Add some doc
This commit is contained in:
Noe Brucy
Noe Brucy
+3
-1
@@ -198,7 +198,9 @@ class BaseProcessor:
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def def_rules(self):
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for rule in self.rules:
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setattr(self, rule, partial(self.process, rule))
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func = partial(self.process, rule)
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func.__doc__ = self.rules[rule].description
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setattr(self, rule, func)
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class HDF5Container(BaseProcessor):
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+171
-124
@@ -1,5 +1,13 @@
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# coding: utf-8
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"""
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This software is a helper to use pysmes tools to read and analyse RAMSES Outputs.
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It's a rule based interface.
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This is the plotter module.
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@author Noé Brucy 2019-2020
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"""
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import sys
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import os
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from functools import partial
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@@ -27,13 +35,24 @@ P.rcParams.update(tex_params)
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class PlotRule(Rule):
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"""
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The rule class, speficic to plot.
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Add an extra method, plot, that take the reference to an open hdf5 file (from pytables)
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"""
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def plot(self, save, arg, **kwargs):
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"""
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Set the plotter's storage to 'save' and exetute the rule
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Parameters
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----------
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save : opended pytables hdf5 file, where to find the data
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arg : main argument of the plotting function
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kargs : optional keyword arguments to the plotting function
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"""
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self.postproc.save = save
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return self.process_fn(arg, **kwargs)
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def is_valid(self, arg):
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return self.is_valid_add(arg)
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class Plotter(Aggregator, BaseProcessor):
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"""
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@@ -50,6 +69,7 @@ class Plotter(Aggregator, BaseProcessor):
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G = 1.0 # Gravitational constant
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# Conversion table from namelist keys (from amses config file) into LaTex strings
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label_convert = {
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"turb_rms": "$f_{rms}$",
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"beta": "$\\beta$",
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@@ -60,6 +80,7 @@ class Plotter(Aggregator, BaseProcessor):
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"comp_frac": "$\\zeta$",
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}
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# Conversion table from namelist values (from amses config file) into LaTex strings
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value_convert = {
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"sfr_avg_window": lambda x: "${:g}$ Myr".format(80 * x),
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"comp_frac": lambda x: "${:g}$".format(1 - x),
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@@ -77,6 +98,22 @@ class Plotter(Aggregator, BaseProcessor):
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**kwargs
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):
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"""
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Create a new Plotter instance. Will select run and outputs via a RunSelector object.
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Parameters
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----------
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path : path to the main folder of the simulations (ex '~/simus/myproject')
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in_runs : list of the runs to consider (ex ['run1', 'run2'])
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in_nums : list or dict of the outputs numbers to consider (ex [3, 5] or {'run1' : [3, 5], 'run2' : [4, 6])
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path_out : Path where the plot will be saved. By default set to `path`
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pp_params : Parameters for postprocessing. See pp_params module.
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selector : Existing instance of RunSelector, that selects runs and outputs. If set, in_runs and in_nums will be ignored
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tag : string to add in the output and data files.
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kwargs : Keyword arguments for RunSelector.
