def fmask_filter_c2(fmask):
mask = np.zeros(fmask.shape, dtype=np.uint8)
col2_nodata = masking.make_mask(fmask, nodata=True)
col2_cloud = masking.make_mask(fmask, cloud_or_cirrus="cloud_or_cirrus")
col2_cloud_shadow = masking.make_mask(fmask, cloud_shadow="cloud_shadow")
mask[col2_cloud.values] += MASKED_CLOUD
mask[col2_cloud_shadow.values] += MASKED_CLOUD_SHADOW
mask[col2_nodata.values] = NO_DATA
return mask
def create_mask(data, flags):
if "or" in flags:
fs = flags["or"]
mask = None
for f in fs.items():
f = {f[0]: f[1]}
if mask is None:
mask = make_mask(data, **f)
else:
mask |= make_mask(data, **f)
else:
fs = flags if "and" not in flags else flags["and"]
mask = make_mask(data, **fs)
return mask
def to_mask(self, data, pq_data, extra_mask=None):
date_count = len(data.coords["time"])
if date_count > 1:
mdh = self.get_multi_date_handler(date_count)
if extra_mask is not None:
extra_mask = mdh.collapse_mask(extra_mask)
if pq_data is not None:
pq_data = mdh.collapse_mask(pq_data)
else:
if extra_mask is not None:
extra_mask = extra_mask.squeeze(dim="time", drop=True)
if pq_data is not None:
pq_data = pq_data.squeeze(dim="time", drop=True)
result = extra_mask
if pq_data is not None:
for mask in self.masks:
odc_mask = make_mask(pq_data, **mask.flags)
mask_data = getattr(odc_mask, self.product.pq_band)
if mask.invert:
mask_data = ~mask_data
if result is None:
result = mask_data
else:
result = result & mask_data
return result
def single_date_make_mask(data, mask):
pq_data = getattr(data, mask.band_name)
if mask.flags:
odc_mask = make_mask(pq_data, **mask.flags)
else:
odc_mask = pq_data == mask.enum
odc_mask = odc_mask.squeeze(dim="time", drop=True)
return odc_mask
def create_long_arrays(ldc, udc, lquery, lquery2):
usgs_names = [
'coastal_aerosol', 'blue', 'green', 'red', 'nir', 'swir1', 'swir2'
]
ls8_temp = ldc.load(product='ls8_nbart_scene', **lquery)
ls8_bigtemp = ldc.load(product='ls8_nbart_scene', **lquery2)
ls8_usgs_temp = udc.load(product='ls8_usgs_l2c1',
measurements=usgs_names,
**lquery)
ls8_usgs_bigtemp = udc.load(product='ls8_usgs_l2c1',
measurements=usgs_names,
**lquery2)
ls8_pq = ldc.load(product='ls8_pq_scene', fuse_func=ga_pq_fuser, **lquery2)
good_quality = masking.make_mask(ls8_pq.pqa,
cloud_acca='no_cloud',
cloud_fmask='no_cloud',
cloud_shadow_acca='no_cloud_shadow',
cloud_shadow_fmask='no_cloud_shadow',
blue_saturated=False,
green_saturated=False,
red_saturated=False,
nir_saturated=False,
swir1_saturated=False,
swir2_saturated=False,
contiguous=True)
ls8_array = ls8_temp.where(good_quality)
ls8_bigarray = ls8_bigtemp.where(good_quality)
ls8_usgs_array = ls8_usgs_temp.where(good_quality)
ls8_usgs_bigarray = ls8_usgs_bigtemp.where(good_quality)
ls8_array = ls8_array.rename({
'1': 'coastal_aerosol',
'2': 'blue',
'3': 'green',
'4': 'red',
'5': 'nir',
'6': 'swir1',
'7': 'swir2'
})
ls8_bigarray = ls8_bigarray.rename({
'1': 'coastal_aerosol',
'2': 'blue',
'3': 'green',
'4': 'red',
'5': 'nir',
'6': 'swir1',
'7': 'swir2'
})
return ls8_array, ls8_usgs_array, ls8_bigarray, ls8_usgs_bigarray
def create_mask(self, data):
if self.values:
mask = None
for v in self.values:
vmask = data == v
if mask is None:
mask = vmask
else:
mask |= vmask
elif self.or_flags:
mask = None
for f in self.flags.items():
f = {f[0]: f[1]}
if mask is None:
mask = make_mask(data, **f)
else:
mask |= make_mask(data, **f)
else:
mask = make_mask(data, **self.flags)
return mask
def make_mask(self, data, mask):
odc_mask = None
for dt in data.coords["time"].values:
tpqdata = getattr(data.sel(time=dt), mask.band_name)
if mask.flags:
dt_mask = make_mask(tpqdata, **mask.flags)
else:
dt_mask = tpqdata == mask.enum
if odc_mask is None:
odc_mask = dt_mask
else:
odc_mask |= dt_mask
return odc_mask
def compute_mosaic(products, measurements, **parsed_expressions):
with Datacube() as dc:
acq_range = parsed_expressions['time']
click.echo("Processing time range {}".format(acq_range))
datasets = []
for prodname in products:
dataset = dc.load(product=prodname,
measurements=measurements,
group_by='solar_day',
**parsed_expressions)
if len(dataset) == 0:
continue
else:
click.echo("Found {} time slices of {} during {}.".format(
len(dataset['time']), prodname, acq_range))
