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Köllőd Csaba
MCC Flow
Commits
66e3ff84
Commit
66e3ff84
authored
Jan 3, 2023
by
Köllőd Csaba
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parent
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mcc-flow/merge_records.py
+109
-51
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mcc-flow/merge_records.py
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109 additions
and
51 deletions
mcc-flow/merge_records.py
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109
−
51
View file @
66e3ff84
from
dataclasses
import
dataclass
,
field
from
datetime
import
datetime
from
datetime
import
datetime
from
pathlib
import
Path
from
pathlib
import
Path
from
struct
import
unpack
from
struct
import
unpack
import
numpy
as
np
import
numpy
as
np
from
matplotlib
import
pyplot
as
plt
from
matplotlib
import
pyplot
as
plt
from
pyedflib
import
EdfWriter
,
FILETYPE_EDFPLUS
HEADER_FS
=
1
EEG_EMG_FS
=
250
GYRO_ACC_FS
=
50
SOUND_FS
=
6000
GSR_FS
=
10
EEG_EMG_SCALE
=
0.04470348358154
# (mV)
GYRO_SCALE
=
0.0152587890625
# (deg/sec)
ACC_SCALE
=
0.00006103515625
# (g)
@dataclass
class
PacketData
:
data
:
np
.
ndarray
type
:
str
unit
:
str
fs
:
int
@property
def
chs
(
self
):
return
self
.
data
.
shape
[
0
]
def
__add__
(
self
,
other
):
assert
self
.
type
==
other
.
type
,
'
Cannot combine PacketDatas with different signal types
'
assert
self
.
unit
==
other
.
unit
,
'
Cannot combine PacketDatas with different units
'
assert
self
.
fs
==
other
.
fs
,
'
Cannot combine PacketDatas with different sampling frequency
'
assert
self
.
chs
==
other
.
chs
,
'
Cannot combine PacketDatas with different number of channels
'
self
.
data
=
np
.
concatenate
((
self
.
data
,
other
.
data
),
axis
=-
1
)
return
self
@dataclass
class
FlowPacket
:
class
FlowPacket
:
header_fs
=
1
date
:
datetime
signal_fs
=
250
duration
:
int
=
field
(
init
=
False
,
default
=
1
)
gyro_acc_fs
=
50
flow
:
PacketData
sound_fs
=
6000
hr
:
PacketData
grs_fs
=
10
spo2
:
PacketData
eeg
:
PacketData
def
__init__
(
self
,
date_
,
flow
,
hr
,
spo2
,
eeg_giro
:
PacketData
# vbat_eeg, vbat_arm,
eeg_acc
:
PacketData
eeg
,
eeg_giro
,
eeg_acc
,
emg
:
PacketData
emg
,
emg_giro
,
emg_acc
,
emg_giro
:
PacketData
sound
,
gsr
):
emg_acc
:
PacketData
self
.
date
=
date_
sound
:
PacketData
self
.
duration
=
1
gsr
:
PacketData
self
.
flow
=
[
flow
]
self
.
hr
=
[
hr
]
self
.
spo2
=
[
spo2
]
self
.
eeg
=
eeg
self
.
eeg_giro
=
eeg_giro
self
.
eeg_acc
=
eeg_acc
self
.
emg
=
emg
self
.
emg_giro
=
emg_giro
self
.
emg_acc
=
emg_acc
self
.
sound
=
sound
self
.
gsr
=
gsr
def
__add__
(
self
,
other
):
def
__add__
(
self
,
other
):
self
.
flow
.
extend
(
other
.
flow
)
self
.
flow
+=
other
.
flow
self
.
hr
.
extend
(
other
.
hr
)
self
.
hr
+=
other
.
hr
self
.
spo2
.
extend
(
other
.
spo2
)
self
.
spo2
+=
other
.
spo2
self
.
eeg
=
np
.
concatenate
((
self
.
eeg
,
other
.
eeg
),
axis
=-
1
)
self
.
eeg
+
=
other
.
eeg
self
.
eeg_giro
=
np
.
concatenate
((
self
.
eeg_giro
,
other
.
eeg_giro
),
axis
=-
1
)
self
.
eeg_giro
+
=
other
.
eeg_giro
self
.
eeg_acc
=
np
.
concatenate
((
self
.
eeg_acc
,
other
.
eeg_acc
),
axis
=-
1
)
self
.
eeg_acc
+
=
other
.
eeg_acc
self
.
emg
=
np
.
concatenate
((
self
.
emg
,
other
.
emg
),
axis
=-
1
)
self
.
emg
+
=
other
.
emg
self
.
emg_giro
=
np
.
concatenate
((
self
.
emg_giro
,
other
.
emg_giro
),
axis
=-
1
)
self
.
emg_giro
+
=
other
.
emg_giro
self
.
emg_acc
=
np
.
concatenate
((
self
.
