add astrophysix support, fix labels

comparator.py

@@ -17,6 +17,7 @@ class Comparator(Aggregator, HDF5Container):
         pp_params=default_params(),
         selector=None,
         tag=None,
+        unit_time=cst.year,
         **kwargs
     ):
         """
@@ -53,7 +54,11 @@ class Comparator(Aggregator, HDF5Container):
 
             for num in self.nums[run]:
                 self.pp[run][num] = PostProcessor(
-                    path_run, num, path_out=path_out_run, pp_params=self.pp_params
+                    path_run,
+                    num,
+                    path_out=path_out_run,
+                    pp_params=self.pp_params,
+                    unit_time=unit_time,
                 )
 
         run0 = self.runs[0]

plotter.py

@@ -17,7 +17,8 @@ from scipy.stats import linregress
 from numpy.polynomial.polynomial import polyfit
 from scipy.ndimage.filters import gaussian_filter1d
 from scipy import optimize
-
+from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
+from astrophysix.utils.file import FileType
 import matplotlib as mpl
 
 if os.environ.get("DISPLAY", "") == "":
@@ -26,12 +27,15 @@ if os.environ.get("DISPLAY", "") == "":
 import pylab as P
 from comparator import *
 import pspec_read
+import datetime
 
-P.rcParams["image.cmap"] = "plasma"
+filetype_from_ext = {ext: ft for ft in FileType for ext in ft.extension_list}
-P.rcParams["savefig.dpi"] = 400
 
-tex_params = {"text.latex.preamble": r"\usepackage{amsmath}"}
+
-P.rcParams.update(tex_params)
+def not_array_error(err):
+    epy2 = "object does not support indexing"
+    epy3 = "object is not subscriptable"
+    return str(err)[-len(epy2) :] == epy2 or str(err)[-len(epy3) :] == epy3
 
 
 class PlotRule(Rule):
@@ -42,7 +46,7 @@ class PlotRule(Rule):
 
     def plot(self, save, arg, **kwargs):
         """
-        Set the plotter's storage to 'save' and exetute the rule
+        Set the plotter's storage to 'save' and execute the rule
 
         Parameters
         ----------
@@ -53,6 +57,12 @@ class PlotRule(Rule):
         self.postproc.save = save
         return self.process_fn(arg, **kwargs)
 
+    def datafile(self, arg):
+        return Datafile(
+            name=self.description + "_" + arg,
+            description=self.description + " ({})".format(arg),
+        )
+
 
 class Plotter(Aggregator, BaseProcessor):
     """
@@ -99,6 +109,7 @@ class Plotter(Aggregator, BaseProcessor):
         pp_params=None,
         selector=None,
         tag=None,
+        unit_time=cst.year,
         **kwargs,
     ):
 
@@ -135,7 +146,13 @@ class Plotter(Aggregator, BaseProcessor):
 
         # Get comparator object
         self.comp = Comparator(
-            path, self.runs, self.nums, path_out, self.pp_params, selector=self.selector
+            path,
+            self.runs,
+            self.nums,
+            path_out,
+            self.pp_params,
+            unit_time=unit_time,
+            selector=self.selector,
         )
 
         # Get postprocesor objets for each run
@@ -147,17 +164,56 @@ class Plotter(Aggregator, BaseProcessor):
         # Define rules
         self.def_rules()
 
+        # generate astrophysix's simulations object
+        self.gen_simus()
+
         self.save = None
 
+    def gen_simus(self):
+        self.simulations = {}
+        simu_fmt = self.pp_params.astrophysix.simu_fmt
+        descr_fmt = self.pp_params.astrophysix.descr_fmt
+        tag = self.pp_params.out.tag
+        for run in self.runs:
+            pp = self.pp[run][self.nums[run][0]]
+            nml = self.comp.namelist[run]
+            name = simu_fmt.format(run=run, tag=tag, nml=nml)
+            exec_time = str(datetime.datetime.fromtimestamp(os.stat(pp.path).st_ctime))
+            description = descr_fmt.format(run=run, tag=tag, nml=nml)
+            simu = Simulation(
+                simu_code=ramses,
+                name=name,
+                alias=name.upper(),
+                description=description,
+                directory_path=pp.path,
+                execution_time=exec_time,
+            )
+
+            for param in ramses.input_parameters:
+                try:
+                    param_setting = ParameterSetting(
+                        input_param=param,
+                        value=self.comp.get_nml(param.key, run),
+                        visibility=ParameterVisibility.BASIC_DISPLAY,
+                    )
+                    simu.parameter_settings.add(param_setting)
+                except KeyError as e:
+                    self._log("key {} not found".format(e), "WARNING")
+                except AttributeError as e:
+                    self._log("{}".format(e), "WARNING")
+
+            self.simulations[run] = simu
+
     def _not_self_dep(self, name, dep, dep_arg, overwrite, **kwargs):
         """
         Check if the dependency belongs to the plotter object or to another one (comp, pp, ..)
         """
         if dep in self.comp.rules:
-            done = self.comp.process(
+            result = self.comp.process(
                 dep, dep_arg, overwrite, overwrite_dep=self.overwrite_dep
             )
-            self.just_done.extend(done)
+            if result is not None:
+                self.just_done.append(done)
         else:
             super(Plotter, self)._not_self_dep(name, dep, dep_arg, overwrite, **kwargs)
 
@@ -172,19 +228,13 @@ class Plotter(Aggregator, BaseProcessor):
         )
 
     def _process_rule(
-        self,
+        self, name, rule, arg, overwrite=False, ax=None, from_cells=False, **kwargs
-        name,
-        rule,
-        arg,
-        overwrite=False,
-        ax=None,
-        movie=False,
-        from_cells=False,
-        **kwargs,
     ):
         """
         Open storage and figure if needed before processing a rule
         """
+
+        # Set full name according to argument
         if not arg is None:
             name_full = (
                 name
@@ -200,28 +250,46 @@ class Plotter(Aggregator, BaseProcessor):
         else:
             name_full = name
 
