Fix box limits when calling athena reader, fix data ordering for Athena

AHFpy/data.py

@@ -207,36 +207,15 @@ def read_h5_dset_athena(fname, data_sym = None,
     if initial_radius == None:
         data_ath = athdf(fname, num_ghost = num_ghost, vertex_centered = True, dtype = np.float64, level = level)
     else:
-        data_ath = athdf(fname, num_ghost = num_ghost, vertex_centered = True, dtype = np.float64, level = level, x1_max = initial_radius, x2_max = initial_radius, x3_max = initial_radius)
+        data_ath = athdf(fname, num_ghost = num_ghost, vertex_centered = True, dtype = np.float64, level = level, x1_max = initial_radius, x2_max = initial_radius, x3_max = initial_radius, x1_min = -initial_radius, x2_min = -initial_radius, x3_min = -initial_radius)
     data['time'] = data_ath["Time"]
     data['coord_x'] = data_ath["x1f"][0:-1]
     data['coord_y'] = data_ath["x2f"][0:-1]
     data['coord_z'] = data_ath["x3f"][0:-1]
     
     for fi in fields:
-        data[fi]     = data_ath["adm.{}".format(fi)]
-    print( np.shape(data['coord_x']) )
-    print( np.shape(data[fi]) )
-    #if data_sym == 'octant':
-    #    x_aux = np.zeros((len(data['coord_x'])*2 - 1))
-    #    y_aux = np.zeros((len(data['coord_y'])*2 - 1))
-    #    z_aux = np.zeros((len(data['coord_z'])*2 - 1))
-
-    #    (nx, ny, nz) = (len(x_aux), len(y_aux), len(z_aux))
-
-    #    x_aux[0:nx//2+1] = -data['coord_x'][::-1]
-    #    y_aux[0:ny//2+1] = -data['coord_y'][::-1]
-    #    z_aux[0:nz//2+1] = -data['coord_z'][::-1]
-    #    x_aux[nx//2::] = data['coord_x']
-    #    y_aux[ny//2::] = data['coord_y']
-    #    z_aux[nz//2::] = data['coord_z']
-    #    data['coord_x'] = x_aux
-    #    data['coord_y'] = y_aux
-    #    data['coord_z'] = z_aux
-    #for fi in fields:
-    #    data[fi]     = data_ath["adm.{}".format(fi)]
-    #    if data_sym == "octant":
-    #        data[fi] = octant_to_full(data[fi])
+        ## Swap axes because Athena output is zyx. 'C' order after that for Cython
+        data[fi] = np.swapaxes(data_ath["adm.{}".format(fi)], 0, 2).copy(order='C')
     return data