def test_filelist(self):
test_oect = oect.OECT(folder='tests/test_device/01')
test_oect.filelist()
assert (os.path.join('tests/test_device/01', 'uc1_kpf6_output_0.txt') in test_oect.files
and os.path.join('tests/test_device/01', 'uc1_kpf6_output_1.txt') in test_oect.files
and os.path.join('tests/test_device/01', 'uc1_kpf6_transfer_0.txt') in test_oect.files
and test_oect.config[0] == os.path.join('tests/test_device/01', 'uc1_kpf6_config.cfg'))
def test_get_metadata(self): test_oect = oect.OECT(folder=os.getcwd()) test_file = 'tests/test_device/metadata_test/uc1_kpf6_output_0.txt' test_oect.get_metadata(test_file) assert (test_oect.Vg == -.5 and test_oect.W == 2000 and test_oect.L == 20)
def test_get_metadata_no_config(self): test_oect = oect.OECT(folder='tests/test_device/metadata_test') test_oect.make_config = True test_file = 'tests/test_device/metadata_test/uc1_kpf6_output_0.txt' test_oect.get_metadata(test_file) assert (test_oect.Vg == -.5 and test_oect.W == 4000 and test_oect.L == 10)
def test_filelist_noconfig(self):
test_oect = oect.OECT(folder='tests/test_device/no_config')
config_check = 'config.cfg' in os.listdir('tests/test_device/no_config')
try:
os.remove('tests/test_device/no_config/config.cfg')
except:
pass
assert config_check
def test_set_params_defaults(self):
test_oect = oect.OECT(folder=os.getcwd())
test_oect.set_params({}, {}, {}, {}) #try defaults
assert (test_oect.options['gm_method'] == 'sg'
and test_oect.options['Reverse'] == True
and test_oect.options['Average'] == False
and test_oect.options['V_low'] == False
and test_oect.options['overwrite'] == False)
def loadOECT(path,
dimDict,
params=None,
gm_plot=True,
plot=True,
options={},
verbose=True,
text_browser=None):
"""
Wrapper function for processing OECT data
params = {W: , L: , d: } for W, L, d of device
USAGE:
device1 = loadOECT(folder_name)
"""
if not path:
path = file_open(caption='Select device subfolder')
device = oect.OECT(path, dimDict, params, options)
device.calc_gms()
device.thresh()
scaling = device.WdL # W *d / L
if verbose:
for key in device.gms:
print(
key, ': {:.2f}'.format(
np.max(device.gms[key].values * 1e-2) / scaling),
'S/cm scaled')
print(key,
': {:.2f}'.format(np.max(device.gms[key].values * 1000)),
'mS max')
if (text_browser):
text_browser.append(key + str(': {:.2f}'.format(
np.max(device.gms[key].values * 1e-2) / scaling)) +
'S/cm scaled')
text_browser.append(key + str(': {:.2f}'.format(
np.max(device.gms[key].values * 1000))) + 'mS max')
if plot:
fig = oect_plot.plot_transfers_gm(device,
gm_plot=gm_plot,
leakage=True)
fig.savefig(path + r'\transfer_leakage.tif', format='tiff')
fig = oect_plot.plot_transfers_gm(device,
gm_plot=gm_plot,
leakage=False)
fig.savefig(path + r'\transfer.tif', format='tiff')
fig = oect_plot.plot_outputs(device, leakage=True)
fig.savefig(path + r'\output_leakage.tif', format='tiff')
fig = oect_plot.plot_outputs(device, leakage=False)
fig.savefig(path + r'\output.tif', format='tiff')
return device
def test_set_params(self): test_oect = oect.OECT(folder='tests/test_device/01') #called in init assert (test_oect.params['W'] == 4000.0 and test_oect.params['L'] == 20.0 and test_oect.params['d'] == 4e-8 and test_oect.params['Preread (ms)'] == 20000 and test_oect.params['First Bias (ms)'] == 120000 and test_oect.params['Vds (V)'] == 0 and test_oect.params['output_Preread (ms)'] == 5000 and test_oect.params['output_First Bias (ms)'] == 200 and test_oect.params['Output Vgs'] == 2 and test_oect.params['Vgs'] == [-0.5, -0.8])
