def generate_protocol_files_from_csv(csv_filename, output_directory=None):
"""
Generates a set of protocol files from csv filename input by
reading protocol file input corresponding to each line of
the csv file. Writes a csv file that.
Args:
csv_filename (str): CSV containing protocol file parameters.
output_directory (str): directory in which to place the output files
"""
# Read csv file
protocol_params_df = pd.read_csv(csv_filename)
new_files = []
names = []
result = ""
message = {"comment": "", "error": ""}
if output_directory is None:
output_directory = PROCEDURE_TEMPLATE_DIR
for index, protocol_params in protocol_params_df.iterrows():
template = protocol_params["template"]
# Filename for the output
filename_prefix = "_".join(
[
protocol_params["project_name"],
"{:06d}".format(protocol_params["seq_num"]),
]
)
# Switch for template invocation
if template == "EXP.000":
protocol = Procedure.from_exp(
**protocol_params[["cutoff_voltage", "charge_rate", "discharge_rate"]]
)
filename = "{}.000".format(filename_prefix)
filename = os.path.join(output_directory, "procedures", filename)
elif template == "diagnosticV2.000":
diag_params_df = pd.read_csv(
os.path.join(PROCEDURE_TEMPLATE_DIR, "PreDiag_parameters - DP.csv")
)
diagnostic_params = diag_params_df[
diag_params_df["diagnostic_parameter_set"]
== protocol_params["diagnostic_parameter_set"]
].squeeze()
# TODO: should these be separated?
protocol = Procedure.from_regcyclev2(protocol_params)
protocol.add_procedure_diagcyclev2(
protocol_params["capacity_nominal"], diagnostic_params
)
filename = "{}.000".format(filename_prefix)
filename = os.path.join(output_directory, "procedures", filename)
# TODO: how are these different?
elif template in ["diagnosticV3.000", "diagnosticV4.000"]:
diag_params_df = pd.read_csv(
os.path.join(PROCEDURE_TEMPLATE_DIR, "PreDiag_parameters - DP.csv")
)
diagnostic_params = diag_params_df[
diag_params_df["diagnostic_parameter_set"]
== protocol_params["diagnostic_parameter_set"]
].squeeze()
template_fullpath = os.path.join(PROCEDURE_TEMPLATE_DIR, template)
protocol = Procedure.generate_procedure_regcyclev3(index,
protocol_params,
template=template_fullpath)
protocol.generate_procedure_diagcyclev3(
protocol_params["capacity_nominal"], diagnostic_params
)
filename = "{}.000".format(filename_prefix)
filename = os.path.join(output_directory, "procedures", filename)
elif template == "drivingV1.000":
diag_params_df = pd.read_csv(
os.path.join(PROCEDURE_TEMPLATE_DIR, "PreDiag_parameters - DP.csv")
)
diagnostic_params = diag_params_df[
diag_params_df["diagnostic_parameter_set"]
== protocol_params["diagnostic_parameter_set"]
].squeeze()
mwf_dir = os.path.join(output_directory, "mwf_files")
waveform_name = insert_driving_parametersv1(protocol_params,
waveform_directory=mwf_dir)
template_fullpath = os.path.join(PROCEDURE_TEMPLATE_DIR, template)
protocol = Procedure.generate_procedure_drivingv1(index,
protocol_params,
waveform_name,
template=template_fullpath)
protocol.generate_procedure_diagcyclev3(
protocol_params["capacity_nominal"], diagnostic_params
)
filename = "{}.000".format(filename_prefix)
filename = os.path.join(output_directory, "procedures", filename)
elif template == "formationV1.mps":
protocol = Settings.from_file(os.path.join(BIOLOGIC_TEMPLATE_DIR, template))
protocol = protocol.formation_protocol_bcs(protocol, protocol_params)
filename = "{}.mps".format(filename_prefix)
filename = os.path.join(output_directory, "settings", filename)
