def test_find_missval():
grid = GridType("my_grid")
assert find_missval(grid) == None
grid.attributes["missing_value"] = np.array([9999])
assert find_missval(grid) == 9999
# _FillValue should take precendence over missing_value
grid.attributes["_FillValue"] = np.array([0])
assert find_missval(grid) == 0
def simple_grid_dataset():
"""
@brief Create a simple dap grid dataset
Just use the pydap interface - passing dicts does not make sense here.
"""
# Convert metadata and data to a dap dataset
ds = DatasetType(name='SimpleGridData')
g = GridType(name='grid')
data = numpy.arange(24.)
data.shape = (4, 2, 3)
# The name in the dictionary must match the name in the basetype
g['a'] = BaseType(name='a',
data=data,
shape=data.shape,
type=Float32,
dimensions=('time', 'x', 'y'))
g['time'] = BaseType(name='time',
data=numpy.arange(4.),
shape=(4, ),
type=Float64)
g['x'] = BaseType(name='x',
data=numpy.arange(2.),
shape=(2, ),
type=Float64)
g['y'] = BaseType(name='y',
data=numpy.arange(3.),
shape=(3, ),
type=Float64)
ds[g.name] = g
return ds
def stream(self):
sz = 10
time = numpy.arange(float(self.index), float(self.index + sz))
self.index += sz
data = numpy.arange(float(sz))
for ind in range(sz):
data[ind] = numpy.random.random()
ds = DatasetType(name='SimpleGridData')
g = GridType(name='Time Series')
# The name in the dictionary must match the name in the basetype
g['timeseries'] = BaseType(name='timeseries',
data=data,
shape=data.shape,
type=Float32,
dimensions=('time'))
g['time'] = BaseType(name='time',
data=time,
shape=(sz, ),
type=Float32)
ds[g.name] = g
msg = dap_tools.ds2dap_msg(ds)
yield self.send(self.deliver, 'data', msg.encode())
def mean(dataset, var, axis=0):
"""Calculate the mean of an array along a given axis.
The input variable should be either a ``GridType`` or ``BaseType``. The
function will return an object of the same type with the mean applied.
"""
if not isinstance(var, (GridType, BaseType)):
raise ConstraintExpressionError(
'Function "mean" should be used on an array or grid.')
axis = int(axis)
dims = tuple(dim for i, dim in enumerate(var.dimensions) if i != axis)
# process basetype
if isinstance(var, BaseType):
return BaseType(name=var.name,
data=np.mean(var.data[:], axis=axis),
dimensions=dims,
attributes=var.attributes)
# process grid
out = GridType(name=var.name, attributes=var.attributes)
out[var.array.name] = BaseType(name=var.array.name,
data=np.mean(var.array.data[:], axis=axis),
dimensions=dims,
attributes=var.array.attributes)
for dim in dims:
out[dim] = BaseType(name=dim,
data=var[dim].data[:],
dimensions=(dim, ),
attributes=var[dim].attributes)
return out
def gridtype_example():
"""Create a simple grid."""
example = GridType("example")
example["a"] = BaseType("a", data=np.arange(30*50).reshape(30, 50))
example["x"] = BaseType("x", data=np.arange(30))
example["y"] = BaseType("y", data=np.arange(50))
return example
def setUp(self):
sz = 12
time = numpy.arange(float(0), float(sz))
data = numpy.arange(float(sz))
for ind in range(sz):
data[ind] = numpy.random.random()
ds = DatasetType(name='SimpleGridData')
g = GridType(name='TimeSeries')
# The name in the dictionary must match the name in the basetype
g['timeseries'] = BaseType(name='timeseries',
data=data,
shape=data.shape,
type=Float32,
dimensions=('time'))
g['time'] = BaseType(name='time',
data=time,
shape=(sz, ),
type=Float32)
ds[g.name] = g
self.ds1 = ds
self.tc = timeseries_consumer.TimeseriesConsumer()
yield self.tc.plc_init()
def setUp(self):
"""Create a simple grid."""
example = GridType("example")
example["a"] = BaseType("a", data=np.arange(30 * 50).reshape(30, 50))
example["x"] = BaseType("x", data=np.arange(30))
example["y"] = BaseType("y", data=np.arange(50))
self.example = example
def grid(self):
"""Parse a DAP grid, returning a ``GridType``."""