-        if rule.is_valid(arg):
+        # Exit if not valid
-            if rule.kind == "classic" or rule.kind == "cells":
+        if not rule.is_valid(arg):
+            self._log("{} is not valid in this context".format(name_full), "ERROR")
+            return
+
+        # get filetype of the output
+        filetype = filetype_from_ext[self.pp_params.out.ext]
+
+        # Select runs and nums
         if "select" in kwargs:
             select = kwargs.pop("select")
             runs, nums = self.selector.select(**select)
-                elif "runs" in kwargs:
-                    runs = kwargs.pop("runs")
-                    if isinstance(runs, RunSelector):
-                        nums = runs.nums
-                        runs = runs.runs
-                    else:
-                        nums = self.nums
         else:
             runs = self.runs
             nums = self.nums
 
-                i = 0
+        datafiles = []
-                for run in runs:
+
-                    files = []
+        # Several plots
-                    for num in nums[run]:
+        if rule.kind == "classic" or rule.kind == "cells":
+            run_num = [(run, num) for run in runs for num in nums[run]]
+        else:
+            run_num = [(run, None) for run in runs]
+
+        for i, (run, num) in enumerate(run_num):
+            # Find filename
             plot_filename = self._find_filename(name_full, run, num)
 
+            # Find ax
+            try:
+                real_ax = ax[i]
+            except TypeError as e:
+                if ax is None:
+                    fig, real_ax = P.subplots(1, 1)
+                elif not_array_error(e):
+                    real_ax = ax
+                else:
+                    raise
+
+            # Find plot save
             if from_cells or rule.kind == "cells":
                 if not os.exists(self.pp[run][num].cells_filename):
                     self.pp[run][num].load_cells()
@@ -231,113 +299,40 @@ class Plotter(Aggregator, BaseProcessor):
                 save = tables.open_file(self.pp[run][num].filename)
             else:
                 save = tables.open_file(self.comp.filename, "r")
-                        try:
-                            self._plot_rule(
-                                rule,
-                                save,
-                                arg,
-                                plot_filename,
-                                overwrite,
-                                ax=ax[i],
-                                run=run,
-                                **kwargs,
-                            )
-                        except TypeError as e:
-                            if str(e) in [
-                                "'LocatableAxes' object does not support indexing",
-                                "'AxesSubplot' object does not support indexing",
-                                "'AxesSubplot' object is not subscriptable",
-                                "'Axes' object is not subscriptable",
-                                "'LocatableAxes' object is not subscriptable",
-                            ]:
-                                self._plot_rule(
-                                    rule,
-                                    save,
-                                    arg,
-                                    plot_filename,
-                                    overwrite,
-                                    ax=ax,
-                                    run=run,
-                                    **kwargs,
-                                )
-                            elif ax is None:
-                                fig = P.figure()
-                                self._plot_rule(
-                                    rule,
-                                    save,
-                                    arg,
-                                    plot_filename,
-                                    overwrite,
-                                    ax=P.gca(),
-                                    run=run,
-                                    **kwargs,
-                                )
-                            else:
-                                raise
-                        finally:
-                            save.close()
-                        i = i + 1
-                        files.append(plot_filename)
-            else:
 
-                if "select" in kwargs and not "runs" in kwargs:
+            # Call plot routine
-                    select = kwargs.pop("select")
-                    runs, nums = self.selector.select(**select)
-                    if not rule.kind == "runs":
-                        kwargs["runs"] = runs
-                elif rule.kind == "runs" and "runs" in kwargs:
-                    runs = kwargs.pop("runs")
-                else:
-                    runs = self.runs
-
-                if ax is None:
-                    ax = P.gca()
-                if rule.kind == "series" and len(runs) == 1:
-                    run = self.runs[0]
-                    plot_filename = self._find_filename(name_full, run)
-                else:
-                    plot_filename = self._find_filename(name_full)
-                save = tables.open_file(self.comp.filename, "r")
             try:
-                    if rule.kind == "runs":
+                plot_info = self._plot_rule(
-                        for i, run in enumerate(runs):
-                            try:
-                                self._plot_rule(
                     rule,
                     save,
                     arg,
                     plot_filename,
                     overwrite,
-                                    ax=ax[i],
+                    ax=real_ax,
                     run=run,
                     **kwargs,
                 )
-                            except TypeError as e:
-                                if str(e) in [
-                                    "'LocatableAxes' object does not support indexing",
-                                    "'AxesSubplot' object does not support indexing",
-                                    "'AxesSubplot' object is not subscriptable",
-                                    "'Axes' object is not subscriptable",
-                                    "'LocatableAxes' object is not subscriptable",
-                                ]:
-                                    self._plot_rule(
-                                        rule,
-                                        save,
-                                        arg,
-                                        plot_filename,
-                                        overwrite,
-                                        ax=ax,
-                                        run=run,
-                                        **kwargs,
-                                    )
-                    else:
-                        self._plot_rule(
-                            rule, save, arg, plot_filename, overwrite, ax, **kwargs
-                        )
             finally:
                 save.close()
-        else:
+
-            self._log("{} is not valid in this context".format(name_full), "ERROR")
+            # Save in astrophysix format
+            df = rule.datafile(arg)
+            df[filetype] = plot_filename
+            if plot_info is not None:
+                df.plot_info = plot_info
+            if num is not None:
+                snap = self.pp[run][num].snapshot
+
+                if overwrite and df.name in snap.datafiles:
+                    del snap.datafiles[df.name]
+                elif df.name not in snap.datafiles:
+                    snap.datafiles.add(df)
+
+                if snap not in self.simulations[run].snapshots:
+                    self.simulations[run].snapshots.add(snap)
+
+            datafiles.append(df)
+        return datafiles
 
     def _plot_rule(self, rule, save, arg, plot_filename, overwrite, ax, **kwargs):
         """
@@ -345,7 +340,7 @@ class Plotter(Aggregator, BaseProcessor):
         """
         P.sca(ax)
         if self._needs_computation(overwrite, plot_filename):
-            rule.plot(save, arg, **kwargs)
+            plot_info = rule.plot(save, arg, **kwargs)
 
             if not self.pp_params.out.interactive:
                 P.tight_layout(pad=1)
@@ -360,6 +355,7 @@ class Plotter(Aggregator, BaseProcessor):
 
             if not self.pp_params.out.interactive:
                 P.close()
+            return plot_info
         else:
             self._log("Plot {} is already done, skipping...".format(plot_filename))
 