pq = dc.load(product=prodname.replace('nbar', 'pq'),
group_by='solar_day',
fuse_func=ga_pq_fuser,
**parsed_expressions)
if len(pq) == 0:
click.echo('No PQ found, skipping')
continue
crs = dataset.attrs['crs']
dataset = dataset.where(dataset != -999)
dataset.attrs['product'] = prodname
dataset.attrs['crs'] = crs
cloud_free = make_mask(pq.pixelquality, ga_good_pixel=True)
dataset = dataset.where(cloud_free)
if len(dataset) == 0:
click.echo("Nothing left after PQ masking")
continue
datasets.append(dataset)
dataset = xr.concat(datasets, dim='time')
return dataset.median(dim='time')
def load_ard(dc,
products=None,
min_gooddata=0.0,
pq_categories_s2=[
'vegetation', 'snow or ice', 'water', 'bare soils',
'unclassified', 'dark area pixels'
],
pq_categories_ls=None,
mask_pixel_quality=True,
ls7_slc_off=True,
predicate=None,
dtype='auto',
scaling='raw',
**kwargs):
'''
Loads and combines Landsat Collections 1 or 2, and Sentinel-2 for
multiple sensors (i.e. ls5t, ls7e and ls8c for Landsat; s2a and s2b for Sentinel-2),
optionally applies pixel quality masks, and drops time steps that
contain greater than a minimum proportion of good quality (e.g. non-
cloudy or shadowed) pixels.
The function supports loading the following DE Africa products:
ls5_usgs_sr_scene
ls7_usgs_sr_scene
ls8_usgs_sr_scene
usgs_ls8c_level2_2
ga_ls8c_fractional_cover_2
s2_l2a
Last modified: March 2020
Parameters
----------
dc : datacube Datacube object
The Datacube to connect to, i.e. `dc = datacube.Datacube()`.
This allows you to also use development datacubes if required.
products : list
A list of product names to load data from. Valid options are
Landsat C1: ['ls5_usgs_sr_scene', 'ls7_usgs_sr_scene', 'ls8_usgs_sr_scene'],
Landsat C2: ['usgs_ls8c_level2_2']
Sentinel-2: ['s2_l2a']
min_gooddata : float, optional
An optional float giving the minimum percentage of good quality
pixels required for a satellite observation to be loaded.
Defaults to 0.0 which will return all observations regardless of
pixel quality (set to e.g. 0.99 to return only observations with
more than 99% good quality pixels).
pq_categories_s2 : list, optional
An optional list of Sentinel-2 Scene Classification Layer (SCL) names
to treat as good quality observations in the above `min_gooddata`
calculation. The default is ['vegetation','snow or ice','water',
'bare soils','unclassified', 'dark area pixels'] which will return
non-cloudy or non-shadowed land, snow, water, veg, and non-veg pixels.
pq_categories_ls : dict, optional
An optional dictionary that is used to generate a good quality
pixel mask from the selected USGS product's pixel quality band (i.e.
'pixel_qa' for USGS Collection 1, and 'quality_l2_aerosol' for
USGS Collection 2). This mask is used for both masking out low
quality pixels (e.g. cloud or shadow), and for dropping
observations entirely based on the above `min_gooddata`
calculation. Default is None, which will apply the following mask
for USGS Collection 1: `{'cloud': 'no_cloud', 'cloud_shadow':
'no_cloud_shadow', 'nodata': False}`, and for USGS Collection 2:
`{'cloud_shadow': 'not_cloud_shadow', 'cloud_or_cirrus':
'not_cloud_or_cirrus', 'nodata': False}.
mask_pixel_quality : bool, optional
An optional boolean indicating whether to apply the good data
mask to all observations that were not filtered out for having
less good quality pixels than `min_gooddata`. E.g. if
`min_gooddata=0.99`, the filtered observations may still contain
up to 1% poor quality pixels. The default of False simply
returns the resulting observations without masking out these
pixels; True masks them and sets them to NaN using the good data
mask. This will convert numeric values to floating point values
which can cause memory issues, set to False to prevent this.
ls7_slc_off : bool, optional
An optional boolean indicating whether to include data from
after the Landsat 7 SLC failure (i.e. SLC-off). Defaults to
True, which keeps all Landsat 7 observations > May 31 2003.
predicate : function, optional
An optional function that can be passed in to restrict the
datasets that are loaded by the function. A filter function
should take a `datacube.model.Dataset` object as an input (i.e.
as returned from `dc.find_datasets`), and return a boolean.
