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MakeIndividualIVs.py
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Created
Thu, Oct 10, 05:23
Size
8 KB
Mime Type
text/x-python
Expires
Sat, Oct 12, 05:23 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
21525973
Attached To
rNPTOOLS Nanopore Tools
MakeIndividualIVs.py
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# -*- coding: utf-8 -*-
import
numpy
as
np
import
scipy
import
scipy.signal
as
sig
import
Functions
as
uf
import
pyqtgraph
as
pg
import
os
import
matplotlib.pyplot
as
plt
import
matplotlib
from
tkinter
import
Tk
from
tkinter.filedialog
import
askopenfilenames
from
matplotlib.font_manager
import
FontProperties
import
platform
import
csv
import
argparse
from
pprint
import
pprint
import
LoadData
#Set font properties
fontP
=
FontProperties
()
fontP
.
set_size
(
'small'
)
props
=
dict
(
boxstyle
=
'round'
,
facecolor
=
'wheat'
,
alpha
=
0.5
)
matplotlib
.
rcParams
[
'pdf.fonttype'
]
=
42
matplotlib
.
rcParams
[
'ps.fonttype'
]
=
42
#Set units formatting
from
matplotlib.ticker
import
EngFormatter
Res
=
EngFormatter
(
unit
=
'Ω'
,
places
=
2
)
Cond
=
EngFormatter
(
unit
=
'S'
,
places
=
2
)
SpesCond
=
EngFormatter
(
unit
=
'S/m'
,
places
=
2
)
size
=
EngFormatter
(
unit
=
'm'
,
places
=
2
)
Tk
()
.
withdraw
()
if
(
platform
.
system
()
==
'Darwin'
):
os
.
system
(
'''/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "python" to true' '''
)
#Define default parameters for size fitting
expname
=
'All'
Parameters
=
{
'Type'
:
'Nanopore'
,
#Nanopore, Nanocapillary, NanocapillaryShrunken
'reversePolarity'
:
0
,
'specificConductance'
:
10.5
,
#10.5 S/m for 1M KCl
'delay'
:
2
,
#seconds for reading current
#Nanopore
'poreLength'
:
1e-9
,
#Nanocapillary
'taperLength'
:
3.3e-3
,
'innerDiameter'
:
0.2e-3
,
'taperLengthShaft'
:
543e-9
,
'innerDiameterShaft'
:
514e-9
,
#Fit option
'CurveFit'
:
'PolyFit'
#PolyFit YorkFit
}
def
GetParameters
():
print
(
"Usage:"
)
print
(
"run(filenames,newParameters={},verbose=False)"
)
print
()
print
(
"Default Parameters:"
)
pprint
(
Parameters
)
def
run
(
filenames
,
newParameters
=
{},
verbose
=
False
):
for
key
in
newParameters
:
Parameters
[
key
]
=
newParameters
[
key
]
Type
=
Parameters
[
'Type'
]
CurveFit
=
Parameters
[
'CurveFit'
]
specificConductance
=
Parameters
[
'specificConductance'
]
for
filename
in
filenames
:
os
.
chdir
(
os
.
path
.
dirname
(
filename
))
print
(
filename
)
#Make Dir to save images
output
=
LoadData
.
OpenFile
(
filename
,
verbose
=
verbose
)
if
Parameters
[
'reversePolarity'
]:
print
(
'Polarity Reversed!!!!'
)
output
[
'i1'
]
=
-
output
[
'i1'
]
output
[
'v1'
]
=
-
output
[
'v1'
]
directory
=
(
str
(
os
.
path
.
split
(
filename
)[
0
])
+
os
.
sep
+
expname
+
'_SavedImages'
)
if
not
os
.
path
.
exists
(
directory
):
os
.
makedirs
(
directory
)
AllData
=
uf
.