grid = GridType('nameless')
self.consume('grid')
self.consume('{')
self.consume('array')
self.consume(':')
array = self.base()
grid[array.name] = array
self.consume('maps')
self.consume(':')
while not self.peek('}'):
var = self.base()
grid[var.name] = var
self.consume('}')
grid.name = quote(self.consume('[^;]+'))
self.consume(';')
return grid
def grid(self):
"""Parse a DAP grid, returning a ``GridType``."""
grid = GridType('nameless')
self.consume('grid')
self.consume('{')
self.consume('array')
self.consume(':')
array = self.base()
grid[array.name] = array
self.consume('maps')
self.consume(':')
while not self.peek('}'):
var = self.base()
grid[var.name] = var
self.consume('}')
grid.name = quote(self.consume('[^;]+'))
self.consume(';')
return grid
def demo_dataset():
"""
@Brief Example methods for creating a dataset
http://pydap.org/developer.html#the-dap-data-model
"""
#Create a dataset object
ds = DatasetType(name='Mine')
#Add Some attributes
ds.attributes['history'] = 'David made a dataset'
ds.attributes['conventions'] = 'OOIs special format'
# Create some data and put it in a variable
varname = 'var1'
data = (1, 2, 3, 4, 5, 8)
shape = (8, )
type = Int32 #
dims = ('time', )
attributes = {'long_name': 'long variable name one'}
ds[varname] = BaseType(name=varname,
data=data,
shape=shape,
dimensions=dims,
type=type,
attributes=attributes)
# Now make a grid data object
g = GridType(name='g')
data = numpy.arange(6.)
data.shape = (2, 3)
# The name in the dictionary must match the name in the basetype
g['a'] = BaseType(name='a',
data=data,
shape=data.shape,
type=Float32,
dimensions=('x', 'y'))
g['x'] = BaseType(name='x',
data=numpy.arange(2.),
shape=(2, ),
type=Float64)
g['y'] = BaseType(name='y',
data=numpy.arange(3.),
shape=(3, ),
type=Float64)
ds[g.name] = g
return ds
def make_grid(self, response, name, data, time_data, attrs, time_attrs,
dims, ttype):
grid = GridType(name=name)
grid[name] = BaseType(name=name,
data=data,
type=ttype,
attributes=attrs,
dimensions=dims,
shape=data.shape)
grid[dims[0]] = BaseType(name=dims[0],
data=time_data,
type=time_data.dtype.char,
attributes=time_attrs,
dimensions=dims,
shape=time_data.shape)
return grid
def __init__(self, filepath):
BaseHandler.__init__(self)
self.filepath = filepath
try:
with netcdf_file(self.filepath, 'r') as source:
self.additional_headers.append(('Last-modified', (formatdate(
time.mktime(time.localtime(
os.stat(filepath)[ST_MTIME]))))))
# shortcuts
vars = source.variables
dims = source.dimensions
# build dataset
name = os.path.split(filepath)[1]
self.dataset = DatasetType(
name, attributes=dict(NC_GLOBAL=attrs(source)))
for dim in dims:
if dims[dim] is None:
self.dataset.attributes['DODS_EXTRA'] = {
'Unlimited_Dimension': dim,
}
break
# add grids
grids = [var for var in vars if var not in dims]
for grid in grids:
self.dataset[grid] = GridType(grid, attrs(vars[grid]))
# add array
self.dataset[grid][grid] = BaseType(
grid, LazyVariable(source, grid, grid, self.filepath),
vars[grid].dimensions, attrs(vars[grid]))
# add maps
for dim in vars[grid].dimensions:
self.dataset[grid][dim] = BaseType(
dim, vars[dim][:], None, attrs(vars[dim]))
# add dims
for dim in dims:
self.dataset[dim] = BaseType(dim, vars[dim][:], None,
attrs(vars[dim]))
except Exception as exc:
raise
message = 'Unable to open file %s: %s' % (filepath, exc)
raise OpenFileError(message)
def add_variables(dataset, h5, level=0):
assert type(h5) in (h5py.File, h5py.Group, h5py.Dataset)
name = h5.name.lstrip('/')
attrs = process_attrs(h5.attrs)
# struct
if type(h5) in (h5py.File, h5py.Group):
foo = StructureType(name, attributes=attrs)
name = foo.name
dataset[name] = foo
for bar in h5.values():
add_variables(dataset[name], bar, level + 1)
return
# Recursion base cases
rank = len(h5.shape)
# basetype
if rank == 0:
dataset[name] = BaseType(name,
data=Hdf5Data(h5),
dimensions=(),
attributes=attrs)
# sequence?
#elif rank == 1:
# dataset[name] = SequenceType(name, data=h5, attributes=h5.attrs)
# grid
elif is_gridded(h5):
parent = dataset[name] = GridType(name, attributes=attrs)
dims = tuple([d.values()[0].name.lstrip('/') for d in h5.dims])
logger.debug("DIMENSIONS: {}".format(dims))
parent[name] = BaseType(
name, data=Hdf5Data(h5), dimensions=dims,
attributes=attrs) # Add the main variable
for dim in h5.dims: # and all of the dimensions
add_variables(
parent, dim[0], level +
1) # Why would dims have more than one h5py.Dataset?
