def check_open_with_grid_workflow(index):
from datacube.api.core import Datacube
dc = Datacube(index=index)
type_name = 'ls5_nbar_albers'
dt = dc.index.datasets.types.get_by_name(type_name)
from datacube.api.grid_workflow import GridWorkflow
gw = GridWorkflow(dc, dt.grid_spec)
cells = gw.list_cells(product=type_name)
assert LBG_CELL in cells
tiles = gw.list_tiles(product=type_name)
assert tiles
assert tiles[LBG_CELL]
ts, tile = tiles[LBG_CELL].popitem()
dataset_cell = gw.load(LBG_CELL, tile, measurements=['blue'])
assert dataset_cell['blue'].size
dataset_cell = gw.load(LBG_CELL, tile)
assert all(m in dataset_cell for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
tiles = gw.list_tile_stacks(product=type_name)
assert tiles
assert tiles[LBG_CELL]
tile = tiles[LBG_CELL]
dataset_cell = gw.load(LBG_CELL, tile, measurements=['blue'])
assert dataset_cell['blue'].size
dataset_cell = gw.load(LBG_CELL, tile)
assert all(m in dataset_cell for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
def check_open_with_grid_workflow(index):
type_name = 'ls5_nbar_albers'
dt = index.datasets.types.get_by_name(type_name)
from datacube.api.grid_workflow import GridWorkflow
gw = GridWorkflow(index, dt.grid_spec)
cells = gw.list_cells(product=type_name)
assert LBG_CELL in cells
tile = cells[LBG_CELL]
dataset_cell = gw.load(tile, measurements=['blue'])
assert dataset_cell['blue'].size
dataset_cell = gw.load(tile)
assert all(m in dataset_cell for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
ts = numpy.datetime64('1992-03-23T23:14:25.500000000')
tile_key = LBG_CELL + (ts,)
tiles = gw.list_tiles(product=type_name)
assert tiles
assert tile_key in tiles
tile = tiles[tile_key]
dataset_cell = gw.load(tile, measurements=['blue'])
assert dataset_cell['blue'].size
dataset_cell = gw.load(tile)
assert all(m in dataset_cell for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
def do_stats(task, config):
source = task['source']
measurement_name = source['measurements'][0]
var_params = get_variable_params(config)
results = create_output_files(config['stats'], config['location'], measurement_name, task, var_params)
for tile_index in tile_iter(task['data'], {'x': 1000, 'y': 1000}):
data = GridWorkflow.load(slice_tile(task['data'], tile_index),
measurements=[measurement_name])[measurement_name]
data = data.where(data != data.attrs['nodata'])
for spec, sources in zip(source['masks'], task['masks']):
mask = GridWorkflow.load(slice_tile(sources, tile_index),
measurements=[spec['measurement']])[spec['measurement']]
mask = make_mask(mask, **spec['flags'])
data = data.where(mask)
del mask
for stat in config['stats']:
data_stats = getattr(data, stat['name'])(dim='time')
results[stat['name']][measurement_name][tile_index][0] = data_stats
print(data_stats)
for nco in config['stats'].values:
nco.close()
def do_stats(task, config):
source = task['source']
measurement_name = source['measurements'][0]
var_params = get_variable_params(config)
results = create_output_files(config['stats'], config['location'],
measurement_name, task, var_params)
for tile_index in tile_iter(task['data'], {'x': 1000, 'y': 1000}):
data = GridWorkflow.load(slice_tile(task['data'], tile_index),
measurements=[measurement_name
])[measurement_name]
data = data.where(data != data.attrs['nodata'])
for spec, sources in zip(source['masks'], task['masks']):
mask = GridWorkflow.load(slice_tile(sources, tile_index),
measurements=[spec['measurement']
])[spec['measurement']]
mask = make_mask(mask, **spec['flags'])
data = data.where(mask)
del mask
for stat in config['stats']:
data_stats = getattr(data, stat['name'])(dim='time')
results[stat['name']][measurement_name][tile_index][0] = data_stats
print(data_stats)
for nco in config['stats'].values:
nco.close()
def check_open_with_grid_workflow(driver_manager):
type_name = 'ls5_nbar_albers'
