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Gregory Ashton
PyFstat
Commits
18bb2b22
Commit
18bb2b22
authored
Sep 20, 2016
by
Gregory Ashton
Browse files
Initial commit adding files and defining the structure
parent
524fe686
Changes
3
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Side-by-side
aux_tools.py
0 → 100644
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18bb2b22
""" Tools used to generate fake data containing glitches """
import
os
import
numpy
as
np
import
logging
import
subprocess
import
lalpulsar
from
glitch_searches
import
initializer
,
BaseSearchClass
logging
.
basicConfig
(
level
=
logging
.
DEBUG
,
format
=
'%(asctime)s %(levelname)-8s: %(message)s'
,
datefmt
=
'%H:%M'
)
class
Writer
(
BaseSearchClass
):
""" Instance object for generating SFT containing glitch signals """
@
initializer
def
__init__
(
self
,
label
=
'Test'
,
tstart
=
700000000
,
duration
=
100
*
86400
,
dtglitch
=
None
,
delta_phi
=
0
,
delta_F0
=
0
,
delta_F1
=
0
,
delta_F2
=
0
,
tref
=
None
,
phi
=
0
,
F0
=
30
,
F1
=
1e-10
,
F2
=
0
,
Alpha
=
5e-3
,
Delta
=
6e-2
,
h0
=
0.1
,
cosi
=
0.0
,
psi
=
0.0
,
Tsft
=
1800
,
outdir
=
"."
,
sqrtSX
=
1
,
Band
=
2
):
"""
Parameters
----------
label: string
a human-readable label to be used in naming the output files
tstart, tend : float
start and end times (in gps seconds) of the total observation span
dtglitch: float
time (in gps seconds) of the glitch after tstart. To create data
without a glitch, set dtglitch=tend-tstart or leave as None
delta_phi, delta_F0, delta_F1: float
instanteneous glitch magnitudes in rad, Hz, and Hz/s respectively
tref: float or None
reference time (default is None, which sets the reference time to
tstart)
phil, F0, F1, F2, Alpha, Delta, h0, cosi, psi: float
pre-glitch phase, frequency, sky-position, and signal properties
Tsft: float
the sft duration
see `lalapps_Makefakedata_v5 --help` for help with the other paramaters
"""
for
d
in
self
.
delta_phi
,
self
.
delta_F0
,
self
.
delta_F1
,
self
.
delta_F2
:
if
np
.
size
(
d
)
==
1
:
d
=
[
d
]
self
.
tend
=
self
.
tstart
+
self
.
duration
if
self
.
dtglitch
is
None
or
self
.
dtglitch
==
self
.
duration
:
self
.
tbounds
=
[
self
.
tstart
,
self
.
tend
]
elif
np
.
size
(
self
.
dtglitch
)
==
1
:
self
.
tbounds
=
[
self
.
tstart
,
self
.
tstart
+
self
.
dtglitch
,
self
.
tend
]
else
:
self
.
tglitch
=
self
.
tstart
+
np
.
array
(
self
.
dtglitch
)
self
.
tbounds
=
[
self
.
tstart
]
+
list
(
self
.
tglitch
)
+
[
self
.
tend
]
if
os
.
path
.
isdir
(
self
.
outdir
)
is
False
:
os
.
makedirs
(
self
.
outdir
)
if
self
.
tref
is
None
:
self
.
tref
=
self
.
tglitch
self
.
tend
=
self
.
tstart
+
self
.
duration
tbs
=
np
.
array
(
self
.
tbounds
)
self
.
durations_days
=
(
tbs
[
1
:]
-
tbs
[:
-
1
])
/
86400
self
.
config_file_name
=
"{}/{}.cff"
.
format
(
outdir
,
label
)
self
.
theta
=
np
.
array
([
phi
,
F0
,
F1
,
F2
])
self
.
delta_thetas
=
np
.
atleast_2d
(
np
.
array
([
delta_phi
,
delta_F0
,
delta_F1
,
delta_F2
]).
T
)
self
.
detector
=
'H1'
numSFTs
=
int
(
float
(
self
.
duration
)
/
self
.
Tsft
)
self
.
sft_filename
=
lalpulsar
.
OfficialSFTFilename
(
'H'
,
'1'
,
numSFTs
,
self
.
