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Maxence Ferrari
IPI_annot
Commits
598683ab
Commit
598683ab
authored
4 years ago
by
ferrari
Browse files
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Add reset fun to change current file
parent
17885a38
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1
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1 changed file
ipi_extract.py
+66
-23
66 additions, 23 deletions
ipi_extract.py
with
66 additions
and
23 deletions
ipi_extract.py
+
66
−
23
View file @
598683ab
...
...
@@ -4,6 +4,7 @@ import matplotlib.pyplot as plt
import
scipy.signal
as
sg
import
soundfile
as
sf
import
os
import
sys
from
matplotlib.widgets
import
Button
,
Cursor
,
MultiCursor
,
CheckButtons
,
RadioButtons
,
AxesWidget
,
TextBox
from
matplotlib.patches
import
Circle
from
fractions
import
Fraction
...
...
@@ -15,6 +16,10 @@ FSSR = 48_000 # Sampling rate of full signal plot
FSPK
=
0.1
# Max distance to detect a click in full sig in seconds
IPIPK
=
0.15
# Max distance to detect a IPI in milliseconds
SPSC
=
80
# Spectrogram scale
EMLN
=
{
'
p1_pos
'
:
np
.
nan
,
'
ipi_sig
'
:
np
.
nan
,
'
ipi_corr_man
'
:
np
.
nan
,
'
ipi_corr_auto
'
:
np
.
nan
,
'
ipi_ceps_man
'
:
np
.
nan
,
'
ipi_ceps_auto
'
:
np
.
nan
,
'
ind_number
'
:
np
.
nan
}
# Empty dataline
def
read
(
file_path
,
always_2d
=
True
):
...
...
@@ -29,6 +34,18 @@ def load_anysound(file_path):
return
np
.
array
(
tmp
.
get_array_of_samples
()).
reshape
(
-
1
,
tmp
.
channels
),
tmp
.
frame_rate
def
load_file
(
in_path
,
channel
,
low
,
high
):
print
(
f
'
Loading and processing
{
in_path
}
'
)
song
,
sr
=
read
(
in_path
,
always_2d
=
True
)
song
=
song
[:,
channel
]
sos
=
sg
.
butter
(
3
,
[
low
,
high
],
'
bandpass
'
,
fs
=
sr
,
output
=
'
sos
'
)
song
=
sg
.
sosfiltfilt
(
sos
,
song
)
frac
=
Fraction
(
FSSR
,
sr
)
song_resample
=
sg
.
resample_poly
(
song
,
frac
.
numerator
,
frac
.
denominator
)
print
(
'
Done processing
'
)
return
song
,
sr
,
song_resample
def
norm
(
x
):
return
x
/
(
np
.
abs
(
x
).
max
()
+
1e-10
)
...
...
@@ -242,6 +259,7 @@ class Callback(object):
self
.
curr_vert
=
3
*
[
0
]
# Current vertical line of sig/spec for each plot
self
.
cursor
=
None
self
.
f_cursor
=
None
self
.
reset_b
=
None
def
shift_left
(
self
,
event
):
self
.
p
=
max
(
0
,
self
.
p
-
FSSR
*
13
)
...
...
@@ -269,10 +287,7 @@ class Callback(object):
if
mpos
/
FSSR
not
in
self
.
offset
[:,
0
]:
self
.
offset
=
np
.
concatenate
([
self
.
offset
,
[[
mpos
/
FSSR
,
self
.
song_resample
[
mpos
]]]],
axis
=
0
)
self
.
scat
.
set_offsets
(
self
.
offset
)
self
.
df
[
mpos
/
FSSR
]
=
{
'
p1_pos
'
:
np
.
nan
,
'
ipi_sig
'
:
np
.
nan
,
'
ipi_corr_man
'
:
np
.
nan
,
'
ipi_corr_auto
'
:
np
.
nan
,
'
ipi_ceps_man
'
:
np
.
nan
,
'
ipi_ceps_auto
'
:
np
.
nan
,
'
ind_number
'
:
np
.
nan
}
self
.
df
[
mpos
/
FSSR
]
=
EMLN
.
copy
()
c
=
[[
0
,
0
,
0
,
1
]]
c
[
0
][
self
.
curr
]
=
1
if
len
(
self
.
offset
)
==
1
:
...
...
@@ -340,6 +355,7 @@ class Callback(object):
self
.
view_data
[
self
.
curr
][
1
][
0
].
set_clim
(
spec
.
max
()
-
SPSC
,
spec
.
max
())
self
.
view_data
[
self
.
curr
][
2
][
0
].
set_ydata
(
norm
(
np
.
correlate
(
click
,
click
,
'
same
'
)[
-
int
(
10e-3
*
self
.
sr
):]))
self
.
view_data
[
self
.
curr
][
3
][
0
].
set_ydata
(
norm_std
(
np
.
abs
(
np
.
fft
.
irfft
(
np
.
log10
(
np
.
abs
(
np
.
fft
.
rfft
(
click
))))[:
int
(
10e-3
*
self
.
sr
)])))
self
.
