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Notes on implementation; scoping compared to draft conformance rules and ugrid-checks #17

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Notes on implementation; scoping compared to draft conformance rules and ugrid-checks #17

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Notes on implementation; scoping compared to draft conformance rules …
pp-mo Apr 21, 2022
08b3ce4
Oddity in dimension checking.
pp-mo Apr 22, 2022
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63 changes: 61 additions & 2 deletions cc_plugin_ugrid/checker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ def _check1_topology_dim(self, mesh):
if not self.meshes[mesh]['topology_dimension']:
m = 'Mesh does not contain the required attribute "topology_dimension"'
messages.append(m)
# PP: "R103" [email protected] check.py::L635

try:
assert self.meshes[mesh]['topology_dimension'] in [1, 2, 3]
Expand All @@ -44,6 +45,8 @@ def _check1_topology_dim(self, mesh):
self.meshes[mesh]['topology_dimension'],
type(self.meshes[mesh]['topology_dimension']))
messages.append(m)
# PP: "R104" [email protected] check.py::L646
# ***BUT ALSO*** ugrid-checks allows =0, rejects=3
else:
score += 1

Expand Down Expand Up @@ -82,6 +85,8 @@ def _check2_connectivity_attrs(self, mesh):
m = 'Mesh does not contain the required attribute "topology_dimension",'+\
' therefore any defined connectivity cannot be verified'
messages.append(m)
# PP: "R104" [email protected] check.py::L646
# ***NOTE*** this test is repeated, also occurs above, L038
out_of += 1
return self.make_result(level, score, out_of, desc, messages)

Expand All @@ -93,6 +98,10 @@ def _check2_connectivity_attrs(self, mesh):
if (not self.meshes[mesh][_conn]) and (self.meshes[mesh]['topology_dimension'] == _dim):
out_of += 1 # increment out_of, do not increment score
m = 'dataset is {}D, so must have "{}"'.format(_dim, _conn)
# PP: various, [email protected] ...
# @@ (_dim=1, _conn=edge_node) : "R112" check.py:L675
# @@ (_dim=2, _conn=face_node) : "R113" check.py:L681
# @@ (_dim=3, _conn=volume_node) : ==UNSUPPORTED==
return self.make_result(level, score, out_of, desc, messages)

# now we test individual connectivities -- here we will be incrementing the score
Expand All @@ -106,6 +115,9 @@ def _check2_connectivity_attrs(self, mesh):
# required per the standard and we want to check it exists
if order == 'nonstd':
self.__check_nonstd_order_dims__(mesh, _conn)
# PP: ???the result is discarded???
# it returns a Result object
# (which presumably may be "empty" ???)

if valid:
score += 1
Expand All @@ -115,6 +127,7 @@ def _check2_connectivity_attrs(self, mesh):

# check for optional attributes edge[face][volume]_coordinates
self.__check_edge_face_coords__(mesh, _conn)
# PP: result is ignored !!

return self.make_result(level, score, out_of, desc, messages)

Expand All @@ -135,7 +148,6 @@ def _check3_ncoords_exist(self, mesh):
Additionally, all node coordinates specified in a mesh must be defined
as variables in the dataset.
"""

level = BaseCheck.HIGH
score = 0
out_of = 0
Expand All @@ -146,13 +158,16 @@ def _check3_ncoords_exist(self, mesh):
self.meshes[mesh]['node_coordinates'] = []
if not self.meshes[mesh].get('topology_dimension'):
msg = 'Failed because no topology dimension exists'
# PP: "R104" [email protected] check.py::L646
# ***NOTE*** this test is repeated, also occurs above, L038, L164
messages.append(msg)
out_of += 1
return self.make_result(level, score, out_of, desc, messages)
else:
try:
ncoords = mesh.node_coordinates.split(' ')
assert len(ncoords) == self.meshes[mesh].get('topology_dimension')
# PP: not necessarily required ?? : see below ...
for nc in ncoords:
try:
out_of += 1
Expand All @@ -161,14 +176,27 @@ def _check3_ncoords_exist(self, mesh):
score += 1
except AssertionError:
msg = 'Node coordinate "{}" in mesh but not in variables'.format(nc)
# PP: "R108" [email protected] check.py::L714
# *and* one of "R105" (invalid) / "R106" (absent var)
# -> [email protected] check.py::L164/173
messages.append(msg)
except AttributeError:
msg = 'This mesh has no node coordinate variables'
# PP: "R108" [email protected] check.py::L714
# *and* "R105" [email protected] check.py::L151
out_of += 1
messages.append(msg)
except AssertionError:
msg = 'The size of mesh\'s node coordinates does not match' +\
' the topology dimension ({})'.format(self.meshes[mesh].get('topology_dimension'))
# from above, L168
# len(ncoords) == self.meshes[mesh].get('topology_dimension')
# PP: "A mesh must have node coordinates the same length as the
# value for mesh's topology dimension."
# ***This is not really true***. E.G. can have x,y,z coords
# defining the points of a 1D or 2D mesh.
# Also, in the message "size of mesh\'s node coordinates", the
# term "size" is very confusing
out_of += 1
messages.append(msg)

Expand Down Expand Up @@ -207,7 +235,14 @@ def _check4_edge_face_conn(self, mesh):
try:
dim1, dim2 = self.ds.variables[efc].shape # unpack the tuple
assert dim1 == self.meshes[mesh]['nedges'].size # compare to nedges
# PP: "R304/305/306/307" [email protected] check.py::L442
# PP: ugrid-checks checks the dims of the variable, **not** the
# shape - so it insists that it use the "correct" dim,
# NOT just one of the right size.
# PP: NOTE - the draft conformance, and ugrid-checks, actually
# allow these dims to be swapped -- might be a mistake ...
assert dim2 == 2 # should be equal to 2
# PP: "R308" [email protected] check.py::L485
score += 1
except AssertionError:
messages.append('Incorrect shape ({}, {}) of edge_face_connectivity array'.format(dim1, dim2))
Expand Down Expand Up @@ -320,6 +355,8 @@ def yield_checks(self):


def __check_edge_face_coords__(self, mesh, cty):
# PP: the whole of this is pointless,
# because when called the result is discarded : see above, L129
"""
Check the edge[face] coordinates of a given mesh.