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"""
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super(Plotter, self).__init__(path, path_out, pp_params, tag)
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# Select runs
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@@ -105,6 +142,7 @@ class Plotter(Aggregator, BaseProcessor):
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self.save = None
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def _not_self_dep(self, name, dep, dep_arg, overwrite, **kwargs):
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""""""
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if dep in self.comp.rules:
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done = self.comp.process(dep, dep_arg, overwrite, overwrite)
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self.just_done.extend(done)
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@@ -874,13 +912,13 @@ class Plotter(Aggregator, BaseProcessor):
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"coldens": PlotRule(
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self,
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partial(self._plot_map, "coldens", label=r"$\Sigma$", unit=cst.coldens),
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"Column density",
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"Column density map",
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dependencies=["coldens"],
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),
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"rho": PlotRule(
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self,
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partial(self._plot_map, "rho", label=r"$\rho$", unit=cst.Msun_pc3),
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"Density slice",
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"Density slice at s = 0, with s = x, y or z.",
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dependencies=["rho"],
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),
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"coldens_l": PlotRule(
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@@ -892,7 +930,7 @@ class Plotter(Aggregator, BaseProcessor):
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unit=cst.coldens,
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overlays=[self._overlay_levels],
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),
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"Column density",
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"Column density with level overlay",
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dependencies=["coldens", "levels"],
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),
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"rho_v": PlotRule(
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@@ -904,7 +942,7 @@ class Plotter(Aggregator, BaseProcessor):
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unit=cst.Msun_pc3,
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overlays=[self._overlay_speed],
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),
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"Density slice",
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"Density slice with speed overlay",
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dependencies=["rho", "speed_h", "speed_v"],
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),
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"jeans_ratio": PlotRule(
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@@ -948,22 +986,145 @@ class Plotter(Aggregator, BaseProcessor):
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xlog=True,
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put_time=False,
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),
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"PDF",
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"Column density PDF, averaged in time",
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kind="runs",
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dependencies={"avg_time_coldens_pdf": "z"},
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),
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"T_pdf": PlotRule(
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self, partial(self._plot_hist, "T_pdf"), "T-PDF", dependencies=["T_pdf"]
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self,
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partial(self._plot_hist, "T_pdf"),
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"T-PDF on a 2D slice",
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dependencies=["T_pdf"],
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),
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"P_pdf": PlotRule(
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self, partial(self._plot_hist, "P_pdf"), "P-PDF", dependencies=["P_pdf"]
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self,
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partial(self._plot_hist, "P_pdf"),
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"P-PDF on a 2D slice ",
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dependencies=["P_pdf"],
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),
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"rho_prof": PlotRule(
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self,
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partial(self._plot, "/profile/axis", "/profile/rho_prof"),
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"Density profile",
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dependencies=["axis", "rho_prof"],
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),
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"pspec": PlotRule(self, self._pspec, dependencies={"pspec": None}),
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"kappa_beta": PlotRule(
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self,
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partial(
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self._plot,
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"/comp/nml_cloud_params/beta_cool",
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"/comp/avg_time_pdf_slope_coldens",
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),
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"Slope of the Sigma-PDF against cooling beta factor",
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kind="comp",
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dependencies={
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"nml": "cloud_params/beta_cool",
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"avg_time_pdf_slope_coldens": None,
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},
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),
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"sink_mass": PlotRule(
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self,
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partial(
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self._plot,
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"/series/sinks_from_log/time",
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"/series/sinks_from_log/mass_sink",
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"Mass of the sinks against time",
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xunit=cst.Myr,
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yunit=cst.Msun,
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),
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kind="series",
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dependencies=["sinks_from_log"],
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),
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"assfr": PlotRule(
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self,
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partial(
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self._plot,
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"/series/sfr_from_log/time",
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"/series/sfr_from_log/sfr",
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ylabel="Averaged surfacic SFR",
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xunit=cst.Myr,
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yunit=cst.ssfr,
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),
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kind="series",
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dependencies=["sfr_from_log"],
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),
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"issfr": PlotRule(
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self,
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partial(
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self._plot,
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"/series/sinks_from_log/time",
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"/series/sinks_from_log/issfr",
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ylabel="Surfacic SFR",
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xunit=cst.Myr,
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yunit=cst.ssfr,
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),
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kind="series",
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dependencies=["issfr"],
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),
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"turb_rms": PlotRule(
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self,
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partial(
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self._plot,
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"/series/rms_from_log/time",
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"/series/rms_from_log/turb_rms",
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xunit=cst.Myr,
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),
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"Turbulent RMS",
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kind="series",
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dependencies=["rms_from_log"],
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),
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"turb_energy": PlotRule(
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self,
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partial(
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self._plot,
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"/series/rms_from_log/time",
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"/series/rms_from_log/turb_energy",
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xunit=cst.Myr,
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),
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"Turbulent energy",
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kind="series",
