diff --git a/pyfstat/core.py b/pyfstat/core.py
index 7ee28da37258a559b7e04b910e5a21ba00de3b93..3a6f99ef0335ff1eaba57451bb583607a8d30b6a 100755
--- a/pyfstat/core.py
+++ b/pyfstat/core.py
@@ -3,7 +3,6 @@ import os
import logging
import copy
import glob
-import subprocess
import numpy as np
import matplotlib.pyplot as plt
@@ -51,27 +50,27 @@ def predict_fstat(h0, cosi, psi, Alpha, Delta, Freq, sftfilepattern,
minStartTime, maxStartTime, IFO=None, assumeSqrtSX=None,
**kwargs):
""" Wrapper to lalapps_PredictFstat """
- c_l = []
- c_l.append("lalapps_PredictFstat")
- c_l.append("--h0={}".format(h0))
- c_l.append("--cosi={}".format(cosi))
- c_l.append("--psi={}".format(psi))
- c_l.append("--Alpha={}".format(Alpha))
- c_l.append("--Delta={}".format(Delta))
- c_l.append("--Freq={}".format(Freq))
-
- c_l.append("--DataFiles='{}'".format(sftfilepattern))
+ cl_pfs = []
+ cl_pfs.append("lalapps_PredictFstat")
+ cl_pfs.append("--h0={}".format(h0))
+ cl_pfs.append("--cosi={}".format(cosi))
+ cl_pfs.append("--psi={}".format(psi))
+ cl_pfs.append("--Alpha={}".format(Alpha))
+ cl_pfs.append("--Delta={}".format(Delta))
+ cl_pfs.append("--Freq={}".format(Freq))
+
+ cl_pfs.append("--DataFiles='{}'".format(sftfilepattern))
if assumeSqrtSX:
- c_l.append("--assumeSqrtSX={}".format(assumeSqrtSX))
+ cl_pfs.append("--assumeSqrtSX={}".format(assumeSqrtSX))
if IFO:
- c_l.append("--IFO={}".format(IFO))
+ cl_pfs.append("--IFO={}".format(IFO))
- c_l.append("--minStartTime={}".format(int(minStartTime)))
- c_l.append("--maxStartTime={}".format(int(maxStartTime)))
- c_l.append("--outputFstat=/tmp/fs")
+ cl_pfs.append("--minStartTime={}".format(int(minStartTime)))
+ cl_pfs.append("--maxStartTime={}".format(int(maxStartTime)))
+ cl_pfs.append("--outputFstat=/tmp/fs")
- logging.debug("Executing: " + " ".join(c_l) + "\n")
- subprocess.check_output(" ".join(c_l), shell=True)
+ cl_pfs = " ".join(cl_pfs)
+ helper_functions.run_commandline(cl_pfs)
d = read_par(filename='/tmp/fs')
return float(d['twoF_expected']), float(d['twoF_sigma'])
@@ -292,13 +291,17 @@ class ComputeFstat(object):
raise ValueError('No data loaded.')
logging.info('Loaded {} data files from detectors {}'.format(
len(SFT_timestamps), detector_names))
+ cl_tconv1 = 'lalapps_tconvert {}'.format(int(SFT_timestamps[0]))
+ output = helper_functions.run_commandline(cl_tconv1)
+ tconvert1 = output.rstrip('\n')
+ cl_tconv2 = 'lalapps_tconvert {}'.format(int(SFT_timestamps[-1]))
+ output = helper_functions.run_commandline(cl_tconv2)
+ tconvert2 = output.rstrip('\n')
logging.info('Data spans from {} ({}) to {} ({})'.format(
int(SFT_timestamps[0]),
- subprocess.check_output('lalapps_tconvert {}'.format(
- int(SFT_timestamps[0])), shell=True).rstrip('\n'),
+ tconvert1,
int(SFT_timestamps[-1]),
- subprocess.check_output('lalapps_tconvert {}'.format(
- int(SFT_timestamps[-1])), shell=True).rstrip('\n')))
+ tconvert2))
return SFTCatalog
def init_computefstatistic_single_point(self):
@@ -1014,12 +1017,9 @@ transientTauDays={:1.3f}\n""")
'The config file {} is older than the sft file {}'.format(
self.config_file_name, self.sftfilepath))
logging.info('Checking contents of cff file')
- logging.info('Execute: {}'.format(
- 'lalapps_SFTdumpheader {} | head -n 20'.format(self.sftfilepath)))
- output = subprocess.check_output(
- 'lalapps_SFTdumpheader {} | head -n 20'.format(self.sftfilepath),
- shell=True)
- calls = [line for line in output.split('\n') if line[:3] == 'lal']
+ cl_dump = 'lalapps_SFTdumpheader {} | head -n 20'.format(self.sftfilepath)
+ output = helper_functions.run_commandline(cl_dump)
+ calls = [line for line in output.split('\n') if line[:3] == 'lal']
if calls[0] == cl:
logging.info('Contents matched, use old sft file')
return True
@@ -1063,56 +1063,54 @@ transientTauDays={:1.3f}\n""")
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(
+ cl_mfd = []
+ cl_mfd.append('lalapps_Makefakedata_v5')
+ cl_mfd.append('--outSingleSFT=TRUE')