MakeIVData
(
output
,
approach
=
'mean'
,
delay
=
Parameters
[
'delay'
])
#, UseVoltageRange = [-0.4, 0.4])
print
(
'uf.MakeIVData'
)
if
AllData
==
0
:
print
(
'!!!! No Sweep in: '
+
filename
)
continue
#Plot Considered Part
#figExtracteParts = plt.figure(1)
#ax1 = figExtracteParts.add_subplot(211)
#ax2 = figExtracteParts.add_subplot(212, sharex=ax1)
#(ax1, ax2) = uf.PlotExtractedPart(output, AllData, current = 'i1', unit=1e9, axis = ax1, axis2=ax2)
#plt.show()
#figExtracteParts.savefig(directory + os.sep + 'PlotExtracted_' + str(os.path.split(filename)[1])[:-4] + '.eps')
#figExtracteParts.savefig(directory + os.sep + 'PlotExtracted_' + str(os.path.split(filename)[1])[:-4] + '.png', dpi=150)
# Plot IV
if
output
[
'graphene'
]:
figIV2
=
plt
.
figure
(
3
,
figsize
=
(
10
,
10
))
figIV2
.
clear
()
ax2IV
=
figIV2
.
add_subplot
(
111
)
ax2IV
=
uf
.
PlotIV
(
output
,
AllData
,
current
=
'i2'
,
unit
=
1e9
,
axis
=
ax2IV
,
WithFit
=
1
)
figIV2
.
tight_layout
()
figIV2
.
savefig
(
directory
+
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
])
+
'_IV_i2.png'
,
dpi
=
300
)
figIV2
.
savefig
(
directory
+
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
])
+
'_IV_i2.eps'
)
figIV
=
plt
.
figure
(
2
,
figsize
=
(
10
,
7
))
ax1IV
=
figIV
.
add_subplot
(
111
)
current
=
'i1'
#ax1IV = uf.PlotIV(output, AllData, current='i1', unit=1, axis = ax1IV, WithFit = 1, useEXP = 0, color ='y',
# labeltxt='MeanFit', PoreSize=[10, 1e-9], title=str(os.path.split(filename)[1]))
Slope
=
AllData
[
current
][
CurveFit
][
'Slope'
]
Yintercept
=
AllData
[
current
][
CurveFit
][
'Yintercept'
]
if
Type
==
'Nanopore'
:
poreLength
=
Parameters
[
'poreLength'
]
textstr
=
'Nanopore Size
\n\n
Specific Conductance: {}
\n
Length: {}
\n\n
Conductance: {}
\n
Diameter: {}'
\
.
format
(
SpesCond
.
format_data
(
specificConductance
),
size
.
format_data
(
poreLength
),
Cond
.
format_data
(
Slope
),
size
.
format_data
(
uf
.
CalculatePoreSize
(
Slope
,
poreLength
,
specificConductance
)))
elif
Type
==
'Nanocapillary'
:
taperLength
=
Parameters
[
'taperLength'
]
innerDiameter
=
Parameters
[
'innerDiameter'
]
textstr
=
'Nanocapillary Size
\n\n
Specific Conductance: {}
\n
Taper lenghth {}:
\n
Inner diameter: {}:
\n\n
Conductance: {}
\n
Diameter: {}'
.
\
format
(
SpesCond
.
format_data
(
specificConductance
),
size
.
format_data
(
taperLength
),
size
.
format_data
(
innerDiameter
),
Cond
.
format_data
(
Slope
),
size
.
format_data
(
uf
.
CalculateCapillarySize
(
Slope
,
innerDiameter
,
taperLength
,
specificConductance
)))
elif
Type
==
'NanocapillaryShrunken'
:
taperLength
=
Parameters
[
'taperLength'
]
innerDiameter
=
Parameters
[
'innerDiameter'
]
taperLengthShaft
=
Parameters
[
'taperLengthShaft'
]
innerDiameterShaft
=
Parameters
[
'innerDiameterShaft'
]
NCSize
=
uf
.