else:
warnings.warn("Unsupported file template {}, skipping.".format(template))
result = "error"
message = {
"comment": "Unable to find template: " + template,
"error": "Not Found",
}
continue
logger.info(filename, extra=s)
if not os.path.isfile(filename):
protocol.to_file(filename)
new_files.append(filename)
names.append(filename_prefix + "_")
elif ".sdu" in template:
logger.warning("Schedule file generation not yet implemented", extra=s)
result = "error"
message = {
"comment": "Schedule file generation is not yet implemented",
"error": "Not Implemented",
}
# This block of code produces the file containing all of the run file
# names produced in this function call. This is to make starting tests easier
_, namefile = os.path.split(csv_filename)
namefile = namefile.split("_")[0] + "_names_"
namefile = namefile + datetime.datetime.now().strftime("%Y%m%d_%H%M") + ".csv"
with open(
os.path.join(output_directory, "names", namefile), "w", newline=""
) as outputfile:
wr = csv.writer(outputfile)
for name in names:
wr.writerow([name])
outputfile.close()
if not result:
result = "success"
message = {
"comment": "Generated {} protocols".format(str(len(new_files))),
"error": "",
}
return new_files, result, message
def test_waveform_from_csv(self):
csv_file = os.path.join(TEST_FILE_DIR, "data-share", "raw",
"parameters", "Drive_parameters - GP.csv")
protocol_params_df = pd.read_csv(csv_file)
# Max power in watts in the profiles (should be less than max power limit on cyclers)
MAX_PROFILE_CURRENT = 15
MIN_PROFILE_VOLTAGE = 2.7
MAX_PROFILE_POWER = MAX_PROFILE_CURRENT * MIN_PROFILE_VOLTAGE
new_files = []
names = []
waveform_names = []
result = ""
message = {"comment": "", "error": ""}
with ScratchDir(".") as scratch_dir:
output_directory = scratch_dir
os.makedirs(os.path.join(output_directory, "procedures"))
for index, protocol_params in protocol_params_df.iterrows():
template = protocol_params["template"]
filename_prefix = "_".join([
protocol_params["project_name"],
"{:06d}".format(protocol_params["seq_num"]),
])
if template == "drivingV1.000":
diag_params_df = pd.read_csv(
os.path.join(PROCEDURE_TEMPLATE_DIR,
"PreDiag_parameters - DP.csv"))
diagnostic_params = diag_params_df[
diag_params_df["diagnostic_parameter_set"] ==
protocol_params["diagnostic_parameter_set"]].squeeze()
mwf_dir = os.path.join(scratch_dir, "mwf_files")
waveform_name = insert_driving_parametersv1(
protocol_params, waveform_directory=mwf_dir)
template_fullpath = os.path.join(PROCEDURE_TEMPLATE_DIR,
template)
protocol = Procedure.generate_procedure_drivingv1(
index,
protocol_params,
waveform_name,
template=template_fullpath)
protocol.generate_procedure_diagcyclev3(
protocol_params["capacity_nominal"], diagnostic_params)
filename = "{}.000".format(filename_prefix)
filename = os.path.join(output_directory, "procedures",
filename)
waveform_names.append(os.path.split(waveform_name)[-1])
if not os.path.isfile(filename):
protocol.to_file(filename)
new_files.append(filename)
names.append(filename_prefix + "_")
waveform_df = pd.read_csv(waveform_name, sep="\t", header=None)
power_df = waveform_df[waveform_df[1] == "P"]
self.assertLessEqual(power_df[2].abs().max(),
MAX_PROFILE_POWER)
self.assertGreaterEqual(power_df[2].abs().max(), 0)
current_df = waveform_df[waveform_df[1] == "I"]
self.assertLessEqual(current_df[2].abs().max(),
MAX_PROFILE_CURRENT)
self.assertGreaterEqual(current_df[2].abs().max(), 0)
discharge_df = waveform_df[waveform_df[0] == "D"]