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dependencies=["rms_from_log"],
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),
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"turb_power": PlotRule(
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self,
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partial(
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self._plot,
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"/series/rms_from_log/time",
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"/series/rms_from_log/turb_power",
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xunit=cst.Myr,
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),
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"Turbulent power",
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kind="series",
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dependencies=["turb_power"],
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),
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"sigma": PlotRule(
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self,
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partial(
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self._plot,
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"/series/time",
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"/series/time_sigma",
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ylabel="$\\sigma$",
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xunit=cst.Myr,
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yunit=cst.km_s,
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),
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"Velocity dispersion",
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kind="series",
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dependencies=["time_sigma"],
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),
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"max_fluct_coldens": PlotRule(
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self,
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partial(
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self._plot,
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"/series/time",
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"/series/time_max_fluct_coldens_z",
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ylabel="$\\max(\Sigma/\overline{\Sigma})$",
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xunit=cst.Myr,
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),
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"Maximal fluctuation of the column density against time",
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kind="series",
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dependencies={"time_max_fluct_coldens": "z"},
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),
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}
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averageables = ["coldens", "rho", "T", "Q"]
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@@ -1006,118 +1167,4 @@ class Plotter(Aggregator, BaseProcessor):
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dependencies=["fit_pdf_" + name],
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)
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self.rules.update(
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{
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"kappa_beta": PlotRule(
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self,
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partial(
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self._plot,
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"/comp/nml_cloud_params/beta_cool",
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"/comp/avg_time_pdf_slope_coldens",
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),
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kind="comp",
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dependencies={
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"nml": "cloud_params/beta_cool",
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"avg_time_pdf_slope_coldens": None,
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},
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),
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"sink_mass": PlotRule(
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self,
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partial(
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self._plot,
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"/series/sinks_from_log/time",
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"/series/sinks_from_log/mass_sink",
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xunit=cst.Myr,
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yunit=cst.Msun,
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),
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kind="series",
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dependencies=["sinks_from_log"],
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),
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"assfr": PlotRule(
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self,
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partial(
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self._plot,
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"/series/sfr_from_log/time",
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"/series/sfr_from_log/sfr",
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ylabel="Averaged surfacic SFR",
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xunit=cst.Myr,
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yunit=cst.ssfr,
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),
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kind="series",
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dependencies=["sfr_from_log"],
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),
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"issfr": PlotRule(
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self,
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partial(
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self._plot,
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"/series/sinks_from_log/time",
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"/series/sinks_from_log/issfr",
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ylabel="Surfacic SFR",
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xunit=cst.Myr,
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yunit=cst.ssfr,
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),
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kind="series",
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dependencies=["issfr"],
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),
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"turb_rms": PlotRule(
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self,
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partial(
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self._plot,
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"/series/rms_from_log/time",
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"/series/rms_from_log/turb_rms",
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xunit=cst.Myr,
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),
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kind="series",
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dependencies=["rms_from_log"],
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),
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"turb_energy": PlotRule(
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self,
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partial(
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self._plot,
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"/series/rms_from_log/time",
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"/series/rms_from_log/turb_energy",
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xunit=cst.Myr,
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),
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kind="series",
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dependencies=["rms_from_log"],
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),
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"turb_power": PlotRule(
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self,
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partial(
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self._plot,
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"/series/rms_from_log/time",
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"/series/rms_from_log/turb_power",
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xunit=cst.Myr,
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),
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kind="series",
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dependencies=["turb_power"],
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),
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"sigma": PlotRule(
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self,
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partial(
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self._plot,
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"/series/time",
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"/series/time_sigma",
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ylabel="$\\sigma$",
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xunit=cst.Myr,
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yunit=cst.km_s,
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),
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kind="series",
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dependencies=["time_sigma"],
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),
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"max_fluct_coldens": PlotRule(
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self,
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partial(
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self._plot,
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"/series/time",
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"/series/time_max_fluct_coldens_z",
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ylabel="$\\max(\Sigma/\overline{\Sigma})$",
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xunit=cst.Myr,
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),
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kind="series",
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dependencies={"time_max_fluct_coldens": "z"},
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),
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}
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)
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super(Plotter, self).def_rules()
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Block a user