def read(filepath):
"""
Takes a filepath, finds out what file type it is, and reads it into two list of lists, fix this! maybe Cell object? or pd array?"""
# Check input file and create proper data thereafter
fn, ext = os.path.splitext(filepath)
LOG.debug(f"Reading file: '{filepath}'")
if ext == ".xlsx":
from ecdh.readers import Neware as NA
df = NA.read_xlsx(filepath)
elif ext == ".csv":
from ecdh.readers import Neware as NA
df = NA.read_csv(
filepath
) #but this gives nested list with V/q data for each cycle.
elif ext == ".mpt":
from ecdh.readers import BioLogic as BL
df = BL.read_mpt(filepath)
elif ext == ".txt":
from ecdh.readers import BatSmall as BS
df = BS.read_txt(filepath)
elif ext == ".ecdh":
from ecdh.readers import Processed as PC
df = PC.read_ecdh(filepath)
else:
LOG.error(f"File format not supported: {ext}")
LOG.error("Exiting..")
exit()
return df
def plot(self):
if not self.plotobj:
LOG.error(
"No plot object supplied to the cell, but cell.plot was still called! Exiting.."
)
import sys
sys.exit()
if self.plotobj.vcplot:
if self.df.experiment_mode == 2:
self.edit_CV()
self.plotobj.plot_CV(self)
elif self.df.experiment_mode == 1:
self.edit_GC()
self.plotobj.plot_GC(self)
if self.plotobj.qcplot:
self.edit_cyclelife()
self.plotobj.plot_cyclelife(self)
if self.plotobj.rawplot:
if self.plotobj.rawplot_capacity:
self.edit_cumulative_capacity()
self.plotobj.plot_raw(self)
if self.plotobj.dqdvplot:
self.edic_dQdV()
self.plotobj.plot_dQdV(self)
def check_files(list):
# Checks that files exist and then returns the ones that does.
return_list = []
for file in list:
filename = file[0]
if os.path.isfile(filename):
return_list.append(file)
else:
LOG.error(
"File not found: '" + str(filename) +
"' Please check that the correct path is typed in your input toml file. Skipping this file."
)
return return_list
def read_config(path):
try:
toml_str = open(path, "r").read()
except Exception as e:
LOG.error(f"Couldn't read config file: {e}")
import sys
sys.exit()
# Check toml string
check_config(toml_str)
# Fill toml config
config = toml.loads(toml_str)
config = fill_config(config)
return config
def edit_cyclelife(self):
import numpy as np
import pandas as pd
#First make sure that we have either CV capacity data or galvanostatic
if self.df.experiment_mode == 2:
if not self.CVdata_capacity:
LOG.error(
"in cell/edit_cyclelife, CVdata_capacity has not been made."
)
self.edit_CV_capacity()
elif self.df.experiment_mode == 1:
#If the GC data doesn't exist, make it.
if not self.GCdata:
self.edit_GC()
#Make temporary dataholders
tmpdat = []
#loop through data and gather capacities
for i, cycle in enumerate(self.GCdata):
chg, dchg = cycle
try:
tmpdat.append([i, chg[0][-1], dchg[0][-1]])
except:
try:
tmpdat.append([i, chg[0][-1], 0])
except:
try:
tmpdat.append([i, 0, dchg[0][-1]])
except:
tmpdat.append([i, 0, 0])
self.cyclelifedata = pd.DataFrame(tmpdat,
columns=[
"cycle",
"charge capacity/mAh",
"discharge capacity/mAh"
])
self.cyclelifedata["coulombic efficiency"] = self.cyclelifedata[
"discharge capacity/mAh"] / self.cyclelifedata[
"charge capacity/mAh"] * 100
def run():
import sys
if len(sys.argv) < 3: #Then no folder is specified, look for toml in local folder.
if os.path.isfile("./ecdh.toml"):
path = "./ecdh.toml"
else:
LOG.error("Could not find an ecdh.toml file in the current directory! \nOptions: \n1. Run ecdh with the argument 'run' followed by the path of your .toml file. \n2. Initiate toml file in this directory with the init argument.")
sys.exit()
elif os.path.isfile(sys.argv[2]):# File was inserted Read toml config
path = sys.argv[2]
else:
LOG.error("Cannot find the .toml configuration file!")
sys.exit()
LOG.debug("Reading config file: '{}'".format(path))
# Read in configuration file
config = read_config(path)
settings = config["settings"]
# Merge cycle range into specific cycles
if settings['cycle_range']:
try:
cyclerange = np.linspace(settings['cycle_range'][0], settings['cycle_range'][1], settings['cycle_range'][1]-settings['cycle_range'][0] + 1).astype(int)
if type(settings['specific_cycles']) is bool:
settings['specific_cycles'] = cyclerange.tolist()
else:
settings['specific_cycles'] += cyclerange.tolist()
LOG.info(f"Specific cycles: {settings['specific_cycles']}")
except Exception as e:
LOG.warning(f"Could not use the cycle range, Error: {e}")
datatreatment = config["datatreatment"]
# Check that files are found
files = check_files(config["files"])
if len(files) == 0:
import sys
LOG.error("Could not load any datafiles. Exiting. Check that the filepaths are typed correctly in the configuration file.")
sys.exit()
LOG.success("Running ECDH: Found {} datafiles!".format(len(files)))
# Define plot specifications
plot = Plot(numfiles=len(files), **settings)
# Run the data reading + plot generation
cells = []
for f in files:
try:
am_mass = f[1]
except:
am_mass = None
try:
nickname = f[2]
except:
nickname = None
cell = Cell(f[0], am_mass, nickname, plot=plot, specific_cycles = settings['specific_cycles'])
cell.get_data()
#cell.edit_GC()
#cell.treat_data(settings)
cell.plot()
#cells.append(cell)
if datatreatment['reduce_data']:
cell.reduce_data(datatreatment)
if datatreatment['smooth_data']:
cell.smooth_data(datatreatment)
if datatreatment['print_capacities']:
if not os.path.isfile("capacity_intervals.json"):
with open("capacity_intervals.json", "w") as f:
f.close()
import json
new_json = cell.get_capacities(datatreatment)
with open("capacity_intervals.json",'r+') as file:
# First we load existing data into a dict.
try:
file_data = json.load(file)
except:
file_data = []
# Join new_data with file_data inside emp_details
file_data.append(new_json)
# Sets file's current position at offset.
file.seek(0)
# convert back to json.
json.dump(file_data, file, indent = 4)
if 'savefig' in settings:
plot.draw(save = settings['savefig'])
else:
plot.draw()
def edit_CV_capacity(self):
import numpy as np
LOG.error(
"Cell.py/edit_CV_capacity has not been made! Creating data with only zeros."
)
self.CVdata_capacity = [(np.array([[0], [0]]), np.array([[0], [0]]))]