def start_measurement(self, comment):
""" Start a measurement """
data_set_saver = DataSetSaver("measurements_dummy", "xy_values_dummy",
"dummy", "dummy")
data_set_saver.start()
data_set_time = time.time()
metadata = {
"Time": CustomColumn(data_set_time, "FROM_UNIXTIME(%s)"),
"comment": comment,
"type": 65,
"preamp_range": 9,
"sem_voltage": -1
}
labels = [
"2W Heater 1", "2W Heater 2", "2W RTD Source", "2W RTD Sense",
"Short circuit check", "RTD Source Sense Left",
"RTD Source Sense Right", "4W RTD", "Temperature", "Temperature 2"
]
for label in labels:
metadata["mass_label"] = label
data_set_saver.add_measurement(label, metadata)
for i in range(0, 99999999):
self.update_values()
for label in labels:
print(
str(i) + ': Channel: ' + label + ': ' +
str(self.data[label]))
data_set_saver.save_point(
label, (time.time() - data_set_time, self.data[label]))
time.sleep(1)
def scan(self, start_energy, end_energy, step, integration_time):
""" Perform a scan """
metadata = {
"Time": CustomColumn(time.time(), "FROM_UNIXTIME(%s)"),
"comment": 'Test',
"type": 2
}
label = 'XPS signal'
self.data_set_saver.add_measurement(label, metadata)
count_string = self.agilent.scpi_comm("SENS:TOT:DATA? (@203)")
meas_time = time.time()
for binding_energy in np.arange(end_energy, start_energy, -1 * step):
kin_energy = str((self.x_ray - binding_energy) / self.calib)
string = "SOURCE:VOLT " + kin_energy + ", (@205)"
self.agilent.scpi_comm(string)
time.sleep(integration_time)
count_string = self.agilent.scpi_comm("SENS:TOT:DATA? (@203)")
count = int(float(count_string.strip()))
int_time = time.time() - meas_time
meas_time = time.time()
count_rate = count / int_time
self.data_set_saver.save_point(label, (binding_energy, count_rate))
def setup_data_set_saver(self):
"""Setup the data set saver"""
sql_time = CustomColumn(time(), 'FROM_UNIXTIME(%s)')
for codename in self.codenames:
metadata = {
'time': sql_time,
'comment': self.config['comment'],
'label': codename[3:],
'type': 1,
'power_supply_channel': self.channel_id,
}
self.data_set_saver.add_measurement(codename, metadata)
def run(self):
"""Run the ramp
This is the main function that contains a loop over the steps in the ramp and the
method that does all the work
"""
self.data_set_saver.start()
# Specify the start time for database
now = time()
now_custom_column = CustomColumn(now, 'FROM_UNIXTIME(%s)')
# Add all measurements
self.metadata['label'] = 'voltage'
self.data_set_saver.add_measurement('voltage', self.metadata)
self.metadata['label'] = 'current'
self.data_set_saver.add_measurement('current', self.metadata)
self.metadata['label'] = 'CO2 flow'
self.data_set_saver.add_measurement('CO2 flow', self.metadata)
# Add the one custom column
self.metadata['time'] = now_custom_column
# Set the current limit on the power supply to 10A
self.cpx.set_current_limit(10)
# Set the pressure on the pressure controller
try:
for step in self.ramp:
# Go through the steps in the ramp file
if step['type'] == 'constant_voltage':
self.run_constant_voltage_step(step)
elif step['type'] == 'voltage_ramp':
self.run_voltage_ramp_step(step)
elif step['type'] == 'constant_current':
self.run_constant_current_step(step)
except KeyboardInterrupt:
print('Program interupted by user')
except IOError as e:
print("I/O error({0}): {1}".format(e.errno, e.strerror))
pass
finally:
# End the data collection and turn off power supply after run or interruption
print('The program has ended')
self.cpx.output_status(False)
self.data_set_saver.wait_for_queue_to_empty()
self.data_set_saver.stop()
def run_measurement(self, v_from, v_to, scan_both_ways):
""" Perform the actual measurement """
metadata = {
"Time": CustomColumn(self.data_set_time, "FROM_UNIXTIME(%s)"),
"comment": self.comment,
"type": 1
}
for label in [
"Ch1",
"Ch2",
"Ch3",
"Ch4",
"Ch5",
"Ch6",
"Ch7",
"Ch8",
]:
metadata["mass_label"] = label
self.data_set_saver.add_measurement(label, metadata)
self.smu.set_voltage(0.0)
self.smu.output_state(True)
for channel in range(1, 9):
print('Channel: ' + str(channel))