dt = driver_manager.index.products.get_by_name(type_name)
from datacube.api.grid_workflow import GridWorkflow
gw = GridWorkflow(None, dt.grid_spec, driver_manager=driver_manager)
cells = gw.list_cells(product=type_name, cell_index=LBG_CELL)
assert LBG_CELL in cells
cells = gw.list_cells(product=type_name)
assert LBG_CELL in cells
tile = cells[LBG_CELL]
assert 'x' in tile.dims
assert 'y' in tile.dims
assert 'time' in tile.dims
assert tile.shape[1] == 4000
assert tile.shape[2] == 4000
assert tile[:1, :100, :100].shape == (1, 100, 100)
dataset_cell = gw.load(tile,
measurements=['blue'],
driver_manager=driver_manager)
assert dataset_cell['blue'].shape == tile.shape
for timestamp, tile_slice in tile.split('time'):
assert tile_slice.shape == (1, 4000, 4000)
dataset_cell = gw.load(tile, driver_manager=driver_manager)
assert all(m in dataset_cell
for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
ts = numpy.datetime64('1992-03-23T23:14:25.500000000')
tile_key = LBG_CELL + (ts, )
tiles = gw.list_tiles(product=type_name)
assert tiles
assert tile_key in tiles
tile = tiles[tile_key]
dataset_cell = gw.load(tile,
measurements=['blue'],
driver_manager=driver_manager)
assert dataset_cell['blue'].size
dataset_cell = gw.load(tile, driver_manager=driver_manager)
assert all(m in dataset_cell
for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
def check_open_with_grid_workflow(index):
from datacube.api.core import Datacube
dc = Datacube(index=index)
type_name = 'ls5_nbar_albers'
dt = dc.index.datasets.types.get_by_name(type_name)
from datacube.api.grid_workflow import GridWorkflow
gw = GridWorkflow(dc, dt.grid_spec)
cells = gw.list_cells(product=type_name)
assert LBG_CELL in cells
tiles = gw.list_tiles(product=type_name)
assert tiles
assert tiles[LBG_CELL]
ts, tile = tiles[LBG_CELL].popitem()
dataset_cell = gw.load(LBG_CELL, tile, measurements=['blue'])
assert dataset_cell['blue'].size
dataset_cell = gw.load(LBG_CELL, tile)
assert all(m in dataset_cell
for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
tiles = gw.list_tile_stacks(product=type_name)
assert tiles
assert tiles[LBG_CELL]
tile = tiles[LBG_CELL]
dataset_cell = gw.load(LBG_CELL, tile, measurements=['blue'])
assert dataset_cell['blue'].size
dataset_cell = gw.load(LBG_CELL, tile)
assert all(m in dataset_cell
for m in ['blue', 'green', 'red', 'nir', 'swir1', 'swir2'])
def do_ndvi_task(config, task):
global_attributes = config['global_attributes']
variable_params = config['variable_params']
file_path = Path(task['filename'])
output_type = config['ndvi_dataset_type']
measurement = output_type.measurements['ndvi']
output_dtype = np.dtype(measurement['dtype'])
nodata_value = np.dtype(output_dtype).type(measurement['nodata'])
if file_path.exists():
raise OSError(errno.EEXIST, 'Output file already exists',
str(file_path))
measurements = ['red', 'nir']
nbar_tile = task['nbar']
nbar = GridWorkflow.load(nbar_tile, measurements)
ndvi = calculate_ndvi(nbar,
nodata=nodata_value,
dtype=output_dtype,
units=measurement['units'])
def _make_dataset(labels, sources):
assert len(sources)
geobox = nbar.geobox
source_data = union_points(
*[dataset.extent.to_crs(geobox.crs).points for dataset in sources])
valid_data = intersect_points(geobox.extent.points, source_data)
dataset = make_dataset(product=output_type,
sources=sources,
extent=geobox.extent,
center_time=labels['time'],
uri=file_path.absolute().as_uri(),
app_info=get_app_metadata(config),
valid_data=GeoPolygon(valid_data, geobox.crs))
return dataset
datasets = xr_apply(nbar_tile.sources, _make_dataset, dtype='O')
ndvi['dataset'] = datasets_to_doc(datasets)
write_dataset_to_netcdf(
dataset=ndvi,
filename=Path(file_path),
global_attributes=global_attributes,
variable_params=variable_params,
)
return datasets
def _do_fc_task(config, task):
"""
Load data, run FC algorithm, attach metadata, and write output.
