Merge branch 'master' into reconnection

python/amun.py

@@ -113,6 +113,9 @@ def amun_attribute(fname, aname):
         ret = np.squeeze(attr).astype(str)
       else:
         ret = np.squeeze(attr)
+    else:
+      print("Attribute '%s' cannot be retrieved from '%s'!" % (aname, fname))
+      ret = False
 
     f.close()
 
@@ -154,6 +157,9 @@ def amun_coordinate(fname, iname):
         ret = np.squeeze(item).astype(str)
       else:
         ret = np.squeeze(item)
+    else:
+      print("Coordinate item '%s' cannot be retrieved from '%s'!" % (iname, fname))
+      ret = False
 
     f.close()
 
@@ -207,13 +213,18 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
     # prepare array to hold data
     #
     ndims = amun_attribute(fname, 'ndims')
-    nb    = amun_attribute(fname, 'ncells')
-    bm    = np.array([nb, nb, nb])
+    nn    = amun_attribute(fname, 'ncells')
+    bm    = np.array([nn, nn, nn])
     if ndims == 2:
       bm[2] = 1
-    rm    = amun_attribute(fname, 'domain_base_dims')
     ng    = amun_attribute(fname, 'nghosts')
     ml    = amun_attribute(fname, 'maxlev')
+    f = h5.File(fname, 'r')
+    if 'rdims' in f['attributes'].attrs:
+      rm    = amun_attribute(fname, 'rdims')
+    else:
+      rm    = amun_attribute(fname, 'domain_base_dims')
+    f.close()
 
     # build the list of supported variables
     #
@@ -225,6 +236,7 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
 
     # add derived variables if possible
     #
+    variables.append('level')
     if 'velx' in variables and 'vely' in variables and 'velz' in variables:
       variables.append('velo')
       variables.append('divv')
@@ -264,12 +276,20 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
       print('The requested variable cannot be extracted from the file datasets!')
       return False
 
-    # check if the shrink parameter is correct
+    # check if the shrink parameter is correct (block dimensions should be
+    # divisible by the shrink factor)
     #
-    sh = bm[0:ndims].min()
-    while(sh > shrink):
-      sh /= 2
-    shrink = int(sh)
+    shrink = max(1, int(shrink))
+    if shrink > 1:
+      if (nn % shrink) != 0:
+        print('The block dimension should be divisible by the shrink factor!')
+        return False
+      sh = shrink
+      while(sh > 2 and sh % 2 == 0):
+        sh = int(sh / 2)
+      if (sh % 2) != 0:
+        print('The shrink factor should be a power of 2!')
+        return False
 
     # prepare dimensions of the output array and allocate it
     #
@@ -292,7 +312,11 @@ def amun_dataset(fname, vname, shrink = 1, progress = False):
         dz     = amun_coordinate(lname, 'dz')
         f = h5.File(lname, 'r')
         g       = f['variables']
-        if vname == 'velo':
+        if vname == 'level':
+          dataset = np.zeros(g[variables[0]].shape)
+          for l in range(dblocks):
+            dataset[:,:,:,l] = levels[l]
+        elif vname == 'velo':
           dataset = np.sqrt(g['velx'][:,:,:,:]**2 \
                           + g['vely'][:,:,:,:]**2 \
                           + g['velz'][:,:,:,:]**2)