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ConcatenateEvents.py
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Fri, Sep 6, 22:11
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13 KB
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text/x-python
Expires
Sun, Sep 8, 22:11 (2 d)
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blob
Format
Raw Data
Handle
20452739
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rNPTOOLS Nanopore Tools
ConcatenateEvents.py
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## Cross-correlation of two channels
import
AnalysisParameters
as
pm
import
numpy
as
np
import
scipy
import
scipy.signal
as
sig
import
Functions
as
fu
import
os
import
matplotlib.pyplot
as
plt
from
matplotlib.backends.backend_pdf
import
PdfPages
from
matplotlib.font_manager
import
FontProperties
import
pandas
as
pd
import
MiscParameters
as
pm
from
matplotlib.ticker
import
EngFormatter
import
h5py
from
tkinter.filedialog
import
askopenfilenames
from
matplotlib
import
rc
rc
(
'mathtext'
,
default
=
'regular'
)
pm
.
init
(
LoadFiles
=
0
)
baseline
=
100
fitOn
=
1
percentage
=
1
plotPoints
=
0
filenames
=
{
'/Users/migraf/SWITCHdrive/PhD/BPS/Poster Resources/Data/17B_1MKCl_IV_80mer_both_Ch25_8_OriginalDB.hdf5'
}
#filenames = askopenfilenames()
for
filename
in
filenames
:
print
(
filename
)
f
=
h5py
.
File
(
filename
,
'r'
)
out
=
fu
.
OpenFile
(
f
[
'General/FileName'
]
.
value
)
file
=
os
.
sep
+
str
(
os
.
path
.
split
(
filename
)[
1
][:
-
5
])
# Graphene Or Not??
if
not
out
[
'graphene'
]:
## Only need to plot i1 and i1_Up and v1
toPlot
=
[
'i1'
,
'i1_Up'
]
for
k
in
toPlot
:
NumberOfEvents
=
f
[
'LowPassSegmentation/'
+
k
+
'/NumberOfEvents'
]
.
value
if
NumberOfEvents
is
not
0
:
pp
=
PdfPages
(
pm
.
OutputFolder
+
file
+
'_Only_'
+
k
+
'_EventPlots.pdf'
)
fig
=
plt
.
figure
()
ax1
=
fig
.
add_subplot
(
211
)
ax2
=
fig
.
add_subplot
(
212
,
sharex
=
ax1
)
ax1
.
set_title
(
'Ionic Current Trace "'
+
k
+
'"'
)
ax2
.
set_title
(
'Ionic Voltage'
)
ax1
.
set_ylabel
(
'Current [nA]'
)
ax2
.
set_ylabel
(
'Voltage [V]'
)
ax1
.
set_xlabel
(
'Time [s]'
)
ax2
.
set_xlabel
(
'Time [s]'
)
ax1
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'A'
,
places
=
1
))
ax2
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'V'
,
places
=
1
))
ax1
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
's'
,
places
=
1
))
ax2
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
's'
,
places
=
1
))
line1
,
=
ax1
.
plot
([])
line2
,
=
ax2
.
plot
([],
'c'
)
if
fitOn
:
line1f
,
=
ax1
.
plot
([],
'r'
)
for
i
in
np
.
linspace
(
0
,
NumberOfEvents
-
1
,
NumberOfEvents
*
percentage
,
dtype
=
np
.
uint64
):
startp_i1
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
k
+
'/'
+
'StartPoints'
]
.
value
[
i
]
-
baseline
)
endp_i1
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
k
+
'/'
+
'EndPoints'
]
.
value
[
i
]
+
baseline
)
if
startp_i1
<
0
:
startp_i1
=
0
if
endp_i1
>
len
(
out
[
'i1'
]):
endp_i1
=
len
(
out
[
'i1'
])
if
fitOn
:
if
plotPoints
:
fit1
=
np
.
concatenate
([
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
k
+
'/LocalBaseline'
]
.
value
[
i
],
f
[
'LowPassSegmentation/'
+
k
+
'/AllEvents/'
+
'{:09d}'
.
