def generate_derived_nbar(self, dataset_types, nbar, pqa, pqa_masks, overwrite=False):
for dataset_type in dataset_types:
filename = self.get_output_filename_derived_nbar(nbar, dataset_type)
_log.info("Generating data from [%s] with pq [%s] and pq mask [%s] to [%s]", nbar.path, pqa and pqa.path or "", pqa and pqa_masks or "", filename)
metadata = get_dataset_metadata(nbar)
data = None
if pqa:
data = get_dataset_data_with_pq(nbar, pqa, pq_masks=pqa_masks)
else:
data = get_dataset_data(nbar)
_log.debug("data is [%s]", data)
if dataset_type == DatasetType.NDVI:
ndvi = calculate_ndvi(data[nbar.bands.RED], data[nbar.bands.NEAR_INFRARED])
raster_create(filename, [ndvi], metadata.transform, metadata.projection, NDV, gdal.GDT_Float32)
elif dataset_type == DatasetType.EVI:
evi = calculate_evi(data[nbar.bands.RED], data[nbar.bands.BLUE], data[nbar.bands.NEAR_INFRARED])
raster_create(filename, [evi], metadata.transform, metadata.projection, NDV, gdal.GDT_Float32)
elif dataset_type == DatasetType.NBR:
nbr = calculate_nbr(data[nbar.bands.NEAR_INFRARED], data[nbar.bands.SHORT_WAVE_INFRARED_2])
raster_create(filename, [nbr], metadata.transform, metadata.projection, NDV, gdal.GDT_Float32)
def retrieve_data(dataset, pq, pq_masks, path, x, y, overwrite=False, stack=False):
_log.info("Retrieving data from [%s] with pq [%s] and pq mask [%s] to [%s]", dataset.path, pq and pq.path or "", pq and pq_masks or "", path)
if os.path.exists(path) and not overwrite:
_log.error("Output file [%s] exists", path)
raise Exception("Output file [%s] already exists" % path)
data = None
metadata = get_dataset_metadata(dataset)
if pq:
data = get_dataset_data_with_pq(dataset, pq, pq_masks=pq_masks)
else:
data = get_dataset_data(dataset)
_log.debug("data is [%s]", data)
raster_create(path, [data[b] for b in dataset.bands],
metadata.transform, metadata.projection, NDV, gdal.GDT_Int16)
# If we are creating a stack then also add to a file list file...
if stack:
path_file_list = os.path.join(os.path.dirname(path), get_filename_file_list(dataset.satellite, dataset.dataset_type, x, y))
_log.info("Also going to write file list to [%s]", path_file_list)
with open(path_file_list, "ab") as f:
print >>f, path
def test_retrieve_data_ls5_mndwi(config=None):
filename = "LS5_TM_MNDWI_{x:03d}_{y:04d}_{date}.{x_offset:04d}_{y_offset:04d}.{x_size:04d}x{y_size:04d}.tif".format(x=CELL_X, y=CELL_Y, date=DATE, x_offset=X_OFFSET, y_offset=Y_OFFSET, x_size=X_SIZE, y_size=Y_SIZE)
tiles = list_tiles_as_list(x=[CELL_X], y=[CELL_Y],
acq_min=ACQ_LS5, acq_max=ACQ_LS5,
satellites=[Satellite.LS5],
dataset_types=[MNDWI_DATASET_TYPE],
config=config)
assert len(tiles) == 1
dataset = tiles[0].datasets[MNDWI_DATASET_TYPE]
data = get_dataset_data(dataset=dataset, x=X_OFFSET, y=Y_OFFSET, x_size=X_SIZE, y_size=Y_SIZE)
assert(data)
_log.info("data is [%s]\n%s", numpy.shape(data), data)
ndv = get_dataset_ndv(dataset)
assert(is_ndv(ndv, MNDWI_NDV))
data_type = get_dataset_datatype(dataset)
assert(data_type == MNDWI_DATA_TYPE)
metadata = generate_dataset_metadata(x=CELL_X, y=CELL_Y, acq_dt=ACQ_LS5,
dataset=dataset, bands=None,
mask_pqa_apply=False, mask_pqa_mask=None,
mask_wofs_apply=False, mask_wofs_mask=None)
raster_create_geotiff(filename, [data[b] for b in dataset.bands], CELL_GEO_TRANSFORM, CELL_PROJECTION, ndv, data_type,
dataset_metadata=metadata, band_ids=[b.name for b in dataset.bands])
assert filecmp.cmp(filename, get_test_data_path(filename))
def doit(self):
shape = (4000, 4000)
masks = [PQ_MASK_CLEAR,
PQ_MASK_SATURATION_OPTICAL,
PQ_MASK_SATURATION_THERMAL,
PQ_MASK_CONTIGUITY,
PQ_MASK_LAND,
PQ_MASK_CLOUD_ACCA,
PQ_MASK_CLOUD_FMASK,
PQ_MASK_CLOUD_SHADOW_ACCA,
PQ_MASK_CLOUD_SHADOW_FMASK]
observation_count = empty_array(shape=shape, dtype=numpy.int16, ndv=0)
observation_count_clear = dict()
for mask in masks:
observation_count_clear[mask] = empty_array(shape=shape, dtype=numpy.int16, ndv=0)
metadata = None
for tile in self.get_tiles():
# Get the PQ mask
pq = tile.datasets[DatasetType.PQ25]
data = get_dataset_data(pq, [Pq25Bands.PQ])[Pq25Bands.PQ]
#
# Count any pixels that are no NDV - don't think we should actually have any but anyway
#
# Mask out any no data pixels - should actually be none but anyway
pq = numpy.ma.masked_equal(data, NDV)
# Count the data pixels - i.e. pixels that were NOT masked out
observation_count += numpy.where(data.mask, 0, 1)
#
# Count and pixels that are not masked due to pixel quality
#
for mask in masks:
# Apply the particular pixel mask
pqm = numpy.ma.masked_where(numpy.bitwise_and(data, mask) != mask, data)
# Count the pixels that were not masked out
observation_count_clear[mask] += numpy.where(pqm.mask, 0, 1)
if not metadata:
metadata = get_dataset_metadata(pq)
# Create the output datasets
# Observation Count
raster_create(self.output()[0].path, [observation_count] + [observation_count_clear[mask] for mask in masks],
metadata.transform, metadata.projection, NDV, GDT_Int16)
def create(
self, x, y, satellites, acq_min, acq_max, dataset_types, bands, months=None, exclude=None, sort=SortType.ASC
):
self.x = x
self.y = y
self.satellites = satellites
self.acq_min = acq_min
self.acq_max = acq_max
self.stack = {}
self.acq_stack = []
self.meta_stack = []
self.bands = bands
self.tile_shape = None
self.shape_stack = []
tiles = list_tiles([x], [y], satellites, acq_min, acq_max, dataset_types, months, exclude, sort)
for tile in tiles:
dataset = DatasetType.ARG25 in tile.datasets and tile.datasets[DatasetType.ARG25] or None
if dataset is None:
continue
tile_metadata = get_dataset_metadata(dataset)
if tile_metadata is None:
continue
pqa = DatasetType.PQ25 in tile.datasets and tile.datasets[DatasetType.PQ25] or None
if pqa is None:
continue
if self.pqa_stack is None:
self.pqa_stack = [pqa]
else:
self.pqa_stack.append(pqa)
data = get_dataset_data(dataset, bands)
need_shape = True
for band in data:
if need_shape:
self.shape_stack.append(np.array(data[band]).shape)
need_shape = False
if band in self.stack:
"""
Append it
"""
self.stack[band] = np.vstack((self.stack[band], np.array(data[band]).ravel()))
else:
self.stack[band] = np.array(data[band]).ravel()
self.acq_stack.append(tile.start_datetime)
self.meta_stack.append(tile_metadata)
del data
del pqa
del tile_metadata
del dataset
def retrieve_pixel_value(dataset, pq, pq_masks, latitude, longitude, ndv=NDV):
_log.debug("Retrieving pixel value(s) at lat=[%f] lon=[%f] from [%s] with pq [%s] and pq mask [%s]", latitude, longitude, dataset.path, pq and pq.path or "", pq and pq_masks or "")
metadata = get_dataset_metadata(dataset)
x, y = latlon_to_xy(latitude, longitude, metadata.transform)
_log.debug("Retrieving value at x=[%d] y=[%d]", x, y)
data = None
if pq:
data = get_dataset_data_with_pq(dataset, pq, x=x, y=y, x_size=1, y_size=1, pq_masks=pq_masks, ndv=ndv)
else:
data = get_dataset_data(dataset, x=x, y=y, x_size=1, y_size=1)
_log.debug("data is [%s]", data)
return data
def run(self):
self.parse_arguments()
config = Config()
_log.debug(config.to_str())
path = self.get_output_filename(self.dataset_type)
_log.info("Output file is [%s]", path)
if os.path.exists(path):
if self.overwrite:
_log.info("Removing existing output file [%s]", path)
os.remove(path)
else:
_log.error("Output file [%s] exists", path)
raise Exception("Output file [%s] already exists" % path)
# TODO
bands = get_bands(self.dataset_type, self.satellites[0])
# TODO once WOFS is in the cube
tiles = list_tiles_as_list(x=[self.x], y=[self.y], acq_min=self.acq_min, acq_max=self.acq_max,
satellites=[satellite for satellite in self.satellites],
