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Commit 5fccdd3e authored by David Keitel's avatar David Keitel
Browse files

use os.path.join instead of manual string joining with "/"

parent 968f9833
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pyfstat/core.py
View file @ 5fccdd3e
......@@ -94,7 +94,7 @@ def read_par(
"""
if filename is None:
filename = "{}/{}.{}".format(outdir, label, suffix)
filename = os.path.join(outdir, "{}.{}".format(label, suffix))
if os.path.isfile(filename) is False:
raise ValueError("No file {} found".format(filename))
d = {}
......@@ -220,7 +220,7 @@ class BaseSearchClass(object):
def _add_log_file(self):
""" Log output to a file, requires class to have outdir and label """
logfilename = "{}/{}.log".format(self.outdir, self.label)
logfilename = os.path.join(self.outdir, self.label + ".log")
fh = logging.FileHandler(logfilename)
fh.setLevel(logging.INFO)
fh.setFormatter(
......@@ -756,7 +756,10 @@ class ComputeFstat(BaseSearchClass):
self.windowRange.tau = self.tauMin
logging.info("Initialising transient FstatMap features...")
self.tCWFstatMapFeatures, self.gpu_context = tcw.init_transient_fstat_map_features(
(
self.tCWFstatMapFeatures,
self.gpu_context,
) = tcw.init_transient_fstat_map_features(
self.tCWFstatMapVersion == "pycuda", self.cudaDeviceName
)
......@@ -942,7 +945,7 @@ class ComputeFstat(BaseSearchClass):
"""
if pfs_input is None:
if os.path.isfile("{}/{}.loudest".format(outdir, label)) is False:
if os.path.isfile(os.path.join(outdir, label + ".loudest")) is False:
raise ValueError("Need a loudest file to add the predicted Fstat")
loudest = read_par(label=label, outdir=outdir, suffix="loudest")
pfs_input = {
......@@ -1089,7 +1092,7 @@ class ComputeFstat(BaseSearchClass):
ax.set_title(title)
if savefig:
plt.tight_layout()
plt.savefig("{}/{}_twoFcumulative.png".format(outdir, label))
plt.savefig(os.path.join(outdir, label + "_twoFcumulative.png"))
return taus, twoFs
else:
return ax
......@@ -1179,7 +1182,7 @@ class SemiCoherentSearch(ComputeFstat):
For all other parameters, see pyfstat.ComputeFStat.
"""
self.fs_file_name = "{}/{}_FS.dat".format(self.outdir, self.label)
self.fs_file_name = os.path.join(self.outdir, self.label + "_FS.dat")
self.set_ephemeris_files()
self.transientWindowType = "rect"
self.t0Band = None
......@@ -1356,7 +1359,7 @@ class SemiCoherentGlitchSearch(ComputeFstat):
For all other parameters, see pyfstat.ComputeFStat.
"""
self.fs_file_name = "{}/{}_FS.dat".format(self.outdir, self.label)
self.fs_file_name = os.path.join(self.outdir, self.label + "_FS.dat")
self.set_ephemeris_files()
self.transientWindowType = "rect"
self.t0Band = None
......
pyfstat/grid_based_searches.py
View file @ 5fccdd3e
......@@ -826,7 +826,7 @@ class SliceGridSearch(GridSearch):
axes[i, i].set_ylabel("$2\mathcal{F}$")
if save:
fig.savefig("{}/{}_slice_projection.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_slice_projection.png"))
else:
return fig, axes
......@@ -1049,7 +1049,9 @@ class SlidingWindow(GridSearch):
def run(self, key="h0", errkey="dh0"):
self.key = key
self.errkey = errkey
out_file = "{}/{}_{}-sliding-window.txt".format(self.outdir, self.label, key)
out_file = os.path.join(
self.outdir, "{}_{}-sliding-window.txt".format(self.label, key)
)
if self.check_old_data_is_okay_to_use(out_file) is False:
self.inititate_search_object()
......@@ -1090,7 +1092,9 @@ class SlidingWindow(GridSearch):
if fig:
fig.savefig(
"{}/{}_{}-sliding-window.png".format(self.outdir, self.label, self.key)
os.path.join(
self.outdir, "{}_{}-sliding-window.png".format(self.label, self.key)
)
)
else:
return ax
......@@ -1239,7 +1243,7 @@ class FrequencySlidingWindow(GridSearch):
ax.set_title(ax.get_title(), y=1.18)
if savefig:
plt.tight_layout()
plt.savefig("{}/{}_sliding_window.png".format(self.outdir, self.label))
plt.savefig(os.path.join(self.outdir, self.label + "_sliding_window.png"))
else:
return ax
......@@ -1454,7 +1458,7 @@ class EarthTest(GridSearch):
y=0.99,
size=14,
)
fig.savefig("{}/{}_projection_matrix.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_projection_matrix.png"))
def plot(self, key, prior_widths=None):
Bsa, FmaxMismatch = self.marginalised_bayes_factor(prior_widths)
......@@ -1479,7 +1483,7 @@ class EarthTest(GridSearch):
)
)
fig.tight_layout()
fig.savefig("{}/{}_1D.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_1D.png"))
class DMoff_NO_SPIN(GridSearch):
......
