def channel_names(dataframe, **kwargs):
"""
Gets a named channel related to a generic ADC channel.
For instance, an ADC with I2C address 48 has three
channels: 0, 1, 2 and 3. 48_0 could corresponde to the working electrode
of a CO sensor, so the channel ADC_48_0 would be copied over to a new
channel named CO_WE. for the ADC_48_1, the CO auxiliary electrode
it would be copied to CO_AE. The naming convention is specified in the
hardware folder
Parameters
----------
channel: string
Channel name, i.e. ADC_48_0
Returns
-------
Channel named accordingly
"""
# Check inputs
flag_error = False
if 'channel' not in kwargs: flag_error = True
if kwargs['channel'] not in dataframe:
std_out(f"Channel {kwargs['channel']} not in dataframe. Ignoring",
'WARNING')
return None
if flag_error:
std_out('Problem with input data', 'ERROR')
return None
# Make copy
df = dataframe.copy()
return df[kwargs['channel']]
def to_csv(self, path=None, forced_overwrite=False):
"""
Exports devices in test to desired path
Parameters
----------
path: string
None
The path (directory) to export the csv(s) into. If None, exports to test_path/processed/
forced_overwrite: boolean
False
To overwrite existing files
Returns
-------
True if export successul
"""
export_ok = True
if path is None: epath = join(self.path, 'processed')
else: epath = path
# Export to csv
for device in self.devices.keys():
export_ok &= self.devices[device].export(
epath, forced_overwrite=forced_overwrite)
if export_ok:
std_out(f'Test {self.full_name} exported successfully', 'SUCCESS')
else:
std_out(f'Test {self.full_name} not exported successfully', 'ERROR')
return export_ok
def fill_template(individual_descriptor,
descriptor_file_name,
upload_type='dataset'):
# Open base template with all keys
if upload_type == 'dataset':
template_file_name = 'template_zenodo_dataset'
elif upload_type == 'publication':
template_file_name = 'template_zenodo_publication'
with open(join('zenodo_templates', f'{template_file_name}.json'),
'r') as template_file:
template = json.load(template_file)
filled_template = template
# Fill it up for each key
for key in individual_descriptor.keys():
value = individual_descriptor[key]
if key in filled_template['metadata'].keys():
filled_template['metadata'][key] = value
with open(
join(config.paths['dataDirectory'], 'uploads',
descriptor_file_name), 'w') as descriptor_json:
json.dump(filled_template, descriptor_json, ensure_ascii=True)
std_out(f'Created descriptor file for {descriptor_file_name}',
'SUCCESS')
return json.dumps(filled_template)
def __update_descriptor__(self):
if self.descriptor == {}: self.std_out('No descriptor file to update')
for field in self._default_fields:
if field not in self.descriptor.keys():
self.descriptor[field] = self._default_fields[field]
# Add details to descriptor, or update them if there is anything in details
for detail in self.details.keys():
self.descriptor[detail] = self.details[detail]
# Add devices to descriptor
for device_name in self.devices.keys():
device = self.devices[device_name]
if device.source == 'csv':
device.processed_data_file = self.full_name + '_' + str(
device.id) + '.csv'
dvars = vars(device).copy()
for discvar in config._discvars:
if discvar in dvars: dvars.pop(discvar)
self.descriptor['devices'][device.id] = dvars
# Create yaml with test description
with open(join(self.path, 'test_description.yaml'), 'w') as yaml_file:
yaml.dump(self.descriptor, yaml_file)
std_out('Descriptor file updated')
def export_csv_file(path, file_name, df, forced_overwrite=False):
'''
Exports pandas dataframe to a csv file
Parameters
----------
path: String
Directory path
file_name: String
File name for the resulting csv
df: pandas.DataFrame
Dataframe to export
forced_overwrite: boolean
False
If file exists, overwrite it or not
Returns
---------