dataset_types=[self.dataset_type],
database=config.get_db_database(),
user=config.get_db_username(),
password=config.get_db_password(),
host=config.get_db_host(), port=config.get_db_port())
raster = None
metadata = None
# TODO - PQ is UNIT16 (others are INT16) and so -999 NDV doesn't work
ndv = self.dataset_type == DatasetType.PQ25 and UINT16_MAX or NDV
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
import itertools
for x, y in itertools.product(range(0, 4000, self.chunk_size_x), range(0, 4000, self.chunk_size_y)):
_log.info("About to read data chunk ({xmin:4d},{ymin:4d}) to ({xmax:4d},{ymax:4d})".format(xmin=x, ymin=y, xmax=x+self.chunk_size_x-1, ymax=y+self.chunk_size_y-1))
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
stack = dict()
for tile in tiles:
if self.list_only:
_log.info("Would summarise dataset [%s]", tile.datasets[self.dataset_type].path)
continue
pqa = None
_log.debug("Reading dataset [%s]", tile.datasets[self.dataset_type].path)
if not metadata:
metadata = get_dataset_metadata(tile.datasets[self.dataset_type])
# Apply PQA if specified
if self.apply_pqa_filter:
data = get_dataset_data_with_pq(tile.datasets[self.dataset_type], tile.datasets[DatasetType.PQ25], bands=bands, x=x, y=y, x_size=self.chunk_size_x, y_size=self.chunk_size_y, pq_masks=self.pqa_mask, ndv=ndv)
else:
data = get_dataset_data(tile.datasets[self.dataset_type], bands=bands, x=x, y=y, x_size=self.chunk_size_x, y_size=self.chunk_size_y)
for band in bands:
if band in stack:
stack[band].append(data[band])
else:
stack[band] = [data[band]]
_log.debug("data[%s] has shape [%s] and MB [%s]", band.name, numpy.shape(data[band]), data[band].nbytes/1000/1000)
_log.debug("stack[%s] has [%s] elements", band.name, len(stack[band]))
# Apply summary method
_log.info("Finished reading {count} datasets for chunk ({xmin:4d},{ymin:4d}) to ({xmax:4d},{ymax:4d}) - about to summarise them".format(count=len(tiles), xmin=x, ymin=y, xmax=x+self.chunk_size_x-1, ymax=y+self.chunk_size_y-1))
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
masked_stack = dict()
for band in bands:
masked_stack[band] = numpy.ma.masked_equal(stack[band], ndv)
_log.debug("masked_stack[%s] is %s", band.name, masked_stack[band])
_log.debug("masked stack[%s] has shape [%s] and MB [%s]", band.name, numpy.shape(masked_stack[band]), masked_stack[band].nbytes/1000/1000)
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
if self.summary_method == TimeSeriesSummaryMethod.MIN:
masked_summary = numpy.min(masked_stack[band], axis=0)
elif self.summary_method == TimeSeriesSummaryMethod.MAX:
masked_summary = numpy.max(masked_stack[band], axis=0)
elif self.summary_method == TimeSeriesSummaryMethod.MEAN:
masked_summary = numpy.mean(masked_stack[band], axis=0)
elif self.summary_method == TimeSeriesSummaryMethod.MEDIAN:
masked_summary = numpy.median(masked_stack[band], axis=0)
# aka 50th percentile
elif self.summary_method == TimeSeriesSummaryMethod.MEDIAN_NON_INTERPOLATED:
masked_sorted = numpy.ma.sort(masked_stack[band], axis=0)
masked_percentile_index = numpy.ma.floor(numpy.ma.count(masked_sorted, axis=0) * 0.95).astype(numpy.int16)
masked_summary = numpy.ma.choose(masked_percentile_index, masked_sorted)
elif self.summary_method == TimeSeriesSummaryMethod.COUNT:
# TODO Need to artificially create masked array here since it is being expected/filled below!!!
masked_summary = numpy.ma.masked_equal(masked_stack[band].count(axis=0), ndv)
elif self.summary_method == TimeSeriesSummaryMethod.SUM:
masked_summary = numpy.sum(masked_stack[band], axis=0)
elif self.summary_method == TimeSeriesSummaryMethod.STANDARD_DEVIATION:
masked_summary = numpy.std(masked_stack[band], axis=0)
elif self.summary_method == TimeSeriesSummaryMethod.VARIANCE:
masked_summary = numpy.var(masked_stack[band], axis=0)
# currently 95th percentile
elif self.summary_method == TimeSeriesSummaryMethod.PERCENTILE:
masked_sorted = numpy.ma.sort(masked_stack[band], axis=0)
masked_percentile_index = numpy.ma.floor(numpy.ma.count(masked_sorted, axis=0) * 0.95).astype(numpy.int16)
masked_summary = numpy.ma.choose(masked_percentile_index, masked_sorted)
elif self.summary_method == TimeSeriesSummaryMethod.YOUNGEST_PIXEL:
# TODO the fact that this is band at a time might be problematic. We really should be considering
# all bands at once (that is what the landsat_mosaic logic did). If PQA is being applied then
# it's probably all good but if not then we might get odd results....
masked_summary = empty_array(shape=(self.chunk_size_x, self.chunk_size_x), dtype=numpy.int16, ndv=ndv)
# Note the reversed as the stack is created oldest first
for d in reversed(stack[band]):
masked_summary = numpy.where(masked_summary == ndv, d, masked_summary)
# If the summary doesn't contain an no data values then we can stop
if not numpy.any(masked_summary == ndv):
break
# TODO Need to artificially create masked array here since it is being expected/filled below!!!
masked_summary = numpy.ma.masked_equal(masked_summary, ndv)
elif self.summary_method == TimeSeriesSummaryMethod.OLDEST_PIXEL:
# TODO the fact that this is band at a time might be problematic. We really should be considering
# all bands at once (that is what the landsat_mosaic logic did). If PQA is being applied then
# it's probably all good but if not then we might get odd results....
masked_summary = empty_array(shape=(self.chunk_size_x, self.chunk_size_x), dtype=numpy.int16, ndv=ndv)
# Note the NOT reversed as the stack is created oldest first
for d in stack[band]:
masked_summary = numpy.where(masked_summary == ndv, d, masked_summary)
# If the summary doesn't contain an no data values then we can stop
if not numpy.any(masked_summary == ndv):
break
# TODO Need to artificially create masked array here since it is being expected/filled below!!!
masked_summary = numpy.ma.masked_equal(masked_summary, ndv)
masked_stack[band] = None
_log.debug("NONE-ing masked stack[%s]", band.name)
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
_log.debug("masked summary is [%s]", masked_summary)
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
# Create the output file
if not os.path.exists(path):
_log.info("Creating raster [%s]", path)
driver = gdal.GetDriverByName("GTiff")
assert driver
raster = driver.Create(path, metadata.shape[0], metadata.shape[1], len(bands), gdal.GDT_Int16)
assert raster
raster.SetGeoTransform(metadata.transform)
raster.SetProjection(metadata.projection)
for b in bands:
raster.GetRasterBand(b.value).SetNoDataValue(ndv)
_log.info("Writing band [%s] data to raster [%s]", band.name, path)
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
raster.GetRasterBand(band.value).WriteArray(masked_summary.filled(ndv), xoff=x, yoff=y)
raster.GetRasterBand(band.value).ComputeStatistics(True)
raster.FlushCache()
masked_summary = None
_log.debug("NONE-ing the masked summary")
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
stack = None
_log.debug("Just NONE-ed the stack")
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
raster = None
_log.debug("Just NONE'd the raster")
_log.debug("Current MAX RSS usage is [%d] MB", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
_log.info("Memory usage was [%d MB]", resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / 1024)
_log.info("CPU time used [%s]", timedelta(seconds=int(resource.getrusage(resource.RUSAGE_SELF).ru_utime)))
def tidal_workflow(tiles,
percentile=10,
xtile=None,
ytile=None,
low_off=0,
high_off=0,
out_fnames=None):
"""
A baseline workflow for doing the baresoil percentile, NBAR, FC
corresponding mosaics.
