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MakeIndividualIVs.py
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Created
Wed, May 1, 22:57
Size
6 KB
Mime Type
text/x-python
Expires
Fri, May 3, 22:57 (2 d)
Engine
blob
Format
Raw Data
Handle
17382261
Attached To
rNPTOOLS Nanopore Tools
MakeIndividualIVs.py
View Options
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
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
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' '''
)
expname
=
'All'
Type
=
'Nanocapillary'
#Nanopore, Nanocapillary, NanocapillaryShrunken
reversePolarity
=
0
specificConductance
=
10.5
#10.5 S/m for 1M KCl
#Nanopore
poreLength
=
1e-9
#Nanocapillary
taperLength
=
3.3e-3
innerDiameter
=
0.2e-3
taperLengthShaft
=
543e-9
innerDiameterShaft
=
514e-9
filenames
=
askopenfilenames
()
# show an "Open" dialog box and return the path to the selected file
#filenames={'/mnt/lben-archive/2018 - CURRENT/Jochem/Chimera/2018/2018-08-27/NCC3_1MKCl_1/IV/IV_NCC_1MKCl_1_20180827_084204.log'}
for
filename
in
filenames
:
print
(
filename
)
#Make Dir to save images
output
=
uf
.
OpenFile
(
filename
)
if
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
,
delay
=
1
)
#, UseVoltageRange = [-0.4, 0.4])
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]))
if
Type
==
'Nanopore'
:
textstr
=
'Nanopore Size
\n\n
Specific Conductance: {}
\n
Lenght: {}
\n\n
Conductance: {}
\n
Diameter: {}'
\
.
format
(
SpesCond
.
format_data
(
specificConductance
),
size
.
format_data
(
poreLength
),
Cond
.
format_data
(
AllData
[
current
][
'YorkFitValues'
][
'Slope'
]),
size
.
format_data
(
uf
.
CalculatePoreSize
(
AllData
[
current
][
'YorkFitValues'
][
'Slope'
],
poreLength
,
specificConductance
)))
elif
Type
==
'Nanocapillary'
:
textstr
=
'Nanocapillary Size
\n\n
Specific Conductance: {}
\n
Taper lenght: {}:
\n
Inner diameter: {}:
\n\n
Conductance: {}
\n
Diameter: {}'
.
\
format
(
SpesCond
.
format_data
(
specificConductance
),
size
.
format_data
(
taperLength
),
size
.
format_data
(
innerDiameter
),
Cond
.
format_data
(
AllData
[
current
][
'YorkFitValues'
][
'Slope'
]),
size
.
format_data
(
uf
.
CalculateCapillarySize
(
AllData
[
current
][
'YorkFitValues'
][
'Slope'
],
innerDiameter
,
taperLength
,
specificConductance
)))
elif
Type
==
'NanocapillaryShrunken'
:
NCSize
=
uf
.
CalculateShrunkenCapillarySize
(
AllData
[
current
][
'YorkFitValues'
][
'Slope'
],
innerDiameter
,
taperLength
,
specificConductance
,
taperLengthShaft
,
innerDiameterShaft
)
textstr
=
'Shrunken Nanocapillary Size
\n\n
Specific Conductance: {}
\n
Taper lenght: {}
\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
(
AllData
[
current
][
'YorkFitValues'
][
'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'
])
p
=
np
.
polyfit
(
AllData
[
current
][
'Voltage'
][
ind
],
AllData
[
current
][
'Mean'
][
ind
],
1
)
ax1IV
.
errorbar
(
AllData
[
current
][
'Voltage'
][
ind
],
AllData
[
current
][
'Mean'
][
ind
],
yerr
=
AllData
[
current
][
'STD'
][
ind
],
fmt
=
'o'
,
color
=
'b'
)
ax1IV
.
plot
(
AllData
[
current
][
'Voltage'
][
ind
],
np
.
polyval
(
p
,
AllData
[
current
][
'Voltage'
][
ind
]),
color
=
'r'
)
ax1IV
.
set_title
(
str
(
os
.
path
.
split
(
filename
)[
1
])
+
'
\n
R='
+
Res
.
format_data
(
1
/
p
[
0
])
+
', G='
+
Cond
.
format_data
(
p
[
0
]))
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
()
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