Tsft
,
self
.
tstart
,
self
.
duration
,
self
.
label
)
self
.
sft_filepath
=
'{}/{}'
.
format
(
self
.
outdir
,
self
.
sft_filename
)
self
.
calculate_fmin_Band
()
def
make_data
(
self
):
''' A convienience wrapper to generate a cff file then sfts '''
self
.
make_cff
()
self
.
run_makefakedata
()
def
get_single_config_line
(
self
,
i
,
Alpha
,
Delta
,
h0
,
cosi
,
psi
,
phi
,
F0
,
F1
,
F2
,
tref
,
tstart
,
duration_days
):
template
=
(
"""[TS{}]
Alpha = {:1.18e}
Delta = {:1.18e}
h0 = {:1.18e}
cosi = {:1.18e}
psi = {:1.18e}
phi0 = {:1.18e}
Freq = {:1.18e}
f1dot = {:1.18e}
f2dot = {:1.18e}
refTime = {:10.6f}
transientWindowType=rect
transientStartTime={:10.3f}
transientTauDays={:1.3f}
\n
"""
)
return
template
.
format
(
i
,
Alpha
,
Delta
,
h0
,
cosi
,
psi
,
phi
,
F0
,
F1
,
F2
,
tref
,
tstart
,
duration_days
)
def
make_cff
(
self
):
"""
Generates an .cff file for a 'glitching' signal
"""
thetas
=
self
.
calculate_thetas
(
self
.
theta
,
self
.
delta_thetas
,
self
.
tbounds
)
content
=
''
for
i
,
(
t
,
d
,
ts
)
in
enumerate
(
zip
(
thetas
,
self
.
durations_days
,
self
.
tbounds
[:
-
1
])):
line
=
self
.
get_single_config_line
(
i
,
self
.
Alpha
,
self
.
Delta
,
self
.
h0
,
self
.
cosi
,
self
.
psi
,
t
[
0
],
t
[
1
],
t
[
2
],
t
[
3
],
self
.
tref
,
ts
,
d
)
content
+=
line
if
self
.
check_if_cff_file_needs_rewritting
(
content
):
config_file
=
open
(
self
.
config_file_name
,
"w+"
)
config_file
.
write
(
content
)
config_file
.
close
()
def
calculate_fmin_Band
(
self
):
self
.
fmin
=
self
.
F0
-
.
5
*
self
.
Band
def
check_cached_data_okay_to_use
(
self
,
cl
):
""" Check if cached data exists and, if it does, if it can be used """
getmtime
=
os
.
path
.
getmtime
if
os
.
path
.
isfile
(
self
.
sft_filepath
)
is
False
:
logging
.
info
(
'No SFT file matching {} found'
.
format
(
self
.
sft_filepath
))
return
False
else
:
logging
.
info
(
'Matching SFT file found'
)
if
getmtime
(
self
.
sft_filepath
)
<
getmtime
(
self
.
config_file_name
):
logging
.
info
(
(
'The config file {} has been modified since the sft file {} '
+
'was created'
).
format
(
self
.
config_file_name
,
self
.
sft_filepath
))
return
False
logging
.
info
(
'The config file {} is older than the sft file {}'
.
format
(
self
.
config_file_name
,
self
.
sft_filepath
))
logging
.
info
(
'Checking contents of cff file'
)
logging
.
info
(
'Execute: {}'
.
format
(
'lalapps_SFTdumpheader {} | head -n 20'
.
format
(
self
.
sft_filepath
)))
output
=
subprocess
.
check_output
(
'lalapps_SFTdumpheader {} | head -n 20'
.
format
(
self
.
sft_filepath
),
shell
=
True
)
calls
=
[
line
for
line
in
output
.
split
(
'
\n
'
)
if
line
[:
3
]
==
'lal'
]
if
calls
[
0
]
==
cl
:
logging
.
info
(
'Contents matched, use old cff file'
)
return
True
else
:
logging
.
info
(
'Contents unmatched, create new cff file'
)
return
False
def
check_if_cff_file_needs_rewritting
(
self
,
content
):
""" Check if the .cff file has changed
Returns True if the file should be overwritten - where possible avoid
overwriting to allow cached data to be used
"""
if
os
.
path
.