For example, a filter function could be used to return True on
only datasets acquired in January:
`dataset.time.begin.month == 1`
dtype : string, optional
An optional parameter that controls the data type/dtype that
layers are coerced to after loading. Valid values: 'native',
'auto', 'float{16|32|64}'. When 'auto' is used, the data will be
converted to `float32` if masking is used, otherwise data will
be returned in the native data type of the data. Be aware that
if data is loaded in its native dtype, nodata and masked
pixels will be returned with the data's native nodata value
(typically -999), not NaN.
scaling : str, optional
If 'normalised', then surface reflectance values are scaled from
their original values to 0-1. If 'raw' then dataset is returned
in its native scaling. WARNING: USGS Landsat Collection 2
surface reflectance values have an offset so normliaed band indices
will return non-sensical results if setting scaling='raw'.
**kwargs :
A set of keyword arguments to `dc.load` that define the
spatiotemporal query used to extract data. This typically
includes `measurements`, `x`, `y`, `time`, `resolution`,
`resampling`, `group_by` and `crs`. Keyword arguments can
either be listed directly in the `load_ard` call like any
other parameter (e.g. `measurements=['nbart_red']`), or by
passing in a query kwarg dictionary (e.g. `**query`). For a
list of possible options, see the `dc.load` documentation:
https://datacube-core.readthedocs.io/en/latest/dev/api/generate/datacube.Datacube.load.html
Returns
-------
combined_ds : xarray Dataset
An xarray dataset containing only satellite observations that
contains greater than `min_gooddata` proportion of good quality
pixels.
'''
#########
# Setup #
#########
# prevent function altering original query object
kwargs = deepcopy(kwargs)
# We deal with `dask_chunks` separately
dask_chunks = kwargs.pop('dask_chunks', None)
requested_measurements = kwargs.pop('measurements', None)
# Warn user if they combine lazy load with min_gooddata
if (min_gooddata > 0.0) and dask_chunks is not None:
warnings.warn("Setting 'min_gooddata' percentage to > 0.0 "
"will cause dask arrays to compute when "
"loading pixel-quality data to calculate "
"'good pixel' percentage. This can "
"slow the return of your dataset.")
# Verify that products were provided and determine if Sentinel-2
# or Landsat data is being loaded
if not products:
raise ValueError(f'Please provide a list of product names '
f'to load data from.')
elif all(['level2' in product for product in products]):
product_type = 'c2'
elif all(['sr' in product for product in products]):
product_type = 'c1'
elif all(['s2' in product for product in products]):
product_type = 's2'
elif all(['fractional_cover' in product for product in products]):
product_type = 'fc'
# If `measurements` are specified but do not include pixel quality bands,
# add these to `measurements` according to collection
if (product_type == 'c2') or (product_type == 'fc'):
print('Using pixel quality parameters for USGS Collection 2')
fmask_band = 'quality_l2_aerosol'
elif product_type == 'c1':
print('Using pixel quality parameters for USGS Collection 1')
fmask_band = 'pixel_qa'
elif product_type == 's2':
print('Using pixel quality parameters for Sentinel 2')
fmask_band = 'SCL'
measurements = requested_measurements.copy(
) if requested_measurements else None
# Deal with "load all" case: pick a set of bands common across
# all products
if measurements is None:
if product_type == 'fc':
measurements = ['pv', 'npv', 'bs', 'ue']
else:
measurements = _common_bands(dc, products)
# If `measurements` are specified but do not include pq, add.
if measurements:
#pass if FC
if product_type == 'fc':
pass
else:
if fmask_band not in measurements:
measurements.append(fmask_band)
# Get list of data and mask bands so that we can later exclude
# mask bands from being masked themselves
if product_type == 'fc':
pass
else:
data_bands = [
band for band in measurements if band not in (fmask_band)
]
mask_bands = [band for band in measurements if band not in data_bands]
#################
# Find datasets #
#################l
# Pull out query params only to pass to dc.find_datasets
query = _dc_query_only(**kwargs)
# Extract datasets for each product using subset of dcload_kwargs
dataset_list = []
# Get list of datasets for each product
print('Finding datasets')
for product in products:
# Obtain list of datasets for product
print(f' {product}')
datasets = dc.find_datasets(product=product, **query)
# Remove Landsat 7 SLC-off observations if ls7_slc_off=False
if not ls7_slc_off and product in [
'ls7_usgs_sr_scene', 'usgs_ls7e_level2_2'
]:
print(' Ignoring SLC-off observations for ls7')
datasets = [
i for i in datasets if
i.time.begin < datetime.datetime(2003, 5, 31, tzinfo=pytz.UTC)
]
# Add any returned datasets to list
dataset_list.extend(datasets)
# Raise exception if no datasets are returned
if len(dataset_list) == 0:
raise ValueError("No data available for query: ensure that "
"the products specified have data for the "
"time and location requested")
# If pedicate is specified, use this function to filter the list
# of datasets prior to load
if predicate:
print(f'Filtering datasets using filter function')
dataset_list = [ds for ds in dataset_list if predicate(ds)]
# Raise exception if filtering removes all datasets
if len(dataset_list) == 0:
raise ValueError("No data available after filtering with "
"filter function")