pyfstat/helper_functions.py
View file @ 5fccdd3e
......@@ -124,7 +124,7 @@ def set_up_command_line_arguments():
def get_ephemeris_files():
""" Returns the earth_ephem and sun_ephem """
config_file = os.path.expanduser("~") + "/.pyfstat.conf"
config_file = os.path.join(os.path.expanduser("~"), ".pyfstat.conf")
env_var = "LALPULSAR_DATADIR"
please = "Please provide the ephemerides paths when initialising searches."
if os.path.isfile(config_file):
......
pyfstat/make_sfts.py
View file @ 5fccdd3e
......@@ -96,7 +96,7 @@ class Writer(BaseSearchClass):
os.makedirs(self.outdir)
if self.tref is None:
self.tref = self.tstart
self.config_file_name = "{}/{}.cff".format(self.outdir, self.label)
self.config_file_name = os.path.join(self.outdir, self.label + ".cff")
self.sftfilenames = [
lalpulsar.OfficialSFTFilename(
dets[0],
......@@ -110,7 +110,7 @@ class Writer(BaseSearchClass):
for dets in self.detectors.split(",")
]
self.sftfilepath = ";".join(
["{}/{}".format(self.outdir, fn) for fn in self.sftfilenames]
[os.path.join(self.outdir, fn) for fn in self.sftfilenames]
)
self.IFOs = ",".join(['"{}"'.format(d) for d in self.detectors.split(",")])
......@@ -354,7 +354,7 @@ transientTau = {:10.0f}\n"""
# Remove old data:
try:
os.unlink("{}/*{}*.sft".format(self.outdir, self.label))
os.unlink(os.path.join(self.outdir, "*" + self.label + "*.sft"))
except OSError:
pass
......@@ -671,24 +671,21 @@ class FrequencyModulatedArtifactWriter(Writer):
int(self.duration),
self.label,
)
SFTFile_fullpath = os.path.join(self.outdir, SFTFilename)
# If the file already exists, simply remove it for now (no caching
# implemented)
helper_functions.run_commandline(
"rm {}/{}".format(self.outdir, SFTFilename), raise_error=False, log_level=10
"rm {}".format(SFTFile_fullpath), raise_error=False, log_level=10
)
cl_splitSFTS = "lalapps_splitSFTs -fs {} -fb {} -fe {} -o {}/{} -i {}/*sft".format(
self.fmin,
self.Band,
self.fmin + self.Band,
self.outdir,
SFTFilename,
self.tmp_outdir,
inpattern = os.path.join(self.tmp_outdir, "*sft")
cl_splitSFTS = "lalapps_splitSFTs -fs {} -fb {} -fe {} -o {} -i {}".format(
self.fmin, self.Band, self.fmin + self.Band, SFTFile_fullpath, inpattern
)
helper_functions.run_commandline(cl_splitSFTS)
helper_functions.run_commandline("rm {} -r".format(self.tmp_outdir))
files = glob.glob("{}/{}*".format(self.outdir, SFTFilename))
files = glob.glob(SFTFile_fullpath + "*")
if len(files) == 1:
fn = files[0]
fn_new = fn.split(".")[0] + ".sft"
......@@ -736,7 +733,7 @@ class FrequencyModulatedArtifactWriter(Writer):
self.maxStartTime = None
self.duration = self.Tsft
self.tmp_outdir = "{}/{}_tmp".format(self.outdir, self.label)
self.tmp_outdir = os.path.join(self.outdir, self.label + "_tmp")
if os.path.isdir(self.tmp_outdir) is True:
raise ValueError(
"Temporary directory {} already exists, please rename".format(
......
