[postprocessor] generalize use of get_value

postprocessor.py

@@ -714,8 +714,8 @@ class PostProcessor(HDF5Container):
         bins : int, number of bins
         logbins : bool, if true, the bins will be logaritmically distributed
         """
-        x = self.save.get_node(group + name_x + "_" + ax_los).read()
-        y = self.save.get_node(group + name_y + "_" + ax_los).read()
+        x = self.get_value(group + name_x + "_" + ax_los)
+        y = self.get_value(group + name_y + "_" + ax_los)
 
         centers, values = mean_by_bins(x, y, bins, logbins)
         # return ({os.path.basename(name_x) : centers, os.path.basename(name_y) : y_mean},
@@ -727,7 +727,7 @@ class PostProcessor(HDF5Container):
         Mean of Ek/Eb in rho bins
         """
         self.load_cells()
-        mean_speed = self.save.get_node("/globals/mwa_speed").read()
+        mean_speed = self.get_value("/globals/mwa_speed")
         mean_speed = mean_speed * self.info["unit_velocity"].express(U.km_s)
         vel_fluct = (self.cells)["vel"] * self.info["unit_velocity"].express(
             U.km_s
@@ -774,7 +774,7 @@ class PostProcessor(HDF5Container):
 
     def cos_vfluct_B(self):
         "return the cos of the angle between the magnetic field and the velocity fluctuation field"
-        mean_speed = self.save.get_node("/globals/mwa_speed").read()
+        mean_speed = self.get_value("/globals/mwa_speed")
 
         def getter_cos_vfluct_B(dset):
             vel_fluct = dset["vel"] - mean_speed
@@ -787,7 +787,7 @@ class PostProcessor(HDF5Container):
         return self._vol_pdf(getter_cos_vfluct_B)
 
     def _mwa_sigma(self, axes=["x", "y", "z"]):
-        mw_speed = self.save.get_node("/globals/mwa_speed").read()
+        mw_speed = self.get_value("/globals/mwa_speed")
 
         if axes == ["x", "y", "z"]:
 
@@ -852,7 +852,7 @@ class PostProcessor(HDF5Container):
     def _temperature(self, ax_los, z=0.0):
         P_op = ScalarOperator(lambda dset: dset["P"], self._ro.info["unit_pressure"])
         dmap_P = (slicing.SliceMap(self._amr, self._cam[ax_los], P_op, z=z)).map.T
-        dmap_rho = self.save.get_node("/maps/slice_rho_{}".format(ax_los)).read()
+        dmap_rho = self.get_value("/maps/slice_rho_{}".format(ax_los))
         return dmap_P / dmap_rho
 
     def _levels(self, ax_los):
@@ -865,14 +865,14 @@ class PostProcessor(HDF5Container):
         return datamap.map.T
 
     def _jeans(self, ax_los):
-        dmap_T = self.save.get_node("/maps/T_" + ax_los).read()
-        dmap_rho = self.save.get_node("/maps/slice_rho_" + ax_los).read()
+        dmap_T = self.get_value("/maps/T_" + ax_los)
+        dmap_rho = self.get_value("/maps/slice_rho_" + ax_los)
         dmap_jeans = np.sqrt(np.pi * dmap_T / dmap_rho)
         return dmap_jeans
 
     def _jeans_ratio(self, ax_los):
-        dmap_jeans = self.save.get_node("/maps/jeans_" + ax_los).read()
-        dmap_levels = self.save.get_node("/maps/levels_" + ax_los).read()
+        dmap_jeans = self.get_value("/maps/jeans_" + ax_los)
+        dmap_levels = self.get_value("/maps/levels_" + ax_los)
         dmap_jeans_ratio = dmap_jeans * 2 ** (dmap_levels)
         return dmap_jeans_ratio
 
@@ -989,7 +989,7 @@ class PostProcessor(HDF5Container):
         return rad_bins
 
     def _radial_centers(self, ax_los="z"):
-        radial_bins = self.save.get_node("/radial/radial_bins_" + ax_los).read()
+        radial_bins = self.get_value("/radial/radial_bins_" + ax_los)
         bin_centers = 0.5 * (radial_bins[1:] + radial_bins[:-1])
         return bin_centers
 