:param dict config: Config object
:param dict task: Dictionary of tasks
:return: Dataset objects representing the generated data that can be added to the index
:rtype: list(datacube.model.Dataset)
"""
global_attributes = config['global_attributes']
variable_params = config['variable_params']
file_path = Path(task['filename'])
output_product = config['fc_product']
if file_path.exists():
raise OSError(errno.EEXIST, 'Output file already exists',
str(file_path))
nbart_tile: Tile = task['nbart']
nbart = GridWorkflow.load(nbart_tile,
['green', 'red', 'nir', 'swir1', 'swir2'])
output_measurements = config['fc_product'].measurements.values()
fc_dataset = _make_fc_tile(nbart, output_measurements,
config.get('sensor_regression_coefficients'))
def _make_dataset(labels, sources):
assert sources
dataset = make_dataset(product=output_product,
sources=sources,
extent=nbart.geobox.extent,
center_time=labels['time'],
uri=file_path.absolute().as_uri(),
app_info=_get_app_metadata(config),
valid_data=polygon_from_sources_extents(
sources, nbart.geobox))
return dataset
datasets = xr_apply(nbart_tile.sources, _make_dataset, dtype='O')
fc_dataset['dataset'] = datasets_to_doc(datasets)
write_dataset_to_netcdf(
dataset=fc_dataset,
filename=file_path,
global_attributes=global_attributes,
variable_params=variable_params,
)
return datasets
def do_ndvi_task(config, task):
global_attributes = config['global_attributes']
variable_params = config['variable_params']
file_path = Path(task['filename'])
output_type = config['ndvi_dataset_type']
measurement = output_type.measurements['ndvi']
output_dtype = np.dtype(measurement['dtype'])
nodata_value = np.dtype(output_dtype).type(measurement['nodata'])
if file_path.exists():
raise OSError(errno.EEXIST, 'Output file already exists', str(file_path))
measurements = ['red', 'nir']
nbar_tile = task['nbar']
nbar = GridWorkflow.load(nbar_tile, measurements)
ndvi = calculate_ndvi(nbar, nodata=nodata_value, dtype=output_dtype, units=measurement['units'])
def _make_dataset(labels, sources):
assert len(sources)
geobox = nbar.geobox
source_data = union_points(*[dataset.extent.to_crs(geobox.crs).points for dataset in sources])
valid_data = intersect_points(geobox.extent.points, source_data)
dataset = make_dataset(product=output_type,
sources=sources,
extent=geobox.extent,
center_time=labels['time'],
uri=file_path.absolute().as_uri(),
app_info=get_app_metadata(config),
valid_data=GeoPolygon(valid_data, geobox.crs))
return dataset
datasets = xr_apply(nbar_tile.sources, _make_dataset, dtype='O')
ndvi['dataset'] = datasets_to_doc(datasets)
write_dataset_to_netcdf(
dataset=ndvi,
filename=Path(file_path),
global_attributes=global_attributes,
variable_params=variable_params,
)
return datasets
def do_fc_task(config, task):
global_attributes = config['global_attributes']
variable_params = config['variable_params']
file_path = Path(task['filename'])
output_product = config['fc_product']
if file_path.exists():
raise OSError(errno.EEXIST, 'Output file already exists', str(file_path))
nbar_tile: Tile = task['nbar']
nbar = GridWorkflow.load(nbar_tile, ['green', 'red', 'nir', 'swir1', 'swir2'])
output_measurements = config['fc_product'].measurements.values()
fc_dataset = make_fc_tile(nbar, output_measurements, config.get('sensor_regression_coefficients'))
def _make_dataset(labels, sources):
assert sources
dataset = make_dataset(product=output_product,
sources=sources,
extent=nbar.geobox.extent,
center_time=labels['time'],
uri=file_path.absolute().as_uri(),
app_info=get_app_metadata(config),
valid_data=GeoPolygon.from_sources_extents(sources, nbar.geobox))
return dataset
datasets = xr_apply(nbar_tile.sources, _make_dataset, dtype='O')
fc_dataset['dataset'] = datasets_to_doc(datasets)
write_dataset_to_netcdf(
dataset=fc_dataset,
filename=file_path,
global_attributes=global_attributes,
variable_params=variable_params,
)
return datasets
def test_gridworkflow():
""" Test GridWorkflow with padding option. """
from mock import MagicMock
import datetime
# ----- fake a datacube -----
# e.g. let there be a dataset that coincides with a grid cell
fakecrs = geometry.CRS('EPSG:4326')