format
(
i
)]
.
value
[
i
],
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
k
+
'/LocalBaseline'
]
.
value
[
i
]])
else
:
fit1
=
np
.
concatenate
([
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
k
+
'/LocalBaseline'
]
.
value
[
i
],
np
.
ones
(
endp_i1
-
startp_i1
-
2
*
baseline
)
*
f
[
'LowPassSegmentation/'
+
k
+
'/FitLevel'
]
.
value
[
i
],
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
k
+
'/LocalBaseline'
]
.
value
[
i
]])
line1f
.
set_data
(
np
.
arange
(
startp_i1
,
endp_i1
)
/
out
[
'samplerate'
],
fit1
)
line1
.
set_data
(
np
.
arange
(
startp_i1
,
endp_i1
)
/
out
[
'samplerate'
],
out
[
'i1'
][
startp_i1
:
endp_i1
])
line2
.
set_data
(
np
.
arange
(
startp_i1
,
endp_i1
)
/
out
[
'samplerate'
],
out
[
'v1'
][
startp_i1
:
endp_i1
])
ax1
.
set_title
(
'{} Event {}
\n
Ionic Current Trace'
.
format
(
filter
,
i
))
ax1
.
relim
()
ax2
.
relim
()
ax1
.
autoscale_view
(
True
,
True
,
True
)
ax2
.
autoscale_view
(
True
,
True
,
True
)
fig
.
canvas
.
draw
()
pp
.
savefig
(
fig
)
print
(
'{}: {} out of {} saved!'
.
format
(
toPlot
,
str
(
i
),
NumberOfEvents
-
1
))
pp
.
close
()
else
:
toPlot
=
[]
#Initialize all the cases
toPlot
.
append
([
'i1'
,
''
,
np
.
uint64
(
f
[
'LowPassSegmentation/i1/OnlyIndexes'
]
.
value
),
np
.
uint64
(
f
[
'LowPassSegmentation/i1/OnlyIndexes'
]
.
value
)])
#toPlot.append(['i1_Up', '', np.uint64(f['LowPassSegmentation/i1_Up/OnlyIndexes'].value), np.uint64(f['LowPassSegmentation/i1_Up/OnlyIndexes'].value)])
#toPlot.append(['', 'i2', np.uint64(f['LowPassSegmentation/i2/OnlyIndexes'].value), np.uint64(f['LowPassSegmentation/i2/OnlyIndexes'].value)])
#toPlot.append(['', 'i2_Up', np.uint64(f['LowPassSegmentation/i2_Up/OnlyIndexes'].value), np.uint64(f['LowPassSegmentation/i2_Up/OnlyIndexes'].value)])
#toPlot.append(['i1', 'i2', np.uint64(f['LowPassSegmentation/i1/CommonIndexesWithi2'].value), np.uint64(f['LowPassSegmentation/i2/CommonIndexesWithi1'].value)])
#toPlot.append(['i1_Up', 'i2', np.uint64(f['LowPassSegmentation/i1_Up/CommonIndexesWithi2'].value), np.uint64(f['LowPassSegmentation/i2/CommonIndexesWithi1_Up'].value)])
#toPlot.append(['i1_Up', 'i2_Up', np.uint64(f['LowPassSegmentation/i1_Up/CommonIndexesWithi2_Up'].value), np.uint64(f['LowPassSegmentation/i2_Up/CommonIndexesWithi1_Up'].value)])
#toPlot.append(['i1', 'i2_Up', np.uint64(f['LowPassSegmentation/i1/CommonIndexesWithi2_Up'].value), np.uint64(f['LowPassSegmentation/i2_Up/CommonIndexesWithi1'].value)])
line1data
=
np
.
array
([])
line2data
=
np
.
array
([])
line3data
=
np
.
array
([])
line4data
=
np
.
array
([])
line1fdata
=
np
.
array
([])
line2fdata
=
np
.
array
([])
for
cases
in
toPlot
:
NumberOfEvents
=
len
(
cases
[
2
])
for
i
in
np
.
