correct bugs

plotter.py

@@ -126,7 +126,7 @@ class Plotter(Aggregator, BaseProcessor):
             name_full = name
 
         if rule.is_valid(arg):
-            if rule.kind == "classic":
+            if rule.kind == "classic" or rule.kind == "runs":
                 try:
                     runs = kwargs.pop("runs")
                     if isinstance(runs, RunSelector):
@@ -136,9 +136,17 @@ class Plotter(Aggregator, BaseProcessor):
                 i = 0
                 for run in runs:
                     files = []
-                    for num in self.nums[run]:
+                    if rule.kind == "classic":
+                        nums = self.nums[run]
+                    else:
+                        nums = [None]
+                    for num in nums:
                         plot_filename = self._find_filename(name_full, run, num)
-                        save = tables.open_file(self.pp[run][num].filename)
+
+                        if rule.kind == "classic":
+                            save = tables.open_file(self.pp[run][num].filename)
+                        else:
+                            save = tables.open_file(self.comp.filename, "r")
                         try:
                             self._plot_rule(
                                 rule,
@@ -265,7 +273,10 @@ class Plotter(Aggregator, BaseProcessor):
             return r"{} = {}".format(prop_label, prop_value_str)
 
         if nml_key is None and label is None:
-            if "attrs" in self.save.root._v_attrs:
+            if (
+                "attrs" in self.save.root._v_attrs
+                and run in self.save.root._v_attrs.attrs
+            ):
                 label_run = r"{}".format(self.save.root._v_attrs.attrs[run].label)
             else:
                 label_run = run
@@ -479,8 +490,9 @@ class Plotter(Aggregator, BaseProcessor):
     def _plot_hist(
         self,
         name,
-        ax_los=None,
-        run="",
+        ax_los,
+        run,
+        group="/hist/",
         label=None,
         unit=None,
         unit_coeff=1.0,
@@ -495,13 +507,15 @@ class Plotter(Aggregator, BaseProcessor):
         color=None,
         colors=None,
         nml_color=None,
+        fit=None,
+        fitlabel=None,
         **kwargs
     ):
 
         if not ax_los is None:
             name = name + "_" + ax_los
 
-        node = self.save.get_node("/hist/" + name)
+        node = self.save.get_node(group + name)
 
         if xlog is None:
             try:
@@ -511,7 +525,12 @@ class Plotter(Aggregator, BaseProcessor):
 
         label, unit_old, unit = self._ax_label_unit(node, label, unit, unit_coeff)
 
-        values, centers = node.read()
+        if "mean" in node:
+            index = node["runs"].read().index(run)
+            values, centers = node["mean"].read()[index]
+        else:
+            values, centers = node.read()
+
         if xlog:
             centers = centers + np.log10(unit_old.express(unit))
         else:
@@ -570,6 +589,11 @@ class Plotter(Aggregator, BaseProcessor):
 
         P.ylim([None, 1.0])
 
+        if not fit is None:
+            self._overlay_fit(
+                centers, values, kind=fit, ls="--", lw=1.5, label=fitlabel
+            )
+
     def _plot(
         self,
         name_x,
@@ -582,6 +606,7 @@ class Plotter(Aggregator, BaseProcessor):
         yunit=None,
         xunit_coeff=1.0,
         yunit_coeff=1.0,
+        ylog=False,
         fit=None,
         fitlabel=None,
         smooth=0,
@@ -618,6 +643,9 @@ class Plotter(Aggregator, BaseProcessor):
         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(
@@ -878,6 +906,19 @@ class Plotter(Aggregator, BaseProcessor):
                 "$\rho$-PDF",
                 dependencies=["rho_pdf"],
             ),
+            "avg_coldens_pdf": PlotRule(
+                self,
+                partial(
+                    self._plot_hist,
+                    "avg_time_coldens_pdf_z",
+                    group="/comp/",
+                    xlog=True,
+                    put_time=False,
+                ),
+                "PDF",
+                kind="runs",
+                dependencies={"avg_time_coldens_pdf": "z"},
+            ),
             "T_pdf": PlotRule(
                 self, partial(self._plot_hist, "T_pdf"), "T-PDF", dependencies=["T_pdf"]
             ),