def _export_geometries():
def aggregate_progress(progresses, count):
p = _sum_dicts(progresses.values(), excluded_keys=['geometry'])
exported = round(100 * p['exported'] / count)
downloaded = round(100 * p['downloaded'] / count)
downloaded_bytes = format_bytes(p['downloaded_bytes'])
processed = round(100 * p['processed'] / count)
return progress(
default_message='Exported {}%, Downloaded {}% ({}), Processed {}%'.format(
exported, downloaded, downloaded_bytes, processed
),
message_key='tasks.retrieve.time_series_to_sepal.progress',
exported=exported,
downloaded=downloaded,
downloaded_bytes=downloaded_bytes,
processed=processed
)
features_collection = _to_features_collection(region)
def export_geometry(geometry, i, geometry_count):
geometry_description = str(i + 1).zfill(len(str(geometry_count)))
return defer(
lambda _: _export_geometry(
geometry,
geometry_description=geometry_description
)
)
return concat(
progress(
default_message='Tiling AOI...',
message_key='tasks.retrieve.time_series_to_sepal.tiling'
),
_extract_feature_indexes(features_collection).pipe(
flat_map(
lambda feature_indexes: _to_geometries(features_collection, feature_indexes).pipe(
flat_map(
lambda geometries: concat(
*[
export_geometry(geometry, i, len(feature_indexes))
for i, geometry in enumerate(geometries)
]
)
),
scan(lambda acc, p: {**acc, p['geometry']: p}, {}),
flat_map(lambda progresses: aggregate_progress(
progresses,
count=len(feature_indexes) * len(year_ranges)
))
)
)
)
)
def _export(create_observable, description, retries):
return concat(
of('PENDING'),
enqueue(queue=_ee_exports,
action=create_observable,
description=description,
retries=retries))
def _export_year(geometry, year_start, year_end, export_description,
year_dir):
stack = _create_stack(geometry, year_start, year_end)
initial_progress = of({
'exported': 0,
'stack_bytes': 0,
'dates_bytes': 0,
'downloaded': 0,
'processed': 0
})
def aggregate_downloaded_bytes(p):
return {
'exported': p['exported'],
'downloaded': p['downloaded'],
'downloaded_bytes': p['stack_bytes'] + p['dates_bytes'],
'processed': p['processed']
}
return concat(
initial_progress,
merge(
_export_and_download_stack(stack, export_description,
year_dir),
_export_and_download_dates(stack, export_description,
year_dir)), _process_year(year_dir),
of({'processed': 1})).pipe(scan(lambda acc, p: {
**acc,
**p
}, {}), map(aggregate_downloaded_bytes))
def events(file_handler, connection_handler, store):
return rx.concat(
_initialize(),
rx.merge(
_new_files(file_handler),
_connection_statuses(connection_handler),
_failed_transfers(store),
))
def recurse(file):
if is_folder(file):
return concat(
of([file]),
list_folder_recursively(credentials, file, retries),
)
else:
return of([file])
def _build_vrt():
return concat(
progress(default_message='Building VRT...',
message_key='tasks.retrieve.image_to_sepal.building_vrt'),
build_vrt(destination=destination_path + '/' + description +
'.vrt',
files=destination_path + '/*.tif').pipe(
flat_map(lambda _: empty())))
def event_for(button: MouseButton) -> Observable:
return self.on_button_release(button).pipe(
ops.map(lambda _: rx.concat(
rx.of(self.position),
rx.never().pipe(
ops.take_until(self.on_button_press(button))))),
ops.exclusive(),
ops.map(lambda p: MouseUpEvent(self.context, p, button)))
def recurse(file):
if is_folder(file):
return concat(
of([file]),
list_folder_recursively(file),
)
else:
return of([file])
def _delete_drive_folder():
return concat(
progress(
default_message='Deleting Google Drive download folder...',
message_key=
'tasks.retrieve.image_to_sepal.deleting_drive_folder'),
delete_file_with_path(credentials, path=drive_folder_path).pipe(
flat_map(lambda _: empty())))
def _create_drive_folder():
return concat(
progress(
default_message='Creating Google Drive download folder...',