linspace
(
0
,
NumberOfEvents
-
1
,
NumberOfEvents
*
percentage
,
dtype
=
np
.
uint64
):
if
not
cases
[
0
]
==
''
:
startp_i1
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/'
+
'StartPoints'
]
.
value
[
cases
[
2
][
i
]]
-
baseline
)
endp_i1
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/'
+
'EndPoints'
]
.
value
[
cases
[
2
][
i
]]
+
baseline
)
else
:
startp_i1
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/'
+
'StartPoints'
]
.
value
[
cases
[
3
][
i
]]
-
baseline
)
endp_i1
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/'
+
'EndPoints'
]
.
value
[
cases
[
3
][
i
]]
+
baseline
)
if
not
cases
[
1
]
==
''
:
startp_i2
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/'
+
'StartPoints'
]
.
value
[
cases
[
3
][
i
]]
-
baseline
)
endp_i2
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/'
+
'EndPoints'
]
.
value
[
cases
[
3
][
i
]]
+
baseline
)
else
:
startp_i2
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/'
+
'StartPoints'
]
.
value
[
cases
[
2
][
i
]]
-
baseline
)
endp_i2
=
np
.
int64
(
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/'
+
'EndPoints'
]
.
value
[
cases
[
2
][
i
]]
+
baseline
)
if
startp_i1
<
0
:
startp_i1
=
0
if
startp_i2
<
0
:
startp_i2
=
0
if
endp_i1
>
len
(
out
[
'i1'
]):
endp_i1
=
len
(
out
[
'i1'
])
if
endp_i2
>
len
(
out
[
'i2'
]):
endp_i2
=
len
(
out
[
'i2'
])
i1
=
out
[
'i1'
][
startp_i1
:
endp_i1
]
v1
=
out
[
'v1'
][
startp_i1
:
endp_i1
]
i2
=
out
[
'i2'
][
startp_i2
:
endp_i2
]
v2
=
out
[
'v2'
][
startp_i2
:
endp_i2
]
diff
=
len
(
i1
)
-
len
(
i2
)
if
diff
>
0
:
#i1 is longer
i1
=
i1
[
0
:
len
(
i2
)]
v1
=
v1
[
0
:
len
(
i2
)]
if
diff
<
0
:
# i2 is longer
i2
=
i2
[
0
:
len
(
i1
)]
v2
=
v2
[
0
:
len
(
i1
)]
line1data
=
np
.
append
(
line1data
,
i1
)
line2data
=
np
.
append
(
line2data
,
i2
)
line3data
=
np
.
append
(
line3data
,
v1
)
line4data
=
np
.
append
(
line4data
,
v2
)
if
fitOn
:
if
not
cases
[
0
]
==
''
:
if
plotPoints
:
fit1
=
np
.
concatenate
([
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/LocalBaseline'
]
.
value
[
cases
[
2
][
i
]],
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/AllEvents/'
+
'{:09d}'
.
format
(
cases
[
2
][
i
])]
.
value
,
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/LocalBaseline'
]
.
value
[
cases
[
2
][
i
]]])
else
:
fit1
=
np
.
concatenate
([
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/LocalBaseline'
]
.
value
[
cases
[
2
][
i
]],
np
.
ones
(
endp_i1
-
startp_i1
-
2
*
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/FitLevel'
]
.
value
[
cases
[
2
][
i
]],
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
0
]
+
'/LocalBaseline'
]
.
value
[
cases
[
2
][
i
]]])
if
diff
>
0
:
# i1 is longer
fit1
=
fit1
[
0
:
len
(
i2
)]
line1fdata
=
np
.
append
(
line1fdata
,
fit1
)
if
not
cases
[
1
]
==
''
:
if
plotPoints
:
fit2
=
np
.
concatenate
([
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/LocalBaseline'
]
.
value
[
cases
[
3
][
i
]],
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/AllEvents/'
+
'{:09d}'
.
format
(
cases
[
3
][
i
])]
.
value
,
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/LocalBaseline'
]
.
value
[
cases
[
3
][
i
]]])
else
:
fit2
=
np
.