@@ -396,7 +392,7 @@ class Plotter(Aggregator, BaseProcessor):
             ext=self.pp_params.out.ext,
         )
 
-    def _label_run(self, run, node, label, nml_key):
+    def _label_run(self, run, node, label, nml_key, time=None):
         """
         Set up a label for the run from the namelist and parameters
         """
@@ -435,7 +431,7 @@ class Plotter(Aggregator, BaseProcessor):
             label_run = label
         return label_run
 
-    def _ax_label_unit(self, node, label, unit, unit_coeff):
+    def _ax_label_unit(self, node, label, unit, unit_coeff, put_units=True):
         """
         Find appropriate labels for axis
         """
@@ -457,6 +453,7 @@ class Plotter(Aggregator, BaseProcessor):
         if unit is None:
             unit = unit_old
 
+        if put_units:
             if not unit_coeff == 1:
                 base = unit
                 unit = unit_coeff * unit
@@ -466,11 +463,28 @@ class Plotter(Aggregator, BaseProcessor):
 
         return label, unit_old, unit
 
+    def _snapshot_title(self, run, node, title, nml_key, put_time, unit_time=cst.Myr):
+        title = self._label_run(run, node, title, nml_key)
+
+        if put_time:
+            time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
+            u_str = unit_str(unit_time, format="{unit}")
+            time_str = self.pp_params.plot.time_fmt.format(
+                time.express(unit_time), u_str
+            )
+            if len(title) > 0:
+                title = title + " | " + time_str
+            else:
+                title = time_str
+        return title
+
     def _plot_map(
         self,
         name,
         ax_los,
         run,
+        xlabel=None,
+        ylabel=None,
         label=None,
         unit=None,
         unit_coeff=1.0,
@@ -480,12 +494,14 @@ class Plotter(Aggregator, BaseProcessor):
         put_title=True,
         nml_key=None,
         put_time=True,
-        time_unit=cst.Myr,
+        unit_time=cst.Myr,
+        put_units=True,
         unit_space=cst.pc,
         cmap="plasma",
         norm="log",
         put_cbar=True,
         autoscale=True,
+        transform=None,
         **kwargs,
     ):
         """
@@ -503,9 +519,13 @@ class Plotter(Aggregator, BaseProcessor):
         node = self.save.get_node("/maps/{}_{}".format(name, ax_los))
         dmap = node.read()
 
-        label, unit_old, unit = self._ax_label_unit(node, label, unit, unit_coeff)
+        label, unit_old, unit = self._ax_label_unit(
+            node, label, unit, unit_coeff, put_units
+        )
 
         dmap = dmap * unit_old.express(unit)
+        if transform is not None:
+            dmap = transform(dmap)
 
         if norm == "log":
             norm = mpl.colors.LogNorm()
@@ -521,32 +541,28 @@ class Plotter(Aggregator, BaseProcessor):
 
         P.locator_params(axis="both", nbins=self.pp_params.plot.ntick)
 
-        P.xlabel(self._ax_title[ax_h] + unit_str(unit_space))
+        if xlabel is None:
-        P.ylabel(self._ax_title[ax_v] + unit_str(unit_space))
+            xlabel = self._ax_title[ax_h]
+        if ylabel is None:
+            ylabel = self._ax_title[ax_v]
+        if put_units:
+            xlabel = xlabel + unit_str(unit_space)
+            ylabel = ylabel + unit_str(unit_space)
+        P.xlabel(xlabel)
+        P.ylabel(ylabel)
 
         try:
             cbar = P.colorbar(im, cax=P.gca().cax)
         except AttributeError:
             cbar = P.colorbar()
 
+        if put_title:
+            title = self._snapshot_title(run, node, title, nml_key, put_time, unit_time)
+            P.title(title)
+
         if not label is None:
             cbar.set_label(label)
 
-        if put_title:
-            title = self._label_run(run, node, title, nml_key)
-
-            if put_time:
-                time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
-                time_str = self.pp_params.plot.time_fmt.format(
-                    time.express(time_unit), time_unit.latex
-                )
-                if len(title) > 0:
-                    title = title + " | " + time_str
-                else:
-                    title = time_str
-
-            P.title(title)
-
         for i, plot_overlay in enumerate(overlays):
             if plot_overlay in self.overlays:
                 plot_overlay = self.overlays[plot_overlay]
@@ -556,6 +572,23 @@ class Plotter(Aggregator, BaseProcessor):
             except:
                 plot_overlay(ax_los, im_extent)
 
+        return PlotInfo(
+            plot_type=PlotType.IMAGE,
+            xaxis_values=np.linspace(im_extent[0], im_extent[1], dmap.shape[0] + 1),
+            yaxis_values=np.linspace(im_extent[2], im_extent[3], dmap.shape[1] + 1),
+            values=dmap,
+            xaxis_log_scale=False,
+            yaxis_log_scale=False,
+            values_log_scale=(norm == mpl.colors.LogNorm()),
+            xaxis_label=xlabel,
+            yaxis_label=ylabel,
+            values_label=label,
+            xaxis_unit=unit_space,
+            yaxis_unit=unit_space,
+            values_unit=unit,
+            plot_title=title,
+        )
+
     def _overlay_contour(
         self,
         ax_los,
@@ -724,7 +757,7 @@ class Plotter(Aggregator, BaseProcessor):
         nml_key=None,
         put_title=True,
         put_time=True,
-        time_unit=cst.Myr,
+        unit_time=cst.Myr,
         **kwargs,
     ):
         """
@@ -749,26 +782,13 @@ class Plotter(Aggregator, BaseProcessor):
         if not ylabel is None:
             P.ylabel(ylabel)
 