# load fmask from C2 for masking FC, and filter if required
# NOTE: This works because only one sensor (ls8) has FC, if/when
# FC is calculated for LS7, LS5, will need to move this section
# into the for loop above.
if product_type == 'fc':
print(' PQ data from USGS C2')
dataset_list_fc_pq = dc.find_datasets(product='usgs_ls8c_level2_2',
**query)
if predicate:
print(f'Filtering datasets using filter function')
dataset_list_fc_pq = [
ds for ds in dataset_list_fc_pq if predicate(ds)
]
#############
# Load data #
#############
# Note we always load using dask here so that
# we can lazy load data before filtering by good data
ds = dc.load(datasets=dataset_list,
measurements=measurements,
dask_chunks={} if dask_chunks is None else dask_chunks,
**kwargs)
if product_type == 'fc':
ds_fc_pq = dc.load(
datasets=dataset_list_fc_pq,
dask_chunks={} if dask_chunks is None else dask_chunks,
**kwargs)
####################
# Filter good data #
####################
# need to distinguish between products due to different
# pq band properties
# collection 2 USGS or FC
if (product_type == 'c2') or (product_type == 'fc'):
if pq_categories_ls is None:
quality_flags_prod = {
'cloud_shadow': 'not_cloud_shadow',
'cloud_or_cirrus': 'not_cloud_or_cirrus',
'nodata': False
}
else:
quality_flags_prod = pq_categories_ls
if product_type == 'fc':
pq_mask = masking.make_mask(ds_fc_pq[fmask_band],
**quality_flags_prod)
else:
pq_mask = masking.make_mask(ds[fmask_band], **quality_flags_prod)
# collection 1 USGS
if product_type == 'c1':
if pq_categories_ls is None:
quality_flags_prod = {
'cloud': 'no_cloud',
'cloud_shadow': 'no_cloud_shadow',
'nodata': False
}
else:
quality_flags_prod = pq_categories_ls
pq_mask = masking.make_mask(ds[fmask_band], **quality_flags_prod)
# sentinel 2
if product_type == 's2':
#currently broken for mask band values >=8
#pq_mask = odc.algo.fmask_to_bool(ds[fmask_band],
# categories=pq_categories_s2)
flags_s2 = dc.list_measurements().loc[
products[0]].loc[fmask_band]['flags_definition']['qa']['values']
pq_mask = ds[fmask_band].isin(
[int(k) for k, v in flags_s2.items() if v in pq_categories_s2])
# The good data percentage calculation has to load in all `fmask`
# data, which can be slow. If the user has chosen no filtering
# by using the default `min_gooddata = 0`, we can skip this step
# completely to save processing time
if min_gooddata > 0.0:
# Compute good data for each observation as % of total pixels
print('Counting good quality pixels for each time step')
data_perc = (pq_mask.sum(axis=[1, 2], dtype='int32') /
(pq_mask.shape[1] * pq_mask.shape[2]))
keep = data_perc >= min_gooddata
# Filter by `min_gooddata` to drop low quality observations
total_obs = len(ds.time)
ds = ds.sel(time=keep)
pq_mask = pq_mask.sel(time=keep)
print(f'Filtering to {len(ds.time)} out of {total_obs} '
f'time steps with at least {min_gooddata:.1%} '
f'good quality pixels')
###############
# Apply masks #
###############
# Generate good quality data mask
mask = None
if mask_pixel_quality:
print('Applying pixel quality/cloud mask')
mask = pq_mask
# Split into data/masks bands, as conversion to float and masking
# should only be applied to data bands
if product_type == 'fc':
ds_data = ds
else:
ds_data = ds[data_bands]
ds_masks = ds[mask_bands]
# Mask data if either of the above masks were generated
if mask is not None:
ds_data = odc.algo.keep_good_only(ds_data, where=mask)
# Automatically set dtype to either native or float32 depending
# on whether masking was requested
if dtype == 'auto':
dtype = 'native' if mask is None else 'float32'
# Set nodata values using odc.algo tools to reduce peak memory
# use when converting data dtype
if dtype != 'native':
ds_data = odc.algo.to_float(ds_data, dtype=dtype)
# Put data and mask bands back together
if product_type == 'fc':
attrs = ds.attrs
ds = ds_data
ds.attrs.update(attrs)
else:
attrs = ds.attrs
ds = xr.merge([ds_data, ds_masks])
ds.attrs.update(attrs)
###############
# Return data #
###############
# Drop bands not originally requested by user
if requested_measurements:
ds = ds[requested_measurements]
