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MakePSDs.py
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Created
Sat, Oct 19, 15:41
Size
3 KB
Mime Type
text/x-python
Expires
Mon, Oct 21, 15:41 (2 d)
Engine
blob
Format
Raw Data
Handle
21749456
Attached To
rNPTOOLS Nanopore Tools
MakePSDs.py
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#Input Stuff
import
AnalysisParameters
as
pm
import
numpy
as
np
import
scipy
import
scipy.signal
as
sig
import
Functions
as
f
import
os
import
matplotlib.pyplot
as
plt
from
matplotlib.backends.backend_pdf
import
PdfPages
from
tkinter
import
Tk
from
tkinter.filedialog
import
askopenfilenames
from
matplotlib.ticker
import
EngFormatter
from
matplotlib.font_manager
import
FontProperties
fontP
=
FontProperties
()
props
=
dict
(
boxstyle
=
'round'
,
facecolor
=
'wheat'
,
alpha
=
0.5
)
import
pyqtgraph
as
pg
fontP
.
set_size
(
'small'
)
pm
.
init
()
root
=
Tk
()
root
.
withdraw
()
os
.
system
(
'''/usr/bin/osascript -e 'tell app "Finder" to set frontmost of process "python" to true' '''
)
SaveAsPDF
=
0
foldername
=
'PSD'
# Load File, empty string prompts a pop.up window for file selection. Else a file-path can be given
root
.
update
()
filenames
=
[
'/Users/migraf/Desktop/Temp/BigBerta_Noise_2.dat'
]
#filenames = askopenfilenames()
root
.
destroy
()
# Make Dir to save images
directory
=
(
str
(
os
.
path
.
split
(
filenames
[
0
])[
0
])
+
os
.
sep
+
foldername
)
if
not
os
.
path
.
exists
(
directory
):
os
.
makedirs
(
directory
)
if
SaveAsPDF
:
pp
=
PdfPages
(
directory
+
os
.
sep
+
'_ALLPSD.pdf'
)
for
filename
in
filenames
:
print
(
filename
)
#filename = '/Users/migraf/Desktop/TestTrace/07B_10mMKClBoth_1kBDN_BothChannels12.dat'
inp
=
f
.
OpenFile
(
filename
)
folder
=
str
(
os
.
path
.
split
(
filename
)[
0
])
+
os
.
sep
+
'PSD'
file
=
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
][:
-
4
])
if
not
os
.
path
.
exists
(
folder
):
os
.
makedirs
(
folder
)
fig1
=
plt
.
figure
()
ax
=
fig1
.
add_subplot
(
211
)
ax2
=
fig1
.
add_subplot
(
212
,
sharex
=
ax
)
fr
,
Pxx_den
=
scipy
.
signal
.
periodogram
(
inp
[
'i1'
],
inp
[
'samplerate'
])
#f, Pxx_den = scipy.signal.welch(input, samplerate, nperseg=10*256, scaling='spectrum')
ax
.
set_ylabel
(
r'PSD of Ionic [$\frac{pA^2}{Hz}$]'
)
ax
.
set_xlabel
(
'Frequency'
)
ax
.
set_yscale
(
'log'
)
ax
.
set_xscale
(
'log'
)
#ax.set_ylim(1e4, 1e17)
#ax.set_xlim(100e-3, 100e3)
ax
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'Hz'
))
ax
.
plot
(
fr
,
Pxx_den
*
1e24
,
'b'
)
ax
.
grid
(
1
)
ax
.
autoscale
()
if
inp
[
'graphene'
]:
print
(
np
.
mean
(
inp
[
'v2'
]))
fr
,
Pxx_den
=
scipy
.
signal
.
periodogram
(
inp
[
'i2'
],
inp
[
'samplerate'
])
ax2
.
plot
(
fr
,
Pxx_den
*
1e24
,
'r'
)
ax2
.
set_ylabel
(
r'PSD of Transverse [$\frac{pA^2}{Hz}$]'
)
ax2
.
set_xlabel
(
'Frequency'
)
ax2
.
set_yscale
(
'log'
)
ax2
.
set_xscale
(
'log'
)
ax2
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'Hz'
))
ax2
.
plot
(
fr
,
Pxx_den
*
1e24
,
'r'
)
ax2
.
grid
(
1
)
ax2
.
autoscale
()
#ax.legend(['Ion', 'Transverse'])
textstr
=
'STD ionic: {}
\n
STD trans: {}'
.
format
(
pg
.
siFormat
(
np
.
std
(
inp
[
'i1'
])),
pg
.
siFormat
(
np
.
std
(
inp
[
'i2'
])))
ax2
.
set_title
(
'STD trans: {}'
.
format
(
pg
.
siFormat
(
np
.
std
(
inp
[
'i2'
]))))
ax
.
set_title
(
'STD ionic: {}'
.
format
(
pg
.
siFormat
(
np
.
std
(
inp
[
'i1'
]))))
else
:
textstr
=
'STD ionic: {}'
.
format
(
pg
.
siFormat
(
np
.
std
(
inp
[
'i1'
])))
ax
.
set_title
(
textstr
)
#ax2.text(0.75, 0.1, textstr, transform=ax.transAxes, fontsize=8,
# verticalalignment='bottom', bbox=props)
fig1
.
tight_layout
()
if
SaveAsPDF
:
pp
.
savefig
(
fig1
)
else
:
fig1
.
savefig
(
directory
+
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
][:
-
4
])
+
'_PSD.png'
,
dpi
=
300
)
fig1
.
clear
()
ax
.
clear
()
plt
.
close
(
fig1
)
if
SaveAsPDF
:
pp
.
close
()
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