+        title = self._snapshot_title(run, node, title, nml_key, put_time, unit_time)
         if put_title:
-            title = self._label_run(run, node, title, nml_key)
-
-            if put_time:
-                time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
-                time_str = self.pp_params.plot.time_fmt.format(
-                    time.express(time_unit), time_unit.latex
-                )
-                if len(title) > 0:
-                    title = title + " | " + time_str
-                else:
-                    title = time_str
-
             P.title(title)
-
+        if label == None:
-        if label is None:
             label = title
-        P.plot(bin_centers, mean_bin, label=label, **kwargs)
 
-        P.plot(bin_centers, mean_bin, label=title, **kwargs)
+        P.plot(bin_centers, mean_bin, label=label, **kwargs)
 
     def _plot_hist(
         self,
@@ -781,10 +801,11 @@ class Plotter(Aggregator, BaseProcessor):
         unit_coeff=1.0,
         ytransform=None,
         label=None,
+        put_title=True,
         title=None,
         nml_key=None,
         put_time=True,
-        time_unit=cst.Myr,
+        unit_time=cst.Myr,
         xlog=None,
         ylog=False,
         kind="bar",
@@ -799,47 +820,41 @@ class Plotter(Aggregator, BaseProcessor):
         """
         Plot an histogram (PDF, etc ...)
         """
+        # Get node
         if not ax_los is None:
             name = name + "_" + ax_los
-
         node = self.save.get_node(group + name)
-
         if xlog is None:
             try:
                 xlog = node._v_attrs_.logbins
             except:
                 xlog = False
 
+        # get label and units
         xlabel, unit_old, unit = self._ax_label_unit(node, label, unit, unit_coeff)
 
+        # Read data
         if "mean" in node:
             index = node["runs"].read().index(run.encode())
             values, centers = node["mean"].read()[index]
         else:
             values, centers = node.read()
-
         if xlog:
             centers = centers + np.log10(unit_old.express(unit))
         else:
             centers = centers * unit_old.express(unit)
-
         if ytransform is not None:
             values = ytransform(values)
+        width = centers[1] - centers[0]
 
-        title = self._label_run(run, node, title, nml_key)
+        # Set title
-
+        title = self._snapshot_title(run, node, title, nml_key, put_time, unit_time)
-        if put_time:
+        if put_title:
-            time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
-            time_str = self.pp_params.plot.time_fmt.format(
-                time.express(time_unit), time_unit.latex
-            )
-            if len(title) > 0:
-                title = title + " | " + time_str
-            else:
-                title = time_str
-
             P.title(title)
+        if label == None:
+            label = title
 
+        # Set colors
         if color is None and not colors is None:
             if nml_color is None:
                 color = colors[run]
@@ -850,11 +865,8 @@ class Plotter(Aggregator, BaseProcessor):
                 except:
                     color = colors(nml)
 
-        if label == None:
+        # Actual plot
-            label = title
-
         if kind == "bar":
-            width = centers[1] - centers[0]
             P.bar(centers, values, width, log=ylog, color=color, label=label, **kwargs)
         elif kind == "step":
             if ylog:
@@ -863,11 +875,13 @@ class Plotter(Aggregator, BaseProcessor):
         else:
             raise ValueError("kind must be 'bar' or 'step'")
 
+        # put labels
         if not label is None:
             P.xlabel(xlabel)
         if not ylabel is None:
             P.ylabel(ylabel)
 
+        # Also diplay fit, previously saved
         if ax_los is not None and "/hist/fit_" + name + "_" + ax_los in self.save:
             slope = node.attrs.slope
             origin = node.attrs.origin
@@ -878,14 +892,27 @@ class Plotter(Aggregator, BaseProcessor):
                 linewidth=2,
                 color="orange",
             )
-
+        # or a new one
-        P.ylim([None, 1.0])
-
         if not fit is None:
             self._overlay_fit(
                 centers, values, kind=fit, ls="--", lw=1.5, label=fitlabel
             )
 
+        # returns PlotInfo (for Galactica)
+        edges = np.append(centers - width / 2.0, centers[-1] + width / 2.0)
+        return PlotInfo(
+            plot_type=PlotType.HISTOGRAM,
+            xaxis_values=edges,
+            yaxis_values=values,
+            xaxis_log_scale=False,
+            yaxis_log_scale=ylog,
+            xaxis_label=xlabel,
+            yaxis_label=ylabel,
+            xaxis_unit=unit,
+            yaxis_unit=cst.none,
+            plot_title=title,
+        )
+
     def _plot(
         self,
         name_x,
@@ -898,19 +925,17 @@ class Plotter(Aggregator, BaseProcessor):
         yunit=None,
         xunit_coeff=1.0,
         yunit_coeff=1.0,
-        ylog=False,
         fit=None,
         fitlabel=None,
         smooth=0,
         nml_key=None,
         run=None,
-        runs=None,
         yerr=None,
         yerr_kind="std",
         sigma_err=2.0,
         grid=False,
         put_time=False,
-        time_unit=cst.Myr,
+        unit_time=cst.Myr,
         colors=None,
         nml_color=None,
         legend=None,
@@ -922,12 +947,15 @@ class Plotter(Aggregator, BaseProcessor):
         Generic plot routine, with name_x and name_y two path in the hdf5 file
         """
 
+        # Get proper hdf5 names
         if not node_arg is None:
             name_x, name_y = name_x + "_" + node_arg, name_y + "_" + node_arg
 
+        # Get hdf5 nodes
         node_x = self.save.get_node(name_x)
         node_y = self.save.get_node(name_y)
 
+        # If the actual data is in a,other file, fetch it
         if subname_x:
             hdf5_x = tables.open_file(node_x.read())
             node_x = hdf5_x.get_node(subname_x)
@@ -935,6 +963,7 @@ class Plotter(Aggregator, BaseProcessor):
             hdf5_y = tables.open_file(node_y.read())
             node_y = hdf5_y.get_node(subname_y)
 
+        # Find proper labels
         xlabel, xunit_old, xunit = self._ax_label_unit(
             node_x, xlabel, xunit, xunit_coeff
         )
@@ -942,58 +971,24 @@ class Plotter(Aggregator, BaseProcessor):
             node_y, ylabel, yunit, yunit_coeff
         )
 