True if exported, False if not (if file exists returns False)
'''
# If path does not exist, create it
if not exists(path):
makedirs(path)
# If file does not exist
if not exists(path + '/' + str(file_name) + '.csv') or forced_overwrite:
df.to_csv(path + '/' + str(file_name) + '.csv', sep=",")
std_out('File saved to: \n' + path + '/' + str(file_name) + '.csv',
'SUCCESS')
else:
std_out(
"File Already exists - delete it first, I was not asked to overwrite anything!",
'ERROR')
return False
return True
def post(self, with_post_info=True):
'''
Posts devices metrics. Only available for parent of ScApiDevice
Parameters
----------
with_post_info: boolean
Default True
Add the post info to the package
Returns
----------
boolean
True if posted ok, False otherwise
'''
post_ok = True
if self.sources[self.source]['handler'] != 'ScApiDevice':
std_out('Only supported processing post is to SmartCitizen API',
'ERROR')
return False
for metric in self.metrics:
if self.metrics[metric]['post'] == True:
# Get single series for post
df = DataFrame(self.readings[metric])
sensor_id = self.metrics[metric]['id']
post_ok &= self.api_device.post_device_data(
df, sensor_id=sensor_id)
# Post info if requested. It should be updated elsewhere
if with_post_info: self.api_device.post_postprocessing_info()
return post_ok
def load_postprocessing_info(self):
if self.source != 'api':
return None
if self.sources[self.source]['handler'] != 'ScApiDevice':
return None
# Request to get postprocessing information
if self.api_device.get_postprocessing_info() is None:
return None
# Put it where it goes
self.hw_id = self.api_device.postprocessing_info['hardware_id']
self.hw_updated_at = self.api_device.postprocessing_info['updated_at']
self.hw_post_blueprint = self.api_device.postprocessing_info[
'postprocessing_blueprint']
self.latest_postprocessing = self.api_device.postprocessing_info[
'latest_postprocessing']
# Use postprocessing info blueprint
if self.hw_post_blueprint in config.blueprints.keys():
std_out(
f'Using hardware postprocessing blueprint: {self.hw_post_blueprint}'
)
self.blueprint = self.hw_post_blueprint
return self.api_device.postprocessing_info
def export(self, path, forced_overwrite=False, file_format='csv'):
'''
Exports Device.readings to file
Parameters
----------
path: String
Path to export file to, does not include filename.
The filename will be the Device.id property
forced_overwrite: boolean
False
Force data export in case of already existing file
file_format: String
'csv'
File format to export. Current supported format CSV
Returns
---------
True if exported ok, False otherwise
'''
# Export device
if file_format == 'csv':
return export_csv_file(path,
str(self.id),
self.readings,
forced_overwrite=forced_overwrite)
else:
std_out('Not supported format', 'ERROR')
return False
def post_postprocessing_info(self):
'''
POST postprocessing info into the device in the SmartCitizen API
Updates all the post info. Changes need to be made info the keys of the postprocessing_info outside of here
# Example postprocessing_info:
# {
# "updated_at": "2020-10-29T04:35:23Z",
# "postprocessing_blueprint": 'sck_21_gps',
# "hardware_id": "SCS20100",
# "latest_postprocessing": "2020-10-29T08:35:23Z"
# }
'''
if 'SC_BEARER' not in environ:
std_out('Cannot post without Auth Bearer', 'ERROR')
return
headers = {'Authorization':'Bearer ' + environ['SC_BEARER'], 'Content-type': 'application/json'}
post_json = dumps(self.postprocessing_info)
std_out(f'Posting post-processing info:\n {post_json}')
response = patch(f'https://api.smartcitizen.me/v0/devices/{self.id}/', data = post_json, headers = headers)
if response.status_code == 200 or response.status_code == 201:
return True
return False
def deconvolution(dataframe, **kwargs):
"""
Calculates pollutant concentration for convolved metrics, such as NO2+O3.