# Scale data 0-1 if requested
if scaling == 'normalised':
if product_type == 'c1':
print("Re-scaling Landsat C1 data")
not_sr_bands = ['pixel_qa', 'sr_aerosol', 'radsat_qa']
for band in ds.data_vars:
if band not in not_sr_bands:
ds[band] = ds[band] / 10000
if product_type == 's2':
print("Re-scaling Sentinel-2 data")
not_sr_bands = [
'scl', 'qa', 'mask', 'water_vapour',
'aerosol_optical_thickness'
]
for band in ds.data_vars:
if band not in not_sr_bands:
ds[band] = ds[band] / 10000
# Collection 2 Landsat raw values aren't useful so rescale,
# need different factors for surface-temp and SR
if product_type == 'c2':
print("Re-scaling Landsat C2 data")
not_sr_bands = [
'thermal_radiance', 'upwell_radiance', 'upwell_radiance',
'atmospheric_transmittance', 'emissivity', 'emissivity_stdev',
'cloud_distance', 'quality_l2_aerosol',
'quality_l2_surface_temperature', 'quality_l1_pixel',
'quality_l1_radiometric_saturation', 'surface_temperature'
]
for band in ds.data_vars:
if band == 'surface_temperature':
ds[band] = ds[band] * 0.00341802 + 149.0 - 273.15
if band not in not_sr_bands:
ds[band] = ds[band] * 2.75e-5 - 0.2
# If user supplied dask_chunks, return data as a dask array without
# actually loading it in
if dask_chunks is not None:
print(f'Returning {len(ds.time)} time steps as a dask array')
return ds
else:
print(f'Loading {len(ds.time)} time steps')
return ds.compute()
def process_data(self, data, parameters):
wofs_mask_flags = [
dict(dry=True),
dict(terrain_or_low_angle=False,
high_slope=False,
cloud_shadow=False,
cloud=False,
sea=False)
]
water = data.data_vars['water']
data = data.drop_vars(['water'])
total = data.count(dim=['x', 'y'])
total_valid = (data != -1).sum(dim=['x', 'y'])
# TODO enable this check, investigate why it fails
# if total_valid <= 0:
# raise ProcessError('query returned no data')
for m in wofs_mask_flags:
mask = make_mask(water, **m)
data = data.where(mask)
total_invalid = (np.isnan(data)).sum(dim=['x', 'y'])
not_pixels = total_valid - (total - total_invalid)
# following robbi's advice, cast the dataset to a dataarray
maxFC = data.to_array(dim='variable', name='maxFC')
# turn FC array into integer only as nanargmax doesn't seem to handle floats the way we want it to
FC_int = maxFC.astype('int16')
# use numpy.nanargmax to get the index of the maximum value along the variable dimension
# BSPVNPV=np.nanargmax(FC_int, axis=0)
BSPVNPV = FC_int.argmax(dim='variable')
FC_mask = np.isfinite(maxFC).all(dim='variable') # pylint: disable=no-member,unexpected-keyword-arg
# #re-mask with nans to remove no-data
BSPVNPV = BSPVNPV.where(FC_mask)
FC_dominant = xarray.Dataset({
'BS': (BSPVNPV == 0).where(FC_mask),
'PV': (BSPVNPV == 1).where(FC_mask),
'NPV': (BSPVNPV == 2).where(FC_mask)
})
FC_count = FC_dominant.sum(dim=['x', 'y'])
# Fractional cover pixel count method
# Get number of FC pixels, divide by total number of pixels per polygon
new_ds = xarray.Dataset({
'BS': (FC_count.BS / total_valid)['BS'] * 100,
'PV': (FC_count.PV / total_valid)['PV'] * 100,
'NPV': (FC_count.NPV / total_valid)['NPV'] * 100,
'Unobservable': (not_pixels / total_valid)['BS'] * 100
})
print('dask compute')
dask_time = default_timer()
new_ds = new_ds.compute()
print('dask took', default_timer() - dask_time, 'seconds')
print(new_ds)
df = new_ds.to_dataframe()
df = df.drop('spatial_ref', axis=1)
df.reset_index(inplace=True)
return df
def load_nbarx(dc,
sensor,
query,
product='nbart',
bands_of_interest='',
filter_pq=True):
"""
Loads NBAR (Nadir BRDF Adjusted Reflectance) or NBAR-T (terrain corrected NBAR) data for a
sensor, masks using pixel quality (PQ), then optionally filters out terrain -999s (for NBAR-T).
Returns an xarray dataset and CRS and Affine objects defining map projection and geotransform
Last modified: May 2018
Author: Bex Dunn
Modified by: Claire Krause, Robbi Bishop-Taylor, Bex Dunn
inputs
dc - Handle for the Datacube to import from. This allows you to also use dev environments
if that have been imported into the environment.
sensor - Options are 'ls5', 'ls7', 'ls8'
query - A dict containing the query bounds. Can include lat/lon, time etc.