pyfstat/mcmc_based_searches.py
View file @ 5fccdd3e
......@@ -188,7 +188,7 @@ class MCMCSearch(core.BaseSearchClass):
logging.info("No sftfilepattern given")
if injectSources:
logging.info("Inject sources: {}".format(injectSources))
self.pickle_path = "{}/{}_saved_data.p".format(self.outdir, self.label)
self.pickle_path = os.path.join(self.outdir, self.label + "_saved_data.p")
self._unpack_input_theta()
self.ndim = len(self.theta_keys)
if self.log10beta_min:
......@@ -609,7 +609,9 @@ class MCMCSearch(core.BaseSearchClass):
fig, axes = self._plot_walkers(sampler, **kwargs)
fig.tight_layout()
fig.savefig(
"{}/{}_init_{}_walkers.png".format(self.outdir, self.label, j)
os.path.join(
self.outdir, "{}_init_{}_walkers.png".format(self.label, j)
)
)
p0 = self._get_new_p0(sampler)
......@@ -629,7 +631,7 @@ class MCMCSearch(core.BaseSearchClass):
try:
fig, axes = self._plot_walkers(sampler, nprod=nprod, **kwargs)
fig.tight_layout()
fig.savefig("{}/{}_walkers.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_walkers.png"))
except RuntimeError as e:
logging.warning("Failed to save walker plots due to Erro {}".format(e))
......@@ -802,7 +804,7 @@ class MCMCSearch(core.BaseSearchClass):
ax.hist(self.samples, bins=50, histtype="stepfilled")
ax.set_xlabel(self.theta_symbols[0])
fig.savefig("{}/{}_corner.png".format(self.outdir, self.label), dpi=dpi)
fig.savefig(os.path.join(self.outdir, self.label + "_corner.png"), dpi=dpi)
return
with plt.rc_context(rc_context):
......@@ -881,7 +883,7 @@ class MCMCSearch(core.BaseSearchClass):
if save_fig:
fig_triangle.savefig(
"{}/{}_corner.png".format(self.outdir, self.label), dpi=dpi
os.path.join(self.outdir, self.label + "_corner.png"), dpi=dpi
)
else:
return fig, axes
......@@ -936,7 +938,7 @@ class MCMCSearch(core.BaseSearchClass):
fig.subplots_adjust(hspace=0.05, wspace=0.05)
if save_fig:
fig.savefig("{}/{}_corner.png".format(self.outdir, self.label), dpi=dpi)
fig.savefig(os.path.join(self.outdir, self.label + "_corner.png"), dpi=dpi)
else:
return fig
......@@ -1023,7 +1025,7 @@ class MCMCSearch(core.BaseSearchClass):
labs = [l.get_label() for l in lns]
axes[0].legend(lns, labs, loc=1, framealpha=0.8)
fig.savefig("{}/{}_prior_posterior.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_prior_posterior.png"))
def plot_cumulative_max(self, **kwargs):
""" Plot the cumulative twoF for the maximum posterior estimate
......@@ -1643,17 +1645,13 @@ class MCMCSearch(core.BaseSearchClass):
def write_par(self, method="med"):
""" Writes a .par of the best-fit params with an estimated std """
logging.info(
"Writing {}/{}.par using the {} method".format(
self.outdir, self.label, method
)
)
filename = os.path.join(self.outdir, self.label + ".par")
logging.info("Writing {} using the {} method".format(filename, method))
median_std_d = self.get_median_stds()
max_twoF_d, max_twoF = self.get_max_twoF()
logging.info("Writing par file with max twoF = {}".format(max_twoF))
filename = "{}/{}.par".format(self.outdir, self.label)
with open(filename, "w+") as f:
f.write("MaxtwoF = {}\n".format(max_twoF))
f.write("tref = {}\n".format(self.tref))
......@@ -1673,9 +1671,10 @@ class MCMCSearch(core.BaseSearchClass):
for key in ["Alpha", "Delta", "F0", "F1"]:
if key not in params:
params[key] = self.theta_prior[key]
filename = os.path.join(self.outdir, self.label + ".loudest")
cmd = (