self.assertGreaterEqual(discharge_df[4].abs().max(),
MIN_PROFILE_VOLTAGE)
self.assertEqual(
protocol.get(
"MaccorTestProcedure.ProcSteps.TestStep.32.StepType"),
'FastWave')
self.assertEqual(
protocol.get(
"MaccorTestProcedure.ProcSteps.TestStep.64.StepType"),
'FastWave')
wave_value = os.path.split(waveform_name)[-1].split(".")[0]
self.assertEqual(
protocol.get(
"MaccorTestProcedure.ProcSteps.TestStep.32.StepValue"),
wave_value)
self.assertEqual(
protocol.get(
"MaccorTestProcedure.ProcSteps.TestStep.64.StepValue"),
wave_value)
self.assertEqual(
len(os.listdir(os.path.join(output_directory, "procedures"))),
36)
self.assertEqual(
len(os.listdir(os.path.join(output_directory, "mwf_files"))),
18)
test_names = [
'US06_x4_24W.MWF', 'LA4_x4_10W.MWF', 'US06_x4_32W.MWF',
'LA4_x4_14W.MWF', 'US06_x4_40W.MWF', 'LA4_x4_18W.MWF',
'US06_x8_24W.MWF', 'LA4_x8_10W.MWF', 'US06_x8_32W.MWF',
'LA4_x8_14W.MWF', 'US06_x8_40W.MWF', 'LA4_x8_18W.MWF',
'US06_x12_24W.MWF', 'LA4_x12_10W.MWF', 'US06_x12_32W.MWF',
'LA4_x12_14W.MWF', 'US06_x12_40W.MWF', 'LA4_x12_18W.MWF',
'US06_x4_24W.MWF', 'LA4_x4_10W.MWF', 'US06_x4_32W.MWF',
'LA4_x4_14W.MWF', 'US06_x4_40W.MWF', 'LA4_x4_18W.MWF',
'US06_x8_24W.MWF', 'LA4_x8_10W.MWF', 'US06_x8_32W.MWF',
'LA4_x8_14W.MWF', 'US06_x8_40W.MWF', 'LA4_x8_18W.MWF',
'US06_x12_24W.MWF', 'LA4_x12_10W.MWF', 'US06_x12_32W.MWF',
'LA4_x12_14W.MWF', 'US06_x12_40W.MWF', 'LA4_x12_18W.MWF'
]
self.assertListEqual(test_names, waveform_names)
def generate_protocol_files_from_csv(csv_filename, output_directory=None):
"""
Generates a set of protocol files from csv filename input by
reading protocol file input corresponding to each line of
the csv file. Writes a csv file that.
Args:
csv_filename (str): CSV containing protocol file parameters.
output_directory (str): directory in which to place the output files
"""
# Read csv file
protocol_params_df = pd.read_csv(csv_filename)
successfully_generated_files = []
file_generation_failures = []
names = []
result = ""
message = {"comment": "", "error": ""}
if output_directory is None:
output_directory = PROCEDURE_TEMPLATE_DIR
for index, protocol_params in protocol_params_df.iterrows():
template = protocol_params["template"]
protocol = None
# Filename for the output
filename_prefix = "_".join(
[
protocol_params["project_name"],
"{:06d}".format(protocol_params["seq_num"]),
]
)
if ".000" in template: # Extension for maccor procedure files
template_fullpath = os.path.join(PROCEDURE_TEMPLATE_DIR, template)
template_length = template_detection(template_fullpath)
if "diagnostic_parameter_set" in protocol_params: # For parameters include diagnostics load those values
diag_params_df = pd.read_csv(
os.path.join(PROCEDURE_TEMPLATE_DIR, "PreDiag_parameters - DP.csv")
)
diagnostic_params = diag_params_df[
diag_params_df["diagnostic_parameter_set"]
== protocol_params["diagnostic_parameter_set"]
].squeeze()
if template_length == 23 and template == "EXP.000": # length and name for initial procedure files
protocol = Procedure.from_exp(
**protocol_params[["cutoff_voltage", "charge_rate", "discharge_rate"]]
)
elif template_length == 72: # length for V1 and V1 diagnostic templates without ending diagnostics
protocol = Procedure.from_regcyclev2(protocol_params)
protocol.add_procedure_diagcyclev2(
protocol_params["capacity_nominal"], diagnostic_params
)
elif template_length == 96: # template length for diagnostic type cycling
mwf_dir = os.path.join(output_directory, "mwf_files")
