Comodo metadata (#39)

* fixed swap_dims

* whats new update

doc/development.rst

@@ -4,6 +4,10 @@ Development
 Release History
 ---------------
 
+v.0.3.0 (???)
+~~~~~~~~~~~~~
+  - Fix to keep proper Comodo metadata when swapping dimensions.
+
 v0.2.0 (2017-02-14)
 ~~~~~~~~~~~~~~~~~~~~
 

xmitgcm/mds_store.py

@@ -226,8 +226,7 @@ def _set_coords(ds):
 def _swap_dimensions(ds, geometry, drop_old=True):
     """Replace logical coordinates with physical ones. Does not work for llc.
     """
-    # TODO: handle metadata correctly such that the new dimension attributes
-    # still conform to comodo conventions
+    keep_attrs = ['axis', 'c_grid_axis_shift']
 
     # this fixes problems
     ds = ds.reset_coords()
@@ -246,6 +245,9 @@ def _swap_dimensions(ds, geometry, drop_old=True):
                     # take the first row / column
                     coord_var = coord_var.isel(**{coord_dim: 0}).drop(coord_dim)
             ds[new_dim] = coord_var
+            for key in keep_attrs:
+                if key in ds[orig_dim].attrs:
+                    ds[new_dim].attrs[key] = ds[orig_dim].attrs[key]
     # then swap dims
     for orig_dim in ds.dims:
         if 'swap_dim' in ds[orig_dim].attrs:

xmitgcm/test/test_mds_store.py

@@ -389,6 +389,17 @@ def test_open_mdsdataset_minimal(all_mds_datadirs):
     ds_expected = xr.Dataset(coords=coords)
     assert ds_expected.equals(ds)
 
+    # check for comodo metadata needed by xgcm
+    assert ds['i'].attrs['axis'] == 'X'
+    assert ds['i_g'].attrs['axis'] == 'X'
+    assert ds['i_g'].attrs['c_grid_axis_shift'] == -0.5
+    assert ds['j'].attrs['axis'] == 'Y'
+    assert ds['j_g'].attrs['axis'] == 'Y'
+    assert ds['j_g'].attrs['c_grid_axis_shift'] == -0.5
+    assert ds['k'].attrs['axis'] == 'Z'
+    assert ds['k_l'].attrs['axis'] == 'Z'
+    assert ds['k_l'].attrs['c_grid_axis_shift'] == -0.5
+
 def test_read_grid(all_mds_datadirs):
     """Make sure we read all the grid variables."""
     dirname, expected = all_mds_datadirs
@@ -508,6 +519,17 @@ def test_swap_dims(all_mds_datadirs):
                     grid_vars_to_coords=True)
 
 
+        # check for comodo metadata needed by xgcm
+        assert ds['XC'].attrs['axis'] == 'X'
+        assert ds['XG'].attrs['axis'] == 'X'
+        assert ds['XG'].attrs['c_grid_axis_shift'] == -0.5
+        assert ds['YC'].attrs['axis'] == 'Y'
+        assert ds['YG'].attrs['axis'] == 'Y'
+        assert ds['YG'].attrs['c_grid_axis_shift'] == -0.5
+        assert ds['Z'].attrs['axis'] == 'Z'
+        assert ds['Zl'].attrs['axis'] == 'Z'
+        assert ds['Zl'].attrs['c_grid_axis_shift'] == -0.5
+
         # add extra layers dimensions if needed
         if 'layers' in expected:
             for layer_name in expected['layers']:

xmitgcm/variables.py

@@ -48,11 +48,11 @@
     k_u = dict(dims=['k_u'], attrs=dict(
                 standard_name="z_grid_index_at_lower_w_location",
                 axis="Z", long_name="z-dimension of the w grid",
-                c_grid_axis_shift=-0.5, swap_dim='Zu')),
+                c_grid_axis_shift=0.5, swap_dim='Zu')),
     k_l = dict(dims=['k_l'], attrs=dict(
                 standard_name="z_grid_index_at_upper_w_location",
                 axis="Z", long_name="z-dimension of the w grid",
-                c_grid_axis_shift=0.5, swap_dim='Zl')),
+                c_grid_axis_shift=-0.5, swap_dim='Zl')),
     # this is complicated because it is offset in both directions - allowed by comodo?
     k_p1 = dict(dims=['k_p1'], attrs=dict(
                 standard_name="z_grid_index_at_w_location",
@@ -384,7 +384,7 @@
        attrs=dict(standard_name='%s_concentration' % trname,
                   long_name="Concentration of %s" % trname,
                   units="kg m-3")
-   ) 
+   )
 
 
 # these aliases are necessary to deal with the LLC output which was saved with