"""
# Get some basic image info
ds_type = DatasetType.ARG25
ds = tiles[0]
dataset = ds.datasets[ds_type]
md = get_dataset_metadata(dataset)
_log.info("low and high offset %s , %s ", low_off, high_off)
if md is None:
_log.info("Tile path not exists %s", dataset.path)
return
samples, lines = md.shape
#_log.info("dataset shape %s for %s", md.shape, out_fnames)
time_slices = len(tiles)
_log.info("length of time slices [%d] for %s", time_slices, out_fnames)
geobox = GriddedGeoBox.from_gdal_dataset(gdal.Open(dataset.path))
lat_lon = ""
for line in out_fnames:
lat_lon = line.split("/")[-2]
break
# Initialise the tiling scheme for processing
if xtile is None:
xtile = samples
if ytile is None:
ytile = lines
chunks = generate_tiles(samples,
lines,
xtile=samples,
ytile=ytile,
generator=False)
# Define no-data
no_data_value = NDV
nan = numpy.float32(numpy.nan) # for the FC dtype no need for float64
# Define the output files
if out_fnames is None:
nbar_outfname = 'nbar_best_pixel'
else:
nbar_outfname = out_fnames[0]
#nbar_outnb = len(TidalProd)
nbar_outnb = len(extraInfo)
#fc_outnb = len(Fc25Bands)
out_dtype = gdal.GDT_Int16
#_log.info("input xtile [%d] ytile [%d] for %s", xtile, ytile, out_fnames)
nbar_outds = TiledOutput(nbar_outfname,
samples=samples,
lines=lines,
bands=nbar_outnb,
dtype=out_dtype,
nodata=no_data_value,
geobox=geobox,
fmt="GTiff")
satellite_code = {Satellite.LS5: 5, Satellite.LS7: 7, Satellite.LS8: 8}
count = 0
# Loop over each spatial tile/chunk and build up the time series
for chunk in chunks:
count = 0
ys, ye = chunk[0]
xs, xe = chunk[1]
ysize = ye - ys
xsize = xe - xs
dims = (time_slices, ysize, xsize)
#_log.info("got chunk [%s] for %s", chunk, out_fnames)
# Initialise the intermediate and best_pixel output arrays
data = {}
median_nbar = {}
stack_tidal = numpy.zeros(dims, dtype='float32')
stack_lowOff = numpy.zeros(dims, dtype='int16')
stack_highOff = numpy.zeros(dims, dtype='int16')
stack_count = numpy.zeros(dims, dtype='int16')
median_lowOff = numpy.zeros((ysize, xsize), dtype='int16')
median_highOff = numpy.zeros((ysize, xsize), dtype='int16')
median_count = numpy.zeros((ysize, xsize), dtype='int16')
median_lowOff.fill(no_data_value)
median_highOff.fill(no_data_value)
median_count.fill(no_data_value)
stack_nbar = {}
#_log.info("all initialised successfully")
for band in Ls57Arg25Bands:
stack_nbar[band] = numpy.zeros(dims, dtype='int16')
median_nbar[band] = numpy.zeros((ysize, xsize), dtype='int16')
median_nbar[band].fill(no_data_value)
for idx, ds in enumerate(tiles):
pqa = ds.datasets[DatasetType.PQ25]
nbar = ds.datasets[DatasetType.ARG25]
mask = get_mask_pqa(pqa, x=xs, y=ys, x_size=xsize, y_size=ysize)
# NBAR
data[DatasetType.ARG25] = get_dataset_data(nbar,
x=xs,
y=ys,
x_size=xsize,
y_size=ysize)
#mask |= numexpr.evaluate("(bare_soil < 0) | (bare_soil > 8000)")A
errcnt = 0
# apply the mask to each dataset and insert into the 3D array
if satellite_code[nbar.satellite] == 8:
for band in Ls57Arg25Bands:
for oband in Ls8Arg25Bands:
try:
if oband.name == band.name:
data[DatasetType.
ARG25][oband][mask] = no_data_value
stack_nbar[band][idx] = data[
DatasetType.ARG25][oband]
break
except ValueError:
errcnt = 1
_log.info("Data converting error LS8")
except IOError:
errcnt = 1
_log.info("reading error LS8")
except KeyError:
errcnt = 1
_log.info("Key error LS8")
except:
errcnt = 1
_log.info("Unexpected error for LS8: %s",
sys.exc_info()[0])
else:
for band in Ls57Arg25Bands:
try:
data[DatasetType.ARG25][band][mask] = no_data_value
stack_nbar[band][idx] = data[DatasetType.ARG25][band]
except ValueError:
errcnt = 1
_log.info("Data converting error LS57")
except IOError:
errcnt = 1
_log.info("NBAR reading error LS57")
except KeyError:
errcnt = 1
_log.info("Key error LS57")
except:
errcnt = 1
_log.info("Unexpected error LS57: %s",
sys.exc_info()[0])
if errcnt != 0:
if errcnt == 1:
_log.info("nbar tile has problem %s", nbar.path)
errcnt = 0
continue
# Add bare soil, satellite and date to the 3D arrays
try:
#_log.info("bare soil for %s %s",bare_soil, out_fnames)
low = int(float(low_off) * 100)
high = int(float(high_off) * 100)
stack_lowOff[idx][:] = low
stack_highOff[idx][:] = high
#_log.info("count observed [%d] on %d", count, dtime)
count1 = int(
numpy.ma.count(numpy.ma.masked_less(stack_nbar, 1)))
if count1 < 1:
_log.info(
"no data present on %d and year %d for tile %s reducing count by one",
mtime, dtime, lat_lon)
else:
count = count + 1
stack_count[idx][:] = count
except:
_log.info("stacking - Unexpected error: %s", sys.exc_info()[0])
# Loop over each time slice and generate a mosaic for each dataset_type
_log.info("checking - flow path: ")
ndv = get_dataset_type_ndv(DatasetType.ARG25)
try:
_log.info("ndv is %s", ndv)
for idx in range(time_slices):
median_count = stack_count[idx]
median_lowOff = stack_lowOff[idx]
median_highOff = stack_highOff[idx]
_log.info("ccccc_data ")
for band in TidalProd:
bn = band.value
if bn == 1:
nbar_outds.write_tile(median_count, chunk, raster_band=bn)
elif bn == 2:
nbar_outds.write_tile(median_lowOff, chunk, raster_band=bn)
elif bn == 3:
nbar_outds.write_tile(median_highOff,
chunk,
raster_band=bn)
except ValueError:
_log.info("Data converting final error")
except IOError:
_log.info("writing error LS57")
except KeyError:
_log.info("Key error final")
except:
_log.info("Final Unexpected error: %s", sys.exc_info()[0])
_log.info("total dataset counts for each chunk is %d for tile %s",
count, lat_lon)
# Close the output files
nbar_outds.close()
def doit(self):
shape = (4000, 4000)
no_data_value = NDV
best_pixel_data = dict()
# TODO
if Satellite.LS8.value in self.satellites:
bands = Ls8Arg25Bands
else:
bands = Ls57Arg25Bands
for band in bands:
best_pixel_data[band] = empty_array(shape=shape, dtype=numpy.int16, ndv=no_data_value)
best_pixel_satellite = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
# best_pixel_epoch = empty_array(shape=shape, dtype=numpy.int32, ndv=NDV)
best_pixel_date = empty_array(shape=shape, dtype=numpy.int32, ndv=NDV)
current_satellite = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
# current_epoch = empty_array(shape=shape, dtype=numpy.int32, ndv=NDV)
current_date = empty_array(shape=shape, dtype=numpy.int32, ndv=NDV)
metadata = None
SATELLITE_DATA_VALUES = {Satellite.LS5: 5, Satellite.LS7: 7, Satellite.LS8: 8}
for tile in self.get_tiles(sort=SortType.DESC):
# Get ARG25 dataset
dataset = tile.datasets[DatasetType.ARG25]
_log.info("Processing ARG tile [%s]", dataset.path)
if not metadata:
metadata = get_dataset_metadata(dataset)
band_data = None
if self.apply_pq_filter:
band_data = get_dataset_data_with_pq(dataset, tile.datasets[DatasetType.PQ25])
else:
band_data = get_dataset_data(dataset)