def test_update_config(self):
test_oect = oect.OECT(folder='tests/test_device/no_config')
#config will be auto generated in init
#default config will be made with values:
# [Dimensions]
# Width (um) = 2000
# Length (um) = 20
# [Transfer]
# Preread (ms) = 30000.0
# First Bias (ms) = 120000.0
# Vds (V) = -0.6
# [Output]
# Preread (ms) = 500.0
# First Bias (ms) = 200.0
# Output Vgs = 4
# Vgs (V) 0 = -0.1
# Vgs (V) 1 = -0.3
# Vgs (V) 2 = -0.5
# Vgs (V) 3 = -0.9
test_oect.W = 4000
test_oect.L = 10
test_oect.Vd = -1
test_oect.Vg_array = [0, .1, .2, .3, .4]
test_oect.update_config()
config = configparser.ConfigParser()
config.read(test_oect.config)
assert (config['Dimensions']['Width (um)'] == '4000'
and config['Dimensions']['Length (um)'] == '10'
and config['Transfer']['Vds (V)'] == '-1'
and config['Output']['Preread (ms)'] == '500.0'
and config['Output']['First Bias (ms)'] == '200.0'
and config['Output']['Vgs (V) 0'] == '0'
and config['Output']['Vgs (V) 1'] == '0.1'
and config['Output']['Vgs (V) 2'] == '0.2'
and config['Output']['Vgs (V) 3'] == '0.3'
and config['Output']['Vgs (V) 4'] == '0.4')
try:
os.remove('tests/test_device/no_config/config.cfg')
except:
pass
def test_reverse_with_sweep(self): test_oect = oect.OECT(folder=os.getcwd()) a = np.arange(start=-1, stop=1.1, step=.1) b = np.arange(start=.9, stop=-1.1, step=-.1) v = np.concatenate((a, b)) assert len(v) // 2, True == test_oect._reverse(v)
import os
import sys
import pytest
import configparser
import numpy as np
sys.path.insert(0, '..')
import oect
test_oect = oect.OECT(folder='test_device/no_config')
print(os.path.isfile(os.path.join('test_device/no_config', 'config.cfg')))
def test_output_curve_wrong_col_names(self): test_oect = oect.OECT(folder=os.getcwd()) with pytest.raises(KeyError): test_file = 'tests/test_device/01/uc1_kpf6_output_0.txt' test_oect.get_metadata(test_file) test_oect.transfer_curve(test_file)
def test_set_params_not_dict(self): test_oect = oect.OECT(folder=os.getcwd()) with pytest.raises(IndexError) or pytest.raises(TypeError): test_oect.set_params([1, 2, 3, 4, 5], [1, 2, 3, 4, 5], [1, 2, 3, 4, 5], [1, 2, 3, 4, 5])
def test_all_outputs(self): test_oect = oect.OECT(folder='tests/test_device/01') #called in init assert test_oect.num_outputs == 4
def test_set_params_add(self):
test_oect = oect.OECT(folder='tests/test_device/01', params={'test_param1': 100},
options={'test_option1': 200})
assert (test_oect.params['test_param1'] == 100
and test_oect.options['test_option1'] == 200)
def test_set_opts(self): test_oect = oect.OECT(folder='tests/test_device/options_test') #called in init assert (test_oect.options['Reverse'] == True and test_oect.options['Average'] == False and test_oect.options['gm_method'] == 'method' and test_oect.options['V_low'] == 10)
def average(dimDict={},
path='',
thickness=40e-9,
plot=True,
text_browser=None):
'''
averages data in this particular path (for folders 'avg')
path: str
string path to folder '.../avg'. Note Windows path are of form r'Path_name'
thickness : float
approximate film thickness. Standard polymers (for Raj) are ~40 nm
plot : bool
Whether to plot or not. Not plotting is very fast!
