fix for 2d diagnostics llc bug (#146)

* fix for 2d diags issue

* remove comment

* remove old numpy env from ci

.travis.yml

@@ -13,8 +13,6 @@ matrix:
     env: CONDA_ENV=py27-xarray0.10.9
   - python: 2.7
     env: CONDA_ENV=py27-xarray0.11.3
-  - python: 2.7
-    env: CONDA_ENV=py27-numpy1.11.1
   - python: 3.5
     env: CONDA_ENV=py35
   - python: 3.6

xmitgcm/mds_store.py

@@ -660,11 +660,14 @@ def load_from_prefix(self, prefix, iternum=None, extra_metadata=None):
             # How should we handle this? Can either eliminate one of the dims
             # or add an extra axis to the data. Let's try the former, on the
             # grounds that it is simpler for the user.
-            if len(dims) == 3 and data.ndim == 2:
+            if ((len(dims) == 3 and data.ndim == 2) or
+                (self.llc and (len(dims) == 3 and data.ndim == 3))):
                 # Deleting the first dimension (z) assumes that 2D data always
                 # corresponds to x,y horizontal data. Is this really true?
                 # The answer appears to be yes: 2D (x|y,z) data retains the
                 # missing dimension as an axis of length 1.
+                # Also handles https://github.com/xgcm/xmitgcm/issues/140
+                # (special case for 2d llc diags)
                 dims = dims[1:]
             elif len(dims) == 1 and data.ndim > 1:
                 # this is for certain profile data like RC, PHrefC, etc.
@@ -928,5 +931,5 @@ def _reshape_for_llc(dims, data):
             # add face dimension to dims
             jdim = dims.index(dim)
             dims.insert(jdim, LLC_FACE_DIMNAME)
-            assert data.ndim==len(dims)
+    assert data.ndim==len(dims), '%r %r' % (data.shape, dims)
     return dims, data

xmitgcm/test/test_mds_store.py

@@ -3,6 +3,7 @@
 import xarray as xr
 from glob import glob
 from shutil import copyfile
+import py
 
 _TESTDATA_FILENAME = 'testdata.tar.gz'
 _TESTDATA_ITERS = [39600, ]
@@ -194,6 +195,39 @@ def test_open_dataset_no_meta(all_mds_datadirs):
             ds = xmitgcm.open_mdsdataset(dirname, prefix=['T', 'Eta'],
                                          nz=nz, **kwargs)
 
+def test_open_dataset_2D_diags(all_mds_datadirs):
+    # convert 3D fields with only 2D diagnostic output
+    # https://github.com/xgcm/xmitgcm/issues/140
+    dirname, expected = all_mds_datadirs
+
+    shape = expected['shape']
+
+    nz = shape[0]
+    ny, nx = shape[-2:]
+    shape_2d = shape[1:]
+    dims_2d = ('j', 'i')
+    if expected['geometry']=='llc':
+        dims_2d = ('face',) + dims_2d
+        ny = nx*shape[-3]
+    dims_3d = dims_2d if nz==1 else ('k',) + dims_2d
+    dims_2d = ('time',) + dims_2d
+    dims_3d = ('time',) + dims_3d
+
+    it = expected['test_iternum']
+    kwargs = dict(iters=it, geometry=expected['geometry'], read_grid=False,
+                  swap_dims=False)
+
+    to_hide = ['T.%010d.meta' % it, 'T.%010d.data' % it]
+    with hide_file(dirname, *to_hide):
+
+        ldir = py.path.local(dirname)
+        old_prefix = 'Eta.%010d' % it
+        new_prefix = 'T.%010d' % it
+        for suffix in ['.data', '.meta']:
+            lp = ldir.join(old_prefix + suffix)
+            lp.copy(ldir.join(new_prefix + suffix))
+
+        ds = xmitgcm.open_mdsdataset(dirname, prefix=['T'], **kwargs)
 
 def test_swap_dims(all_mds_datadirs):
     """See if we can swap dimensions."""