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Merge pull request #33 from lewismc/ISSUE-26
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ISSUE-26 Weird error message about missing axis attribute
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@RileyWilliams
RileyWilliams authored Jul 16, 2017
2 parents 60a3e2d + 617769a commit 258436d
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Showing 3 changed files with 42 additions and 51 deletions.
2 changes: 0 additions & 2 deletions pycovjson/cli/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,6 @@ def main():
if interactive:
axis = input('Which Axis?', Reader.get_axis(variable))



if tiled and len(tile_shape) == 0:
reader = Reader(inputfile)
shape_list = reader.get_shape(variable)
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12 changes: 5 additions & 7 deletions pycovjson/read_netcdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -261,8 +261,7 @@ def get_axis(self, variable):
axis = list(map(str.lower, list(axis)))
return axis
except:
print("Error occured: Variable '%s' has no axis attribute" % (variable))
pass
print("Variable '%s' has no axis attribute, executing fallback for manual axis value detection." % (variable))
try:
axes_list = []
axes_dict = self.get_axes()
Expand All @@ -272,10 +271,12 @@ def get_axis(self, variable):
list(axes_dict.values()).index(dim)])

axes_list.append(index)


print("Manually detected axis as: '%s'" % (axes_list))
return axes_list
except:
print('Error in axes_dict')

def get_dims(self, variable):
try:
dims = self.dataset[variable].dims
Expand Down Expand Up @@ -358,16 +359,13 @@ def get_axes(self):
except:
pass

# if coord in x_list or self.dataset[coord].standard_name in x_list: axes_dict['x'] = coord
# if coord in y_list or self.dataset[coord].standard_name in y_list: axes_dict['y'] = coord
try:
if coord in t_list or self.dataset[coord].standard_name in t_list or self.dataset[coord].name in t_list:
axes_dict['t'] = coord
if coord in z_list or self.dataset[coord].standard_name in z_list or self.dataset[coord].name in z_list:
axes_dict['z'] = coord
except:
print("Error: DataArray does not include standard name.")
pass
print("Error: DataArray does not include 'standard name' or 'name'.")

if len(axes_dict) < 2:
print('Error: File does not conform to CF Conventions')
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79 changes: 37 additions & 42 deletions pycovjson/write.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@

from pycovjson.model import *
from pycovjson.model import Coverage, Domain, Parameter, Range, Reference, SpatialReferenceSystem2d, SpatialReferenceSystem3d, TemporalReferenceSystem, TileSet
from pycovjson.read_netcdf import NetCDFReader as Reader
import time
import json
Expand All @@ -20,18 +19,17 @@ def __init__(self, output_name: object, dataset_path: object, vars_to_write: obj
:parameter tile_shape: List containing shape of tiles
"""
self.output_name = output_name
self.dataset_path = dataset_path
self.tile_shape = tile_shape
self.vars_to_write = vars_to_write
self.urlTemplate = 'localhost:8080/{t}.covjson'
self.url_template = 'localhost:8080/{t}.covjson'
self.tiled = tiled
if tiled:
self.range_type = 'TiledNdArray'
else:
self.range_type = 'NdArray'
self.dataset_path = dataset_path
self.Reader = Reader(dataset_path)
self.axis_dict = self.Reader.get_axes()
self.reader = Reader(dataset_path)
self.axis_dict = self.reader.get_axes()
self.axis_list = list(self.axis_dict.keys())
self.ref_list = []
if 't' in self.axis_list and 'z' in self.axis_list:
Expand All @@ -55,7 +53,6 @@ def write(self):
else:
self._save_covjson(coverage, self.output_name)

pass

def _construct_coverage(self):
"""
Expand All @@ -73,18 +70,18 @@ def _construct_domain(self):
"""

domain_type = 'Grid'
x_values = self.Reader.get_x().flatten().tolist()
y_values = self.Reader.get_y().flatten().tolist()
x_values = self.reader.get_x().flatten().tolist()
y_values = self.reader.get_y().flatten().tolist()
t_values = []
z_values = []

if 't' in self.axis_list:

t_values = self.Reader.get_t()
t_values = self.reader.get_t()

if 'z' in self.axis_list:

z_values = self.Reader.get_z().flatten().tolist()
z_values = self.reader.get_z().flatten().tolist()

domain = Domain(domain_type, x_values, y_values, z_values, t_values)

Expand All @@ -96,10 +93,10 @@ def _construct_params(self):
:return: Parameter object
"""
for variable in self.vars_to_write:
description = self.Reader.get_std_name(variable)
unit = self.Reader.get_units(variable)
symbol = self.Reader.dataset[variable].units
label = self.Reader.dataset[variable].long_name
description = self.reader.get_std_name(variable)
unit = self.reader.get_units(variable)
symbol = self.reader.dataset[variable].units
label = self.reader.dataset[variable].long_name
params = Parameter(description=description, variable_name=variable,
symbol=symbol, unit=unit, observed_property=label)