# Create the provenance datasets
# NOTE: need to do this BEFORE selecting the pixel since it is actually using the fact that the
# selected pixel currently doesn't have a value
# NOTE: band values are propagated "as a job lot" so can just check any band
# TODO better way than just saying....RED....?
band = bands.RED
# Satellite
current_satellite.fill(SATELLITE_DATA_VALUES[dataset.satellite])
best_pixel_satellite = numpy.where(best_pixel_data[band] == no_data_value, current_satellite, best_pixel_satellite)
# # Epoch dataset
#
# current_epoch.fill(calendar.timegm(tile.end_datetime.timetuple()))
# best_pixel_epoch = numpy.where(best_pixel_data[band] == no_data_value, current_epoch, best_pixel_epoch)
# Date dataset (20150101)
current_date.fill(tile.end_datetime.year * 10000 + tile.end_datetime.month * 100 + tile.end_datetime.day)
best_pixel_date = numpy.where(best_pixel_data[band] == no_data_value, current_date, best_pixel_date)
for band in bands:
data = band_data[band]
# _log.debug("data = \n%s", data)
# Replace any NO DATA best pixels with data pixels
# TODO should I explicitly do the AND data is not NO DATA VALUE?
best_pixel_data[band] = numpy.where(best_pixel_data[band] == no_data_value, data, best_pixel_data[band])
# _log.debug("best pixel = \n%s", best_pixel_data[band])
still_no_data = numpy.any(numpy.array([best_pixel_data[b] for b in bands]) == no_data_value)
# _log.debug("still no data pixels = %s", still_no_data)
if not still_no_data:
break
# Now want to mask out values in the provenance datasets if we haven't actually got a value
# TODO better way than just saying....RED....?
band = bands.RED
mask = numpy.ma.masked_equal(best_pixel_data[band], NDV).mask
best_pixel_satellite = numpy.ma.array(best_pixel_satellite, mask=mask).filled(NDV)
# best_pixel_epoch = numpy.ma.array(best_pixel_epoch, mask=mask).fill(NDV)
best_pixel_date = numpy.ma.array(best_pixel_date, mask=mask).filled(NDV)
# Composite NBAR dataset
raster_create(self.get_output_path("NBAR"), [best_pixel_data[b] for b in bands],
metadata.transform, metadata.projection, NDV, gdal.GDT_Int16)
# Provenance (satellite) dataset
raster_create(self.get_output_path("SAT"),
[best_pixel_satellite],
metadata.transform, metadata.projection, no_data_value,
gdal.GDT_Int16)
# # Provenance (epoch) dataset
#
# raster_create(self.get_output_path("EPOCH"),
# [best_pixel_epoch],
# metadata.transform, metadata.projection, no_data_value,
# gdal.GDT_Int32)
# Provenance (day of month) dataset
raster_create(self.get_output_path("DATE"),
[best_pixel_date],
metadata.transform, metadata.projection, no_data_value,
gdal.GDT_Int32)
def doit(self):
_log.debug("Bare Soil Cell Task - doit()")
shape = (4000, 4000)
no_data_value = NDV
best_pixel_fc = dict()
for band in Fc25Bands:
best_pixel_fc[band] = empty_array(shape=shape, dtype=numpy.int16, ndv=INT16_MIN)
best_pixel_nbar = dict()
for band in Ls57Arg25Bands:
best_pixel_nbar[band] = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
best_pixel_satellite = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
best_pixel_year = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
best_pixel_month = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
best_pixel_epoch = empty_array(shape=shape, dtype=numpy.int32, ndv=NDV)
current_satellite = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
current_year = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
current_month = empty_array(shape=shape, dtype=numpy.int16, ndv=NDV)
current_epoch = empty_array(shape=shape, dtype=numpy.int32, ndv=NDV)
SATELLITE_DATA_VALUES = {Satellite.LS5: 5, Satellite.LS7: 7, Satellite.LS8: 8}
metadata_nbar = None
metadata_fc = None
for tile in self.get_tiles():
# Get the PQ mask
pq = tile.datasets[DatasetType.PQ25]
data_pq = get_dataset_data(pq, [Pq25Bands.PQ])[Pq25Bands.PQ]
mask_pq = get_pq_mask(data_pq)
# Get NBAR dataset
nbar = tile.datasets[DatasetType.ARG25]
_log.info("Processing NBAR tile [%s]", nbar.path)
if not metadata_nbar:
metadata_nbar = get_dataset_metadata(nbar)
data_nbar = get_dataset_data_with_pq(nbar, Ls57Arg25Bands, tile.datasets[DatasetType.PQ25])
# Get the NDVI mask
red = data_nbar[Ls57Arg25Bands.RED]
nir = data_nbar[Ls57Arg25Bands.NEAR_INFRARED]
ndvi_data = calculate_ndvi(red, nir)
ndvi_data = numpy.ma.masked_equal(ndvi_data, NDV)
ndvi_data = numpy.ma.masked_outside(ndvi_data, 0, 0.3, copy=False)
mask_ndvi = ndvi_data.mask
# Get FC25 dataset
fc = tile.datasets[DatasetType.FC25]
_log.info("Processing FC tile [%s]", fc.path)
if not metadata_fc:
metadata_fc = get_dataset_metadata(fc)
_log.debug("metadata fc is %s", metadata_fc)
data_fc = get_dataset_data(fc, Fc25Bands)
data_bare_soil = data_fc[Fc25Bands.BS]
data_bare_soil = numpy.ma.masked_equal(data_bare_soil, -999)
data_bare_soil = numpy.ma.masked_outside(data_bare_soil, 0, 8000)
data_bare_soil.mask = (data_bare_soil.mask | mask_pq | mask_ndvi)
data_bare_soil = data_bare_soil.filled(NDV)
# Compare the bare soil value from this dataset to the current "best" value
best_pixel_fc[Fc25Bands.BS] = numpy.fmax(best_pixel_fc[Fc25Bands.BS], data_bare_soil)
# Now update the other best pixel datasets/bands to grab the pixels we just selected
for band in Ls57Arg25Bands:
best_pixel_nbar[band] = propagate_using_selected_pixel(best_pixel_fc[Fc25Bands.BS],
data_bare_soil,
data_nbar[band],
best_pixel_nbar[band])
for band in [Fc25Bands.PV, Fc25Bands.NPV, Fc25Bands.ERROR]:
best_pixel_fc[band] = propagate_using_selected_pixel(best_pixel_fc[Fc25Bands.BS],
data_bare_soil,
data_fc[band],
best_pixel_fc[band])
# And now the other "provenance" data
current_satellite.fill(SATELLITE_DATA_VALUES[fc.satellite])
best_pixel_satellite = propagate_using_selected_pixel(best_pixel_fc[Fc25Bands.BS],
data_bare_soil,
current_satellite,
best_pixel_satellite)
current_year.fill(tile.end_datetime_year)
best_pixel_year = propagate_using_selected_pixel(best_pixel_fc[Fc25Bands.BS],
data_bare_soil,
current_year,
best_pixel_year)
current_month.fill(tile.end_datetime_month)
best_pixel_month = propagate_using_selected_pixel(best_pixel_fc[Fc25Bands.BS],
data_bare_soil,
current_month,
best_pixel_month)
current_epoch.fill(calendar.timegm(tile.end_datetime.timetuple()))
best_pixel_epoch = propagate_using_selected_pixel(best_pixel_fc[Fc25Bands.BS],
data_bare_soil,
current_epoch,
best_pixel_epoch)
# Create the output datasets
# FC composite
raster_create(self.get_dataset_filename("FC"),
[best_pixel_fc[b] for b in Fc25Bands],
metadata_fc.transform, metadata_fc.projection, metadata_fc.bands[Fc25Bands.BS].no_data_value,
metadata_fc.bands[Fc25Bands.BS].data_type)
# NBAR composite
raster_create(self.get_dataset_filename("NBAR"),
[best_pixel_nbar[b] for b in Ls57Arg25Bands],
metadata_nbar.transform, metadata_nbar.projection,
metadata_nbar.bands[Ls57Arg25Bands.BLUE].no_data_value,
metadata_nbar.bands[Ls57Arg25Bands.BLUE].data_type)
# "Provenance" composites
raster_create(self.get_dataset_filename("SAT"),
[best_pixel_satellite],
metadata_nbar.transform, metadata_nbar.projection, no_data_value,
gdal.GDT_Int16)
raster_create(self.get_dataset_filename("YEAR"),
[best_pixel_year],
metadata_nbar.transform, metadata_nbar.projection, no_data_value,
gdal.GDT_Int16)
raster_create(self.get_dataset_filename("MONTH"),
[best_pixel_month],
metadata_nbar.transform, metadata_nbar.projection, no_data_value,
gdal.GDT_Int16)
raster_create(self.get_dataset_filename("EPOCH"),
[best_pixel_epoch],
metadata_nbar.transform, metadata_nbar.projection, no_data_value,
gdal.GDT_Int32)
def bs_workflow(tiles, percentile=90, xtile=None, ytile=None,
out_fnames=None):
"""
A baseline workflow for doing the baresoil percentile, NBAR, FC
corresponding mosaics.
