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Correct bugs, add extractor for turb_rms

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This commit is contained in:
Noe Brucy
2019-12-05 10:52:18 +01:00
parent 7d5aa9d911
commit 10600f53df
3 changed files with 73 additions and 32 deletions
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plotter.py
+12 -1
View File
@@ -680,6 +680,17 @@ class Plotter(Aggregator, BaseProcessor):
kind="series",
dependencies=["issfr"],
),
"turb_rms": PlotRule(
self,
partial(
self._plot,
"/series/rms_from_log/time",
"/series/rms_from_log/turb_rms",
xunit=cst.Myr,
),
kind="series",
dependencies=["rms_from_log"],
),
"sigma": PlotRule(
self,
partial(
@@ -691,7 +702,7 @@ class Plotter(Aggregator, BaseProcessor):
yunit=cst.km_s,
),
kind="comp",
dependencies=["time", "time_sigma"],
dependencies=["time_sigma"],
),
"plot": PlotRule(
self, lambda arg, **kwargs: self._plot(*arg, **kwargs), kind="comp"
postprocessor.py
+51 -14
View File
@@ -20,7 +20,7 @@ from pymses.analysis import ScalarOperator, FractionOperator, MaxLevelOperator
from mypool import MyPool as Pool
from functools import partial
from abc import ABCMeta, abstractmethod
import contextlib
import bunch
from run_selector import *
@@ -77,7 +77,7 @@ class BaseProcessor:
__metaclass__ = ABCMeta
log_id = ""
rules = dict()
rules = {}
solve_self_dep = True
def __init__(self, path, path_out=None, pp_params=None, tag=None):
@@ -98,6 +98,7 @@ class BaseProcessor:
self.path_out = path_out
def _log(self, string, status=""):
if self.pp_params.process.verbose:
if len(status) > 0:
print(status + ": " + self.log_id + string)
else:
@@ -165,7 +166,7 @@ class BaseProcessor:
def _not_self_dep(self, name, dep, dep_arg, overwrite, **kwargs):
self._log("Dependency {} for {} is unknown".format(dep, name), "ERROR")
def _check_existing(self, overwrite, name_full):
def _needs_computation(self, overwrite, name_full):
return overwrite or not (name_full in self.save)
def _process_rule(self, name, rule, arg, overwrite=False, **kwargs):
@@ -176,7 +177,7 @@ class BaseProcessor:
if rule.is_valid(arg):
if not name_full in self.just_done:
if self._check_existing(overwrite, name_full):
if self._needs_computation(overwrite, name_full):
self._log("Processing {}".format(name_full))
data = rule.process(arg, **kwargs)
self._save_data(name_full, data, rule.description, rule.unit)
@@ -278,7 +279,7 @@ class HDF5Container(BaseProcessor):
try:
node = self.save.get_node(node_name)
if node._v_attrs.CLASS == "GROUP":
value = dict()
value = {}
for child_name in node._v_children:
value[child_name] = self.get_value(node_name + "/" + child_name)
else:
@@ -353,7 +354,7 @@ class PostProcessor(HDF5Container):
path=None,
num=None,
path_out=None,
pp_params=default_params(),
pp_params=None,
tag=None,
variables=["rho", "vel", "Br", "Bl", "P", "g", "phi"],
):
@@ -364,8 +365,8 @@ class PostProcessor(HDF5Container):
super(PostProcessor, self).__init__(path, path_out, pp_params, tag)
# Open outfile
if not pp_params.out.tag == "":
tag_name = pp_params.out.tag + "_"
if not self.pp_params.out.tag == "":
tag_name = self.pp_params.out.tag + "_"
else:
tag_name = ""
@@ -426,7 +427,7 @@ class PostProcessor(HDF5Container):
self.save.root.maps._v_attrs.im_extent = im_extent
# Initialize cameras
self._cam = dict()
self._cam = {}
for ax_los in self._ax_nb: # los = line of sight
ax_h = self._axes_h[ax_los]
ax_v = self._axes_v[ax_los]
@@ -463,8 +464,15 @@ class PostProcessor(HDF5Container):
self.label = self.run
self.save.root._v_attrs.label = self.label
# def open_pymlog(self):
# if self.pp_params.pymses.verbose:
# return sys.stdout
# else:
# return open(os.devnull, "w")
def load_cells(self):
