def check_force_resume(cls, output, info=None):
"""
Performs the necessary checks on existing files if resuming or forcing
(including deleting some output files when forcing).
"""
if not output:
return
resuming: Optional[bool]
if mpi.is_main_process():
resuming = False
if output.force:
cls.delete_output_files(output, info=info)
elif any(find_with_regexp(regexp, root or output.folder) for (regexp, root)
in cls.output_files_regexps(output=output, info=info, minimal=True)):
if output.is_resuming():
output.log.info("Found an old sample. Resuming.")
resuming = True
else:
raise LoggedError(
output.log, "Delete the previous output manually, automatically "
"('-%s', '--%s', '%s: True')" % (
"force"[0], "force", "force") +
" or request resuming ('-%s', '--%s', '%s: True')" % (
"resume"[0], "resume", "resume"))
else:
if output.is_resuming():
output.log.info(
"Did not find an old sample. Cleaning up and starting anew.")
# Clean up old files, and set resuming=False,
# regardless of requested value
cls.delete_output_files(output, info=info)
else:
resuming = None
output.set_resuming(resuming)
def delete_with_regexp(self, regexp, root=None):
"""
Deletes all files compatible with the given `regexp`.
If `regexp` is `None` and `root` is defined, deletes the `root` folder.
"""
if root is None:
root = self.folder
if regexp is not None:
file_names = find_with_regexp(regexp, root)
if file_names:
self.log.debug(
"From regexp %r in folder %r, deleting files %r",
regexp.pattern, root, file_names)
else:
file_names = [root]
self.log.debug("Deleting folder %r", root)
for f in file_names:
try:
os.remove(f)
except IsADirectoryError:
try:
shutil.rmtree(f)
except:
raise
except OSError:
pass
def delete_with_regexp(self, regexp, root=None):
"""
Deletes all files compatible with the given `regexp`.
If `regexp` is `None` and `root` is defined, deletes the `root` folder.
"""
if root is None:
root = self.folder
if regexp is not None:
file_names = find_with_regexp(regexp, root)
if file_names:
self.log.debug(
"From regexp %r in folder %r, deleting files %r", regexp.pattern,
root, file_names)
else:
file_names = [root]
self.log.debug("Deleting folder %r", root)
for f in file_names:
self.delete_file_or_folder(f)
def process_raw_output(self):
"""
Loads the sample of live points from ``PolyChord``'s raw output and writes it
(if ``txt`` output requested).
"""
if is_main_process():
self.log.info(
"Loading PolyChord's results: samples and evidences.")
self.dump_paramnames(self.raw_prefix)
self.collection = self.save_sample(self.raw_prefix + ".txt", "1")
# Load clusters, and save if output
if self.pc_settings.do_clustering:
self.clusters = {}
clusters_raw_regexp = re.compile(
re.escape(self.pc_settings.file_root + "_") + r"\d+\.txt")
cluster_raw_files = sorted(
find_with_regexp(clusters_raw_regexp,
os.path.join(self.pc_settings.base_dir,
self._clusters_dir),
walk_tree=True))
for f in cluster_raw_files:
i = int(f[f.rfind("_") + 1:-len(".txt")])
if self.output:
old_folder = self.output.folder
self.output.folder = self.clusters_folder
sample = self.save_sample(f, str(i))
if self.output:
self.output.folder = old_folder
self.clusters[i] = {"sample": sample}
# Prepare the evidence(s) and write to file
pre = "log(Z"
active = "(Still active)"
with open(self.raw_prefix + ".stats", "r",
encoding="utf-8-sig") as statsfile:
lines = [l for l in statsfile.readlines() if l.startswith(pre)]
for l in lines:
logZ, logZstd = [
float(n.replace(active, ""))
for n in l.split("=")[-1].split("+/-")
]
component = l.split("=")[0].lstrip(pre + "_").rstrip(") ")
if not component:
self.logZ, self.logZstd = logZ, logZstd
elif self.pc_settings.do_clustering:
i = int(component)
self.clusters[i]["logZ"], self.clusters[i][
"logZstd"] = logZ, logZstd
self.log.debug(
"RAW log(Z) = %g +/- %g ; RAW Z in [%.8g, %.8g] (68%% C.L. log-gaussian)",
self.logZ, self.logZstd,
*[np.exp(self.logZ + n * self.logZstd) for n in [-1, 1]])
self._correct_unphysical_fraction()
if self.output:
out_evidences = dict(logZ=self.logZ, logZstd=self.logZstd)
if getattr(self, "clusters", None):
out_evidences["clusters"] = {}
for i in sorted(list(self.clusters)):
out_evidences["clusters"][i] = dict(
logZ=self.clusters[i]["logZ"],
logZstd=self.clusters[i]["logZstd"])
fname = os.path.join(self.output.folder,
self.output.prefix + _evidence_extension)
yaml_dump_file(fname,
out_evidences,
comment="log-evidence",
error_if_exists=False)
# TODO: try to broadcast the collections
# if get_mpi():
# bcast_from_0 = lambda attrname: setattr(self,
# attrname, get_mpi_comm().bcast(getattr(self, attrname, None), root=0))
# map(bcast_from_0, ["collection", "logZ", "logZstd", "clusters"])
if is_main_process():
self.log.info(
"Finished! Raw PolyChord output stored in '%s', "
"with prefix '%s'", self.pc_settings.base_dir,
self.pc_settings.file_root)
self.log.info(
"log(Z) = %g +/- %g ; Z in [%.8g, %.8g] (68%% C.L. log-gaussian)",
self.logZ, self.logZstd,
*[np.exp(self.logZ + n * self.logZstd) for n in [-1, 1]])