"""
# Get some basic image info
ds_type = DatasetType.FC25
ds = tiles[0]
dataset = ds.datasets[ds_type]
md = get_dataset_metadata(dataset)
if md is None:
_log.info("Tile path not exists %s",dataset.path)
return
samples, lines = md.shape
#_log.info("dataset shape %s for %s", md.shape, out_fnames)
time_slices = len(tiles)
_log.info("length of time slices [%d] for %s", time_slices, out_fnames)
geobox = GriddedGeoBox.from_gdal_dataset(gdal.Open(dataset.path))
lat_lon = ""
for line in out_fnames:
lat_lon = line.split("/")[-2]
break;
# Initialise the tiling scheme for processing
if xtile is None:
xtile = samples
if ytile is None:
ytile = lines
chunks = generate_tiles(samples, lines, xtile=samples, ytile=ytile,
generator=False)
# Define no-data
no_data_value = NDV
nan = numpy.float32(numpy.nan) # for the FC dtype no need for float64
# Define the output files
if out_fnames is None:
nbar_outfname = 'nbar_best_pixel'
all_outfname = 'all_best_pixel'
#fc_outfname = 'fc_best_pixel'
#sat_outfname = 'sat_best_pixel'
#date_outfnme = 'date_best_pixel'
#count_outfnme = 'count_best_pixel'
else:
nbar_outfname = out_fnames[0]
all_outfname = out_fnames[1]
#fc_outfname = out_fnames[1]
#sat_outfname = out_fnames[2]
#date_outfnme = out_fnames[3]
#count_outfnme = out_fnames[4]
nbar_outnb = len(Ls57Arg25Bands)
all_outnb = len(BareSoil)
#fc_outnb = len(Fc25Bands)
out_dtype = gdal.GDT_Int16
#_log.info("input xtile [%d] ytile [%d] for %s", xtile, ytile, out_fnames)
nbar_outds = TiledOutput(nbar_outfname, samples=samples, lines=lines,
bands=nbar_outnb, dtype=out_dtype,
nodata=no_data_value, geobox=geobox, fmt="GTiff")
all_outds = TiledOutput(all_outfname, samples=samples, lines=lines,
bands=all_outnb, dtype=out_dtype,
nodata=no_data_value, geobox=geobox, fmt="GTiff")
satellite_code = {Satellite.LS5: 5, Satellite.LS7: 7, Satellite.LS8: 8}
fc_bands_subset = [Fc25Bands.PHOTOSYNTHETIC_VEGETATION,
Fc25Bands.NON_PHOTOSYNTHETIC_VEGETATION,
Fc25Bands.UNMIXING_ERROR]
count=0
# Loop over each spatial tile/chunk and build up the time series
for chunk in chunks:
count=0
ys, ye = chunk[0]
xs, xe = chunk[1]
ysize = ye - ys
xsize = xe - xs
dims = (time_slices, ysize, xsize)
#_log.info("got chunk [%s] for %s", chunk, out_fnames)
# Initialise the intermediate and best_pixel output arrays
data = {}
best_pixel_nbar = {}
best_pixel_fc = {}
stack_bare_soil = numpy.zeros(dims, dtype='float32')
stack_sat = numpy.zeros(dims, dtype='int16')
#stack_date = numpy.zeros(dims, dtype='int32')
stack_year = numpy.zeros(dims, dtype='int16')
stack_md = numpy.zeros(dims, dtype='int16')
stack_count = numpy.zeros(dims, dtype='int16')
best_pixel_satellite = numpy.zeros((ysize, xsize), dtype='int16')
#best_pixel_date = numpy.zeros((ysize, xsize), dtype='int32')
best_pixel_year = numpy.zeros((ysize, xsize), dtype='int16')
best_pixel_md = numpy.zeros((ysize, xsize), dtype='int16')
best_pixel_count = numpy.zeros((ysize, xsize), dtype='int16')
best_pixel_satellite.fill(no_data_value)
#best_pixel_date.fill(no_data_value)
best_pixel_count.fill(no_data_value)
stack_nbar = {}
#_log.info("all initialised successfully")
for band in Ls57Arg25Bands:
stack_nbar[band] = numpy.zeros(dims, dtype='int16')
best_pixel_nbar[band] = numpy.zeros((ysize, xsize),
dtype='int16')
best_pixel_nbar[band].fill(no_data_value)
stack_fc = {}
for band in fc_bands_subset:
stack_fc[band] = numpy.zeros(dims, dtype='int16')
best_pixel_fc[band] = numpy.zeros((ysize, xsize),
dtype='int16')
best_pixel_fc[band].fill(no_data_value)
for idx, ds in enumerate(tiles):
pqa = ds.datasets[DatasetType.PQ25]
nbar = ds.datasets[DatasetType.ARG25]
fc = ds.datasets[DatasetType.FC25]
#_log.info("Processing nbar for index %d ", idx)
try:
wofs = ds.datasets[DatasetType.WATER]
except KeyError:
print "Missing water for:\n {}".format(ds.end_datetime)
wofs = None
# mask = numpy.zeros((ysize, xsize), dtype='bool')
# TODO update to use the api's version of extract_pq
#pq_data = get_dataset_data(pqa, x=xs, y=ys, x_size=xsize,
# y_size=ysize)[Pq25Bands.PQ]
#mask = extract_pq_flags(pq_data, combine=True)
#mask = ~mask
mask = get_mask_pqa(pqa, x=xs, y=ys, x_size=xsize, y_size=ysize)
# WOfS
if wofs is not None:
mask = get_mask_wofs(wofs, x=xs, y=ys, x_size=xsize,
y_size=ysize, mask=mask)
# NBAR
data[DatasetType.ARG25] = get_dataset_data(nbar, x=xs, y=ys,
x_size=xsize,
y_size=ysize)
# NDVI
'''
red = None
nir = None
if satellite_code[fc.satellite] == 8:
red = data[DatasetType.ARG25][Ls8Arg25Bands.RED]
nir = data[DatasetType.ARG25][Ls8Arg25Bands.NEAR_INFRARED]
else:
red = data[DatasetType.ARG25][Ls57Arg25Bands.RED]
nir = data[DatasetType.ARG25][Ls57Arg25Bands.NEAR_INFRARED]
ndvi = calculate_ndvi(red, nir)
ndvi[mask] = no_data_value
#mask |= numexpr.evaluate("(ndvi < 0.0) | (ndvi > 0.3)")
'''
# FC
data[DatasetType.FC25] = get_dataset_data(fc, x=xs, y=ys,
x_size=xsize,
y_size=ysize)
bare_soil = data[DatasetType.FC25][Fc25Bands.BARE_SOIL]
#mask |= numexpr.evaluate("(bare_soil < 0) | (bare_soil > 8000)")
errcnt=0
# apply the mask to each dataset and insert into the 3D array
if satellite_code[fc.satellite] == 8:
for band in Ls57Arg25Bands:
for oband in Ls8Arg25Bands:
try:
if oband.name == band.name:
data[DatasetType.ARG25][oband][mask] = no_data_value
stack_nbar[band][idx] = data[DatasetType.ARG25][oband]
break
except ValueError:
errcnt=1
_log.info("Data converting error LS8")
except IOError:
errcnt=1
_log.info("reading error LS8")
except KeyError:
errcnt=1
_log.info("Key error LS8")
except:
errcnt=1
_log.info("Unexpected error for LS8: %s",sys.exc_info()[0])
else:
for band in Ls57Arg25Bands:
try:
data[DatasetType.ARG25][band][mask] = no_data_value
stack_nbar[band][idx] = data[DatasetType.ARG25][band]
except ValueError:
errcnt=1
_log.info("Data converting error LS57")
except IOError:
errcnt=1
_log.info("NBAR reading error LS57")
except KeyError:
errcnt=1
_log.info("Key error LS57")
except:
errcnt=1
_log.info("Unexpected error LS57: %s",sys.exc_info()[0])
for band in fc_bands_subset:
try:
data[DatasetType.FC25][band][mask] = no_data_value
stack_fc[band][idx] = data[DatasetType.FC25][band]
except ValueError:
errcnt=2
_log.info("FC Data converting error")
except IOError:
errcnt=2
_log.info("FC reading error LS57")
except KeyError:
errcnt=2
_log.info("FC Key error")
except:
errcnt=2
_log.info("FC Unexpected error: %s",sys.exc_info()[0])
if errcnt != 0:
if errcnt == 1:
_log.info("nbar tile has problem %s",nbar.path)
else:
_log.info("fc tile has problem %s",fc.path)
errcnt=0
continue
# Add bare soil, satellite and date to the 3D arrays
try:
#_log.info("bare soil for %s %s",bare_soil, out_fnames)
stack_bare_soil[idx] = bare_soil
stack_bare_soil[idx][mask] = nan
stack_sat[idx][:] = satellite_code[fc.satellite]
#dtime = int(ds.end_datetime.strftime('%Y%m%d'))
dtime = int(ds.end_datetime.strftime('%Y'))
#_log.info("year of acquisition %d",dtime)
stack_year[idx][:] = dtime
#stack_date[idx][:] = dtime
mtime = int(ds.end_datetime.strftime('%m%d'))
stack_md[idx][:] = mtime
count = count+1
#count = int(numpy.ma.count(numpy.ma.masked_less(bare_soil, 1),axis=0)[0])
#_log.info("count observed [%d] on %d", count, dtime)
count1 = int(numpy.ma.count(numpy.ma.masked_less(bare_soil, 1)))
if count1 < 1 :
_log.info("no data present on %d and year %d for tile %s reducing count by one", mtime, dtime, lat_lon )