Needs convolved metric, and target pollutant sensitivities
Parameters
----------
source: string
Name of convolved metric containing both pollutants (such as NO2+O3)
base: string
Name of one of the already deconvolved pollutants (for instance NO2)
id: int
Sensor ID
pollutant: string
Pollutant name. Must be included in the corresponding LUTs for unit convertion and additional parameters:
MOLECULAR_WEIGHTS, config._background_conc, CHANNEL_LUT
Returns
-------
calculation of pollutant based on: 6.36 * sensitivity(working - zero_working)/(auxiliary - zero_auxiliary)
"""
result = Series()
baseline = Series()
flag_error = False
if 'source' not in kwargs: flag_error = True
if 'base' not in kwargs: flag_error = True
if 'id' not in kwargs: flag_error = True
if 'pollutant' not in kwargs: flag_error = True
if flag_error:
std_out('Problem with input data', 'ERROR')
return None
sensitivity_1 = config.calibrations.loc[kwargs['id'], 'sensitivity_1']
sensitivity_2 = config.calibrations.loc[kwargs['id'], 'sensitivity_2']
target_1 = config.calibrations.loc[kwargs['id'], 'target_1']
target_2 = config.calibrations.loc[kwargs['id'], 'target_2']
nWA = config.calibrations.loc[kwargs['id'],
'w_zero_current'] / config.calibrations.loc[
kwargs['id'], 'aux_zero_current']
if target_1 != kwargs['pollutant']:
std_out(
f"Sensor {kwargs['id']} doesn't coincide with calibration data",
'ERROR')
return None
factor_unit_1 = get_units_convf(kwargs['pollutant'], from_units='ppm')
factor_unit_2 = get_units_convf(kwargs['base'], from_units='ppm')
result = factor_unit_1 * (
config._alphadelta_pcb * dataframe[kwargs['source']] -
dataframe[kwargs['base']] / factor_unit_2 *
abs(sensitivity_2)) / abs(sensitivity_1)
# Add Background concentration
result += config._background_conc[kwargs['pollutant']]
return result
def add_content(self,
title,
figure=None,
text=None,
iframe=None,
show_title=True,
force=False):
'''
Adds content for the rendered flask template of the test. Content is a dict()
which contains a key per title (replacing ' ' with '_') and the content in it.
Parameters
----------
title
None
Content title. Needs to not be None
figure
None
matplotlib or similar figure that can be converted to base64
text
None
Text to be converted to <p> html tag with additional inner html (jinja2 safe rendered)
iframe
None
HTML iframe contanining anything
show_title
True
show title in HTML <h3> tag
force
If already added content with this title
Returns
----------
True if content added, false otherwise
'''
title_cor = sub('\W|^(?=\d)', '_', title)
if title_cor not in self.content or force:
self.content[title_cor] = dict()
if title is not None:
self.content[title_cor]['title'] = title
if figure is not None:
self.content[title_cor]['image'] = to_png_b64(figure)
if text is not None:
self.content[title_cor]['text'] = text
if iframe is not None:
self.content[title_cor]['iframe'] = iframe
self.content[title_cor]['show_title'] = show_title
std_out('Item added', 'SUCCESS')
return True
else:
std_out('Item not added as its already in content', 'ERROR')
return False
def add_device(self, device):
'''
Adds a device to the test. The device has to be an instance of 'scdata.device.Device'
'''
if device.id not in self.devices.keys():
self.devices[device.id] = device
else:
std_out(f'Device {device.id} is duplicated', 'WARNING')
def post_device_data(self, df, sensor_id, clean_na = 'drop'):
'''
POST data in the SmartCitizen API
Parameters
----------
df: pandas DataFrame
Contains data in a DataFrame format.