_set_label
()
plt
.
draw
()
return
for
i
in
range
(
3
):
# Look if a click plot was clicked and which one
...
...
@@ -365,7 +381,7 @@ class Callback(object):
if
self
.
view_data
[
i
][
0
][
1
][
1
].
get_visible
():
ipi_man
=
self
.
view_data
[
i
][
0
][
1
][
1
].
get_xdata
()[
0
]
-
self
.
view_data
[
i
][
0
][
1
][
0
].
get_xdata
()[
0
]
self
.
df
[
self
.
offset
[
self
.
curr_ind
[
i
],
0
]][
'
ipi_sig
'
]
=
ipi_man
self
.
view_ax
[
i
][
0
].
set_xlabel
(
f
'
IPI
man:
{
ipi_man
:
.
5
f
}
'
)
self
.
view_ax
[
i
][
0
].
set_xlabel
(
f
'
Sig
man:
{
ipi_man
:
.
5
f
}
'
)
else
:
self
.
view_data
[
i
][
j
][
1
].
set_xdata
((
event
.
xdata
,
event
.
xdata
))
self
.
view_data
[
i
][
j
][
1
].
set_visible
(
True
)
...
...
@@ -375,12 +391,14 @@ class Callback(object):
col
=
'
ipi_
'
+
(
'
corr
'
if
j
==
2
else
'
ceps
'
)
self
.
df
[
self
.
offset
[
self
.
curr_ind
[
i
],
0
]][
col
+
'
_man
'
]
=
event
.
xdata
self
.
df
[
self
.
offset
[
self
.
curr_ind
[
i
],
0
]][
col
+
'
_auto
'
]
=
ipi_auto
*
1e3
/
self
.
sr
self
.
view_ax
[
i
][
j
].
set_xlabel
(
f
'
IPI
man:
{
event
.
xdata
:
.
3
f
}
auto:
{
ipi_auto
*
1e3
/
self
.
sr
:
.
3
f
}
'
)
self
.
view_ax
[
i
][
j
].
set_xlabel
(
f
'
{
"
Corr
"
if
j
==
2
else
"
Ceps
"
}
man:
{
event
.
xdata
:
.
3
f
}
auto:
{
ipi_auto
*
1e3
/
self
.
sr
:
.
3
f
}
'
)
plt
.
draw
()
def
change_curr
(
self
,
label
):
self
.
curr
=
int
(
label
[
-
1
])
self
.
f_cursor
.
linev
.
set_color
(
'
rgb
'
[
self
.
curr
])
self
.
reset_b
.
label
.
set_c
(
'
rgb
'
[
self
.
curr
])
plt
.
draw
()
def
play
(
self
,
event
):
sound
=
(
norm
(
self
.
song_resample
[
self
.
p
:
self
.
p
+
FSSR
*
20
])
*
(
2
**
15
-
1
)).
astype
(
np
.
int16
)
...
...
@@ -395,22 +413,40 @@ class Callback(object):
plt
.
pause
(
0.2
)
self
.
fax
.
get_figure
().
set_constrained_layout
(
False
)
def
_set_label
(
self
,
ind
=
None
,
dic
=
None
):
if
ind
is
None
:
ind
=
self
.
curr
if
dic
is
None
:
dic
=
self
.
df
[
self
.
offset
[
self
.
curr_ind
[
ind
],
0
]]
self
.
view_ax
[
ind
][
0
].
set_xlabel
(
f
'
Sig man:
{
dic
[
"
ipi_sig
"
]
:
.
3
f
}
'
)
self
.
view_ax
[
ind
][
2
].
set_xlabel
(
f
'
Corr man:
{
dic
[
"
ipi_corr_man
"
]
:
.
3
f
}
auto:
{
dic
[
"
ipi_corr_auto
"
]
:
.
3
f
}
'
)
self
.
view_ax
[
ind
][
3
].
set_xlabel
(
f
'
Ceps man:
{
dic
[
"
ipi_ceps_man
"
]
:
.
3
f
}
auto:
{
dic
[
"
ipi_ceps_auto
"
]
:
.
3
f
}
'
)
def
reset_curr
(
self
,
event
):
self
.
df
[
self
.
offset
[
self
.
curr_ind
[
self
.
curr
],
0
]]
=
EMLN
.
copy
()
self
.
