From 267122178d3525e320c9fb0f8fa75d974724b1e4 Mon Sep 17 00:00:00 2001 From: Noe Brucy Date: Wed, 10 Jun 2020 09:11:55 +0200 Subject: [PATCH] Add some doc --- baseprocessor.py | 4 +- plotter.py | 295 +++++++++++++++++++++++++++-------------------- 2 files changed, 174 insertions(+), 125 deletions(-) diff --git a/baseprocessor.py b/baseprocessor.py index ef1b1bf..28202b7 100644 --- a/baseprocessor.py +++ b/baseprocessor.py @@ -198,7 +198,9 @@ class BaseProcessor: def def_rules(self): for rule in self.rules: - setattr(self, rule, partial(self.process, rule)) + func = partial(self.process, rule) + func.__doc__ = self.rules[rule].description + setattr(self, rule, func) class HDF5Container(BaseProcessor): diff --git a/plotter.py b/plotter.py index 3dd3849..03998b4 100644 --- a/plotter.py +++ b/plotter.py @@ -1,5 +1,13 @@ # coding: utf-8 +""" +This software is a helper to use pysmes tools to read and analyse RAMSES Outputs. +It's a rule based interface. +This is the plotter module. + +@author Noé Brucy 2019-2020 +""" + import sys import os from functools import partial @@ -27,13 +35,24 @@ P.rcParams.update(tex_params) class PlotRule(Rule): + """ + The rule class, speficic to plot. + Add an extra method, plot, that take the reference to an open hdf5 file (from pytables) + """ + def plot(self, save, arg, **kwargs): + """ + Set the plotter's storage to 'save' and exetute the rule + + Parameters + ---------- + save : opended pytables hdf5 file, where to find the data + arg : main argument of the plotting function + kargs : optional keyword arguments to the plotting function + """ self.postproc.save = save return self.process_fn(arg, **kwargs) - def is_valid(self, arg): - return self.is_valid_add(arg) - class Plotter(Aggregator, BaseProcessor): """ @@ -50,6 +69,7 @@ class Plotter(Aggregator, BaseProcessor): G = 1.0 # Gravitational constant + # Conversion table from namelist keys (from amses config file) into LaTex strings label_convert = { "turb_rms": "$f_{rms}$", "beta": "$\\beta$", @@ -60,6 +80,7 @@ class Plotter(Aggregator, BaseProcessor): "comp_frac": "$\\zeta$", } + # Conversion table from namelist values (from amses config file) into LaTex strings value_convert = { "sfr_avg_window": lambda x: "${:g}$ Myr".format(80 * x), "comp_frac": lambda x: "${:g}$".format(1 - x), @@ -77,6 +98,22 @@ class Plotter(Aggregator, BaseProcessor): **kwargs ): + """ + Create a new Plotter instance. Will select run and outputs via a RunSelector object. + + Parameters + ---------- + + path : path to the main folder of the simulations (ex '~/simus/myproject') + in_runs : list of the runs to consider (ex ['run1', 'run2']) + in_nums : list or dict of the outputs numbers to consider (ex [3, 5] or {'run1' : [3, 5], 'run2' : [4, 6]) + path_out : Path where the plot will be saved. By default set to `path` + pp_params : Parameters for postprocessing. See pp_params module. + selector : Existing instance of RunSelector, that selects runs and outputs. If set, in_runs and in_nums will be ignored + tag : string to add in the output and data files. + kwargs : Keyword arguments for RunSelector. + """ + super(Plotter, self).__init__(path, path_out, pp_params, tag) # Select runs @@ -105,6 +142,7 @@ class Plotter(Aggregator, BaseProcessor): self.save = None def _not_self_dep(self, name, dep, dep_arg, overwrite, **kwargs): + """""" if dep in self.comp.rules: done = self.comp.process(dep, dep_arg, overwrite, overwrite) self.just_done.extend(done) @@ -874,13 +912,13 @@ class Plotter(Aggregator, BaseProcessor): "coldens": PlotRule( self, partial(self._plot_map, "coldens", label=r"$\Sigma$", unit=cst.coldens), - "Column density", + "Column density map", dependencies=["coldens"], ), "rho": PlotRule( self, partial(self._plot_map, "rho", label=r"$\rho$", unit=cst.Msun_pc3), - "Density slice", + "Density slice at s = 0, with s = x, y or z.", dependencies=["rho"], ), "coldens_l": PlotRule( @@ -892,7 +930,7 @@ class Plotter(Aggregator, BaseProcessor): unit=cst.coldens, overlays=[self._overlay_levels], ), - "Column density", + "Column density with level overlay", dependencies=["coldens", "levels"], ), "rho_v": PlotRule( @@ -904,7 +942,7 @@ class Plotter(Aggregator, BaseProcessor): unit=cst.Msun_pc3, overlays=[self._overlay_speed], ), - "Density slice", + "Density slice with speed overlay", dependencies=["rho", "speed_h", "speed_v"], ), "jeans_ratio": PlotRule( @@ -948,22 +986,145 @@ class Plotter(Aggregator, BaseProcessor): xlog=True, put_time=False, ), - "PDF", + "Column density PDF, averaged in time", kind="runs", dependencies={"avg_time_coldens_pdf": "z"}, ), "T_pdf": PlotRule( - self, partial(self._plot_hist, "T_pdf"), "T-PDF", dependencies=["T_pdf"] + self, + partial(self._plot_hist, "T_pdf"), + "T-PDF