if not self.cells_loaded:
# with self.open_pymlog() as f, contextlib.redirect_stdout(f):
cell_source = CellsToPoints(self._amr)
self.cells = cell_source.flatten()
self.cells_loaded = True
@@ -1022,18 +1030,30 @@ class Comparator(Aggregator, HDF5Container):
# Define rules
self.def_rules()
def _check_existing(self, overwrite, name_full):
def _needs_computation(self, overwrite, name_full):
"""
Returns True if a new computation of the rule is needed
"""
if overwrite or not (name_full in self.save):
return True
elif not "runs" in self.save.get_node(name_full)._v_attrs:
elif not "nums" in self.save.get_node(name_full)._v_attrs:
return True
else:
saved_runs = self.save.get_node(name_full)._v_attrs.runs
return len([run for run in self.runs if not run in saved_runs]) == 0
saved_nums = self.save.get_node(name_full)._v_attrs.nums
missing_runs = len([run for run in self.nums if not run in saved_nums]) > 0
missing_nums = missing_runs and all(
[
len([num for num in self.nums[run] if not num in saved_nums[run]])
> 0
for run in self.nums
if run in saved_nums
]
)
return missing_nums
def _save_data(self, name_full, data, description, unit):
super(Comparator, self)._save_data(name_full, data, description, unit)
self.save.get_node(name_full)._v_attrs.runs = self.runs
self.save.get_node(name_full)._v_attrs.nums = self.nums
def _time_series(self, getter):
series = {}
@@ -1122,6 +1142,14 @@ class Comparator(Aggregator, HDF5Container):
series["sfr"][run].append(sfr)
return series
def _extract_rms_from_log(self, series, log_filename, run):
cmd_grep = "grep 'turbulent rms' {} -B 1".format(log_filename)
content = os.popen(cmd_grep).readlines()
for i in range(0, len(content), 3):
series["time"][run].append(np.float(content[i].split("=")[2].split()[0]))
series["turb_rms"][run].append(np.float(content[i + 1].split(":")[1]))
return series
def _from_log(self, keys, extractor):
nums = self.nums
@@ -1265,6 +1293,15 @@ class Comparator(Aggregator, HDF5Container):
"sfr": "Averaged surfacic star formation rate",
},
),
"rms_from_log": Rule(
self,
partial(
self._from_log, ["time", "turb_rms"], self._extract_rms_from_log
),
group="/series",
unit={"time": self.info["unit_time"], "turb_rms": cst.none},
description={"time": "Time", "turb_rms": "Computed turbulent RMS"},
),
# Read from outputs
"time": Rule(
self,
run_selector.py
+6 -13
View File
@@ -14,7 +14,6 @@ class RunSelector:
in_runs=None,
in_nums="all",
pp_params=default_params(),
number_run="[0-9]*_",
name_run="*",
namelist_cond={},
sort_run_by=None,
@@ -25,9 +24,7 @@ class RunSelector:
self.pp_params = pp_params
self.namelist = {}
self.runs = self.get_runs(
in_runs, number_run, name_run, namelist_cond, sort_run_by
)
self.runs = self.get_runs(in_runs, name_run, namelist_cond, sort_run_by)
self.info = {}
for run in self.runs:
@@ -54,14 +51,7 @@ class RunSelector:
res = res[key]
return res
def get_runs(
self,
in_runs=None,
number_run="[0-9]*_",
name_run="*",
namelist_cond={},
sort_run_by=None,
):
def get_runs(self, in_runs=None, name_run="*", namelist_cond={}, sort_run_by=None):
def try_load_nml(run):
try:
self.namelist[run] = self.load_namelist(run)
@@ -71,7 +61,8 @@ class RunSelector:
return success
runs = map(
os.path.basename, glob.glob(self.path_in + "/" + number_run + name_run)
os.path.basename,
filter(os.path.isdir, glob.glob(self.path_in + "/" + name_run)),
)
if not in_runs is None:
runs = filter(lambda n: n in runs, in_runs)
@@ -140,6 +131,8 @@ class RunSelector:
)
nums = map(lambda n: int(n.split("/")[-1].split("_")[1]), names)
if type(in_nums) == int:
in_nums = [in_nums]
if type(in_nums) == list:
nums = filter(lambda n: n in nums, in_nums)