_set_label
()
plt
.
draw
()
def
load_file
(
in_path
,
channel
,
low
,
high
):
print
(
f
'
Loading and processing
{
in_path
}
'
)
song
,
sr
=
read
(
in_path
,
always_2d
=
True
)
song
=
song
[:,
channel
]
sos
=
sg
.
butter
(
3
,
[
low
,
high
],
'
bandpass
'
,
fs
=
sr
,
output
=
'
sos
'
)
song
=
sg
.
sosfiltfilt
(
sos
,
song
)
frac
=
Fraction
(
FSSR
,
sr
)
song_resample
=
sg
.
resample_poly
(
song
,
frac
.
numerator
,
frac
.
denominator
)
print
(
'
Done processing
'
)
return
song
,
sr
,
song_resample
def
reset
(
self
,
song
,
sr
,
song_resample
):
self
.
p
=
0
self
.
df
=
dict
()
self
.
line
.
set_ydata
(
song_resample
[:
FSSR
*
20
])
self
.
song
=
song
self
.
song_resample
=
song_resample
self
.
sr
=
sr
self
.
curr
=
0
# current view selected
self
.
offset
=
np
.
zeros
((
0
,
2
))
self
.
scat
.
set_offsets
(
self
.
offset
)
self
.
curr_ind
=
3
*
[
None
]
# Ind of click for each plot
self
.
curr_vert
=
3
*
[
0
]
# Current vertical line of sig/spec for each plot
for
i
in
range
(
3
):
self
.
_set_label
(
i
,
EMLN
)
plt
.
draw
()
def
init
(
in_path
,
channel
,
low
=
2e3
,
high
=
20e3
):
song
,
sr
,
song_resample
=
load_file
(
in_path
,
channel
,
low
,
high
)
fig
=
plt
.
figure
(
'
IPI
'
,
figsize
=
[
16
,
9
],
constrained_layout
=
True
)
fig
=
plt
.
figure
(
'
IPI
of
'
+
in_path
.
rsplit
(
'
/
'
,
1
)[
-
1
]
,
figsize
=
[
16
,
9
],
constrained_layout
=
True
)
gs
=
fig
.
add_gridspec
(
12
,
20
)
full_sig
=
plt
.
subplot
(
gs
[:
2
,
1
:
-
1
])
...
...
@@ -466,7 +502,13 @@ def init(in_path, channel, low=2e3, high=20e3):
resize_b
=
Button
(
resize_b_ax
,
'
Resize plot
'
)
resize_b
.
on_clicked
(
callback
.
resize
)
# text_b_ax = plt.subplot(gs[-1,4:6])
reset_b_ax
=
plt
.
subplot
(
gs
[
-
1
,
4
:
6
])
reset_b
=
Button
(
reset_b_ax
,
'
Reset current
'
)
reset_b
.
label
.
set_c
(
'
r
'
)
reset_b
.
on_clicked
(
callback
.
reset_curr
)
callback
.
reset_b
=
reset_b
# text_b_ax = plt.subplot(gs[-1,6:8])
# text_b = TextBox(text_b_ax, 'Individue #\nof current')
# # text_b.on_clicked(callback.resize)
...
...
@@ -523,21 +565,22 @@ def init(in_path, channel, low=2e3, high=20e3):
fig
.
set_constrained_layout
(
False
)
return
{
'
callback
'
:
callback
,
'
fig
'
:
fig
,
'
buttons
'
:
{
'
b_left
'
:
b_left
,
'
b_right
'
:
b_right
,
'
play_b
'
:
play_b
,
'
resize_b
'
:
resize_b
,
'
r_button
'
:
r_button
,
'
fs_click
'
:
cid
}}
# Needed to keep the callbacks alive
'
fs_click
'
:
cid
,
'
reset_b
'
:
reset_b
}}
# Needed to keep the callbacks alive
def
reset
(
in_path
,
channel
,
low
=
2e3
,
high
=
20e3
):
def
reset
(
callback
,
in_path
,
channel
,
low
=
2e3
,
high
=
20e3
):
song
,
sr
,
song_resample
=
load_file
(
in_path
,
channel
,
low
,
high
)
callback
.
reset
(
song
,
sr
,
song_resample
)
def
main
(
args
):
if
args
.
out
==
''
:
outpath
=
args
.
o
ut
.
rsplit
(
'
.
'
,
1
)[
0
]
+
'
.pred.h5
'
outpath
=
args
.
inp
ut
.
rsplit
(
'
.
'
,
1
)[
0
]
+
'
.pred.h5
'
else
:
outpath
=
args
.
out
if
os
.
path
.
isfile
(
outpath
)
and
not
args
.
erase
:
print
(
f
'
Out file
{
outpath
}
already exist and erase option isn
\'
t set.
'
)
return
1
ref_dict
=
init
(
args
.
input
,
args
.
channel
)
plt
.
show
()
...
...
@@ -555,4 +598,4 @@ if __name__ == '__main__':
"
the computation will be halted
"
)
args
=
parser
.
parse_args
()
main
(
args
)
sys
.
exit
(
main
(
args
)
)
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