if protocol_params["project_name"] == "RapidC": # Project with charging waveform
waveform_name = insert_charging_parametersv1(protocol_params,
waveform_directory=mwf_dir)
protocol = Procedure.generate_procedure_chargingv1(index,
protocol_params,
waveform_name,
template=template_fullpath)
elif protocol_params["project_name"] == "Drive": # Project with discharging waveform
waveform_name = insert_driving_parametersv1(protocol_params,
waveform_directory=mwf_dir)
protocol = Procedure.generate_procedure_drivingv1(index,
protocol_params,
waveform_name,
template=template_fullpath)
else: # Use the default parameterization for PreDiag/Prediction Diagnostic projects
protocol = Procedure.generate_procedure_regcyclev3(index,
protocol_params,
template=template_fullpath)
protocol.generate_procedure_diagcyclev3(
protocol_params["capacity_nominal"], diagnostic_params
)
else: # Case where its not possible to match the procedure template
failure = {
"comment": "Unable to find template: " + template,
"error": "Not Found",
}
file_generation_failures.append(failure)
warnings.warn("Unsupported file template {}, skipping.".format(template))
result = "error"
continue
filename = "{}.000".format(filename_prefix)
filename = os.path.join(output_directory, "procedures", filename)
elif ".mps" in template and template == "formationV1.mps": # biologic settings template and formation project
protocol = Settings.from_file(os.path.join(BIOLOGIC_TEMPLATE_DIR, template))
protocol = protocol.formation_protocol_bcs(protocol_params)
filename = "{}.mps".format(filename_prefix)
filename = os.path.join(output_directory, "settings", filename)
elif ".sdu" in template: # No schedule file templates implemented
failure = {
"comment": "Schedule file generation is not yet implemented",
"error": "Not Implemented"
}
file_generation_failures.append(failure)
logger.warning("Schedule file generation not yet implemented", extra=s)
result = "error"
continue
else: # Unable to match to any known template format
failure = {
"comment": "Unable to find template: " + template,
"error": "Not Found",
}
file_generation_failures.append(failure)
warnings.warn("Unsupported file template {}, skipping.".format(template))
result = "error"
continue
logger.info(filename, extra=s)
protocol.to_file(filename)
successfully_generated_files.append(filename)
names.append(filename_prefix + "_")
# This block of code produces the file containing all of the run file
# names produced in this function call. This is to make starting tests easier
_, namefile = os.path.split(csv_filename)
namefile = namefile.split("_")[0] + "_names_"
namefile = namefile + datetime.datetime.now().strftime("%Y%m%d_%H%M") + ".csv"
names_dir = os.path.join(output_directory, "names")
os.makedirs(names_dir, exist_ok=True)
with open(os.path.join(names_dir, namefile), "w", newline="") as outputfile:
wr = csv.writer(outputfile)
for name in names:
wr.writerow([name])
outputfile.close()
num_generated_files = len(successfully_generated_files)
num_generation_failures = len(file_generation_failures)
num_files = num_generated_files + num_generation_failures
message = {
"comment": "Generated {} of {} protocols".format(num_generated_files, num_files),
"error": ""
}
if not result:
result = "success"
else:
message["error"] = "Failed to generate {} of {} protocols".format(num_generation_failures, num_files)
logger.error(message["error"])
return successfully_generated_files, file_generation_failures, result, message