[plotter] [postprocessor] make particles scatter actually work

plotter.py

@@ -695,9 +695,10 @@ class Plotter(Aggregator, BaseProcessor):
         """
 
         # Open particle HDF5 file
-        filename = self.save.get_node("/hdf5/particles").read()
+        filename = self.save.get_node("/hdf5/particles").read()[0].decode()
-        hdf5_parts = tables.open(filename, "r")
+        hdf5_parts = tables.open_file(filename, "r")
         part_pos = hdf5_parts.get_node("/data/pos").read()
+        hdf5_parts.close()
 
         # index of the horizontal axis
         ih = self._ax_nb[self._axes_h[ax_los]]
@@ -713,7 +714,7 @@ class Plotter(Aggregator, BaseProcessor):
         part_v = im_extent[2] + (im_extent[3] - im_extent[2]) * part_v
 
         # Scatter plot
-        plt.scatter(part_h, part_v)
+        plt.scatter(part_h, part_v, **kwargs)
 
     def _overlay_speed(
         self, ax_los, im_extent, unit=U.km_s, unit_coeff=1.0, key_v=None, **kwargs

postprocessor.py

@@ -183,6 +183,7 @@ class PostProcessor(HDF5Container):
     G = 1.0  # Gravitational constant
 
     cells_loaded = False
+    parts_loaded = False
 
     def __init__(
         self,
@@ -241,7 +242,7 @@ class PostProcessor(HDF5Container):
             verbose=self.pp_params.pymses.verbose,
         )
         self._amr = self._ro.amr_source(self.pp_params.pymses.variables)
-        self._part = self._ro.part_source(["vel", "mass"])
+        self._part = self._ro.particle_source(["vel", "mass"])
 
         if self.pp_params.pymses.filter:
             self.min_coords = np.array(self.pp_params.pymses.min_coords)
@@ -358,14 +359,14 @@ class PostProcessor(HDF5Container):
         Load data from the source file in the memory.
         (Long and memory heavy)
         """
-        if not self.part_loaded:
+        if not self.parts_loaded:
             if os.path.exists(filename):
                 hdf5 = tables.open_file(filename, mode="r")
                 try:
                     node = hdf5.get_node("/data")
                     data = {}
                     for key in node._v_children:
-                        self.part[key] = hdf5.get_node("/data/" + key).read()
+                        data[key] = hdf5.get_node("/data/" + key).read()
                 finally:
                     hdf5.close()
             else:
@@ -373,7 +374,10 @@ class PostProcessor(HDF5Container):
                 data = {}
                 for key in data_pymses.fields:
                     data[key] = data_pymses[key]
+                try:
                     data["dx"] = data_pymses.get_sizes()
+                except AttributeError:
+                    pass
                 data["pos"] = data_pymses.points
 
                 if save:
@@ -1164,7 +1168,7 @@ class PostProcessor(HDF5Container):
         """Ensure particles are written in the hdf5 file"""
         self.load_parts()
         self.unload_parts()
-        return self.parts_filename
+        return np.array([self.parts_filename])
 
     def _filaments(self):
 

pp_params.yml

@@ -89,7 +89,7 @@ process: # General setting of the post-processor module
     verbose : False                    # Give more infos on what is going on
     num_process : 1                    # Number of forks
     save_cells : True                  # Save cells structure on disk
-    save_particles : True              # Save particles on disk
+    save_parts : True                  # Save particles on disk
     unload_cells : True                # Save memory usage
 
 rules: # Specific rules parameters