Data is posted regardless the name of the dataframe
It uses the sensor id provided, not the name
Data is posted in UTC TZ so dataframe needs to have located
timestamp
sensor_id: int
The sensor id
clean_na: string, optional
'drop'
'drop', 'fill'
Returns
-------
True if the data was posted succesfully
'''
if 'SC_ADMIN_BEARER' not in environ:
std_out('Cannot post without Auth Bearer', 'ERROR')
return
headers = {'Authorization':'Bearer ' + environ['SC_ADMIN_BEARER'], 'Content-type': 'application/json'}
# Get sensor name
sensor_name = list(df.columns)[0]
# Clean df of nans
df = clean(df, clean_na, how = 'all')
# Process dataframe
df['id'] = sensor_id
df.index.name = 'recorded_at'
df.rename(columns = {sensor_name: 'value'}, inplace = True)
df.columns = MultiIndex.from_product([['sensors'], df.columns])
j = (df.groupby('recorded_at', as_index = True)
.apply(lambda x: x['sensors'][['value', 'id']].to_dict('r'))
)
# Prepare json post
payload = {"data":[]}
for item in j.index:
payload["data"].append(
{
"recorded_at": localise_date(item, 'UTC').strftime('%Y-%m-%dT%H:%M:%SZ'),
"sensors": j[item]
}
)
payload_json = dumps(payload)
response = post(f'https://api.smartcitizen.me/v0/devices/{self.id}/readings', data = payload_json, headers = headers)
if response.status_code == 200 or response.status_code == 201:
return True
return False
def get_device_added_at(self):
if self.added_at is None:
if self.get_device_json() is not None:
self.added_at = self.devicejson['added_at']
std_out('Device {} was added at {}'.format(self.id, self.added_at))
return self.added_at
def get_device_last_reading(self, update = False):
if self.last_reading_at is None or update:
if self.get_device_json(update) is not None:
self.last_reading_at = self.devicejson['last_reading_at']
std_out ('Device {} has last reading at {}'.format(self.id, self.last_reading_at))
return self.last_reading_at
def del_metric(self, metricn=''):
if 'metrics' not in vars(self): return
if metricn in self.metrics: self.metrics.pop(metricn, None)
if metricn in self.readings.columns: self.readings.__delitem__(metricn)
if metricn not in self.readings and metricn not in self.metrics:
std_out(f'Metric {metricn} removed from metrics', 'SUCCESS')
return True
return False
def check_existing(self, comment):
l = []
c = self.cron.find_comment(comment)
for item in c: l.append(c)
if l:
std_out(f'{comment} already running')
return True
else:
std_out(f'{comment} not running')
return False
def get_device_location(self):
if self.location is None:
latitude, longitude = self.get_device_lat_long()
# Localize it
self.location = tz_where.tzNameAt(latitude, longitude)
std_out('Device {} timezone is {}'.format(self.id, self.location))
return self.location
def prepare(self, measurand, inputs, options=dict()):
"""
Prepares a test for a regression model
Parameters
----------
measurand: dict
measurand = {'8019043': ['NO2']}
inputs: dict
inputs per device and reading
inputs = {'devicename': ['reading-1', 'reading-2']}
options: dict
Options including data processing. Defaults in config._model_def_opt
Returns
-------
df = pandas Dataframe
measurand_name = string
"""
options = dict_fmerge(options, config._model_def_opt)
# Measurand
measurand_device = list(measurand.keys())[0]
measurand_metric = measurand[measurand_device][0]
measurand_name = measurand[measurand_device][0] + '_' + measurand_device
df = DataFrame()
df[measurand_name] = self.devices[measurand_device].readings[
measurand_metric]
for input_device in inputs.keys():
combined_df = self.combine(devices=[input_device],
readings=inputs[input_device])
df = df.combine_first(combined_df)