grid = 100 # spatial frequency in crs units
pixel = 10 # square pixel linear dimension in crs units
# if cell(0,0) has lower left corner at grid origin,
# and cell indices increase toward upper right,
# then this will be cell(1,-2).
gridspec = GridSpec(crs=fakecrs,
tile_size=(grid, grid),
resolution=(-pixel, pixel)) # e.g. product gridspec
fakedataset = MagicMock()
fakedataset.extent = geometry.box(left=grid,
bottom=-grid,
right=2 * grid,
top=-2 * grid,
crs=fakecrs)
fakedataset.center_time = t = datetime.datetime(2001, 2, 15)
fakedataset.id = uuid.uuid4()
fakeindex = PickableMock()
fakeindex._db = None
fakeindex.datasets.get_field_names.return_value = [
'time'
] # permit query on time
fakeindex.datasets.search_eager.return_value = [fakedataset]
# ------ test without padding ----
from datacube.api.grid_workflow import GridWorkflow
gw = GridWorkflow(fakeindex, gridspec)
# Need to force the fake index otherwise the driver manager will
# only take its _db
gw.index = fakeindex
query = dict(product='fake_product_name',
time=('2001-1-1 00:00:00', '2001-3-31 23:59:59'))
# test backend : that it finds the expected cell/dataset
assert list(gw.cell_observations(**query).keys()) == [(1, -2)]
# again but with geopolygon
assert list(
gw.cell_observations(**query,
geopolygon=gridspec.tile_geobox(
(1, -2)).extent).keys()) == [(1, -2)]
with pytest.raises(ValueError) as e:
list(
gw.cell_observations(**query,
tile_buffer=(1, 1),
geopolygon=gridspec.tile_geobox(
(1, -2)).extent).keys())
assert str(
e.value) == 'Cannot process tile_buffering and geopolygon together.'
# test frontend
assert len(gw.list_tiles(**query)) == 1
# ------ introduce padding --------
assert len(gw.list_tiles(tile_buffer=(20, 20), **query)) == 9
# ------ add another dataset (to test grouping) -----
# consider cell (2,-2)
fakedataset2 = MagicMock()
fakedataset2.extent = geometry.box(left=2 * grid,
bottom=-grid,
right=3 * grid,
top=-2 * grid,
crs=fakecrs)
fakedataset2.center_time = t
fakedataset2.id = uuid.uuid4()
def search_eager(lat=None, lon=None, **kwargs):
return [fakedataset, fakedataset2]
fakeindex.datasets.search_eager = search_eager
# unpadded
assert len(gw.list_tiles(**query)) == 2
ti = numpy.datetime64(t, 'ns')
assert set(gw.list_tiles(**query).keys()) == {(1, -2, ti), (2, -2, ti)}
# padded
assert len(gw.list_tiles(tile_buffer=(20, 20), **
query)) == 12 # not 18=2*9 because of grouping
# -------- inspect particular returned tile objects --------
# check the array shape
tile = gw.list_tiles(**query)[1, -2, ti] # unpadded example
assert grid / pixel == 10
assert tile.shape == (1, 10, 10)
padded_tile = gw.list_tiles(tile_buffer=(20, 20),
**query)[1, -2, ti] # padded example
# assert grid/pixel + 2*gw2.grid_spec.padding == 14 # GREG: understand this
assert padded_tile.shape == (1, 14, 14)
# count the sources
assert len(tile.sources.isel(time=0).item()) == 1
assert len(padded_tile.sources.isel(time=0).item()) == 2
# check the geocoding
assert tile.geobox.alignment == padded_tile.geobox.alignment
assert tile.geobox.affine * (0, 0) == padded_tile.geobox.affine * (2, 2)
assert tile.geobox.affine * (10, 10) == padded_tile.geobox.affine * (
10 + 2, 10 + 2)
# ------- check loading --------
# GridWorkflow accesses the load_data API
# to ultimately convert geobox,sources,measurements to xarray,
# so only thing to check here is the call interface.
measurement = dict(nodata=0, dtype=numpy.int)
fakedataset.type.lookup_measurements.return_value = {'dummy': measurement}
fakedataset2.type = fakedataset.type
from mock import patch
with patch('datacube.api.core.Datacube.load_data') as loader:
data = GridWorkflow.load(tile)
data2 = GridWorkflow.load(padded_tile)
# Note, could also test Datacube.load for consistency (but may require more patching)
assert data is data2 is loader.return_value
assert loader.call_count == 2
# Note, use of positional arguments here is not robust, could spec mock etc.
for (args, kwargs), loadable in zip(loader.call_args_list,
[tile, padded_tile]):
args = list(args)
assert args[0] is loadable.sources
assert args[1] is loadable.geobox
assert list(args[2].values())[0] is measurement
assert 'resampling' in kwargs
# ------- check single cell index extract -------
tile = gw.list_tiles(cell_index=(1, -2), **query)
assert len(tile) == 1
assert tile[1, -2, ti].shape == (1, 10, 10)
assert len(tile[1, -2, ti].sources.values[0]) == 1
padded_tile = gw.list_tiles(cell_index=(1, -2),
tile_buffer=(20, 20),
**query)
assert len(padded_tile) == 1
assert padded_tile[1, -2, ti].shape == (1, 14, 14)
assert len(padded_tile[1, -2, ti].sources.values[0]) == 2