-        P.xlabel(xlabel)
+        # If relevent, get time
-        P.ylabel(ylabel)
-
-        if grid:
-            P.grid()
-
-        if ylog:
-            P.yscale("log")
-
         if put_time:
             time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
             time_str = self.pp_params.plot.time_fmt.format(
-                time.express(time_unit), time_unit.latex
+                time.express(unit_time), unit_time.latex
             )
             if label is not None and len(label) > 0:
                 label = label + " | " + time_str
             else:
                 label = time_str
 
+        # Manage the different forms in which the data may be stored :
+        # Possibilities are : plain array, dict of arrays (mean, std, ..) or dict of array (runs)
         if node_y._v_attrs.CLASS == "ARRAY":
             x = node_x.read() * xunit_old.express(xunit)
             y = node_y.read() * yunit_old.express(yunit)
             mask = np.isfinite(x) & np.isfinite(y)
             x, y = x[mask], y[mask]
-            if smooth > 0:
-                y = gaussian_filter1d(y, sigma=smooth)
-            if not run is None:
-                label = self._label_run(run, node_y, label, nml_key)
-            if colors is None:
-                (base_line,) = P.plot(x, y, label=label, **kwargs)
-            else:
-                if nml_color is None:
-                    color = colors[run]
-                elif nml_color == "time":
-                    time = (
-                        self.save.root._v_attrs.time * self.comp.info["unit_time"]
-                    ).express(time_unit)
-                    color = colors(time)
-                else:
-                    nml = self.comp.get_nml(nml_color, run)
-                    try:
-                        color = colors[nml]
-                    except:
-                        color = colors(nml)
-                if yerr is None:
-                    (base_line,) = P.plot(x, y, label=label, color=color, **kwargs)
-                else:
-                    if isinstance(yerr, str):
-                        yerr = self.save.get_node(yerr).read()
-
-                    base_line, _, _ = P.errorbar(x, y, yerr=yerr, label=label, **kwargs)
-
         elif "mean" in node_y:
             x = node_x.read() * xunit_old.express(xunit)
             y = node_y.mean.read() * yunit_old.express(yunit)
@@ -1014,7 +1009,6 @@ class Plotter(Aggregator, BaseProcessor):
             else:
                 yerr_min = y
                 yerr_max = y
-
             yerr = yerr_max - yerr_min
             mask = np.isfinite(x) & np.isfinite(y) & np.isfinite(yerr)
             x, y, yerr, yerr_min, yerr_max = (
@@ -1024,44 +1018,51 @@ class Plotter(Aggregator, BaseProcessor):
                 yerr_min[mask],
                 yerr_max[mask],
             )
+        else:
+            x, y = node_x[run], node_y[run]
+            mask = np.isfinite(x) & np.isfinite(y)
+            x, y = x[mask], y[mask]
+
+        if isinstance(yerr, str):
+            yerr = self.save.get_node(yerr).read()
+
+        if smooth > 0:
+            y = gaussian_filter1d(y, sigma=smooth)
         if not run is None:
             label = self._label_run(run, node_y, label, nml_key)
 
-            if yerr_kind is None:
+        # Look if special colors method is used
-                yerr = None
+        if colors is None:
+            if yerr is None:
                 (base_line,) = P.plot(x, y, label=label, **kwargs)
             else:
-                base_line, _, _ = P.errorbar(
+                base_line, _, _ = P.errorbar(x, y, yerr=yerr, label=label, **kwargs)
-                    x, y, yerr=[y - yerr_min, yerr_max - y], label=label, **kwargs
-                )
-
-        else:
-            if runs is None:
-                runs = self.runs
-            for i, run in enumerate(runs):
-                x_run, y_run = node_x[run], node_y[run]
-                x = x_run.read() * xunit_old.express(xunit)
-                y = y_run.read() * yunit_old.express(yunit)
-                mask = np.isfinite(x) & np.isfinite(y)
-                x, y = x[mask], y[mask]
-                if smooth > 0:
-                    y = gaussian_filter1d(y, sigma=smooth)
-                label_run = self._label_run(run, y_run, label, nml_key)
-                if colors is None:
-                    (base_line,) = P.plot(x, y, label=label_run, **kwargs)
         else:
             if nml_color is None:
-                        color = colors[i % len(colors)]
+                color = colors[run]
+            elif nml_color == "time":
+                time = (
+                    self.save.root._v_attrs.time * self.comp.info["unit_time"]
+                ).express(unit_time)
+                color = colors(time)
             else:
                 nml = self.comp.get_nml(nml_color, run)
                 try:
                     color = colors[nml]
                 except:
                     color = colors(nml)
-                    (base_line,) = P.plot(x, y, label=label_run, color=color, **kwargs)
+            if yerr is None:
-            if legend is None:
+                (base_line,) = P.plot(x, y, label=label, color=color, **kwargs)
-                legend = True
+            else:
+                base_line, _, _ = P.errorbar(
+                    x, y, yerr=yerr, color=color, label=label, **kwargs
+                )
 
+        # Ax decorations
+        P.xlabel(xlabel)
+        P.ylabel(ylabel)
+        if grid:
+            P.grid()
         if legend:
             P.legend()
 
@@ -1076,6 +1077,7 @@ class Plotter(Aggregator, BaseProcessor):
                 color=base_line.get_color(),
                 label=fitlabel,
             )
+
         if subname_x:
             hdf5_x.close()
         if subname_y:
@@ -1603,11 +1605,16 @@ class Plotter(Aggregator, BaseProcessor):
                 dependencies=["radial_bins", "rad_avg_" + name],
             )
 