message_key=
'tasks.retrieve.time_series_to_sepal.creating_drive_folder'),
create_folder_with_path(credentials, drive_folder_path).pipe(
flat_map(lambda _: empty())))
def download_file(f, dest):
total_bytes = int(f['size'])
def next_chunk(downloader):
status, done = downloader.next_chunk()
logging.debug('downloaded chunk from {} to {}: {}'.format(
file, destination, status))
return 1.0 if done else status.progress()
def download_from_drive(destination_file):
def create_downloader():
request = get_service(credentials).files().get_media(
fileId=f['id'])
return MediaIoBaseDownload(fd=destination_file,
request=request,
chunksize=CHUNK_SIZE)
downloader = create_downloader()
return forever().pipe(
map(lambda _: next_chunk(downloader)),
take_while(lambda p: p < 1, inclusive=True),
flat_map(lambda p: progress(
default_message=
'Downloaded {downloaded_files} of {total_files} files ({downloaded} of {total})',
message_key='tasks.drive.download_folder',
downloaded_bytes=int(total_bytes * p),
downloaded=format_bytes(int(total_bytes * p)),
total_bytes=total_bytes,
total=format_bytes(total_bytes),
file=f)))
def action():
return using_file(file=dest,
mode='wb',
to_observable=download_from_drive)
os.makedirs(os.path.dirname(dest), exist_ok=True)
initial_progress = progress(
default_message=
'Downloaded {downloaded_files} of {total_files} files ({downloaded} of {total})',
message_key='tasks.drive.download_folder',
downloaded_bytes=0,
downloaded='0 bytes',
total_bytes=total_bytes,
total=format_bytes(total_bytes),
file=f)
touch_stream = interval(TOUCH_PERIOD).pipe(
flat_map(lambda _: touch(credentials, f)))
download_stream = enqueue(credentials,
queue=_drive_downloads,
action=action,
retries=retries,
description='Download {} to {}'.format(
f, dest)).pipe(aside(touch_stream))
return concat(initial_progress, download_stream, delete_downloaded(f))
def _export(credentials, create_observable, description, retries):
return concat(
progress(
default_message='Submitting export task to Google Earth Engine...',
message_key='tasks.ee.export.pending'),
enqueue(credentials,
queue=_ee_exports,
action=create_observable,
description=description,
retries=retries))
def __add__(self, other):
"""Pythonic version of concat.
Example:
>>> zs = xs + ys
Returns:
self.concat(other)"""
from rx import concat
return concat(self, other)
def __add__(self, other):
"""Pythonic version of concat.
Example:
>>> zs = xs + ys
Returns:
self.concat(other)"""
from rx import concat
return concat(self, other)
def test_double_subscribe_to_iterable(self):
iterable_finite = [1, 2, 3]
scheduler = TestScheduler()
obs = rx.from_(iterable_finite)
results = scheduler.start(lambda: rx.concat(obs, obs))
assert results.messages == [
on_next(200, 1), on_next(200, 2), on_next(200, 3),
on_next(200, 1), on_next(200, 2), on_next(200, 3),
on_completed(200)]
def __iadd__(self, other):
"""Pythonic use of concat.
Example:
xs += ys
Returns:
rx.concat(self, other)
"""
from rx import concat
return concat(self, other)
def __iadd__(self, other):
"""Pythonic use of concat.
Example:
xs += ys
Returns:
rx.concat(self, other)
"""
from rx import concat
return concat(self, other)
def concat(source: Observable) -> Observable:
"""Concatenates all the observable sequences.
Examples:
>>> op = concat(xs, ys, zs)
Returns:
An operator function that takes one or more observable sources and
returns an observable sequence that contains the elements of
each given sequence, in sequential order.
"""
return rx.concat(source, *sources)
def concat(source: Observable) -> Observable:
"""Concatenates all the observable sequences.
Examples:
>>> op = concat(xs, ys, zs)
Returns:
An operator function that takes one or more observable sources and
returns an observable sequence that contains the elements of
each given sequence, in sequential order.