Returns
-------
pixels : dict of OECT
Contains the various OECT class devices
Id_Vg : pandas dataframe
Contains the averaged Id vs Vg (drain current vs gate voltage, transfer)
Id_Vd : pandas dataframe
Contains the averaged Id vs Vg (drain current vs drain voltages, output)
'''
if not path:
path = file_open(caption='Select avg subfolder')
print('Loading from', path)
filelist = os.listdir(path)
# removes all but the folders in pixel_names
f = filelist[:]
for k in filelist:
try:
sub_num = int(k)
except:
print('Ignoring', k)
f.remove(k)
filelist = f[:]
del f
paths = [os.path.join(path, name) for name in filelist]
# removes random files instead of the sub-folders
for p in paths:
if not os.path.isdir(p):
paths.remove(p)
pixels = {}
# loads all the folders
for p, f in zip(paths, filelist):
dv = loadOECT(dimDict,
p,
params={'d': thickness},
gm_plot=plot,
plot=plot,
text_browser=text_browser)
pixels[f] = dv
# average Id-Vg
Id_Vg = []
first_pxl = pixels[list(pixels.keys())[0]]
for dv in pixels:
if not any(Id_Vg):
Id_Vg = pixels[dv].transfers.values
else:
Id_Vg += pixels[dv].transfers.values
Id_Vg /= len(pixels)
Id_Vg = pd.DataFrame(data=Id_Vg)
try:
Id_Vg = Id_Vg.set_index(first_pxl.transfers.index)
except:
Id_Vg = Id_Vg.set_index(pixels[list(pixels.keys())[-1]])
# find gm of the average
temp_dv = oect.OECT(dimDict, paths[0], {'d': thickness})
_gm_fwd, _gm_bwd = temp_dv._calc_gm(Id_Vg)
Id_Vg['gm_fwd'] = _gm_fwd
if not _gm_bwd.empty:
Id_Vg['gm_bwd'] = _gm_bwd
Id_Vg = Id_Vg.rename(columns={0: 'Id average'}) # fix a naming bug
if temp_dv.reverse:
Id_Vg.reverse = True
Id_Vg.rev_point = temp_dv.rev_point
# average Id-Vd at max Vd
Id_Vd = []
# finds column corresponding to lowest voltage (most doping), but these are strings
idx = np.argmin(np.array([float(i) for i in first_pxl.outputs.columns]))
volt = first_pxl.outputs.columns[idx]
for dv in pixels:
if not any(Id_Vd):
Id_Vd = pixels[dv].outputs[volt].values
else:
Id_Vd += pixels[dv].outputs[volt].values
Id_Vd /= len(pixels)
Id_Vd = pd.DataFrame(data=Id_Vd)
try:
Id_Vd = Id_Vd.set_index(pixels[list(
pixels.keys())[0]].outputs[volt].index)
except:
Id_Vd = Id_Vd.set_index(pixels[list(
pixels.keys())[-1]].outputs[volt].index)
if plot:
fig = oect_plot.plot_transfer_avg(Id_Vg, temp_dv.WdL)
fig.savefig(path + r'\transfer_avg.tif', format='tiff')
fig = oect_plot.plot_output_avg(Id_Vd)
fig.savefig(path + r'\output_avg.tif', format='tiff')
return pixels, Id_Vg, Id_Vd, temp_dv.WdL
def test_reverse_no_sweep(self): test_oect = oect.OECT(folder=os.getcwd()) v = np.arange(start=-1, stop=.1, step=.1) assert len(v) // 2, False == test_oect._reverse(v)
def test_all_transfers(self): test_oect = oect.OECT(folder='tests/test_device/01') #called in init assert test_oect.num_transfers == 2
def test_all_outputs_append(self): test_oect = oect.OECT(folder='tests/test_device/01') #called in init test_oect.all_outputs() #call again assert test_oect.num_outputs == 8
