}
s = yaml_utils.dump(x, default_flow_style=False)
y = yaml_utils.load(s)
self.assertEqual(x, y)
def load_training_settings(training_name):
file_path = get_training_settings_file_path(training_name)
logging.info(f'Loading annotator settings from "{file_path}"...')
text = file_path.read_text()
dict_ = yaml_utils.load(text)
return Settings.create_from_dict(dict_)
def _load_extensions_if_needed(self):
if self._extensions is None:
spec = yaml_utils.load(self._extensions_spec)
self._extensions = dict(
(type_name, _load_extension_classes(module_class_names))
for type_name, module_class_names in spec.items())