'lalapps_ComputeFstatistic_v2 -a {} -d {} -f {} -s {} -D "{}"'
' --refTime={} --outputLoudest="{}/{}.loudest" '
' --refTime={} --outputLoudest="{}" '
"--minStartTime={} --maxStartTime={}"
).format(
params["Alpha"],
......@@ -1684,8 +1683,7 @@ class MCMCSearch(core.BaseSearchClass):
params["F1"],
self.sftfilepattern,
params["tref"],
self.outdir,
self.label,
filename,
self.minStartTime,
self.maxStartTime,
)
......@@ -1693,7 +1691,7 @@ class MCMCSearch(core.BaseSearchClass):
def write_prior_table(self):
""" Generate a .tex file of the prior """
with open("{}/{}_prior.tex".format(self.outdir, self.label), "w") as f:
with open(os.path.join(self.outdir, self.label + "_prior.tex"), "w") as f:
f.write(
r"\begin{tabular}{c l c} \hline" + "\n"
r"Parameter & & & \\ \hhline{====}"
......@@ -1860,7 +1858,7 @@ class MCMCSearch(core.BaseSearchClass):
)
ax2.set_xlabel(r"$\beta_{\textrm{min}}$")
plt.tight_layout()
fig.savefig("{}/{}_beta_lnl.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_beta_lnl.png"))
return log10evidence, log10evidence_err
......@@ -1966,7 +1964,7 @@ class MCMCGlitchSearch(MCMCSearch):
"Set-up MCMC glitch search with {} glitches for model {}" " on data {}"
).format(self.nglitch, self.label, self.sftfilepattern)
)
self.pickle_path = "{}/{}_saved_data.p".format(self.outdir, self.label)
self.pickle_path = os.path.join(self.outdir, self.label + "_saved_data.p")
self._unpack_input_theta()
self.ndim = len(self.theta_keys)
if self.log10beta_min:
......@@ -2189,7 +2187,7 @@ class MCMCGlitchSearch(MCMCSearch):
ax.plot(ts + taus, twoFs)
ax.set_xlabel("GPS time")
fig.savefig("{}/{}_twoFcumulative.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_twoFcumulative.png"))
class MCMCSemiCoherentSearch(MCMCSearch):
......@@ -2309,7 +2307,7 @@ class MCMCSemiCoherentSearch(MCMCSearch):
self.label, self.sftfilepattern
)
)
self.pickle_path = "{}/{}_saved_data.p".format(self.outdir, self.label)
self.pickle_path = os.path.join(self.outdir, self.label + "_saved_data.p")
self._unpack_input_theta()
self.ndim = len(self.theta_keys)
if self.log10beta_min:
......@@ -2508,7 +2506,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
self.label, self.sftfilepattern
)
)
self.pickle_path = "{}/{}_saved_data.p".format(self.outdir, self.label)
self.pickle_path = os.path.join(self.outdir, self.label + "_saved_data.p")
self._unpack_input_theta()
self.ndim = len(self.theta_keys)
if self.log10beta_min:
......@@ -2603,7 +2601,9 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
if run_setup is None:
logging.info("No run_setup provided")
run_setup_input_file = "{}/{}_run_setup.p".format(self.outdir, self.label)
run_setup_input_file = os.path.join(
self.outdir, self.label + "_run_setup.p"
)
if os.path.isfile(run_setup_input_file):
logging.info(
......@@ -2699,7 +2699,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
)
if gen_tex_table:
filename = "{}/{}_run_setup.tex".format(self.outdir, self.label)
filename = os.path.join(self.outdir, self.label + "_run_setup.tex")
with open(filename, "w+") as f:
f.write(r"\begin{tabular}{c|ccc}" + "\n")
f.write(
......@@ -2884,7 +2884,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
if return_fig:
return fig, axes
else:
fig.savefig("{}/{}_walkers.png".format(self.outdir, self.label))
fig.savefig(os.path.join(self.outdir, self.label + "_walkers.png"))
class MCMCTransientSearch(MCMCSearch):
......