+            self.rules["avg_map_" + name] = PlotRule(
+                self,
+                partial(self._plot_map, "avg_map_" + name),
+                "Map of the radial average of {}".format(name),
+                dependencies=["avg_map_" + name],
+            )
+
             self.rules["fluct_" + name] = PlotRule(
                 self,
-                partial(
+                partial(self._plot_map, "fluct_" + name, cmap="RdBu_r"),
-                    self._plot_map, "fluct_" + name, vmin=0.01, vmax=100, cmap="RdBu_r"
-                ),
                 "Fluctuation of {}".format(name),
                 dependencies=["fluct_" + name],
             )
@@ -1666,7 +1673,7 @@ class Plotter(Aggregator, BaseProcessor):
 
                 # Radial
                 generic_rule(field + "r")
-                # Othoradial
+                # Orthoradial
                 generic_rule(field + "phi")
                 # Norm
                 generic_rule(field + "_norm")

postprocessor.py

@@ -149,7 +149,15 @@ class PostProcessor(HDF5Container):
 
     cells_loaded = False
 
-    def __init__(self, path=None, num=None, path_out=None, pp_params=None, tag=None):
+    def __init__(
+        self,
+        path=None,
+        num=None,
+        path_out=None,
+        pp_params=None,
+        tag=None,
+        unit_time=cst.year,
+    ):
         """
         Creates the basic structures needed for the outputs
         """
@@ -170,6 +178,14 @@ class PostProcessor(HDF5Container):
             self.path_out + "/cells_" + tag_name + format(num, "05") + ".h5"
         )
 
+        self.pspec_filename = (
+            self.path_out + "/pspec_" + tag_name + format(num, "05") + ".h5"
+        )
+
+        self.filaments_filename = (
+            self.path_out + "/filaments_" + tag_name + format(num, "05") + ".pickle"
+        )
+
         if not os.path.exists(self.path_out):
             os.makedirs(self.path_out)
 
@@ -213,7 +229,7 @@ class PostProcessor(HDF5Container):
         if not self.pp_params.pymses.multiprocessing:
             self._rt.disable_multiprocessing()
 
-        # Set the extend of the image
+        # Set the extent of the image
         self._radius = 0.5 / self.pp_params.pymses.zoom
         self.lbox = self.info["boxlen"]
 
@@ -273,12 +289,23 @@ class PostProcessor(HDF5Container):
 
         self.log_id = "[{}, {}] ".format(self.run, self.num)
 
-        if os.path.exists(self.path_out + "/filaments.pickle"):
+        if os.path.exists(self.filaments_filename):
-            with open(self.path_out + "/filaments.pickle", "rb") as f:
+            with open(self.filaments_filename, "rb") as f:
                 self.fil = pickle.load(f)
         else:
             self.fil = None
 
+        self.snapshot = Snapshot(
+            name=str(self.num),
+            description="",
+            time=(
+                self.info["time"] * self.info["unit_time"].express(unit_time),
+                unit_time,
+            ),
+            directory_path=self.path,
+            data_reference="OUTPUT_{}".format(self.num),
+        )
+
         self.def_rules()
 
     def load_cells(self):
@@ -964,12 +991,22 @@ class PostProcessor(HDF5Container):
             )
 
             bins = np.zeros(r.shape, dtype=int)
-            for r0 in radial_bins[1:]:
+            for r0 in radial_bins[1:-1]:
                 bins = bins + (r >= r0).astype(int)
 
             vr_mean = mean_bin_vr[bins]
             vphi_mean = mean_bin_vphi[bins]
 
+            # use linear interpolation
+            # v = ((r[i+1] - r)v[i] + (r - r[i])v[i + 1]) / (r[i+1] - r[i])
+            vr_mean = (radial_bins[bins + 1] - r) * vr_mean
+            vr_mean = vr_mean + (r - radial_bins[bins]) * mean_bin_vr[bins + 1]
+            vr_mean = vr_mean / (radial_bins[bins + 1] - radial_bins[bins])
+
+            vphi_mean = (radial_bins[bins + 1] - r) * vphi_mean
+            vphi_mean = vphi_mean + (r - radial_bins[bins]) * mean_bin_vphi[bins + 1]
+            vphi_mean = vphi_mean / (radial_bins[bins + 1] - radial_bins[bins])
+
             vr = self.oct_getter_vr(dset)
             vphi = self.oct_getter_vphi(dset)
             alpha = (vphi - vphi_mean) * (vr - vr_mean)
@@ -1055,7 +1092,7 @@ class PostProcessor(HDF5Container):
         return sinks_dict
 
     def _pspec(self):
-        outfile = self.path_out + "/pspec.h5"
+        outfile = self.pspec_filename
         pspec_new.pspec(repo=self.path, iouts=[self.num], outfile=outfile)
         return True
 
@@ -1086,9 +1123,10 @@ class PostProcessor(HDF5Container):
         self.fil.create_mask(
             verbose=verbose,
             smooth_size=1 * u.pix,
-            adapt_thresh=2 * u.pix,
+            adapt_thresh=4 * u.pix,
             size_thresh=size_thresh * u.pix ** 2,
             glob_thresh=glob_thresh,
+            fill_hole_size=0.1 * u.pix ** 2,
         )
         self.fil.medskel(verbose=verbose)
         self.fil.analyze_skeletons(
@@ -1099,8 +1137,7 @@ class PostProcessor(HDF5Container):
         self.fil.exec_rht()
         self.fil.find_widths()
 
-        outfile = self.path_out + "/filaments.pickle"
+        with open(self.filaments_filename, "wb") as f:
-        with open(outfile, "wb") as f:
             pickle.dump(self.fil, f, pickle.HIGHEST_PROTOCOL)
         return True
 
@@ -1121,7 +1158,7 @@ class PostProcessor(HDF5Container):
 
     def _filaments_forces(self):
         """
-        Compute forces within a filament (for disks)
+        Compute forces within a filament (for disks), within the slice at z=0
         """
 
         GM = self.G * self.pp_params.disk.mass_star  # Mass parameter
@@ -1134,11 +1171,11 @@ class PostProcessor(HDF5Container):
         i_center, j_center = self._filaments_center()
 