concatenate
([
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/LocalBaseline'
]
.
value
[
cases
[
3
][
i
]],
np
.
ones
(
endp_i2
-
startp_i2
-
2
*
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/FitLevel'
]
.
value
[
cases
[
3
][
i
]],
np
.
ones
(
baseline
)
*
f
[
'LowPassSegmentation/'
+
cases
[
1
]
+
'/LocalBaseline'
]
.
value
[
cases
[
3
][
i
]]])
if
diff
<
0
:
# i2 is longer
fit2
=
fit2
[
0
:
len
(
i1
)]
line2fdata
=
np
.
append
(
line2fdata
,
fit2
)
fig
=
plt
.
figure
()
ax1
=
fig
.
add_subplot
(
311
)
ax2
=
fig
.
add_subplot
(
312
,
sharex
=
ax1
)
ax3
=
fig
.
add_subplot
(
313
,
sharex
=
ax1
)
ax4
=
ax3
.
twinx
()
ax4
.
set_title
(
'Voltage Trace'
)
ax1
.
set_ylabel
(
'Current [nA]'
)
ax2
.
set_ylabel
(
'Current [nA]'
)
ax3
.
set_ylabel
(
'Ionic Voltage [V]'
)
ax3
.
set_xlabel
(
'Time [s]'
)
ax1
.
set_xlabel
(
'Time [s]'
)
ax2
.
set_xlabel
(
'Time [s]'
)
ax1
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'A'
,
places
=
1
))
ax2
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'A'
,
places
=
1
))
ax3
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'V'
,
places
=
1
))
ax4
.
yaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
'V'
,
places
=
1
))
ax3
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
's'
,
places
=
1
))
ax1
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
's'
,
places
=
1
))
ax2
.
xaxis
.
set_major_formatter
(
EngFormatter
(
unit
=
's'
,
places
=
1
))
ax4
.
set_ylabel
(
'Tr. Voltage [V]'
)
t
=
np
.
arange
(
len
(
line1data
))
/
out
[
'samplerate'
]
t2
=
np
.
arange
(
len
(
line2data
))
/
out
[
'samplerate'
]
ax1
.
plot
(
t
,
line1data
)
ax2
.
plot
(
t2
,
line2data
)
ax3
.
plot
(
t
,
line3data
,
'c'
)
ax4
.
plot
(
t2
,
line4data
,
'y'
)
if
fitOn
:
ax1
.
plot
(
t
,
line1fdata
,
'r'
)
#ax2.plot(t2, line2fdata, 'r')
ax4
.
tick_params
(
axis
=
'y'
,
colors
=
'y'
)
ax4
.
yaxis
.
label
.
set_color
(
'y'
)
ax3
.
tick_params
(
axis
=
'y'
,
colors
=
'c'
)
ax3
.
yaxis
.
label
.
set_color
(
'c'
)
ax1
.
set_title
(
'Event {} of {}
\n
Ionic Current Trace "{}"'
.
format
(
i
,
NumberOfEvents
,
cases
[
0
]))
ax1
.
relim
()
ax2
.
relim
()
ax3
.
relim
()
ax4
.
relim
()
ax1
.
autoscale_view
(
True
,
True
,
True
)
ax2
.
autoscale_view
(
True
,
True
,
True
)
# voltage plots
ax3
.
autoscale_view
(
True
,
True
,
False
)
ax4
.
autoscale_view
(
True
,
True
,
False
)
ax3
.
set_ylim
(
np
.
min
(
line3data
)
-
np
.
mean
(
line3data
)
*
5
/
10
,
np
.
max
(
line3data
)
+
np
.
mean
(
line3data
)
*
1
/
10
)
ax4
.
set_ylim
([
np
.
min
(
line4data
)
-
np
.
mean
(
line4data
)
*
2
/
10
,
np
.
max
(
line4data
)
+
np
.
mean
(
line4data
)
*
5
/
10
])
fig
.
tight_layout
()
fig
.
canvas
.
draw
()
plt
.
show
()
Event Timeline
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