Expand All @@ -120,41 +117,39 @@ def _construct_range(self):
:return: range
"""
for variable in self.vars_to_write:
print("wrote variable:", variable)
print("Constructing Range from variable:", variable)

axis_names = list(map(str.lower, list(self.Reader.get_axis(variable))))
axis_names = list(map(str.lower, list(self.reader.get_axis(variable))))

if self.tiled:
tile_set_obj = TileSet(self.tile_shape, self.urlTemplate)
variable_type = self.Reader.get_type(variable)
variable_shape = self.Reader.get_shape(variable)
variable_type = self.reader.get_type(variable)
variable_shape = self.reader.get_shape(variable)
print('Variable shape:', variable_shape)

count = 0
for tile in tile_set_obj.get_tiles(self.tile_shape, self.Reader.dataset[variable].values):
for tile in tile_set_obj.get_tiles(self.tile_shape, self.reader.dataset[variable].values):
count += 1
range = {'ranges': Range('NdArray', data_type=variable_type, axes=tile[
covrange = {'ranges': Range('NdArray', data_type=variable_type, axes=tile[
1], shape=variable_shape, values=tile[0].flatten().tolist()).to_dict()}
self.save_covjson_range(range, str(count) + '.covjson')
self.save_covjson_range(covrange, str(count) + '.covjson')
url_template = tile_set_obj.generate_url_template(base_url='localhost:8080',
axis_names=['t'])
tileset = TileSet(variable_shape, url_template).create_tileset(self.tile_shape)
# tileset = [{'tileShape': [None, 173, 301],
# 'urlTemplate': 'http://localhost:8080/{t}.covjson'}]

range = Range('TiledNdArray', data_type=variable_type, variable_name=variable,
covrange = Range('TiledNdArray', data_type=variable_type, variable_name=variable,
axes=axis_names, tile_sets=tileset, shape=variable_shape)
return range
return covrange
else:

shape = self.Reader.get_shape(variable)
values = self.Reader.get_values(variable).flatten().tolist()
data_type = self.Reader.get_type(variable)
axes = self.Reader.get_axis(variable)
range = Range(range_type='NdArray', data_type=data_type, values=values, shape=shape,
shape = self.reader.get_shape(variable)
values = self.reader.get_values(variable).flatten().tolist()
data_type = self.reader.get_type(variable)
axes = self.reader.get_axis(variable)
covrange = Range(range_type='NdArray', data_type=data_type, values=values, shape=shape,
variable_name=variable, axes=axis_names)

return range
return covrange

# Adapted from
# https://github.com/the-iea/ecem/blob/master/preprocess/ecem/util.py -
Expand All @@ -167,7 +162,7 @@ def _save_json(self, obj, path, **kw):
jsonstr = json.dumps(obj, fp, cls=CustomEncoder, **kw)
fp.write(jsonstr)
stop = time.clock()
print("Completed in: ", (stop - start), "seconds.")
print("Completed in: '%s' seconds." % (stop - start))

def _save_covjson(self, obj, path):
"""
Expand All @@ -181,9 +176,9 @@ def _save_covjson(self, obj, path):
self.compact(axis, 'values')
for ref in obj['domain']['referencing']:
self.no_indent(ref, 'coordinates')
for range in obj['ranges'].values():
self.no_indent(range, 'axisNames', 'shape')
self.compact(range, 'values')
for covrange in obj['ranges'].values():
self.no_indent(covrange, 'axisNames', 'shape')
self.compact(covrange, 'values')
self.save_json(obj, path, indent=2)

def save_covjson_tiled(self, obj, path):
Expand All @@ -203,17 +198,17 @@ def save_covjson_tiled(self, obj, path):

def save_json(self, obj, path, **kw):
with open(path, 'w') as fp:
print("Converting....")
print("Attempting to write CovJSON manifestation to '%s'" % (path))
start = time.clock()
jsonstr = json.dumps(obj, fp, cls=CustomEncoder, **kw)
jsonstr = json.dumps(obj, cls=CustomEncoder, **kw)
fp.write(jsonstr)
stop = time.clock()
print("Completed in: ", (stop - start), "seconds.")
print("Completed in: '%s' seconds." % (stop - start))

def save_covjson_range(self, obj, path):
for range in obj['ranges'].values():
self.no_indent(range, 'axisNames', 'shape')
self.compact(range, 'values')
for covrange in obj['ranges'].values():
self.no_indent(covrange, 'axisNames', 'shape')
self.compact(covrange, 'values')
self.save_json(obj, path, indent=2)

def compact(self, obj, *names):
Expand Down

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