self.mux.scpi_comm('ROUTE:CLOSE (@10' + str(channel) + ')')
time.sleep(0.2)
voltage, current = self.smu.iv_scan(v_from=v_from,
v_to=v_to,
steps=10,
settle_time=0)
for i in range(0, len(current)):
self.data_set_saver.save_point('Ch' + str(channel),
(voltage[i], current[i]))
if scan_both_ways:
voltage, current = self.smu.iv_scan(v_from=v_to,
v_to=v_from,
steps=50,
settle_time=0)
for i in range(0, len(current)):
self.data_set_saver.save_point('Ch' + str(channel),
(voltage[i], current[i]))
self.mux.scpi_comm('ROUTE:OPEN (@10' + str(channel) + ')')
self.smu.set_voltage(0.0)
self.smu.output_state(False)
time.sleep(0.2)
def init_logging(self):
if self.log_data:
self.comment = 'Run'
self.data_set_saver = DataSetSaver('measurements_mailscan',
'xy_values_mailscan',
credentials.user,
credentials.passwd)
self.data_set_saver.start()
# PyExpLabSys does does not excell in db-normalization - add
# metadata to all channels
metadata = {
"Time": CustomColumn(self.start_time, "FROM_UNIXTIME(%s)"),
"comment": self.comment,
"type": 1,
"label": None,
"processes": self.number_of_threads()[1]
}
metadata['label'] = 'Avg export speed'
self.data_set_saver.add_measurement(metadata['label'], metadata)
metadata['label'] = 'Total export size'
self.data_set_saver.add_measurement(metadata['label'], metadata)
metadata['label'] = 'Total users'
self.data_set_saver.add_measurement(metadata['label'], metadata)
metadata['label'] = 'Total memory'
self.data_set_saver.add_measurement(metadata['label'], metadata)
metadata['label'] = 'Total CPU'
self.data_set_saver.add_measurement(metadata['label'], metadata)
metadata['label'] = 'Total Mails'
self.data_set_saver.add_measurement(metadata['label'], metadata)
for scanner in self.amqp_messages.keys():
if scanner == 'global':
continue
metadata['processes'] = 1
metadata['label'] = '{} memory'.format(scanner)
self.data_set_saver.add_measurement(metadata['label'],
metadata)
metadata['label'] = '{} exported users'.format(scanner)
self.data_set_saver.add_measurement(metadata['label'],
metadata)
comment = "First run"
## EDIT HERE
# Create data set saver object
data_set_saver = DataSetSaver(
"measurements_dummy",
"xy_values_dummy",
credentials.USERNAME,
credentials.PASSWORD,
)
data_set_saver.start()
# Create measurement specs i.e. entires entries in the metadata table
data_set_time = time.time()
metadata = {
"time": CustomColumn(data_set_time, "FROM_UNIXTIME(%s)"),
"comment": comment,
"type": 64,
"preamp_range": 0,
"sem_voltage": 0
}
# Only the labels differ, so we generate the metadata with a loop
for label in [
"p_korr", "i_korr", "total_korr", "ph_setpoint", "ph_value",
"pump_rate"
]:
metadata["mass_label"] = label
data_set_saver.add_measurement(label, metadata)
# http://pyexplabsys.readthedocs.io/common/database_saver.html#PyExpLabSys.common.database_saver.DataSetSaver.save_point
"""
import time
from PyExpLabSys.common.database_saver import DataSetSaver, CustomColumn
import credentials
data_set_saver = DataSetSaver(
'measurements_large_CO2_MEA',
'xy_values_large_CO2_MEA',
credentials.USERNAME,
credentials.PASSWORD,
)
data_set_saver.start()
now = time.time()
now_custom_column = CustomColumn(now, 'FROM_UNIXTIME(%s)')
#CREATE TABLE `measurements_large_CO2_MEA` (
# `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
# `time` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
# `type` int(10) unsigned NOT NULL COMMENT 'Type of measurement, as found in the types table',
# `comment` varchar(128) NOT NULL COMMENT 'Comment',
# `cathode_gas_type` varchar(128) NOT NULL COMMENT 'Cathode gas type',
# `anode_gas_type` varchar(128) NOT NULL COMMENT 'Anode gas type',
# `cathode_catalyst_description` varchar(128) NOT NULL COMMENT 'Cathode catalyst description',
# `anode_catalyst_description` varchar(128) NOT NULL COMMENT 'Anode catalyst description',
# `label` varchar(45) NOT NULL,
# PRIMARY KEY (`id`)
#) ENGINE=MyISAM DEFAULT CHARSET=latin1 COMMENT='A single record pr. measurent run'
metadata = {
def run(self):
"""Run the ramp
This is the main function that contains a loop over the steps in the ramp and the