emg_acc
,
other
.
emg_acc
),
axis
=-
1
)
self
.
emg_acc
+
=
other
.
emg_acc
self
.
sound
=
np
.
concatenate
((
self
.
sound
,
other
.
sound
),
axis
=-
1
)
self
.
sound
+
=
other
.
sound
self
.
gsr
=
np
.
concatenate
((
self
.
gsr
,
other
.
gsr
),
axis
=-
1
)
self
.
gsr
+
=
other
.
gsr
self
.
duration
+=
other
.
duration
self
.
duration
+=
other
.
duration
return
self
return
self
def
_plot
(
self
,
data
,
title
):
def
_plot
(
self
,
pkt_data
,
title
):
data
=
pkt_data
.
data
plt
.
figure
()
plt
.
figure
()
plt
.
suptitle
(
title
)
plt
.
suptitle
(
title
)
chs
=
data
.
shape
[
0
]
chs
=
data
.
shape
[
0
]
for
i
in
range
(
chs
):
for
i
in
range
(
chs
):
plt
.
subplot
(
chs
,
1
,
i
+
1
)
plt
.
subplot
(
chs
,
1
,
i
+
1
)
plt
.
plot
(
np
.
linspace
(
0
,
self
.
duration
,
data
.
shape
[
1
]),
data
[
i
,
:])
plt
.
plot
(
np
.
linspace
(
0
,
self
.
duration
,
data
.
shape
[
1
]),
data
[
i
,
:])
if
chs
>
1
:
plt
.
title
(
f
'
ch
{
i
+
1
}
'
)
plt
.
title
(
f
'
ch
{
i
+
1
}
'
)
plt
.
xlabel
(
'
time (s)
'
)
plt
.
xlabel
(
'
time (s)
'
)
...
@@ -62,9 +85,32 @@ class FlowPacket:
...
@@ -62,9 +85,32 @@ class FlowPacket:
self
.
_plot
(
self
.
eeg
,
'
EEG
'
)
self
.
_plot
(
self
.
eeg
,
'
EEG
'
)
self
.
_plot
(
self
.
eeg_giro
,
'
EEG Gyro
'
)
self
.
_plot
(
self
.
eeg_giro
,
'
EEG Gyro
'
)
self
.
_plot
(
self
.
emg
,
'
EMG
'
)
self
.
_plot
(
self
.
emg
,
'
EMG
'
)
self
.
_plot
(
self
.
spo2
,
'
SPO2
'
)
plt
.
show
()
plt
.
show
()
def
to_edf
(
self
,
filename
):
to_save
=
[
self
.
eeg
,
self
.
eeg_giro
,
self
.
eeg_acc
,
self
.
emg
,
self
.
emg_giro
,
self
.
emg_acc
,
self
.
flow
,
self
.
hr
,
self
.
spo2
,
self
.
sound
,
self
.
gsr
]
with
EdfWriter
(
filename
,
sum
(
pkt
.
chs
for
pkt
in
to_save
),
FILETYPE_EDFPLUS
)
as
edf
:
data_buffer
=
[]
sig
=
0
for
pkt
in
to_save
:
for
i
,
ch_dat
in
enumerate
(
pkt
.
data
):
print
(
sig
)
# edf.setPhysicalMaximum(sig, 2**7 * EEG_EMG_SCALE)
# edf.setPhysicalMinimum(sig, -2**7 * EEG_EMG_SCALE)
# edf.setDigitalMaximum(sig, 2**7)
# edf.setDigitalMinimum(sig, -2**7)
edf
.
setPhysicalDimension
(
sig
,
pkt
.
unit
)
edf
.
setSamplefrequency
(
sig
,
pkt
.
fs
)
edf
.
setLabel
(
sig
,
f
'
{
pkt
.
type
}{
i
}
'
)
data_buffer
.
append
(
ch_dat
)
sig
+=
1
edf
.
writeSamples
(
data_buffer
)
def
_read_block_data
(
file
,
shape
,
format_
,
format_size
):
def
_read_block_data
(
file
,
shape
,
format_
,
format_size
):
sh
=
np
.
prod
(
shape
)
sh
=
np
.
prod
(
shape
)
...
@@ -82,26 +128,37 @@ def read_packet(file):
...