+ cl_mfd.append('--outSFTdir="{}"'.format(self.outdir))
+ cl_mfd.append('--outLabel="{}"'.format(self.label))
+ cl_mfd.append('--IFOs={}'.format(
",".join(['"{}"'.format(d) for d in self.detectors.split(",")])))
if self.add_noise:
- cl.append('--sqrtSX="{}"'.format(self.sqrtSX))
+ cl_mfd.append('--sqrtSX="{}"'.format(self.sqrtSX))
if self.minStartTime is None:
- cl.append('--startTime={:0.0f}'.format(float(self.tstart)))
+ cl_mfd.append('--startTime={:0.0f}'.format(float(self.tstart)))
else:
- cl.append('--startTime={:0.0f}'.format(float(self.minStartTime)))
+ cl_mfd.append('--startTime={:0.0f}'.format(float(self.minStartTime)))
if self.maxStartTime is None:
- cl.append('--duration={}'.format(int(self.duration)))
+ cl_mfd.append('--duration={}'.format(int(self.duration)))
else:
data_duration = self.maxStartTime - self.minStartTime
- cl.append('--duration={}'.format(int(data_duration)))
- cl.append('--fmin={}'.format(int(self.fmin)))
- cl.append('--Band={}'.format(self.Band))
- cl.append('--Tsft={}'.format(self.Tsft))
+ cl_mfd.append('--duration={}'.format(int(data_duration)))
+ cl_mfd.append('--fmin={}'.format(int(self.fmin)))
+ cl_mfd.append('--Band={}'.format(self.Band))
+ cl_mfd.append('--Tsft={}'.format(self.Tsft))
if self.h0 != 0:
- cl.append('--injectionSources="{}"'.format(self.config_file_name))
+ cl_mfd.append('--injectionSources="{}"'.format(self.config_file_name))
- cl = " ".join(cl)
+ cl_mfd = " ".join(cl_mfd)
- if self.check_cached_data_okay_to_use(cl) is False:
- logging.info("Executing: " + cl)
- os.system(cl)
- os.system('\n')
+ if self.check_cached_data_okay_to_use(cl_mfd) is False:
+ helper_functions.run_commandline(cl_mfd)
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(
+ cl_pfs = []
+ cl_pfs.append("lalapps_PredictFstat")
+ cl_pfs.append("--h0={}".format(self.h0))
+ cl_pfs.append("--cosi={}".format(self.cosi))
+ cl_pfs.append("--psi={}".format(self.psi))
+ cl_pfs.append("--Alpha={}".format(self.Alpha))
+ cl_pfs.append("--Delta={}".format(self.Delta))
+ cl_pfs.append("--Freq={}".format(self.F0))
+
+ cl_pfs.append("--DataFiles='{}'".format(
self.outdir+"/*SFT_"+self.label+"*sft"))
- c_l.append("--assumeSqrtSX={}".format(self.sqrtSX))
+ cl_pfs.append("--assumeSqrtSX={}".format(self.sqrtSX))
- c_l.append("--minStartTime={}".format(int(self.minStartTime)))
- c_l.append("--maxStartTime={}".format(int(self.maxStartTime)))
+ cl_pfs.append("--minStartTime={}".format(int(self.minStartTime)))
+ cl_pfs.append("--maxStartTime={}".format(int(self.maxStartTime)))
- logging.info("Executing: " + " ".join(c_l) + "\n")
- output = subprocess.check_output(" ".join(c_l), shell=True)
+ cl_pfs = " ".join(cl_pfs)
+ output = helper_functions.run_commandline(cl_pfs)
twoF = float(output.split('\n')[-2])
return float(twoF)
diff --git a/pyfstat/helper_functions.py b/pyfstat/helper_functions.py
index 3a1a02e4249278fdadba7fb5ea45357a5d5a4b5c..25a560198e4b70697bc2a06e5cfc6502639f1708 100644
--- a/pyfstat/helper_functions.py
+++ b/pyfstat/helper_functions.py
@@ -4,6 +4,7 @@ Provides helpful functions to facilitate ease-of-use of pyfstat
import os
import sys
+import subprocess
import argparse
import logging
import inspect
@@ -183,3 +184,22 @@ def compute_pstar(twoFcheck_obs, twoFstarcheck_obs, m0, plot=False):
fig.savefig('test')
pstar_l = np.trapz(P_twoFstarcheck[:idx+1]/C, twoFstarcheck_vals[:idx+1])
return 2*np.min([pstar_l, 1-pstar_l])
+
+
+def run_commandline (cl):
+ """Run a string commandline as a subprocess, check for errors and return output."""
+
+ logging.info('Now executing: ' + cl)
+ try:
+ out = subprocess.check_output(cl, # what to run
+ stderr=subprocess.STDOUT, # catch errors
+ shell=True, # proper environment etc
+ universal_newlines=True # properly display linebreaks in error/output printing
+ )
+ except subprocess.CalledProcessError as e:
+ logging.error('Execution failed:')
+ logging.error(e.output)
+ raise
+ os.system('\n')
+
+ return(out)