tests.py
View file @ 5fccdd3e
......@@ -64,7 +64,9 @@ class Writer(Test):
def test_make_cff(self):
Writer = pyfstat.Writer(self.label, outdir=self.outdir)
Writer.make_cff()
self.assertTrue(os.path.isfile("./{}/{}.cff".format(self.outdir, self.label)))
self.assertTrue(
os.path.isfile(os.path.join(".", self.outdir, self.label + ".cff"))
)
def test_run_makefakedata(self):
Writer = pyfstat.Writer(self.label, outdir=self.outdir, duration=3600)
......@@ -72,7 +74,9 @@ class Writer(Test):
Writer.run_makefakedata()
self.assertTrue(
os.path.isfile(
"./{}/H-2_H1_1800SFT_TestWriter-700000000-3600.sft".format(self.outdir)
os.path.join(
".", self.outdir, "H-2_H1_1800SFT_TestWriter-700000000-3600.sft"
)
)
)
......@@ -107,11 +111,10 @@ class par(Test):
label = "TestPar"
def test(self):
os.system('echo "x=100\ny=10" > {}/{}.par'.format(self.outdir, self.label))
parfile = os.path.join(self.outdir, self.label + ".par")
os.system('echo "x=100\ny=10" > ' + parfile)
par = pyfstat.core.read_par(
"{}/{}.par".format(self.outdir, self.label), return_type="Bunch"
)
par = pyfstat.core.read_par(parfile, return_type="Bunch")
self.assertTrue(par.x == 100)
self.assertTrue(par.y == 10)
......@@ -186,9 +189,10 @@ class ComputeFstat(Test):
Writer.make_data()
predicted_FS = Writer.predict_fstat()
sftfilepattern = os.path.join(Writer.outdir, "*{}*sft".format(Writer.label))
search_H1L1 = pyfstat.ComputeFstat(
tref=Writer.tref,
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
tref=Writer.tref, sftfilepattern=sftfilepattern,
)
FS = search_H1L1.get_fullycoherent_twoF(
Writer.tstart,
......@@ -206,7 +210,7 @@ class ComputeFstat(Test):
search_H1 = pyfstat.ComputeFstat(
tref=Writer.tref,
detectors="H1",
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
sftfilepattern=sftfilepattern,
SSBprec=lalpulsar.SSBPREC_RELATIVISTIC,
)
FS = search_H1.get_fullycoherent_twoF(
......@@ -235,7 +239,7 @@ class ComputeFstat(Test):
search = pyfstat.ComputeFstat(
tref=Writer.tref,
assumeSqrtSX=1,
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
sftfilepattern=os.path.join(Writer.outdir, "*{}*sft".format(Writer.label)),
)
FS = search.get_fullycoherent_twoF(
Writer.tstart,
......@@ -324,7 +328,7 @@ class SemiCoherentSearch(Test):
label=self.label,
outdir=self.outdir,
nsegs=2,
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
sftfilepattern=os.path.join(Writer.outdir, "*{}*sft".format(Writer.label)),
tref=Writer.tref,
minStartTime=Writer.tstart,
maxStartTime=Writer.tend,
......@@ -365,7 +369,7 @@ class SemiCoherentSearch(Test):
label=self.label,
outdir=self.outdir,
nsegs=2,
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
sftfilepattern=os.path.join(Writer.outdir, "*{}*sft".format(Writer.label)),
tref=Writer.tref,
minStartTime=Writer.tstart,
maxStartTime=Writer.tend,
......@@ -407,7 +411,7 @@ class SemiCoherentGlitchSearch(Test):
search = pyfstat.SemiCoherentGlitchSearch(
label=self.label,
outdir=self.outdir,
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
sftfilepattern=os.path.join(Writer.outdir, "*{}*sft".format(Writer.label)),
tref=Writer.tref,
minStartTime=Writer.tstart,
maxStartTime=Writer.tend,
......@@ -490,7 +494,7 @@ class MCMCSearch(Test):
outdir=self.outdir,
theta_prior=theta,
tref=tref,
sftfilepattern="{}/*{}*sft".format(Writer.outdir, Writer.label),
sftfilepattern=os.path.join(Writer.outdir, "*{}*sft".format(Writer.label)),
minStartTime=minStartTime,
maxStartTime=maxStartTime,
nsteps=[100, 100],
......
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