isfile
(
self
.
config_file_name
)
is
False
:
logging
.
info
(
'No config file {} found'
.
format
(
self
.
config_file_name
))
return
True
else
:
logging
.
info
(
'Config file {} already exists'
.
format
(
self
.
config_file_name
))
with
open
(
self
.
config_file_name
,
'r'
)
as
f
:
file_content
=
f
.
read
()
if
file_content
==
content
:
logging
.
info
(
'File contents match, no update of {} required'
.
format
(
self
.
config_file_name
))
return
False
else
:
logging
.
info
(
'File contents unmatched, updating {}'
.
format
(
self
.
config_file_name
))
return
True
def
run_makefakedata
(
self
):
""" Generate the sft data from the configuration file """
# Remove old data:
try
:
os
.
unlink
(
"{}/*{}*.sft"
.
format
(
self
.
outdir
,
self
.
label
))
except
OSError
:
pass
cl
=
[]
cl
.
append
(
'lalapps_Makefakedata_v5'
)
cl
.
append
(
'--outSingleSFT=TRUE'
)
cl
.
append
(
'--outSFTdir="{}"'
.
format
(
self
.
outdir
))
cl
.
append
(
'--outLabel="{}"'
.
format
(
self
.
label
))
cl
.
append
(
'--IFOs="{}"'
.
format
(
self
.
detector
))
cl
.
append
(
'--sqrtSX="{}"'
.
format
(
self
.
sqrtSX
))
cl
.
append
(
'--startTime={:10.9f}'
.
format
(
float
(
self
.
tstart
)))
cl
.
append
(
'--duration={}'
.
format
(
int
(
self
.
duration
)))
cl
.
append
(
'--fmin={}'
.
format
(
self
.
fmin
))
cl
.
append
(
'--Band={}'
.
format
(
self
.
Band
))
cl
.
append
(
'--Tsft={}'
.
format
(
self
.
Tsft
))
cl
.
append
(
'--injectionSources="./{}"'
.
format
(
self
.
config_file_name
))
cl
=
" "
.
join
(
cl
)
if
self
.
check_cached_data_okay_to_use
(
cl
)
is
False
:
logging
.
info
(
"Executing: "
+
cl
)
os
.
system
(
cl
)
os
.
system
(
'
\n
'
)
def
predict_fstat
(
self
):
""" Wrapper to lalapps_PredictFstat """
c_l
=
[]
c_l
.
append
(
"lalapps_PredictFstat"
)
c_l
.
append
(
"--h0={}"
.
format
(
self
.
h0
))
c_l
.
append
(
"--cosi={}"
.
format
(
self
.
cosi
))
c_l
.
append
(
"--psi={}"
.
format
(
self
.
psi
))
c_l
.
append
(
"--Alpha={}"
.
format
(
self
.
Alpha
))
c_l
.
append
(
"--Delta={}"
.
format
(
self
.
Delta
))
c_l
.
append
(
"--Freq={}"
.
format
(
self
.
F0
))
c_l
.
append
(
"--DataFiles='{}'"
.
format
(
self
.
outdir
+
"/*SFT_"
+
self
.
label
+
"*sft"
))
c_l
.
append
(
"--assumeSqrtSX={}"
.
format
(
self
.
sqrtSX
))
c_l
.
append
(
"--minStartTime={}"
.
format
(
self
.
tstart
))
c_l
.
append
(
"--maxStartTime={}"
.
format
(
self
.
tend
))
logging
.
info
(
"Executing: "
+
" "
.
join
(
c_l
)
+
"
\n
"
)
output
=
subprocess
.
check_output
(
" "
.
join
(
c_l
),
shell
=
True
)
twoF
=
float
(
output
.
split
(
'
\n
'
)[
-
2
])
return
float
(
twoF
)
pyfstat.py
0 → 100755
View file @
18bb2b22
This diff is collapsed.
Click to expand it.
setup.py
0 → 100644
View file @
18bb2b22
#!/usr/bin/env python
from
distutils.core
import
setup
setup
(
name
=
'PyFstat'
,
version
=
'0.1'
,
author
=
'Gregory Ashton'
,
author_email
=
'gregory.ashton@ligo.org'
,
py_modules
=
[
'pyfstat'
],
)
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