optional
product - 'nbar' or 'nbart'. Defaults to nbart unless otherwise specified
bands_of_interest - List of strings containing the bands to be read in; defaults to all bands,
options include 'red', 'green', 'blue', 'nir', 'swir1', 'swir2'
filter_pq - boolean. Will filter clouds and saturated pixels using PQ unless set to False
outputs
ds - Extracted and optionally PQ filtered dataset
crs - CRS object defining dataset coordinate reference system
affine - Affine object defining dataset affine transformation
"""
product_name = '{}_{}_albers'.format(sensor, product)
mask_product = '{}_{}_albers'.format(sensor, 'pq')
print('Loading {}'.format(product_name))
# If bands of interest are given, assign measurements in dc.load call
if bands_of_interest:
ds = dc.load(product=product_name,
measurements=bands_of_interest,
group_by='solar_day',
**query)
# If no bands of interest given, run without specifying measurements
else:
ds = dc.load(product=product_name, group_by='solar_day', **query)
# Proceed if the resulting call returns data
if ds.variables:
crs = ds.crs
affine = ds.affine
print('Loaded {}'.format(product_name))
# If pixel quality filtering is enabled, extract PQ data to use as mask
if filter_pq:
sensor_pq = dc.load(product=mask_product,
fuse_func=ga_pq_fuser,
group_by='solar_day',
**query)
# If PQ call returns data, use to mask input data
if sensor_pq.variables:
print('Generating mask {}'.format(mask_product))
good_quality = masking.make_mask(
sensor_pq.pixelquality,
cloud_acca='no_cloud',
cloud_shadow_acca='no_cloud_shadow',
cloud_shadow_fmask='no_cloud_shadow',
cloud_fmask='no_cloud',
blue_saturated=False,
green_saturated=False,
red_saturated=False,
nir_saturated=False,
swir1_saturated=False,
swir2_saturated=False,
contiguous=True)
# Apply mask to preserve only good data
ds = ds.where(good_quality)
ds.attrs['crs'] = crs
ds.attrs['affine'] = affine
# Replace nodata values with nans
ds = masking.mask_invalid_data(ds)
return ds, crs, affine
else:
print('Failed to load {}'.format(product_name))
return None, None, None
def load_clearlandsat(dc,
query,
sensors=('ls5', 'ls7', 'ls8'),
product='nbart',
dask_chunks={'time': 1},
lazy_load=False,
bands_of_interest=None,
masked_prop=0.0,
mask_dict=None,
mask_pixel_quality=True,
mask_invalid_data=True,
ls7_slc_off=False,
satellite_metadata=False):
"""Loads Landsat NBAR, NBART or FC25 and PQ data for multiple sensors (i.e. ls5, ls7, ls8) and returns a single
xarray dataset containing only observations that contain greater than a given proportion of good quality pixels.
This function can be used to extract visually appealing time series of observations that are not affected by cloud,
for example as an input to the `animated_timeseries` function from `DEAPlotting`.
The proportion of clear pixels is calculated by summing the pixels that are marked as being good quality
in the Landsat PQ25 layer. By default cloud, cloud shadow, saturated pixels and pixels missing data for any band
are considered poor quality data, but this can be customised using the `mask_dict` parameter.
Last modified: March 2019
Author: Robbi Bishop-Taylor, Bex Dunn
Parameters
----------
dc : datacube Datacube object
A specific Datacube to import from, i.e. `dc = datacube.Datacube(app='Clear Landsat')`. This allows you to
also use development datacubes if they have been imported into the environment.
query : dict
A dict containing the query bounds. Can include lat/lon, time etc. If no `time` query is given, the
function defaults to all timesteps available to all sensors (e.g. 1987-2018)
sensors : list, optional
An optional list of Landsat sensor names to load data for. Options are 'ls5', 'ls7', 'ls8'; defaults to all.
product : str, optional
An optional string specifying 'nbar', 'nbart' or 'fc'. Defaults to 'nbart'. For information on the difference,
see the '02_DEA_datasets/Introduction_to_Landsat' or '02_DEA_datasets/Introduction_to_Fractional_Cover'
notebooks from DEA-notebooks.
dask_chunks : dict, optional
An optional dictionary containing the coords and sizes you wish to create dask chunks over. Usually
used in combination with lazy_load=True (see below). example: dask_chunks = {'x': 500, 'y': 500}
lazy_load : boolean, optional
Setting this variable to 'True' will delay the computation of the function until you explicitly
run ds.compute(). If used in conjuction with dask.distributed.Client() will allow
for automatic parallel computation.
bands_of_interest : list, optional
An optional list of strings containing the bands to be read in; options include 'red', 'green', 'blue',
'nir', 'swir1', 'swir2'; defaults to all available bands if no bands are specified.
masked_prop : float, optional
An optional float giving the minimum percentage of good quality pixels required for a Landsat observation to
be loaded. Defaults to 0.0 which will return all observations regardless of pixel quality (set to e.g. 0.99
to return only observations with more than 99% good quality pixels).
mask_dict : dict, optional
An optional dict of arguments to the `masking.make_mask` function that can be used to identify poor
quality pixels from the PQ layer using alternative masking criteria. The default value of None masks
out pixels flagged as cloud or cloud shadow by either the ACCA or Fmask algorithms, any saturated pixels,
or any pixels that are missing data in any band (equivalent to: `mask_dict={'cloud_acca': 'no_cloud',
'cloud_shadow_acca': 'no_cloud_shadow', 'cloud_shadow_fmask': 'no_cloud_shadow', 'cloud_fmask': 'no_cloud',
'blue_saturated': False, 'green_saturated': False, 'red_saturated': False, 'nir_saturated': False,
'swir1_saturated': False, 'swir2_saturated': False, 'contiguous': True}`. See the
`02_DEA_datasets/Introduction_to_LandsatPQ.ipynb` notebook on DEA Notebooks for a list of all possible options.