# BaseType
else:
dataset[name] = BaseType(name,
data=Hdf5Data(h5),
attributes=attrs)
def handle_dds(self, coverage, dataset, fields):
cov = coverage
try:
time_name = coverage.temporal_parameter_name
time_context = coverage.get_parameter_context(time_name)
time_attrs = self.get_attrs(cov, time_name)
time_base = BaseType(time_name,
type=self.dap_type(time_context),
attributes=time_attrs,
dimensions=(time_name, ),
shape=(coverage.num_timesteps, ))
dataset[time_name] = time_base
except:
log.exception('Problem reading cov %s', str(cov))
raise # Can't do much without time
for var in fields:
while var:
name, slice_ = var.pop(0)
name = urllib.unquote(name)
if name == time_name:
continue # Already added to the dataset
try:
grid = GridType(name=name)
context = coverage.get_parameter_context(name)
attrs = self.get_attrs(cov, name)
grid[name] = BaseType(name=name,
type=self.dap_type(context),
attributes=attrs,
dimensions=(time_name, ),
shape=(coverage.num_timesteps, ))
grid[cov.temporal_parameter_name] = time_base
dataset[name] = grid
except Exception:
log.exception('Problem reading cov %s', str(cov))
continue
return dataset
("float", 1000.0),
]))
SimpleStructure['types']['b'] = BaseType('b', np.array(0, np.byte))
SimpleStructure['types']['i32'] = BaseType('i32', np.array(1, np.int32))
SimpleStructure['types']['ui32'] = BaseType('ui32', np.array(0, np.uint32))
SimpleStructure['types']['i16'] = BaseType('i16', np.array(0, np.int16))
SimpleStructure['types']['ui16'] = BaseType('ui16', np.array(0, np.uint16))
SimpleStructure['types']['f32'] = BaseType('f32', np.array(0.0, np.float32))
SimpleStructure['types']['f64'] = BaseType('f64', np.array(1000., np.float64))
SimpleStructure['types']['s'] = BaseType(
's', np.array("This is a data test string (pass 0)."))
SimpleStructure['types']['u'] = BaseType('u', np.array("http://www.dods.org"))
# test grid
rain = DatasetType('test')
rain['rain'] = GridType('rain')
rain['rain']['rain'] = BaseType('rain',
np.arange(6).reshape(2, 3),
dimensions=('y', 'x'))
rain['rain']['x'] = BaseType('x', np.arange(3), units='degrees_east')
rain['rain']['y'] = BaseType('y', np.arange(2), units='degrees_north')
# test for ``bounds`` function
bounds = DatasetType('test')
bounds['sequence'] = SequenceType('sequence')
bounds['sequence']['lon'] = BaseType('lon', axis='X')
bounds['sequence']['lat'] = BaseType('lat', axis='Y')
bounds['sequence']['depth'] = BaseType('depth', axis='Z')
bounds['sequence']['time'] = BaseType('time',
axis='T',
units="days since 1970-01-01")
SimpleStructure['types']['ub'] = BaseType('ub', np.array(10, np.ubyte))
SimpleStructure['types']['i32'] = BaseType('i32', np.array(-10, np.int32))
SimpleStructure['types']['ui32'] = BaseType('ui32', np.array(10, np.uint32))
SimpleStructure['types']['i16'] = BaseType('i16', np.array(-10, np.int16))
SimpleStructure['types']['ui16'] = BaseType('ui16', np.array(10, np.uint16))
SimpleStructure['types']['f32'] = BaseType('f32', np.array(100.0, np.float32))
SimpleStructure['types']['f64'] = BaseType('f64', np.array(1000., np.float64))
SimpleStructure['types']['s'] = BaseType(
's', np.array("This is a data test string (pass 0)."))