method that does all the work
"""
self.data_set_saver.start()
# Specify the start time for database
now = time()
now_custom_column = CustomColumn(now, 'FROM_UNIXTIME(%s)')
# Add all measurements
self.metadata['label'] = 'voltage'
self.data_set_saver.add_measurement('voltage', self.metadata)
self.metadata['label'] = 'current'
self.data_set_saver.add_measurement('current', self.metadata)
self.metadata['label'] = 'CO2 flow'
self.data_set_saver.add_measurement('CO2 flow', self.metadata)
# If another flow meter is used collect the flow here
#self.metadata['label'] = 'cell outlet flow'
#self.data_set_saver.add_measurement('cell outlet flow', self.metadata)
# Collect the pressure reading from the pressure controller
#self.metadata['label'] = 'pressure'
#self.data_set_saver.add_measurement('pressure', self.metadata)
# Add the one custom column
self.metadata['time'] = now_custom_column
# Set the current limit on the power supply to 10A
self.cpx.set_current_limit(10)
# Change address to CO2 flow controller
self.red_flow_meter.set_address(42)
# Set the CO2 flow to the specified value
self.red_flow_meter.write_value('setpoint_gas_flow', self.setpoint_gas_flow)
# Set the pressure on the pressure controller
#self.message = 'json_wn#' + json.dumps({'A': 0.0, 'B': self.setpoint_pressure })
#self.sock.sendto(message.encode('ascii'), (self.host, self.port))
try:
for step in self.ramp:
# Go through the steps in the ramp file
if step['type'] == 'constant_voltage':
self.run_constant_voltage_step(step)
elif step['type'] == 'voltage_ramp':
self.run_voltage_ramp_step(step)
elif step['type'] == 'constant_current':
self.run_constant_current_step(step)
except KeyboardInterrupt:
print('Program interupted by user')
finally:
# End the data collection and turn off power supply after run or interruption
print('The program has ended')
self.cpx.output_status(False)
self.red_flow_meter.set_address(42)
self.red_flow_meter.write_value('setpoint_gas_flow', 0.0)
#self.message = 'json_wn#' + json.dumps({'A': 0.0, 'B': 0.0})
#self.sock.sendto(message.encode('ascii'), (self.host, self.port))
self.data_set_saver.wait_for_queue_to_empty()
self.data_set_saver.stop()
def main():
"""Main function"""
parser = argparse.ArgumentParser(
description='Run the infamous ph control script.')
# ph_setpoint, ph_direction (string [up, down]), kick_in_rate (float)
# Main (constant), secondary (regulation)
# python ph_increment.py 10.0 --direction up --main-offset=24.0 --second-min=10.0 --second-max=40.0 --second-offset=17.0
parser.add_argument('setpoint', type=float, help='The Ph setpoint.')
parser.add_argument('--direction',
default=None,
help='Pumping direction. Must be up or down.',
required=True)
parser.add_argument('--main-offset',
type=float,
default=None,
help='Start pumping speed for the main pump.',
required=True)
parser.add_argument('--second-min',
type=float,
default=None,
help='Minimum pumping speed for the secondary pump.',
required=True)
parser.add_argument('--second-max',
type=float,
default=None,
help='Maximum pumping speed for the secondary pump.',
required=True)
parser.add_argument('--second-offset',
type=float,
default=None,
help='Start pumping value for the secondary pump.',
required=True)
parser.add_argument('--comment',
default=None,
help='Optional comment',
required=True)
args = parser.parse_args()
## Edit comment
comment = "pH " + str(args.setpoint) + " // p: 0.02 // start rate " + str(
args.second_offset) + " // " + args.comment
## Edit comment
# raise SystemExit('All good')
# Init pumps, Omegabus, PID and data saver
pump_main = AL1000(
"/dev/serial/by-id/usb-FTDI_USB-RS232_Cable_FTV9X9TM-if00-port0")
pump_second = AL1000(
"/dev/serial/by-id/usb-FTDI_USB-RS232_Cable_FTWZCJLU-if00-port0")
obus = OmegaBus(
"/dev/serial/by-id/usb-FTDI_USB-RS232_Cable_FTWZCGSW-if00-port0",
baud=9600,
)
data_set_saver = DataSetSaver("measurements_dummy", "xy_values_dummy",
"dummy", "dummy")
pid = PID(pid_p=0.04, pid_i=0.0, pid_d=0, p_max=9999, p_min=-9)
pid.update_setpoint(args.setpoint)
# time_start = time.time()
#Pre flight check.