count=count-1
stack_count[idx][:] = count
except:
_log.info("stacking - Unexpected error: %s",sys.exc_info()[0])
# Calcualte the percentile
pct_fc = numpy.nanpercentile(stack_bare_soil, percentile,
axis=0, interpolation='nearest')
# Loop over each time slice and generate a mosaic for each dataset_type
try:
for idx in range(time_slices):
pct_idx = pct_fc == stack_bare_soil[idx]
for band in Ls57Arg25Bands:
band_data = stack_nbar[band]
best_pixel_nbar[band][pct_idx] = band_data[idx][pct_idx]
for band in fc_bands_subset:
band_data = stack_fc[band]
best_pixel_fc[band][pct_idx] = band_data[idx][pct_idx]
best_pixel_satellite[pct_idx] = stack_sat[idx][pct_idx]
#best_pixel_date[pct_idx] = stack_date[idx][pct_idx]
best_pixel_year[pct_idx] = stack_year[idx][pct_idx]
best_pixel_md[pct_idx] = stack_md[idx][pct_idx]
best_pixel_count[pct_idx] = stack_count[idx][pct_idx]
#best_pixel_count[pct_idx] = time_slices
# Output the current spatial chunk for each dataset
for band in Ls57Arg25Bands:
bn = band.value
band_data = best_pixel_nbar[band]
nbar_outds.write_tile(band_data, chunk, raster_band=bn)
'''
for band in fc_bands_subset:
bn = band.value
band_data = best_pixel_fc[band]
fc_outds.write_tile(band_data, chunk, raster_band=bn)
'''
for band in BareSoil:
bn = band.value
if bn < 5:
if bn == 1:
all_outds.write_tile(pct_fc, chunk,raster_band=BareSoil.BARE_SOIL.value)
for oband in fc_bands_subset:
if oband.name == band.name:
band_data = best_pixel_fc[oband]
all_outds.write_tile(band_data, chunk, raster_band=bn)
break
elif bn < 11:
for oband in Ls57Arg25Bands:
if oband.name == band.name:
band_data = best_pixel_nbar[oband]
all_outds.write_tile(band_data, chunk, raster_band=bn)
break
elif bn == 11:
all_outds.write_tile(best_pixel_satellite, chunk, raster_band=bn)
elif bn == 12:
all_outds.write_tile(best_pixel_year, chunk, raster_band=bn)
elif bn == 13:
all_outds.write_tile(best_pixel_md, chunk, raster_band=bn)
elif bn == 14:
all_outds.write_tile(best_pixel_count, chunk, raster_band=bn)
except ValueError:
_log.info("Data converting final error")
except IOError:
_log.info("writing error LS57")
except KeyError:
_log.info("Key error final")
except:
_log.info("Final Unexpected error: %s",sys.exc_info()[0])
_log.info("total dataset counts for each chunk is %d for tile %s", count, lat_lon)
# Close the output files
nbar_outds.close()
all_outds.close()
def go(self):
import numpy
from datacube.api.query import list_cells_as_list, list_tiles_as_list
from datacube.config import Config
x_min, x_max, y_max, y_min = self.extract_bounds_from_vector()
_log.debug("The bounds are [%s]", (x_min, x_max, y_min, y_max))
cells_vector = self.extract_cells_from_vector()
_log.debug("Intersecting cells_vector are [%d] [%s]", len(cells_vector), cells_vector)
config = Config()
_log.debug(config.to_str())
x_list = range(x_min, x_max + 1)
y_list = range(y_min, y_max + 1)
_log.debug("x = [%s] y=[%s]", x_list, y_list)
cells_db = list()
for cell in list_cells_as_list(x=x_list, y=y_list, acq_min=self.acq_min, acq_max=self.acq_max,
satellites=[satellite for satellite in self.satellites],
dataset_types=[self.dataset_type]):
cells_db.append((cell.x, cell.y))
_log.debug("Cells from DB are [%d] [%s]", len(cells_db), cells_db)
cells = intersection(cells_vector, cells_db)
_log.debug("Combined cells are [%d] [%s]", len(cells), cells)
for (x, y) in cells:
_log.info("Processing cell [%3d/%4d]", x, y)
tiles = list_tiles_as_list(x=x_list, y=y_list, acq_min=self.acq_min, acq_max=self.acq_max,
satellites=[satellite for satellite in self.satellites],
dataset_types=[self.dataset_type])
_log.info("There are [%d] tiles", len(tiles))
if self.list_only:
for tile in tiles:
_log.info("Would process [%s]", tile.datasets[self.dataset_type].path)
continue
# Calculate the mask for the cell
mask_aoi = self.get_mask_aoi_cell(x, y)
pixel_count = 4000 * 4000
pixel_count_aoi = (mask_aoi == False).sum()
_log.debug("mask_aoi is [%s]\n[%s]", numpy.shape(mask_aoi), mask_aoi)
metadata = None
with self.get_output_file() as csv_file:
csv_writer = csv.writer(csv_file)
import operator
header = reduce(operator.add, [["DATE", "INSTRUMENT", "# PIXELS", "# PIXELS IN AOI"]] + [
["%s - # DATA PIXELS" % band_name,
"%s - # DATA PIXELS AFTER PQA" % band_name,
"%s - # DATA PIXELS AFTER PQA WOFS" % band_name,
"%s - # DATA PIXELS AFTER PQA WOFS AOI" % band_name,
"%s - MIN" % band_name, "%s - MAX" % band_name, "%s - MEAN" % band_name] for band_name in self.bands])
csv_writer.writerow(header)
for tile in tiles:
_log.info("Processing tile [%s]", tile.datasets[self.dataset_type].path)
if self.list_only:
continue
if not metadata:
metadata = get_dataset_metadata(tile.datasets[self.dataset_type])
# Apply PQA if specified
pqa = None
mask_pqa = None
if self.mask_pqa_apply and DatasetType.PQ25 in tile.datasets:
pqa = tile.datasets[DatasetType.PQ25]
mask_pqa = get_mask_pqa(pqa, self.mask_pqa_mask)
_log.debug("mask_pqa is [%s]\n[%s]", numpy.shape(mask_pqa), mask_pqa)
# Apply WOFS if specified
wofs = None
mask_wofs = None
if self.mask_wofs_apply and DatasetType.WATER in tile.datasets:
wofs = tile.datasets[DatasetType.WATER]
mask_wofs = get_mask_wofs(wofs, self.mask_wofs_mask)
_log.debug("mask_wofs is [%s]\n[%s]", numpy.shape(mask_wofs), mask_wofs)
dataset = tile.datasets[self.dataset_type]
bands = []
dataset_band_names = [b.name for b in dataset.bands]
for b in self.bands:
if b in dataset_band_names:
bands.append(dataset.bands[b])
data = get_dataset_data(tile.datasets[self.dataset_type], bands=bands)
_log.debug("data is [%s]\n[%s]", numpy.shape(data), data)
pixel_count_data = dict()
pixel_count_data_pqa = dict()
pixel_count_data_pqa_wofs = dict()
pixel_count_data_pqa_wofs_aoi = dict()
mmin = dict()
mmax = dict()
mmean = dict()
for band_name in self.bands:
# Add "zeroed" entries for non-present bands - should only be if outputs for those bands have been explicitly requested
if band_name not in dataset_band_names:
pixel_count_data[band_name] = 0
pixel_count_data_pqa[band_name] = 0
pixel_count_data_pqa_wofs[band_name] = 0
pixel_count_data_pqa_wofs_aoi[band_name] = 0
mmin[band_name] = numpy.ma.masked
mmax[band_name] = numpy.ma.masked
mmean[band_name] = numpy.ma.masked
continue
band = dataset.bands[band_name]
data[band] = numpy.ma.masked_equal(data[band], NDV)
_log.debug("masked data is [%s] [%d]\n[%s]", numpy.shape(data), numpy.ma.count(data), data)
pixel_count_data[band_name] = numpy.ma.count(data[band])
if pqa:
data[band].mask = numpy.ma.mask_or(data[band].mask, mask_pqa)
_log.debug("PQA masked data is [%s] [%d]\n[%s]", numpy.shape(data[band]), numpy.ma.count(data[band]), data[band])
pixel_count_data_pqa[band_name] = numpy.ma.count(data[band])
if wofs:
data[band].mask = numpy.ma.mask_or(data[band].mask, mask_wofs)
_log.debug("WOFS masked data is [%s] [%d]\n[%s]", numpy.shape(data[band]), numpy.ma.count(data[band]), data[band])
pixel_count_data_pqa_wofs[band_name] = numpy.ma.count(data[band])
data[band].mask = numpy.ma.mask_or(data[band].mask, mask_aoi)
_log.debug("AOI masked data is [%s] [%d]\n[%s]", numpy.shape(data[band]), numpy.ma.count(data[band]), data[band])
pixel_count_data_pqa_wofs_aoi[band_name] = numpy.ma.count(data[band])
mmin[band_name] = numpy.ma.min(data[band])
mmax[band_name] = numpy.ma.max(data[band])
mmean[band_name] = numpy.ma.mean(data[band])