SimpleStructure['types']['u'] = BaseType('u', np.array("http://www.dods.org"))
SimpleStructure['types']['U'] = BaseType('U',
np.array(u"test unicode", np.unicode))
# test grid
rain = DatasetType('test')
rain['rain'] = GridType('rain')
rain['rain']['rain'] = BaseType('rain',
np.arange(6).reshape(2, 3),
dimensions=('y', 'x'))
rain['rain']['x'] = BaseType('x', np.arange(3), units='degrees_east')
rain['rain']['y'] = BaseType('y', np.arange(2), units='degrees_north')
# test for ``bounds`` function
bounds = DatasetType('test')
bounds['sequence'] = SequenceType('sequence')
bounds['sequence']['lon'] = BaseType('lon', axis='X')
bounds['sequence']['lat'] = BaseType('lat', axis='Y')
bounds['sequence']['depth'] = BaseType('depth', axis='Z')
bounds['sequence']['time'] = BaseType('time',
axis='T',
units="days since 1970-01-01")
def dataset_from_str(name,
buffer_str,
mtime,
directory='.',
buffer_cache={},
dataset_cache={},
mtimes={},
known_infiles={}):
from fstd2nc import Buffer
from fstd2nc.mixins import _var_type, _axis_type, _dim_type
from pydap.model import DatasetType, GridType, BaseType
from os.path import basename, getmtime
import numpy as np
from collections import OrderedDict
from datetime import datetime
from argparse import ArgumentParser
from os import chdir, path
import shlex
from glob import glob
# Set the directory (to properly evaluate relative paths).
chdir(directory)
# Parse the arguments from the string.
parser = ArgumentParser()
parser.add_argument('infile', nargs='+')
Buffer._cmdline_args(parser)
buffer_args = shlex.split(buffer_str)
buffer_args = parser.parse_args(buffer_args)
buffer_args = vars(buffer_args)
infiles = buffer_args.pop('infile')
# Apply wildcard expansion to filenames.
infiles = [
f for filepattern in infiles
for f in sorted(glob(filepattern)) or [filepattern]
]
# Make sure the filenames are strings (not unicode).
infiles = list(map(str, infiles))
# Look at modification times of individual files.
mtime = max(map(getmtime, infiles))
# Return a cached version of the dataset if nothing about the file(s) have
# changed since last time.
if name in dataset_cache and mtime <= mtimes[name] and known_infiles[
name] == infiles:
return dataset_cache[name]
mtimes[name] = mtime
known_infiles[name] = infiles
# Construct an fstd2nc Buffer object with the decoded FST data.
buf = Buffer(infiles, **buffer_args)
# Save a reference to the Buffer so the file reference(s) remain valid.
buffer_cache[name] = buf
# Get global metadata.
global_metadata = buf._metadata.get('global', {})
# Add history to global metadata.
timestamp = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
history = timestamp + ": %s via Pydap+fstd2dap" % path.basename(name)
global_metadata = {"history": history}
# Construct a pydap Dataset object.
dataset = DatasetType(name=path.basename(name),
attributes=dict(NC_GLOBAL=global_metadata))
# Save this so it can be immediately returned next time it's requested.
dataset_cache[name] = dataset
# Split into vars / dims.
buf = list(buf)
variables = OrderedDict((var.name, var) for var in buf
if not isinstance(var, (_axis_type, _dim_type)))
dims = OrderedDict((var.name, var) for var in buf
if isinstance(var, (_axis_type, _dim_type)))
# Based loosely on pydap's builtin netcdf handler.
for var in variables.values():
# Add grids.
dataset[var.name] = GridType(var.name, var.atts)
# Add array.
dataset[var.name][var.name] = BaseType(var.name, var.array, var.dims,
var.atts)
# Add maps.
for dim in var.dims:
if dim in dims:
if hasattr(dims[dim], 'array'):
array = dims[dim].array
atts = dims[dim].atts
else:
# Add "dummy" dimensions (or they're not interpreted properly by some
# clients like Panoply).
array = np.arange(len(dims[dim]))
if hasattr(dims[dim], 'atts'):
atts = dims[dim].atts
else:
atts = {}
dataset[var.name][dim] = BaseType(dim, array, None, atts)
for dim in dims.values():
if hasattr(dim, 'array'):
array = dim.array
else:
# Add "dummy" dimensions (or they're not interpreted properly by some
# clients like Panoply).
array = np.arange(len(dim))
if hasattr(dim, 'atts'):
atts = dim.atts
else:
atts = {}
dataset[dim.name] = BaseType(dim.name, array, None, atts)
# Handle unlimited dimension.
if dim.name == 'time':
dataset.attributes['DODS_EXTRA'] = {
'Unlimited_Dimension': dim.name,
}
return dataset