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[misc] May last round of bug corrections

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This commit is contained in:
Noe Brucy
2022-05-31 16:15:33 +02:00
parent 6c912a5294
commit 124f24f92c
6 changed files with 129 additions and 107 deletions
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plotter.py
+15 -16
View File
@@ -109,15 +109,15 @@ def quiver(ax, map_h, map_v, extent, key_v=None, label="", **kwargs):
# add vector key
if key_v is None:
key_v = (max_v + min_v) / 2.0
ax.quiverkey(
vec_field,
0.6,
0.98,
key_v,
f"${key_v:g}$ {label}",
labelpos="E",
coordinates="figure",
)
ax.quiverkey(
vec_field,
0.6,
0.98,
key_v,
f"${key_v:g}$ {label}",
labelpos="E",
coordinates="figure",
)
def line_integral_convolution(ax, map_h, map_v, extent, **kwargs):
@@ -793,7 +793,7 @@ class Plotter(Aggregator, BaseProcessor):
except AttributeError:
cbar = plt.colorbar()
if label is not None:
if text_embeded:
if colorbar_embeded:
cbar.set_label(" " + label, color=overtext_color, loc="bottom")
else:
cbar.set_label(label)
@@ -824,14 +824,13 @@ class Plotter(Aggregator, BaseProcessor):
plot_overlay = self.overlays[plot_overlay]
xlim = plt.xlim()
ylim = plt.ylim()
try:
if len(overlays_kwargs) > i:
plot_overlay(ax_los, im_extent, **overlays_kwargs[i])
except IndexError:
else:
plot_overlay(ax_los, im_extent)
finally:
# Restore previous limits in case overlays changed it
plt.xlim(xlim)
plt.ylim(ylim)
plt.xlim(xlim)
plt.ylim(ylim)
return PlotInfo(
plot_type=PlotType.IMAGE,
pspec_new.py
+3 -3
View File
@@ -434,7 +434,7 @@ parser.add_argument(
"repo", help="RAMSES output repository", type=str, default=".", nargs="?"
)
parser.add_argument(
"iouts", help="output numbers", type=args.selection, default=":", nargs="?"
"iouts", help="output numbers", type=int, default=[1], nargs="+"
)
parser.add_argument(
"outfile",
@@ -520,7 +520,7 @@ def main(arg):
iouts = arg.iouts # tools.select_outputs(arg.repo, arg.iouts)
for iout in iouts:
print("Output %d" % iout)
print(f"Output {iout}")
print("Load data")
read_lvl = None
if True:
@@ -933,7 +933,7 @@ if __name__ == "__main__":
def pspec(**kwargs):
arg = parser.parse_args("")
arg = parser.parse_args("1")
for kwarg in kwargs:
setattr(arg, kwarg, kwargs[kwarg])
main(arg)
run_selector.py
+80 -63
View File
@@ -56,39 +56,38 @@ class RunSelector:
Select runs and outputs with several filter options.
By default, all runs and outputs within path_in are considered
Parameters
---------
Args:
1. Define the set of runs and outputs considered
1. Define the set of runs and outputs considered
path_in : str, path to the folder of the runs
path_in : str, path to the folder of the runs
2. Filter runs and outputs
2. Filter runs and outputs
in_runs : str or list of str. The name runs to consider. Default: all.
in_nums : int or list of int or str.
The output numbers to consider.
"last" select only the last output.
"all" preselect all outputs (default)
in_runs : str or list of str. The name runs to consider. Default: all.
in_nums : int or list of int or str.
The output numbers to consider.
"last" select only the last output.
"all" preselect all outputs (default)
nml_filename : str name of the namelist (should be the same for all outputs)
nml_filename : str name of the namelist (should be the same for all outputs)
filter_name : str, filter runs by name. Default "*"
filter_nml : tuple or list of tupple.
Filter runs by namelist.
tuples are in the following form:
(nml_key, operator, nml_value)
with nml_key a key from the namelist (eg. "cloud_params/dens0")
operator within ("=", "!=", "<", ">", "in")
and nml_value a string, float or int
time_min : float, select output where time >= time_min (in code units)
time_max : float, select output where time <= time_min (in code units)
time : float or list of float. For each value, select the output closer to it.
unit_time : astrophysix.Unit, unit for the time above. None is code unit.
filter_name : str, filter runs by name. Default "*"
filter_nml : tuple or list of tupple.