on a 2D slice", + dependencies=["T_pdf"], ), "P_pdf": PlotRule( - self, partial(self._plot_hist, "P_pdf"), "P-PDF", dependencies=["P_pdf"] + self, + partial(self._plot_hist, "P_pdf"), + "P-PDF on a 2D slice ", + dependencies=["P_pdf"], ), "rho_prof": PlotRule( self, partial(self._plot, "/profile/axis", "/profile/rho_prof"), + "Density profile", dependencies=["axis", "rho_prof"], ), "pspec": PlotRule(self, self._pspec, dependencies={"pspec": None}), + "kappa_beta": PlotRule( + self, + partial( + self._plot, + "/comp/nml_cloud_params/beta_cool", + "/comp/avg_time_pdf_slope_coldens", + ), + "Slope of the Sigma-PDF against cooling beta factor", + kind="comp", + dependencies={ + "nml": "cloud_params/beta_cool", + "avg_time_pdf_slope_coldens": None, + }, + ), + "sink_mass": PlotRule( + self, + partial( + self._plot, + "/series/sinks_from_log/time", + "/series/sinks_from_log/mass_sink", + "Mass of the sinks against time", + xunit=cst.Myr, + yunit=cst.Msun, + ), + kind="series", + dependencies=["sinks_from_log"], + ), + "assfr": PlotRule( + self, + partial( + self._plot, + "/series/sfr_from_log/time", + "/series/sfr_from_log/sfr", + ylabel="Averaged surfacic SFR", + xunit=cst.Myr, + yunit=cst.ssfr, + ), + kind="series", + dependencies=["sfr_from_log"], + ), + "issfr": PlotRule( + self, + partial( + self._plot, + "/series/sinks_from_log/time", + "/series/sinks_from_log/issfr", + ylabel="Surfacic SFR", + xunit=cst.Myr, + yunit=cst.ssfr, + ), + 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, + ), + "Turbulent RMS", + kind="series", + dependencies=["rms_from_log"], + ), + "turb_energy": PlotRule( + self, + partial( + self._plot, + "/series/rms_from_log/time", + "/series/rms_from_log/turb_energy", + xunit=cst.Myr, + ), + "Turbulent energy", + kind="series", + dependencies=["rms_from_log"], + ), + "turb_power": PlotRule( + self, + partial( + self._plot, + "/series/rms_from_log/time", + "/series/rms_from_log/turb_power", + xunit=cst.Myr, + ), + "Turbulent power", + kind="series", + dependencies=["turb_power"], + ), + "sigma": PlotRule( + self, + partial( + self._plot, + "/series/time", + "/series/time_sigma", + ylabel="$\\sigma$", + xunit=cst.Myr, + yunit=cst.km_s, + ), + "Velocity dispersion", + kind="series", + dependencies=["time_sigma"], + ), + "max_fluct_coldens": PlotRule( + self, + partial( + self._plot, + "/series/time", + "/series/time_max_fluct_coldens_z", + ylabel="$\\max(\Sigma/\overline{\Sigma})$", + xunit=cst.Myr, + ), + "Maximal fluctuation of the column density against time", + kind="series", + dependencies={"time_max_fluct_coldens": "z"}, + ), } averageables = ["coldens", "rho", "T", "Q"] @@ -1006,118 +1167,4 @@ class Plotter(Aggregator, BaseProcessor): dependencies=["fit_pdf_" + name], ) - self.rules.update( - { - "kappa_beta": PlotRule( - self, - partial( - self._plot, - "/comp/nml_cloud_params/beta_cool", - "/comp/avg_time_pdf_slope_coldens", - ), - kind="comp", - dependencies={ - "nml": "cloud_params/beta_cool", - "avg_time_pdf_slope_coldens": None, - }, - ), - "sink_mass": PlotRule( - self, - partial( - self._plot, - "/series/sinks_from_log/time", - "/series/sinks_from_log/mass_sink", - xunit=cst.Myr, - yunit=cst.Msun, - ), - kind="series", - dependencies=["sinks_from_log"], - ), - "assfr": PlotRule( - self, - partial( - self._plot, - "/series/sfr_from_log/time", - "/series/sfr_from_log/sfr", - ylabel="Averaged surfacic SFR", - xunit=cst.Myr, - yunit=cst.ssfr, - ), - kind="series", - dependencies=["sfr_from_log"], - ), - "issfr": PlotRule( - self, - partial( - self._plot, - "/series/sinks_from_log/time", - "/series/sinks_from_log/issfr", - ylabel="Surfacic SFR", - xunit=cst.Myr, - yunit=cst.ssfr, - ), - 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"], - ), - "turb_energy": PlotRule( - self, - partial( - self._plot, - "/series/rms_from_log/time", - "/series/rms_from_log/turb_energy", - xunit=cst.Myr, - ), - kind="series", - dependencies=["rms_from_log"], - ), - "turb_power": PlotRule( - self, - partial( - self._plot, - "/series/rms_from_log/time", - "/series/rms_from_log/turb_power", - xunit=cst.Myr, - ), - kind="series", - dependencies=["turb_power"], - ), - "sigma": PlotRule( - self, - partial( - self._plot, - "/series/time", - "/series/time_sigma", - ylabel="$\\sigma$", - xunit=cst.Myr, - yunit=cst.km_s, - ), - kind="series", - dependencies=["time_sigma"], - ), - "max_fluct_coldens": PlotRule( - self, - partial( - self._plot, - "/series/time", - "/series/time_max_fluct_coldens_z", - ylabel="$\\max(\Sigma/\overline{\Sigma})$", - xunit=cst.Myr, - ), - kind="series", - dependencies={"time_max_fluct_coldens": "z"}, - ), - } - ) - super(Plotter, self).def_rules()