# Convert the mean to an int...taking into account masking....
if not numpy.ma.is_masked(mmean[band_name]):
mmean[band_name] = mmean[band_name].astype(numpy.int16)
pixel_count_data_pqa_wofs_aoi_all_bands = reduce(operator.add, pixel_count_data_pqa_wofs_aoi.itervalues())
if pixel_count_data_pqa_wofs_aoi_all_bands == 0 and not self.output_no_data:
_log.info("Skipping dataset with no non-masked data values in ANY band")
continue
row = reduce(
operator.add,
[[tile.end_datetime,
self.decode_satellite_as_instrument(tile.datasets[self.dataset_type].satellite),
pixel_count, pixel_count_aoi]] +
[[pixel_count_data[band_name], pixel_count_data_pqa[band_name],
pixel_count_data_pqa_wofs[band_name], pixel_count_data_pqa_wofs_aoi[band_name],
mmin[band_name], mmax[band_name], mmean[band_name]] for band_name in self.bands])
csv_writer.writerow(row)
def tidal_workflow(tiles, percentile=10, xtile=None, ytile=None, low_off=0, high_off=0,
out_fnames=None):
"""
A baseline workflow for doing the baresoil percentile, NBAR, FC
corresponding mosaics.
"""
# Get some basic image info
ds_type = DatasetType.ARG25
ds = tiles[0]
dataset = ds.datasets[ds_type]
md = get_dataset_metadata(dataset)
_log.info("low and high offset %s , %s ", low_off, high_off)
if md is None:
_log.info("Tile path not exists %s",dataset.path)
return
samples, lines = md.shape
#_log.info("dataset shape %s for %s", md.shape, out_fnames)
time_slices = len(tiles)
_log.info("length of time slices [%d] for %s", time_slices, out_fnames)
geobox = GriddedGeoBox.from_gdal_dataset(gdal.Open(dataset.path))
lat_lon = ""
for line in out_fnames:
lat_lon = line.split("/")[-2]
break;
# Initialise the tiling scheme for processing
if xtile is None:
xtile = samples
if ytile is None:
ytile = lines
chunks = generate_tiles(samples, lines, xtile=samples, ytile=ytile,
generator=False)
# Define no-data
no_data_value = NDV
nan = numpy.float32(numpy.nan) # for the FC dtype no need for float64
# Define the output files
if out_fnames is None:
nbar_outfname = 'nbar_best_pixel'
else:
nbar_outfname = out_fnames[0]
#nbar_outnb = len(TidalProd)
nbar_outnb = len(extraInfo)
#fc_outnb = len(Fc25Bands)
out_dtype = gdal.GDT_Int16
#_log.info("input xtile [%d] ytile [%d] for %s", xtile, ytile, out_fnames)
nbar_outds = TiledOutput(nbar_outfname, samples=samples, lines=lines,
bands=nbar_outnb, dtype=out_dtype,
nodata=no_data_value, geobox=geobox, fmt="GTiff")
satellite_code = {Satellite.LS5: 5, Satellite.LS7: 7, Satellite.LS8: 8}
count=0
# Loop over each spatial tile/chunk and build up the time series
for chunk in chunks:
count=0
ys, ye = chunk[0]
xs, xe = chunk[1]
ysize = ye - ys
xsize = xe - xs
dims = (time_slices, ysize, xsize)
#_log.info("got chunk [%s] for %s", chunk, out_fnames)
# Initialise the intermediate and best_pixel output arrays
data = {}
median_nbar = {}
stack_tidal = numpy.zeros(dims, dtype='float32')
stack_lowOff = numpy.zeros(dims, dtype='int16')
stack_highOff = numpy.zeros(dims, dtype='int16')
stack_count = numpy.zeros(dims, dtype='int16')
median_lowOff = numpy.zeros((ysize, xsize), dtype='int16')
median_highOff = numpy.zeros((ysize, xsize), dtype='int16')
median_count = numpy.zeros((ysize, xsize), dtype='int16')
median_lowOff.fill(no_data_value)
median_highOff.fill(no_data_value)
median_count.fill(no_data_value)
stack_nbar = {}
#_log.info("all initialised successfully")
for band in Ls57Arg25Bands:
stack_nbar[band] = numpy.zeros(dims, dtype='int16')
median_nbar[band] = numpy.zeros((ysize, xsize), dtype='int16')
median_nbar[band].fill(no_data_value)
for idx, ds in enumerate(tiles):
pqa = ds.datasets[DatasetType.PQ25]
nbar = ds.datasets[DatasetType.ARG25]
mask = get_mask_pqa(pqa, x=xs, y=ys, x_size=xsize, y_size=ysize)
# NBAR
data[DatasetType.ARG25] = get_dataset_data(nbar, x=xs, y=ys,
x_size=xsize,
y_size=ysize)
#mask |= numexpr.evaluate("(bare_soil < 0) | (bare_soil > 8000)")A
errcnt=0
# apply the mask to each dataset and insert into the 3D array
if satellite_code[nbar.satellite] == 8:
for band in Ls57Arg25Bands:
for oband in Ls8Arg25Bands:
try:
if oband.name == band.name:
data[DatasetType.ARG25][oband][mask] = no_data_value
stack_nbar[band][idx] = data[DatasetType.ARG25][oband]
break
except ValueError:
errcnt=1
_log.info("Data converting error LS8")
except IOError:
errcnt=1
_log.info("reading error LS8")
except KeyError:
errcnt=1
_log.info("Key error LS8")
except:
errcnt=1
_log.info("Unexpected error for LS8: %s",sys.exc_info()[0])
else:
for band in Ls57Arg25Bands:
try:
data[DatasetType.ARG25][band][mask] = no_data_value
stack_nbar[band][idx] = data[DatasetType.ARG25][band]
except ValueError:
errcnt=1
_log.info("Data converting error LS57")
except IOError:
errcnt=1
_log.info("NBAR reading error LS57")
except KeyError:
errcnt=1
_log.info("Key error LS57")
except:
errcnt=1
_log.info("Unexpected error LS57: %s",sys.exc_info()[0])
if errcnt != 0:
if errcnt == 1:
_log.info("nbar tile has problem %s",nbar.path)
errcnt=0
continue
# Add bare soil, satellite and date to the 3D arrays
try:
#_log.info("bare soil for %s %s",bare_soil, out_fnames)
low=int(float(low_off) * 100)
high = int(float(high_off) * 100)
stack_lowOff[idx][:] = low
stack_highOff[idx][:] = high
#_log.info("count observed [%d] on %d", count, dtime)
count1 = int(numpy.ma.count(numpy.ma.masked_less(stack_nbar, 1)))
if count1 < 1 :
_log.info("no data present on %d and year %d for tile %s reducing count by one", mtime, dtime, lat_lon )
else:
count=count+1
stack_count[idx][:] = count
except:
_log.info("stacking - Unexpected error: %s",sys.exc_info()[0])
# Loop over each time slice and generate a mosaic for each dataset_type
_log.info("checking - flow path: ")
ndv = get_dataset_type_ndv(DatasetType.ARG25)
try:
_log.info("ndv is %s", ndv)
for idx in range(time_slices):
median_count = stack_count[idx]
median_lowOff = stack_lowOff[idx]
median_highOff = stack_highOff[idx]
_log.info("ccccc_data ")
for band in TidalProd:
bn = band.value
if bn == 1:
nbar_outds.write_tile(median_count, chunk, raster_band=bn)
elif bn == 2:
nbar_outds.write_tile(median_lowOff, chunk, raster_band=bn)
elif bn == 3:
nbar_outds.write_tile(median_highOff, chunk, raster_band=bn)
except ValueError:
_log.info("Data converting final error")
except IOError:
_log.info("writing error LS57")
except KeyError:
_log.info("Key error final")
except:
_log.info("Final Unexpected error: %s",sys.exc_info()[0])
_log.info("total dataset counts for each chunk is %d for tile %s", count, lat_lon)
# Close the output files
nbar_outds.close()
def go(self):
import numpy
from datacube.api.query import list_cells_as_list, list_tiles_as_list
from datacube.config import Config
# Verify that all the requested satellites have the same band combinations
dataset_bands = get_bands(self.dataset_type, self.satellites[0])
_log.info("dataset bands is [%s]", " ".join([b.name for b in dataset_bands]))
for satellite in self.satellites:
if dataset_bands != get_bands(self.dataset_type, satellite):
_log.error("Satellites [%s] have differing bands", " ".join([satellite.name for satellite in self.satellites]))
raise Exception("Satellites with different band combinations selected")
bands = []
dataset_bands_list = list(dataset_bands)
if not self.bands:
bands = dataset_bands_list
else:
for b in self.bands:
bands.append(dataset_bands_list[b - 1])
_log.info("Using bands [%s]", " ".join(band.name for band in bands))
x_min, x_max, y_max, y_min = self.extract_bounds_from_vector()
_log.debug("The bounds are [%s]", (x_min, x_max, y_min, y_max))
cells_vector = self.extract_cells_from_vector()
_log.debug("Intersecting cells_vector are [%d] [%s]", len(cells_vector), cells_vector)
config = Config(os.path.expanduser("~/.datacube/config"))
_log.debug(config.to_str())
x_list = range(x_min, x_max + 1)
y_list = range(y_min, y_max + 1)
_log.debug("x = [%s] y=[%s]", x_list, y_list)
cells_db = list()
for cell in list_cells_as_list(x=x_list, y=y_list, acq_min=self.acq_min, acq_max=self.acq_max,
satellites=[satellite for satellite in self.satellites],
dataset_types=[self.dataset_type]):
cells_db.append((cell.x, cell.y))
_log.debug("Cells from DB are [%d] [%s]", len(cells_db), cells_db)
cells = intersection(cells_vector, cells_db)
_log.debug("Combined cells are [%d] [%s]", len(cells), cells)
for (x, y) in cells:
_log.info("Processing cell [%3d/%4d]", x, y)
tiles = list_tiles_as_list(x=x_list, y=y_list, acq_min=self.acq_min, acq_max=self.acq_max,
satellites=[satellite for satellite in self.satellites],
dataset_types=[self.dataset_type])
_log.info("There are [%d] tiles", len(tiles))
if self.list_only:
for tile in tiles:
_log.info("Would process [%s]", tile.datasets[self.dataset_type].path)
continue
# Calculate the mask for the cell
mask_aoi = self.get_mask_aoi_cell(x, y)
pixel_count = 4000 * 4000
pixel_count_aoi = (mask_aoi == False).sum()
_log.debug("mask_aoi is [%s]\n[%s]", numpy.shape(mask_aoi), mask_aoi)
metadata = None
with self.get_output_file() as csv_file:
csv_writer = csv.writer(csv_file)
import operator
header = reduce(operator.add, [["DATE", "INSTRUMENT", "# PIXELS", "# PIXELS IN AOI"]] + [
["%s - # DATA PIXELS" % b.name,
"%s - # DATA PIXELS AFTER PQA" % b.name,
"%s - # DATA PIXELS AFTER PQA WOFS" % b.name,
"%s - # DATA PIXELS AFTER PQA WOFS AOI" % b.name,
"%s - MIN" % b.name, "%s - MAX" % b.name, "%s - MEAN" % b.name] for b in bands])
csv_writer.writerow(header)
for tile in tiles:
_log.info("Processing tile [%s]", tile.datasets[self.dataset_type].path)
if self.list_only:
continue
if not metadata:
metadata = get_dataset_metadata(tile.datasets[self.dataset_type])
# Apply PQA if specified
pqa = None
mask_pqa = None
if self.mask_pqa_apply and DatasetType.PQ25 in tile.datasets:
pqa = tile.datasets[DatasetType.PQ25]
mask_pqa = get_mask_pqa(pqa, self.mask_pqa_mask)
_log.debug("mask_pqa is [%s]\n[%s]", numpy.shape(mask_pqa), mask_pqa)
# Apply WOFS if specified
wofs = None
mask_wofs = None
if self.mask_wofs_apply and DatasetType.WATER in tile.datasets:
wofs = tile.datasets[DatasetType.WATER]
mask_wofs = get_mask_wofs(wofs, self.mask_wofs_mask)
_log.debug("mask_wofs is [%s]\n[%s]", numpy.shape(mask_wofs), mask_wofs)
data = get_dataset_data(tile.datasets[self.dataset_type], bands=bands)
_log.debug("data is [%s]\n[%s]", numpy.shape(data), data)
pixel_count_data = dict()
pixel_count_data_pqa = dict()
pixel_count_data_pqa_wofs = dict()
pixel_count_data_pqa_wofs_aoi = dict()
mmin = dict()
mmax = dict()
mmean = dict()
for band in bands:
data[band] = numpy.ma.masked_equal(data[band], NDV)
_log.debug("masked data is [%s] [%d]\n[%s]", numpy.shape(data), numpy.ma.count(data), data)
pixel_count_data[band] = numpy.ma.count(data[band])
if pqa:
data[band].mask = numpy.ma.mask_or(data[band].mask, mask_pqa)
_log.debug("PQA masked data is [%s] [%d]\n[%s]", numpy.shape(data[band]), numpy.ma.count(data[band]), data[band])
pixel_count_data_pqa[band] = numpy.ma.count(data[band])
if wofs:
data[band].mask = numpy.ma.mask_or(data[band].mask, mask_wofs)
_log.debug("WOFS masked data is [%s] [%d]\n[%s]", numpy.shape(data[band]), numpy.ma.count(data[band]), data[band])
pixel_count_data_pqa_wofs[band] = numpy.ma.count(data[band])
data[band].mask = numpy.ma.mask_or(data[band].mask, mask_aoi)
_log.debug("AOI masked data is [%s] [%d]\n[%s]", numpy.shape(data[band]), numpy.ma.count(data[band]), data[band])
pixel_count_data_pqa_wofs_aoi[band] = numpy.ma.count(data[band])
mmin[band] = numpy.ma.min(data[band])
mmax[band] = numpy.ma.max(data[band])
mmean[band] = numpy.ma.mean(data[band])
# Convert the mean to an int...which is actually trickier than you would expect due to masking....
if numpy.ma.count(mmean[band]) != 0:
mmean[band] = mmean[band].astype(numpy.int16)
# Should we output if no data values found?
pixel_count_data_pqa_wofs_aoi_all_bands = reduce(operator.add, pixel_count_data_pqa_wofs_aoi.itervalues())
if pixel_count_data_pqa_wofs_aoi_all_bands == 0 and not self.output_no_data:
_log.info("Skipping dataset with no non-masked data values in ANY band")
continue
row = reduce(
operator.add,
[[tile.end_datetime,
self.decode_satellite_as_instrument(tile.datasets[self.dataset_type].satellite),
pixel_count, pixel_count_aoi]] +
[[pixel_count_data[band], pixel_count_data_pqa[band],
pixel_count_data_pqa_wofs[band], pixel_count_data_pqa_wofs_aoi[band],
mmin[band], mmax[band], mmean[band]] for band in bands])
csv_writer.writerow(row)