Expand Down Expand Up @@ -349,6 +386,7 @@ def __check_edge_face_coords__(self, mesh, cty):
messages = []
desc = 'Edge coordinates point to aux coordinate variables representing' +\
' locations of edges (usually midpoint)'
# PP: test name "desc" needs generalising to "face or edge"

coordmap = {
'edge_node_connectivity': 'edge_coordinates',
Expand All @@ -359,11 +397,14 @@ def __check_edge_face_coords__(self, mesh, cty):
'edge_coordinates': 'nedges',
'face_coordinates': 'nfaces',
}
# PP: don't get this at all -- seems to require fixed names
# for face/edge dimensions ???

# do(es) the mesh(es) have appropriate connectivity? If not, pass
if (not self.meshes[mesh][cty]):
messages.append('No {}?'.format(cty))
return self.make_result(level, score, out_of, desc, messages)
# PP: in this case, out_of should = 0 ??

# first ensure the _coordinates variable exists
_c = coordmap[cty]
Expand All @@ -372,13 +413,18 @@ def __check_edge_face_coords__(self, mesh, cty):
except AttributeError:
messages.append('Optional attribute, not required')
return self.make_result(level, score, out_of, desc, messages)
# PP: in this case, out_of should = 0 ??

# if it exists, verify its length is equivalent to nedges
try:
for coord in coords.split(' '): # split the string
_coord_len = len(self.ds.variables[coord])
# PP: fails if named vars are missing from dataset ??
_dim_len = len(self.ds.dimensions[varmap[_c]])
# PP: don't get this at all -- seems to require fixed names
# for face/edge dimensions ???
assert _coord_len == _dim_len
# PP: prefer testing var.dimensions over var.shape ??
score += 1
except AssertionError:
m = '{} should have length of {}'.format(_c, varmap[_c])
Expand Down Expand Up @@ -493,10 +539,13 @@ def __check_edge_face_dim__(self, mesh, dim_var):
except AttributeError:
msg = 'Mesh does not contain {}, '.format(dim_var)+\
'required when connectivity in non-standard order.'
# PP: "" [email protected] check.py::L836
return False, msg
except KeyError:
msg = 'Edge dimension defined in mesh, not defined in dataset ' +\
'dimensions'
# PP: message should say "face or edge dimension defined..." ??
# PP: "R115/117" [email protected] check.py::L781
return False, msg


Expand All @@ -522,18 +571,27 @@ def _validate_nc_shape(self, mesh, cty):
assert cty in ['edge_node_connectivity', 'face_node_connectivity', 'volume_node_connectivity']
conn_array_name = mesh.getncattr(cty)
except AssertionError:
# PP: CAN'T happen, given the possible args this is called with
# - see above, L94
return False, None # should never get this, right?
except AttributeError:
return False, None

# use name of array to get that variable from the dataset
_array = self.ds.variables.get(conn_array_name)
# PP: this seems unsafe -- if a connectivity variable specified in
# a mesh does not exist, checker falls over ?!?
# This does NOT happen for coordinates.
# : See cc_plugin_ugrid/tests/checker_test.py:176

_d1name, _d2name = _array.dimensions # tuple of strings
# PP: likewise, unsafe if var doesn't have exactly 2 dims
dim1 = self.ds.dimensions[_d1name] # access the dimension objects
dim2 = self.ds.dimensions[_d2name]

# check against dimensions of dataset
try:
# PP: surely CAN'T fail, as dims came from an actual variable ??
assert dim1.name in self.ds.dimensions.keys()
assert dim2.name in self.ds.dimensions.keys()
except AssertionError:
Expand All @@ -550,6 +608,7 @@ def _validate_nc_shape(self, mesh, cty):
_dim2size = 2
elif cty == 'face_node_connectivity':
_dim1 = 'nfaces'
# PP: does not support quad meshes ???
_dim2size = 3
else:
raise NotImplementedError # haven't dealt with real 3D grids yet
Expand Down
3 changes: 2 additions & 1 deletion cc_plugin_ugrid/tests/checker_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,8 @@ def nc(self, ncpath):
def setUp(self):
"""Method to run before every test"""

dspath = os.path.join(os.getcwd(), 'cc_plugin_ugrid', 'resources', 'ugrid.nc')
# dspath = os.path.join(os.getcwd(), 'cc_plugin_ugrid', 'resources', 'ugrid.nc')
dspath = '/home/h05/itpp/git/ioos_cc-plugin-ugrid/cc_plugin_ugrid/resources/ugrid.nc'
dataset = self.nc(dspath)
self.checker = UgridChecker()
self.checker.setup(dataset) # initializes dict of meshes
Expand Down