pump_main_check = pump_main.get_firmware()
print("main: " + pump_main_check)
pump_second_check = pump_second.get_firmware()
print("second: " + pump_second_check)
obus_check = obus.read_value(1)
obus_check = current_to_ph(obus_check)
if pump_main_check != "NE1000V3.923":
print("Main pump failed")
raise SystemExit(1)
if pump_second_check != "NE1000V3.923":
print("Secondary pump failed")
raise SystemExit(1)
if obus_check < 0:
print("OmegaBus failed")
raise SystemExit(1)
#Set initial condition for pumps
pump_second.set_direction("INF")
pump_main.set_direction("INF")
if args.direction == "up":
pump_second.set_rate(args.second_offset)
rate_second = args.second_offset
pump_main.set_rate(0)
rate_main = 0
if args.direction == "down":
pump_second.set_rate(0)
rate_second = 0
pump_main.set_rate(args.main_offset)
rate_main = args.main_offset
pump_second.set_vol(9999)
pump_main.set_vol(9999)
pump_second.start_program()
pump_main.start_program()
# Setup database saver
data_set_saver.start()
data_set_time = time.time()
metadata = {
"Time": CustomColumn(data_set_time, "FROM_UNIXTIME(%s)"),
"comment": comment,
"type": 64,
"preamp_range": 0,
"sem_voltage": 0
}
for label in [
"p_korr", "i_korr", "total_korr", "ph_setpoint", "ph_value",
"pump_rate"
]:
metadata["mass_label"] = label
data_set_saver.add_measurement(label, metadata)
# Run PID
try:
time_start = time.time()
run(pump_second, pump_main, obus, pid, data_set_saver, time_start,
args.setpoint, rate_second, rate_main, args.second_offset,
args.main_offset, args.second_min, args.second_max, args.direction,
minutes)
except KeyboardInterrupt:
# Clean up
pump_main.set_rate(0)
pump_second.set_rate(0)
pump_main.stop_program()
pump_second.stop_program()
data_set_saver.stop()
raise SystemExit(" Sequence stopped.")
# Clean up
pump_main.set_rate(0)
pump_second.set_rate(0)
pump_main.stop_program()
pump_second.stop_program()
# Log pH during ageing
try:
while True:
value = obus.read_value(1)
value = current_to_ph(value)
print("pH: " + str(round(value, 3)))
data_set_saver.save_point("ph_value",
(time.time() - time_start, value))
data_set_saver.save_point(
"ph_setpoint", (time.time() - time_start, args.setpoint))
time.sleep(8)
except KeyboardInterrupt:
data_set_saver.stop()
pass
# Load the sequence
print('Found new sequence for upload: {} '.format(relative_path))
try:
sequence = Sequence(root)
except ValueError as exception:
if exception.args[0].startswith('No injections in sequence'):
print(' ... No injections in this sequence')
continue
else:
raise exception
# Upload the sequence summary data
metadata = sequence.metadata.copy()
metadata['relative_path'] = relative_path
metadata['time'] = CustomColumn(time.mktime(metadata.pop('sequence_start')), 'FROM_UNIXTIME(%s)')
metadata['type'] = 20
# We don't use these columns, but they are setup in the database without default
# values, so to avoid warnings we fill them in
metadata['sem_voltage'] = 0.0
metadata['preamp_range'] = 0.0
data_set = sequence.full_sequence_dataset()
for label, data in data_set.items():
data_set_metadata = metadata.copy()
data_set_metadata['label'] = label
codename = relative_path+label
x, y = zip(*data)
data_set_saver.add_measurement(codename, data_set_metadata)
data_set_saver.save_points_batch(codename, x, y)
print(' Summary datasets uploaded........: {}'.format(len(data_set)))