Filter runs by namelist.
tuples are in the following form:
(nml_key, operator, nml_value)
with nml_key a key from the namelist (eg. "cloud_params/dens0")
operator within ("=", "!=", "<", ">", "in")
and nml_value a string, float or int
time_min : float, select output where time >= time_min (in code units)
time_max : float, select output where time <= time_min (in code units)
time : float or list of float. For each value, select the output closer to it.
unit_time : astrophysix.Unit, unit for the time above. None is code unit.
3. Sort the runs
3. Sort the runs
sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
"""
@@ -146,37 +145,35 @@ class RunSelector:
"""
Sub-select runs and outputs from already selected runs and outputs
Parameters
---------
runs : str or list of str. The name runs to consider. Default: all.
nums : int or list of int or str.
The output numbers to consider.
"last" select only the last output.
"all" preselect all outputs (default)
Args:
filter_name : str.
glob pattern used to filter run names.
default is "*" (all runs)
runs : str or list of str. The name runs to consider. Default: all.
nums : int or list of int or str.
The output numbers to consider.
"last" select only the last output.
"all" preselect all outputs (default)
filter_nml : tuple or list of tupple.
Filter runs by namelist.
tuples are in the following form:
(nml_key, operator, nml_value)
with nml_key a key from the namelist (eg. "cloud_params/dens0")
operator within ("=", "!=", "<", ">", "in")
and nml_value a string, float or int
time_min : float, select output where time >= time_min (in code units)
time_max : float, select output where time <= time_min (in code units)
time : float or list of float. For each value, select the output closer to it.
unit_time : astrophysix.Unit, unit for the time above. None is code unit.
filter_name : str.
glob pattern used to filter run names.
default is "*" (all runs)
filter_nml : tuple or list of tupple.
Filter runs by namelist.
tuples are in the following form:
(nml_key, operator, nml_value)
with nml_key a key from the namelist (eg. "cloud_params/dens0")
operator within ("=", "!=", "<", ">", "in")
and nml_value a string, float or int
time_min : float, select output where time >= time_min (in code units)
time_max : float, select output where time <= time_min (in code units)
time : float or list of float. For each value, select the output closer to it.
unit_time : astrophysix.Unit, unit for the time above. None is code unit.
sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
sort_run_by : str, a key from the namelist used to sort the runs (by ascending order)
Returns
-------
(selected_runs, selected_nums)
Returns:
(selected_runs, selected_nums)
"""
if runs is None:
@@ -301,20 +298,19 @@ class RunSelector:
"""
Select snapshots from the disk
Parameters
---------
Args:
in_nums : int or list of int or str.
The output numbers to consider.
"last" select only the last output.
"all" preselect all outputs (default)
in_nums : int or list of int or str.
The output numbers to consider.
"last" select only the last output.
"all" preselect all outputs (default)
time_min : float, select output where time >= time_min (in code units)
time_max : float, select output where time <= time_min (in code units)
time : float or list of float. For each value, select the output closer to it.
unit_time : astrophysix.Unit, unit for the time above. None is code unit.
time_min : float, select output where time >= time_min (in code units)
time_max : float, select output where time <= time_min (in code units)
time : float or list of float. For each value, select the output closer to it.
unit_time : astrophysix.Unit, unit for the time above. None is code unit.
do_tests : test if the snapshots are actually on disk. Not needed when subselecting snapshots.
do_tests : test if the snapshots are actually on disk. Not needed when subselecting snapshots.
"""
# -- Initialize info loader --
@@ -382,7 +378,7 @@ class RunSelector:
if position == "left":
return ileft
elif position == "right":
return nums[iright]
return iright
else:
dleft = np.abs(get_time(nums[ileft]) - time)
dright = np.abs(get_time(nums[iright]) - time)
@@ -457,3 +453,24 @@ class RunSelector:
nums = list(filter(try_load_info, nums))
return nums
def write_paths(self, prefix=None, filename="~/list_file"):
"""
Write the paths of the selected runs on a file
Args:
prefix (str, optional): Prefix for the pathscd si. Defaults to path_in.
filename (str, optional): F. Defaults to "~/list_file".