         # Get slices and projections at z = 0
-        vphi = self.save.get_node("/maps/slice_velphi_z").read()
+        vphi = self.get_value("/maps/slice_velphi_z")
-        gr = self.save.get_node("/maps/slice_gr_z").read()
+        gr = self.get_value("/maps/slice_gr_z")
-        Pz = self.save.get_node("/maps/slice_P_z").read()
+        Pz = self.get_value("/maps/slice_P_z")
-        coldens = self.save.get_node("/maps/coldens_z").read()
+        rho = self.get_value("/maps/slice_rho_z")
-        vr = self.save.get_node("/maps/slice_velr_z").read()
+        vr = self.get_value("/maps/slice_velr_z")
 
         # Get coordinates
         im_extent = np.array(self.save.root.maps._v_attrs.im_extent) * self.lbox
@@ -1167,7 +1204,7 @@ class PostProcessor(HDF5Container):
         # Thermal support
         GPx, GPy = np.gradient(Pz)
         gradPr = (xx * GPx + yy * GPy) / rr
-        fP = gradPr / coldens
+        fP = gradPr / rho
 
         # Gravitational field
         e2 = (1.0 / 512) ** 2
@@ -1371,7 +1408,7 @@ class PostProcessor(HDF5Container):
                     "slice_velphi": "z",
                     "slice_gr": "z",
                     "slice_P": "z",
-                    "coldens": "z",
+                    "slice_rho": "z",
                     "slice_velr": "z",
                 },
             ),

pp_params.yml

@@ -22,22 +22,22 @@ disk: # Disk speficic parameters
 
 
 pdf: # parameters for probability density functions
-    nb_bin    : 200                   # Number of bins for the PDF
+    nb_bin    : 100                   # Number of bins for the PDF
     range     : [-1.5, 2.5]           # Range of the PDF (log of fluctuation)
-    xmin_fit  : 0.1                   # Lower boundary of the fit (log of fluctuation)
+    xmin_fit  : 0.3                   # Lower boundary of the fit (log of fluctuation)
     xmax_fit  : 1.5                   # Upper boundary of the fit (log of fluctuation)
     fit_cut   : 1e-4                  # Exclude value that are < fit_cut * maximum
 
 
 filaments:  # parameters for FilFinder
-     datamap : "rho_avg"
+     datamap : "fluct_coldens"
      verbose : False
      rmin    : 0.15 # In fraction of the box (zoom to be taken into account)
      rmax    : 0.45 # In fraction of the box (idem)
-     size_thresh   : 200 # in pixels**2
+     size_thresh   : 400 # in pixels**2
-     skel_thresh   : 100 # in pixels
+     skel_thresh   : 50 # in pixels
-     branch_thresh : 100 # in pixels
+     branch_thresh : 50 # in pixels
-     glob_thresh   : 40  # in map unit
+     glob_thresh   : 1.5  # in datamap unit
 
 pymses: # Parameters for Pymses reader
 
@@ -80,7 +80,7 @@ out: # Parameters for post processing
     # {ext} : Extension defined above
     # {name} : Name of the rule
     # {tag} : Tag defined above
-    # {nml[nml_key]} : The value of nml_key in the namelist (ex: amr_params/levelmin)
+    # {nml[nml_key]} : The value of nml_key in the namelist (ex: {nml[amr_params/levelmin]})
 
 
 process: # General setting of the post-processor module
@@ -91,3 +91,12 @@ process: # General setting of the post-processor module
 
 rules: # Specific rules parameters
     turb_energy_threshold : -1       # Remove invalid data (<0 = no threshold)
+
+
+astrophysix: # Parameters for astrophysix and galactica
+    simu_fmt          : "{tag}_{run}"      # Format of the name of simulation
+    descr_fmt         : "{tag}_{run}"      # Format of the default description
+    # The following keys are accepted
+    # {run} : Name of the relevant run
+    # {tag} : Tag defined above
+    # {nml[nml_key]} : The value of nml_key in the namelist (ex: {nml[amr_params/levelmin]})

ramses_astrophysix.py

@@ -0,0 +1,92 @@
+# coding: utf-8
+
+
+from astrophysix.simdm.protocol import (
+    SimulationCode,
+    AlgoType,
+    Algorithm,
+    InputParameter,
+    PhysicalProcess,
+    Physics,
+)
+
+
+# Simulation code definition  #
+ramses = SimulationCode(
+    name="Ramses 3 (MHD)",
+    code_name="Ramses",
+    code_version="3.10.1",
+    alias="RAMSES_3",
+    url="https://www.ics.uzh.ch/~teyssier/ramses/RAMSES.html",
+    description="Ramses MHD code",
+)
+# => Add algorithms : available algorithm types are :
+# - AlgoType.AdaptiveMeshRefinement
+# - AlgoType.VoronoiMovingMesh
+# - AlgoType.SmoothParticleHydrodynamics
+# - AlgoType.Godunov
+# - AlgoType.PoissonMultigrid
+# - AlgoType.PoissonConjugateGradient
+# - AlgoType.ParticleMesh
+# - AlgoType.FriendOfFriend
+# - AlgoType.HLLCRiemann
+# - AlgoType.RayTracer
+ramses.algorithms.add(
+    Algorithm(algo_type=AlgoType.AdaptiveMeshRefinement, description="AMR")
+)
+ramses.algorithms.add(
+    Algorithm(algo_type=AlgoType.Godunov, description="Godunov scheme")
+)
+ramses.algorithms.add(
+    Algorithm(algo_type=AlgoType.HLLCRiemann, description="HLLC Riemann solver")
+)
+ramses.algorithms.add(
+    Algorithm(
+        algo_type=AlgoType.PoissonMultigrid, description="Multigrid Poisson solver"
+    )
+)
+# => Add input parameters
+ramses.input_parameters.add(
+    InputParameter(
+        key="amr_params/levelmin",
+        name="lmin",
+        description="min. level of AMR refinement",
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="amr_params/levelmax",
+        name="lmax",
+        description="max. level of AMR refinement",
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="amr_params/jeans_refine",
+        name="jeans_refine",
+        description="Array, number of cells needed to resolve the Jeans lenght at each level from lmin",
+    )
+)
+ramses.input_parameters.add(
+    InputParameter(
+        key="cloud_params/beta_cool", name="beta", description="Cooling parameter"
+    )
+)
+
+
+# => Add physical processes : available physics are :
+# - Physics.SelfGravity
+# - Physics.Hydrodynamics
+# - Physics.MHD
+# - Physics.StarFormation
+# - Physics.SupernovaeFeedback
+# - Physics.AGNFeedback
+# - Physics.MolecularCooling
+ramses.physical_processes.add(
+    PhysicalProcess(
+        physics=Physics.Hydrodynamics, description="Hydrodynamical equations are solved"
+    )
+)
+ramses.physical_processes.add(
+    PhysicalProcess(physics=Physics.SelfGravity, description="Self-Gravity is applied.")
+)