@@ -82,26 +128,37 @@ def read_packet(file):
flow
=
int
.
from_bytes
(
flow
,
'
big
'
)
flow
=
int
.
from_bytes
(
flow
,
'
big
'
)
date_
=
datetime
.
fromisoformat
(
f
'
{
date_
[
:
4
]
}
-
{
date_
[
4
:
6
]
}
-
{
date_
[
6
:
]
}
T
{
time_
[
:
2
]
}
:
{
time_
[
2
:
4
]
}
:
{
time_
[
4
:
]
}
'
)
date_
=
datetime
.
fromisoformat
(
f
'
{
date_
[
:
4
]
}
-
{
date_
[
4
:
6
]
}
-
{
date_
[
6
:
]
}
T
{
time_
[
:
2
]
}
:
{
time_
[
2
:
4
]
}
:
{
time_
[
4
:
]
}
'
)
spo2
/=
10.
spo2
/=
10.
print
(
date_
,
flow
,
hr
,
spo2
,
vbat_eeg
,
vbat_arm
)
flow
=
PacketData
(
np
.
array
([[
flow
]]),
'
flow
'
,
'
unit
'
,
HEADER_FS
)
hr
=
PacketData
(
np
.
array
([[
hr
]]),
'
hr
'
,
'
unit
'
,
HEADER_FS
)
spo2
=
PacketData
(
np
.
array
([[
spo2
]]),
'
spo2
'
,
'
unit
'
,
HEADER_FS
)
# print(date_, flow, hr, spo2, vbat_eeg, vbat_arm)
# eeg
# eeg
eeg
=
_read_block_data
(
file
,
(
250
,
4
),
'
i
'
,
4
).
T
eeg
=
_read_block_data
(
file
,
(
250
,
4
),
'
i
'
,
4
).
T
*
EEG_EMG_SCALE
eeg_giro
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
eeg_giro
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
*
GYRO_SCALE
eeg_acc
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
eeg_acc
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
*
ACC_SCALE
print
(
eeg
.
shape
,
eeg_giro
.
shape
,
eeg_acc
.
shape
)
eeg
=
PacketData
(
eeg
,
'
eeg
'
,
'
uV
'
,
EEG_EMG_FS
)
eeg_giro
=
PacketData
(
eeg_giro
,
'
eeg_giro
'
,
'
unit
'
,
GYRO_ACC_FS
)
eeg_acc
=
PacketData
(
eeg_acc
,
'
eeg_acc
'
,
'
unit
'
,
GYRO_ACC_FS
)
# print(eeg, eeg_giro, eeg_acc)
# emg
# emg
emg
=
_read_block_data
(
file
,
(
250
,
6
),
'
i
'
,
4
).
T
emg
=
_read_block_data
(
file
,
(
250
,
6
),
'
i
'
,
4
).
T
*
EEG_EMG_SCALE
emg_giro
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
emg_giro
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
*
GYRO_SCALE
emg_acc
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
emg_acc
=
_read_block_data
(
file
,
(
50
,
3
),
'
h
'
,
2
).
T
*
ACC_SCALE
print
(
emg
.
shape
,
emg_giro
.
shape
,
emg_acc
.
shape
)
emg
=
PacketData
(
emg
,
'
emg
'
,
'
uV
'
,
EEG_EMG_FS
)
emg_giro
=
PacketData
(
emg_giro
,
'
emg_giro
'
,
'
unit
'
,
GYRO_ACC_FS
)
emg_acc
=
PacketData
(
emg_acc
,
'
emg_acc
'
,
'
unit
'
,
GYRO_ACC_FS
)
# print(emg, emg_giro, emg_acc)
# extra
# extra
sound
=
_read_block_data
(
file
,
(
6000
,
1
),
'
h
'
,
2
).
T
sound
=
_read_block_data
(
file
,
(
6000
,
1
),
'
h
'
,
2
).
T
gsr
=
_read_block_data
(
file
,
(
10
,
1
),
'
h
'
,
2
).
T
gsr
=
_read_block_data
(
file
,
(
10
,
1
),
'
h
'
,
2
).
T
print
(
sound
.
shape
,
gsr
.
shape
)
sound
=
PacketData
(
sound
,
'
sound
'
,
'
unit
'
,
SOUND_FS
)
gsr
=
PacketData
(
gsr
,
'
gsr
'
,
'
unit
'
,
GSR_FS
)
# print(sound, gsr)
packet
=
FlowPacket
(
date_
,
flow
,
hr
,
spo2
,
# vbat_eeg, vbat_arm,
packet
=
FlowPacket
(
date_
,
flow
,
hr
,
spo2
,
eeg
,
eeg_giro
,
eeg_acc
,
eeg
,
eeg_giro
,
eeg_acc
,
emg
,
emg_giro
,
emg_acc
,
emg
,
emg_giro
,
emg_acc
,
sound
,
gsr
)
sound
,
gsr
)
...
@@ -125,7 +182,8 @@ def read_data(path):
...
@@ -125,7 +182,8 @@ def read_data(path):
for
file
in
files
:
for
file
in
files
:
with
open
(
file
,
'
rb
'
)
as
f
:
with
open
(
file
,
'
rb
'
)
as
f
:
data
=
read_dat_file
(
f
)
data
=
read_dat_file
(
f
)
data
.
plot
()
# data.plot()
data
.
to_edf
(
'
test.edf
'
)
exit
(
12
)
exit
(
12
)
...
...
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