mask_pixel_quality : bool, optional
An optional boolean indicating whether to apply the pixel quality mask to all observations that were not
filtered out for having less good quality pixels that `masked_prop`. For example, if `masked_prop=0.99`, the
filtered images may still contain up to 1% poor quality pixels. The default of False simply returns the
resulting observations without masking out these pixels; True masks them out and sets them to NaN using the
pixel quality mask, but has the side effect of changing the data type of the output arrays from int16 to
float32 which can cause memory issues. To reduce memory usage, set to False.
mask_invalid_data : bool, optional
An optional boolean indicating whether invalid -999 nodata values should be replaced with NaN. Defaults to
True; this has the side effect of changing the data type of the output arrays from int16 to float32 which
can cause memory issues. To reduce memory usage, set to False.
ls7_slc_off : bool, optional
An optional boolean indicating whether to include data from after the Landsat 7 SLC failure (i.e. SLC-off).
Defaults to False, which removes all Landsat 7 observations after May 31 2003.
satellite_metadata : bool, optional
An optional boolean indicating whether to return the dataset with a `satellite` variable that gives the name
of the satellite that made each observation in the timeseries (i.e. ls5, ls7, ls8). Defaults to False.
Returns
-------
combined_ds : xarray Dataset
An xarray dataset containing only Landsat observations that contain greater than `masked_prop`
proportion of clear pixels.
Notes
-----
Memory issues: For large data extractions, it is recommended that you set both `mask_pixel_quality=False` and
`mask_invalid_data=False`. Otherwise, all output variables will be coerced to float32 when NaN values are
inserted into the array, potentially causing your data to use 2x as much memory. Be aware that the resulting
arrays will contain invalid -999 values which should be considered in analyses.
Example
-------
>>> # Import modules
>>> import datacube
>>> import sys
>>> # Import dea-notebooks functions using relative link to 10_Scripts directory
>>> sys.path.append('../10_Scripts')
>>> import DEADataHandling
>>> # Connect to a datacube containing Landsat data
>>> dc = datacube.Datacube(app='load_clearlandsat')
>>> # Set up spatial and temporal query
>>> query = {'x': (954163, 972163),
... 'y': (-3573891, -3555891),
... 'time': ('2011-06-01', '2013-06-01'),
... 'crs': 'EPSG:3577'}
>>> # Load observations with more than 75% good quality pixels from ls5, ls7 and ls8 as a combined dataset
>>> landsat_ds = DEADataHandling.load_clearlandsat(dc=dc, query=query, sensors=['ls5', 'ls7', 'ls8'],
... bands_of_interest=['red', 'green', 'blue'],
... masked_prop=0.75, mask_pixel_quality=True, ls7_slc_off=True)
Loading ls5
Loading 4 filtered ls5 timesteps
Loading ls7
Loading 29 filtered ls7 timesteps
Loading ls8
Loading 3 filtered ls8 timesteps
Combining and sorting ls5, ls7, ls8 data
Replacing invalid -999 values with NaN (data will be coerced to float32)
>>> # Test that function returned data
>>> len(landsat_ds.time) > 0
True
"""
#######################
# Process each sensor #
#######################
#warn if loading a pq bitstring product and attempting to mask it (and therefore cast to float)
if product == 'pq' and (mask_invalid_data or mask_pixel_quality):
warnings.warn(
"""You are attempting to load pixel quality product with a mask flag
(mask_invalid_data or mask_pixel_quality). Pixel quality is a bitstring
(only makes sense as int) and masking
casts to float32.""")
# Dictionary to save results from each sensor
filtered_sensors = {}
# Iterate through all sensors, returning only observations with > mask_prop clear pixels
for sensor in sensors:
# Load PQ data using dask
print(f'Loading {sensor}')