units.py

@@ -1,14 +1,16 @@
 # coding: utf-8
 
-import pymses.utils.constants as cst
+import astrophysix.units as cst
+
+create_unit = cst.Unit.create_unit
 
 
 def parse_exp_unit(u):
     splitted = u.split("^")
-    name_u = cst.Unit.from_name(splitted[0]).latex
+    name_u = cst.Unit.from_name(splitted[0]).latex.replace("text", "math")
     exp = ""
     if len(splitted) > 1:
-        exp = "$^{" + str(splitted[1]) + "}$"
+        exp = "^{" + str(splitted[1]) + "}"
     return name_u + exp
 
 
@@ -17,66 +19,78 @@ def convert_exp(number, digits=4):
     splitted = "{num:.{digits}g}".format(num=number, digits=digits).split("e")
     # If no need of scientific notation (low number of digits)
     if len(splitted) == 1:
-        return "${}$".format(splitted[0])
+        return "{}".format(splitted[0])
     else:
         coeff = splitted[0]
         exp = splitted[1]
         exp_str = "10^{" + str(int(exp)) + "}"
         if float(coeff) == 1.0:
-            return "$" + exp_str + "$"
+            return exp_str
         else:
-            return "${}\\times {}$".format(coeff, exp_str)
+            return "{}\\times {}".format(coeff, exp_str)
 
 
-def unit_str(unit, base=None, prefix=""):
+def unit_str(unit, base=None, prefix="", format=" [{unit}]"):
+    """
+    Format a unit in matplotlib parsable latex
+
+    unit : astrophysics.units.unit.Unit
+    base : astrophysics.units.unit.Unit to use as base unit (if None `unit` is used)
+    prefix : str to put befor the unit
+    format : str with the {unit} key, to put external decoration
+    """
     if unit == cst.none:
         return ""
     elif not base is None:
         coeff = unit.express(base)
-        return unit_str(base, prefix=convert_exp(coeff) + " ")
+        u_str = unit_str(base, prefix=convert_exp(coeff) + " ")
     elif len(unit.latex) > 0:
-        if ("." in unit.latex or "^" in unit.latex) and not "$" in unit.latex:
+        if "." in unit.latex or "^" in unit.latex:
             base_str = ".".join(map(parse_exp_unit, unit.name.split(".")))
-            return r" [{}{}]".format(prefix, base_str)
+            u_str = r"${}{}$".format(prefix, base_str)
         else:
-            return r" [{}{}]".format(prefix, unit.latex)
+            u_str = r"${}{}$".format(prefix, unit.latex.replace("text", "math"))
     elif len(unit.name) > 0:
         try:
             base_str = ".".join(map(parse_exp_unit, unit.name.split(".")))
-            u_str = r" [{}{}]".format(prefix, base_str)
+            u_str = r"${}{}$".format(prefix, base_str)
         except:
-            u_str = r" [{}{}]".format(prefix, unit.name)
+            u_str = r"${}{}$".format(prefix, unit.name)
-        return u_str
     else:
         base_str = ".".join(
             map(parse_exp_unit, unit._decompose_base_units().split("."))
         )
-        return r" [{}{} {}]".format(prefix, unit.coeff, base_str)
+        u_str = r"${}{} {}$".format(prefix, unit.coeff, base_str)
+    return format.format(unit=u_str)
 
 
-cst.Msun_pc3 = cst.create_unit(
+cst.coldens = create_unit(
+    "Msun.pc^-2", base_unit=cst.Msun / cst.pc ** 2, descr="Column density"
+)
+cst.km_s = create_unit("km.s^-1", base_unit=cst.km / cst.s, descr="Speed")
+
+
+cst.Msun_pc3 = create_unit(
     "Msun.pc^-3", base_unit=cst.Msun / cst.pc ** 3, descr="Density"
 )
 
-cst.Msun_pc3 = cst.create_unit(
+cst.kg_m3 = create_unit("kg.m^-3", base_unit=cst.kg / cst.m ** 3, descr="Density")
-    "Msun.pc^-3", base_unit=cst.Msun / cst.pc ** 3, descr="Density"
-)
 
-cst.ssfr = cst.create_unit(
+cst.ssfr = create_unit(
-    "Msun.yr^-1.pc^-2",
+    "Msun.year^-1.pc^-2",
     base_unit=cst.Msun / cst.year / cst.pc ** 2,
     descr="Surfacic SFR",
-    latex="M$_{\odot}$.yr$^{-1}$.pc$^{-2}$",
 )
+# latex='M$_{\odot}$.yr$^{-1}$.pc$^{-2}$')
 
-cst.ssfrG = cst.create_unit(
+cst.ssfrG = create_unit(
     "Msun.Gyr^-1.pc^-2",
     base_unit=1e-9 * cst.Msun / cst.year / cst.pc ** 2,
     descr="Surfacic SFR",
-    latex="M$_{\odot}$.Gyr$^{-1}$.pc$^{-2}$",
+    latex="\mathrm{M}_{\odot}.\mathrm{Gyr}^{-1}.\mathrm{pc}^{-2}",
 )
 
 
-cst.uG = cst.create_unit(
+cst.uG = create_unit(
-    "μG", base_unit=1e-10 * cst.T, descr="Micro Gauss", latex="$\mu\mathrm{G}$"
+    "μG", base_unit=1e-10 * cst.T, descr="Micro Gauss", latex="\\mu\\mathrm{G}"
 )