CalculateShrunkenCapillarySize
(
Slope
,
innerDiameter
,
taperLength
,
specificConductance
,
taperLengthShaft
,
innerDiameterShaft
)
textstr
=
'Shrunken Nanocapillary Size
\n\n
Specific Conductance: {}
\n
Taper length: {}
\n
Inner diameter: {}
\n
Taper length at shaft: {}'
\
'
\n
Inner Diameter at shaft: {}:
\n\n
Conductance: {}
\n
Diameter: {}'
.
\
format
(
SpesCond
.
format_data
(
specificConductance
),
size
.
format_data
(
taperLength
),
size
.
format_data
(
innerDiameter
),
size
.
format_data
(
taperLengthShaft
),
size
.
format_data
(
innerDiameterShaft
),
Cond
.
format_data
(
Slope
),
size
.
format_data
(
NCSize
))
ax1IV
.
text
(
0.05
,
0.95
,
textstr
,
transform
=
ax1IV
.
transAxes
,
fontsize
=
12
,
verticalalignment
=
'top'
,
bbox
=
dict
(
boxstyle
=
'round'
,
facecolor
=
'wheat'
,
alpha
=
0.5
))
ind
=
np
.
argsort
(
AllData
[
current
][
'Voltage'
])
ax1IV
.
errorbar
(
AllData
[
current
][
'Voltage'
][
ind
],
AllData
[
current
][
'Mean'
][
ind
],
yerr
=
AllData
[
current
][
'SE'
][
ind
],
fmt
=
'o'
,
color
=
'b'
)
ax1IV
.
plot
(
AllData
[
current
][
'Voltage'
][
ind
],
np
.
polyval
([
Slope
,
Yintercept
],
AllData
[
current
][
'Voltage'
][
ind
]),
color
=
'r'
)
ax1IV
.
set_title
(
str
(
os
.
path
.
split
(
filename
)[
1
])
+
'
\n
R='
+
Res
.
format_data
(
1
/
Slope
)
+
', G='
+
Cond
.
format_data
(
Slope
))
ax1IV
.
set_ylabel
(
'Current'
)
ax1IV
.
set_xlabel
(
'Voltage'
)
ax1IV
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'V'
))
ax1IV
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'A'
))
figIV
.
savefig
(
directory
+
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
])
+
Type
+
'IV_i1.pdf'
,
transparent
=
True
)
x
=
AllData
[
current
][
'Voltage'
][
ind
]
y
=
AllData
[
current
][
'Mean'
][
ind
]
csvfile
=
directory
+
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
])
+
Type
+
'IV_i1.csv'
with
open
(
csvfile
,
'w'
)
as
output
:
writer
=
csv
.
writer
(
output
,
lineterminator
=
'
\n
'
)
for
i
in
range
(
len
(
x
)):
writer
.
writerow
([
x
[
i
]
,
y
[
i
]])
plt
.
show
()
figIV
.
clear
()
if
__name__
==
'__main__'
:
parser
=
argparse
.
ArgumentParser
()
parser
.
add_argument
(
'-i'
,
'--input'
,
help
=
'input file'
)
parser
.
add_argument
(
'-c'
,
'--coeff'
,
help
=
'Coefficients for calculating pore size'
,
nargs
=
'+'
)
parser
args
=
parser
.
parse_args
()
inputData
=
args
.
input
if
inputData
==
None
:
inputData
=
askopenfilenames
()
else
:
inputData
=
{
inputData
}
newParameters
=
{}
if
args
.
coeff
is
not
None
:
if
len
(
args
.
coeff
)
%
2
==
0
:
for
i
in
range
(
0
,
len
(
args
.
coeff
),
2
):
if
i
<=
len
(
args
.
coeff
):
newParameters
[
str
(
args
.
coeff
[
i
])]
=
args
.
coeff
[
i
+
1
]
run
(
inputData
,
newParameters
)
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