# If bands of interest are given, assign measurements in dc.load call. This is
# for compatibility with the existing dea-notebooks load_nbarx function.
if bands_of_interest:
# Lazily load Landsat data using dask
data = dc.load(product=f'{sensor}_{product}_albers',
measurements=bands_of_interest,
group_by='solar_day',
dask_chunks=dask_chunks,
**query)
# If no bands of interest given, run without specifying measurements, and
# therefore return all available bands
else:
# Lazily load Landsat data using dask
data = dc.load(product=f'{sensor}_{product}_albers',
group_by='solar_day',
dask_chunks=dask_chunks,
**query)
# Load PQ data
pq = dc.load(product=f'{sensor}_pq_albers',
group_by='solar_day',
fuse_func=ga_pq_fuser,
dask_chunks=dask_chunks,
**query)
# If resulting dataset has data, continue:
if data.variables:
# Remove Landsat 7 SLC-off from PQ layer if ls7_slc_off=False
if not ls7_slc_off and sensor == 'ls7':
print(' Ignoring SLC-off observations for ls7')
data = data.sel(time=data.time < np.datetime64('2003-05-30'))
# If more than 0 timesteps
if len(data.time) > 0:
# Return only Landsat observations that have matching PQ data
time = (data.time - pq.time).time
data = data.sel(time=time)
pq = pq.sel(time=time)
# If a custom dict is provided for mask_dict, use these values to make mask from PQ
if mask_dict:
# Mask PQ using custom values by unpacking mask_dict **kwarg
good_quality = masking.make_mask(pq.pixelquality,
**mask_dict)
else:
# Identify pixels with no clouds in either ACCA for Fmask
good_quality = masking.make_mask(
pq.pixelquality,
cloud_acca='no_cloud',
cloud_shadow_acca='no_cloud_shadow',
cloud_shadow_fmask='no_cloud_shadow',
cloud_fmask='no_cloud',
blue_saturated=False,
green_saturated=False,
red_saturated=False,
nir_saturated=False,
swir1_saturated=False,
swir2_saturated=False,
contiguous=True)
# Compute good data for each observation as a percentage of total array pixels. Need to
# sum over x and y axes individually so that the function works with lat-lon dimensions,
# and because it isn't currently possible to pass a list of axes (bug with xarray?)
data_perc = good_quality.sum(axis=1).sum(
axis=1) / (good_quality.shape[1] * good_quality.shape[2])
# Add data_perc data to Landsat dataset as a new xarray variable
data['data_perc'] = xr.DataArray(data_perc,
[('time', data.time)])
# Filter by data_perc to drop low quality observations and finally import data using dask
filtered = data.sel(time=data.data_perc >= masked_prop)
print(
f' Loading {len(filtered.time)} filtered {sensor} timesteps'
)
# Optionally apply pixel quality mask to all observations that were not dropped in previous step
if mask_pixel_quality:
# First change dtype to float32, then mask out values using
# `.where()`. By casting to float32, we prevent `.where()`
# from automatically casting to float64, using 2x the memory
# We also need to manually reset attributes due to a possible
# bug in recent xarray version
filtered = filtered.astype(
np.float32).assign_attrs(crs=filtered.crs)
filtered = filtered.where(good_quality)
# Optionally add satellite name variable
if satellite_metadata:
filtered['satellite'] = xr.DataArray(
[sensor] * len(filtered.time),
[('time', filtered.time)])
# Add result to dictionary
if lazy_load == True:
filtered_sensors[sensor] = filtered
else:
filtered_sensors[sensor] = filtered.compute()
# Close datasets
filtered = None
good_quality = None
data = None
pq = None
else:
# If there is no data for sensor or if another error occurs:
print(f' Skipping {sensor}; no valid data for query')
else:
# If there is no data for sensor or if another error occurs:
print(f' Skipping {sensor}; no valid data for query')
############################
# Combine multiple sensors #
############################
# Proceed with concatenating only if there is more than 1 sensor processed
if len(filtered_sensors) > 1:
# Concatenate all sensors into one big xarray dataset, and then sort by time
sensor_string = ", ".join(filtered_sensors.keys())
print(f'Combining and sorting {sensor_string} data')
combined_ds = xr.concat(filtered_sensors.values(), dim='time')
combined_ds = combined_ds.sortby('time')
# Optionally filter to replace no data values with nans
if mask_invalid_data:
print(
' Replacing invalid -999 values with NaN (data will be coerced to float32)'
)
# First change dtype to float32, then mask out values using
# `.where()`. By casting to float32, we prevent `.where()`
# from automatically casting to float64, using 2x the memory
# We also need to manually reset attributes due to a possible
# bug in recent xarray version
combined_ds = (combined_ds.astype(
np.float32).assign_attrs(crs=combined_ds.crs))
combined_ds = masking.mask_invalid_data(combined_ds)
# reset pixel quality attributes
if product == 'pq':
combined_ds.pixelquality.attrs.update(
list(filtered_sensors.values())[0].pixelquality.attrs)
# Return combined dataset
return combined_ds
# Return the single dataset if only one sensor was processed
elif len(filtered_sensors) == 1:
sensor_string = ", ".join(filtered_sensors.keys())
print(f'Returning {sensor_string} data')
sensor_ds = list(filtered_sensors.values())[0]
# Optionally filter to replace no data values with nans
if mask_invalid_data:
print(
' Replacing invalid -999 values with NaN (data will be coerced to float32)'
)
# First change dtype to float32, then mask out values using
# `.where()`. By casting to float32, we prevent `.where()`
# from automatically casting to float64, using 2x the memory
# We also need to manually reset attributes due to a possible
# bug in recent xarray version
sensor_ds = (sensor_ds.astype(
np.float32).assign_attrs(crs=sensor_ds.crs))
sensor_ds = masking.mask_invalid_data(sensor_ds)
return sensor_ds
else:
print(
f'No data returned for query for any sensor in {", ".join(sensors)} '
f'and time range {"-".join(query["time"])}')