if options['common_avg']:
common_channels = inputs[list(inputs.keys())[0]]
for input_device in inputs.keys():
common_channels = list(
set(common_channels).intersection(set(inputs[input_device])))
std_out(f'Performing avg in common columns {common_channels}')
for channel in common_channels:
columns_list = [
channel + '_' + device for device in list(inputs.keys())
]
df[channel + '_AVG'] = df[columns_list].mean(axis=1)
df = df.loc[:,
df.columns.str.contains("_AVG")
| df.columns.str.contains(measurand_name)]
if options['clean_na'] is not None:
df = clean(df, options['clean_na'], how='any')
return df, measurand_name
def __fill_metrics__(self):
if self.hw_id in config.hardware_info:
std_out('Hardware ID found in history', "SUCCESS")
hw_info = config.hardware_info[self.hw_id]
else:
std_out(f"Hardware id: {self.hw_id} not found in hardware_info",
'ERROR')
return False
# Now go through sensor versions and parse them
for version in hw_info.keys():
from_date = hw_info[version]["from"]
to_date = hw_info[version]["to"]
for slot in hw_info[version]["ids"]:
# Alphasense type
if slot.startswith('AS'):
sensor_id = hw_info[version]["ids"][slot]
as_type = config._as_sensor_codes[sensor_id[0:3]]
pollutant = as_type[as_type.index('_') + 1:]
platform_sensor_id = config._platform_sensor_ids[pollutant]
# TODO - USE POLLUTANT OR PLATFORM SENSOR ID?
process = 'alphasense_803_04'
wen = f"ADC_{slot.strip('AS_')[:slot.index('_')]}_{slot.strip('AS_')[slot.index('_')+1]}"
aen = f"ADC_{slot.strip('AS_')[:slot.index('_')]}_{slot.strip('AS_')[slot.index('_')+2]}"
# metric_name = f'{pollutant}_V{version}_S{list(hw_info[version]["ids"]).index(slot)}'
metric_name = f'{pollutant}'
metric = {
metric_name: {
'process': process,
'desc':
f'Calculation of {pollutant} based on AAN 803-04',
'units': 'ppb', # always for alphasense sensors,
'id': platform_sensor_id,
'post': True,
'kwargs': {
'from_date': from_date,
'to_date': to_date,
'id': sensor_id,
'we': wen,
'ae': aen,
't': 'EXT_TEMP', # With external temperature?
'location': self.location
}
}
}
self.add_metric(metric)
def apply_regressor(dataframe, **kwargs):
'''
Applies a regressor model based on a pretrained model
Parameters
----------
model: sklearn predictor
Model with .predict method
options: dict
Options for data preprocessing. Defaults in config.model_def_opt
variables: dict
variables dictionary with:
{
'measurand': {
'measurand-device-name': ['measurand']
},
'inputs': {'input-device-names': ['input-1', 'input_2', 'input-3']
}
}
Returns
----------
pandas series containing the prediction
'''
inputs = list()
for device in kwargs['variables']['inputs']:
inputs = list(
set(inputs).union(set(kwargs['variables']['inputs'][device])))
try:
inputdf = dataframe[inputs].copy()
inputdf = inputdf.reindex(sorted(inputdf.columns), axis=1)
except KeyError:
std_out('Inputs not in dataframe', 'ERROR')
pass
return None
if 'model' not in kwargs:
std_out('Model not in inputs', 'ERROR')
else:
model = kwargs['model']
if 'options' not in kwargs:
options = config.model_def_opt
else:
options = dict_fmerge(config.model_def_opt, kwargs['options'])
# Remove na
inputdf = clean(inputdf, options['clean_na'], how='any')
features = array(inputdf)
result = DataFrame(model.predict(features)).set_index(inputdf.index)
return result
def __check_sensors__(self):
remove_sensors = list()
for sensor in self.sensors:
if sensor not in self.readings.columns:
remove_sensors.append(sensor)
if remove_sensors != []:
std_out(f'Removing sensors from device: {remove_sensors}',
'WARNING')
for sensor_to_remove in remove_sensors:
self.sensors.pop(sensor_to_remove, None)