"""
if prefix is None:
prefix = self.path_in
paths = []
for run in self.nums:
for num in nums[run]:
paths.append(f"{prefix}/{run}/output_{num:05}\n")
f = open(os.path.expanduser(filename), "w")
f.writelines(paths)
f.close()
select_runs.py
+22 -21
View File
@@ -2,10 +2,6 @@ from run_selector import RunSelector
from plotter import Plotter, U
import os
path_from_home = "simus/ismfeed/allmode"
names = "n6_st_2e5_seed3_T5Myr_nsink1e3_comp*"
def prep_mcons(study):
study.coarse_step_from_log()
@@ -18,12 +14,19 @@ def time_mcons(study, run, target=0.2):
return time_target
def find_nums(study, prep_function, time_function):
def find_nums(study, prep_function, time_function, time_min=0):
"""
Once other filter are applied, select one output based on the time given by time function
Args:
prep_function (study:studyProcessor -> None): prepare a study object
time_function (study:studyProcessor, run:str -> time:float): compute selected time from the object
"""
nums = {}
prep_function(study)
for run in study.runs:
time_target = time_function(study, run)
rs = RunSelector(path_in=in_dir, in_runs=run, time=time_target, unit_time=U.Myr)
time_target = max(time_min, time_function(study, run))
rs = RunSelector(path_in=study.path, in_runs=run, time_min=time_min, time=time_target, unit_time=U.Myr)
nums.update(rs.nums)
return nums
@@ -38,18 +41,16 @@ def write_paths(nums, path_from_home, filename="~/list_file"):
f.close()
in_dir = os.path.expanduser(f"~/{path_from_home}")
study = Plotter(
in_dir,
filter_name=names,
nums="first",
tag="select",
).study
if __name__ == '__main__':
path_from_home = "simus/ismfeed/allmode"
names = "n6_st_2e5_seed3_T5Myr_nsink1e3_comp*"
nums = find_nums(study, prep_mcons, time_mcons)
write_paths(nums, ".")
pl = Plotter(in_dir, runs=nums.keys(), nums=nums)
pl.rho_pdf()
in_dir = os.path.expanduser(f"~/{path_from_home}")
study = Plotter(
in_dir,
filter_name=names,
nums="first",
tag="select",
).study
nums = find_nums(study, prep_mcons, time_mcons)
write_paths(nums, ".")
snapshotprocessor.py
+1 -1
View File
@@ -1340,7 +1340,7 @@ class SnapshotProcessor(HDF5Container):
second_line = f.readline()
f.close()
if first_line[1] == "#":
if len(first_line) > 0 and first_line[1] == "#":
header = first_line[3:-2].split(",")
units = second_line[3:-2].split(",")
df = pd.read_csv(csv_name, header=None, names=header, skiprows=2)
studyprocessor.py
+8 -3
View File
@@ -269,7 +269,7 @@ class StudyProcessor(Aggregator, HDF5Container):
return series
def _extract_stellar_from_log(self, stellar_objects, log_filename, run):
cmd_grep = f"grep stellar {log_filename} -n"
cmd_grep = f"grep 'stellar objects:' {log_filename} -n"
content = os.popen(cmd_grep).readlines()
nb_stellar = list(map(lambda s: int(s.split()[1]), content))
line_numbers = list(map(lambda s: int(s.split(":")[0]), content))
@@ -440,8 +440,13 @@ class StudyProcessor(Aggregator, HDF5Container):
def get_coldens0(self, run):
mp = 1.4 * 1.66 * 10**(-24) * U.g
z0 = self.get_nml("galbox_params/height0", run) * U.pc
n0 = self.get_nml("galbox_params/dens0", run) * U.cm**(-3)
try:
z0 = self.get_nml("galbox_params/height0", run) * U.pc
n0 = self.get_nml("galbox_params/dens0", run) * U.cm**(-3)
except KeyError:
z0 = self.get_nml("cloud_params/height0", run) * U.pc
n0 = self.get_nml("cloud_params/dens0", run) * U.cm**(-3)
return (np.sqrt(2 * np.pi) * mp * z0 * n0).express(U.coldens)
def total_mass(self):