@@ -1016,8 +1016,8 @@ class PostProcessor(HDF5Container):
         return rr
 
     def _bins_on_map(self, ax_los="z"):
-        rad_bins = self.save.get_node("/radial/radial_bins_" + ax_los).read()
-        rr = self.save.get_node("/maps/rr_" + ax_los).read()
+        rad_bins = self.get_value("/radial/radial_bins_" + ax_los)
+        rr = self.get_value("/maps/rr_" + ax_los)
 
         # Find appropriate bin for each coordinate set
         bins = np.zeros(rr.shape, dtype=int)
@@ -1080,7 +1080,7 @@ class PostProcessor(HDF5Container):
 
     def _fluct_map(self, name, ax_los="z", mass_weighted=False):
 
-        dmap = self.save.get_node("/maps/" + name + "_" + ax_los).read()
+        dmap = self.get_value("/maps/" + name + "_" + ax_los)
         if mass_weighted:
             avg_map = self.get_value("/maps/mwavg_map_" + name + "_" + ax_los)
         else:
@@ -1147,8 +1147,8 @@ class PostProcessor(HDF5Container):
         return np.stack([values, centers])
 
     def _fit_pdf(self, name, ax_los="z"):
-        pdf = self.save.get_node("/hist/pdf_" + name + "_" + ax_los)
-        values, centers = pdf.read()
+        pdf = self.get_value("/hist/pdf_" + name + "_" + ax_los)
+        values, centers = pdf
         mask_fit = (
             (centers > self.pp_params.pdf.xmin_fit)
             & (centers < self.pp_params.pdf.xmax_fit)
@@ -1171,15 +1171,13 @@ class PostProcessor(HDF5Container):
 
         # Mean part
 
-        T_avg = self.save.get_node("/maps/avg_map_T_mwavg_z").read()
+        T_avg = self.get_value("/maps/avg_map_T_mwavg_z")
 
-        radial_bins = self.save.get_node("/radial/radial_bins_" + ax_los).read()
-        mean_bin_vr = self.save.get_node(
-            "/radial/rad_avg_" + "slice_velr" + "_" + ax_los
-        ).read()
-        mean_bin_vphi = self.save.get_node(
+        radial_bins = self.get_value("/radial/radial_bins_" + ax_los)
+        mean_bin_vr = self.get_value("/radial/rad_avg_" + "slice_velr" + "_" + ax_los)
+        mean_bin_vphi = self.get_value(
             "/radial/rad_avg_" + "slice_velphi" + "_" + ax_los
-        ).read()
+        )
         mean_bin_vr = np.concatenate((mean_bin_vr, [mean_bin_vr[-1]]))
         mean_bin_vphi = np.concatenate((mean_bin_vphi, [mean_bin_vr[-1]]))
 
@@ -1223,8 +1221,8 @@ class PostProcessor(HDF5Container):
         "Map of the gravitational contribution to the Shakura&Sunaev alpha parameter for disks"
         assert ax_los == "z"
 
-        T_avg = self.save.get_node("/maps/avg_map_T_mwavg_z").read()
-        coldens = self.save.get_node("/maps/avg_map_coldens_z").read()
+        T_avg = self.get_value("/maps/avg_map_T_mwavg_z")
+        coldens = self.get_value("/maps/avg_map_coldens_z")
 
         def getter_alpha_grav(dset):
             r2 = np.sum((self.lbox * self.oct_getter_pos_disk(dset)) ** 2, axis=2)
@@ -1284,7 +1282,7 @@ class PostProcessor(HDF5Container):
     def _pspec(self, **kwargs):
         outfile = self.pspec_filename
         pspec_new.pspec(repo=self.path, iouts=[self.num], outfile=outfile, **kwargs)
-        return True
+        return np.array([self.pspec_filename])
 
     def _particles(self):
         """Ensure particles are written in the hdf5 file"""
@@ -1303,7 +1301,7 @@ class PostProcessor(HDF5Container):
         branch_thresh = self.pp_params.filaments.branch_thresh
         glob_thresh = self.pp_params.filaments.glob_thresh
 
-        datamap = self.save.get_node("/maps/" + datamap_name + "_z").read()
+        datamap = self.get_value("/maps/" + datamap_name + "_z")
         shape = datamap.shape
         x = np.arange(shape[0]) - shape[0] / 2
         y = np.arange(shape[1]) - shape[1] / 2