std_out(f'Device sensors after removal: {list(self.sensors.keys())}')
def get_device_location(self, update = False):
if self.location is None or update:
latitude, longitude = self.get_device_lat_long(update)
# Localize it
if latitude is not None and longitude is not None:
self.location = tz_where.tzNameAt(latitude, longitude)
std_out ('Device {} timezone is {}'.format(self.id, self.location))
return self.location
def get_device_json(self, update = False):
if self.devicejson is None or update:
try:
deviceR = get(self.API_BASE_URL + '{}/'.format(self.id))
if deviceR.status_code == 200 or deviceR.status_code == 201:
self.devicejson = deviceR.json()
else:
std_out('API reported {}'.format(deviceR.status_code), 'ERROR')
except:
std_out('Failed request. Probably no connection', 'ERROR')
pass
return self.devicejson
def dispersion_summary(self):
self._dispersion_summary = dict()
if self.dispersion_df is None:
std_out('Perform dispersion analysis first!', 'ERROR')
return None
for channel in self.common_channels:
if channel in config._dispersion['ignore_channels']: continue
# Calculate
self._dispersion_summary[channel] = self.dispersion_df[channel +
'_STD'].mean()
return self._dispersion_summary
def get_user_json_by_username(self):
if self.userjson is None:
try:
userR = get(self.API_BASE_URL + '{}/'.format(self.username), headers = self.headers)
print (userR)
if userR.status_code == 200 or userR.status_code == 201:
self.userjson = userR.json()
else:
std_out('API reported {}'.format(userR.status_code), 'ERROR')
except:
std_out('Failed request. Probably no connection', 'ERROR')
pass
return self.userjson
def get_device_json(self):
if self.devicejson is None:
try:
s = get(self.API_BASE_URL + f'codi_eoi={self.id}')
if s.status_code == 200 or s.status_code == 201:
self.devicejson = read_csv(StringIO(s.content.decode('utf-8')))
else:
std_out('API reported {}'.format(s.status_code), 'ERROR')
except:
std_out('Failed request. Probably no connection', 'ERROR')
pass
return self.devicejson
def set_descriptor_attrs(self):
# Descriptor attributes
for ditem in self.description.keys():
if ditem not in vars(self):
std_out(f'Ignoring {ditem} from input')
continue
if type(self.__getattribute__(ditem)) == dict:
self.__setattr__(
ditem,
dict_fmerge(self.__getattribute__(ditem),
self.description[ditem]))
else:
self.__setattr__(ditem, self.description[ditem])
def dprocess(device, dryrun=False):
'''
This function processes a device from SC API assuming there
is postprocessing information in it and that it's valid for doing
so
'''
std_out(f'[CHUPIFLOW] Processing instance for device {device}')
# Create device from SC API
d = Device(descriptor={'source': 'api', 'id': f'{device}'})
if d.validate():
# Load only unprocessed
if d.load(only_unprocessed=True, max_amount=config._max_load_amount):
# Process it
d.process()
# Post results
d.post_metrics(dry_run=dry_run,
max_retries=config._max_forward_retries)
# Forward it if requested
if d.forwarding_request is not None:
std_out(f'[CHUPIFLOW] Forwarding {device}')
d.forward(dry_run=dry_run,
max_retries=config._max_forward_retries)
d.update_postprocessing(dry_run=dry_run)
else:
std_out(f'[CHUPIFLOW] Device {device} not valid', 'ERROR')
std_out(f'[CHUPIFLOW] Concluded job for {device}')
def process(self, only_new=False):
'''
Calculates all the metrics in each of the devices
Returns True if done OK
'''
process_ok = True
for device in self.devices:
process_ok &= self.devices[device].process(only_new=only_new)
# Cosmetic output
if process_ok: std_out(f'Test {self.full_name} processed', 'SUCCESS')
else: std_out(f'Test {self.full_name} not processed', 'ERROR')
return process_ok