"""
return rx.concat(source, *sources)
def start_with(source: Observable) -> Observable:
"""Partially applied start_with operator.
Prepends a sequence of values to an observable sequence.
Example:
>>> start_with(source)
Returns:
The source sequence prepended with the specified values.
"""
start = rx.from_iterable(args)
sequence = [start, source]
return rx.concat(*sequence)
def _set_band_names():
band_names_stream = of(band_names) if band_names else get_band_names(
credentials, image)
return concat(
progress(
default_message='Setting band names...',
message_key='tasks.retrieve.image_to_sepal.setting_band_names'
),
band_names_stream.pipe(
flat_map(lambda names: set_band_names(
band_names=names,
files=
[destination_path + '/*.tif', destination_path + '/*.vrt'])
), flat_map(lambda _: empty())))
def __iadd__(self, other) -> 'Observable':
"""Pythonic use of :func:`concat <rx.concat>`.
Example:
>>> xs += ys
Args:
other: The second observable sequence in the concatenation.
Returns:
Concatenated observable sequence.
"""
from rx import concat
return concat(self, other)
def on_mouse_over(self) -> Observable:
position = MouseInput.input(self).observe("position")
local_pos = position.pipe(ops.map(lambda p: p - self.offset))
return self.on_mouse_move.pipe(
ops.map(lambda e: e.position),
ops.map(lambda p: rx.concat(
rx.of(p),
rx.never().pipe(
ops.take_until(
local_pos.pipe(
ops.filter(lambda l: not self.bounds.contains(l)))
)))), ops.exclusive(),
ops.map(lambda p: MouseOverEvent(self, p)))
def start_with(source: Observable) -> Observable:
"""Partially applied start_with operator.
Prepends a sequence of values to an observable sequence.
Example:
>>> start_with(source)
Returns:
The source sequence prepended with the specified values.
"""
start = rx.from_iterable(args)
sequence = [start, source]
return rx.concat(*sequence)
def while_do(source: Observable) -> Observable:
"""Repeats source as long as condition holds emulating a while
loop.
Args:
source: The observable sequence that will be run if the
condition function returns true.
Returns:
An observable sequence which is repeated as long as the
condition holds.
"""
source = rx.from_future(source) if is_future(source) else source
return rx.concat(
itertools.takewhile(condition, (source for x in infinite())))
def _export_and_download_dates(stack, export_description, year_dir):
table_drive_description = 'dates_' + export_description
dates_drive_folder = '{}-{}'.format(table_drive_description,
str(uuid.uuid4()))
dates_drive_path = '{}/{}'.format(drive_folder_path,
dates_drive_folder)
create_dates_drive_folder = create_folder_with_path(
credentials, dates_drive_path).pipe(flat_map(lambda _: empty()))
export_dates = _export_dates(stack.bandNames(),
table_drive_description,
dates_drive_folder)
download_dates_from_drive = _download_from_drive(
path=dates_drive_path, destination=year_dir).pipe(
map(lambda p: {'dates_bytes': p.downloaded_bytes}))
return concat(create_dates_drive_folder, export_dates,
download_dates_from_drive)
def _export_geometry(geometry, geometry_description):
export_years = combine_latest(
*[_export_year(
geometry=geometry,
year_start=year_range[0],
year_end=year_range[1],
export_description='{}_{}_{}'.format(geometry_description, year_range[0].year, description),
year_dir='/'.join([download_dir, description, geometry_description, str(year_range[0].year)])
) for year_range in year_ranges]
).pipe(
map(lambda progresses: _sum_dicts(progresses)),
map(lambda p: {**p, 'geometry': geometry_description})
)
process_geometry = _process_geometry('/'.join([download_dir, description, geometry_description]))
return concat(
export_years,
process_geometry
)
def __init__(self, context: Context, visible: bool = True) -> None:
super().__init__(context, visible)
# noinspection PyTypeChecker
self.hover = rx.merge(
self.on_mouse_over.pipe(ops.map(lambda _: True)),
self.on_mouse_out.pipe(ops.map(lambda _: False))).pipe(ops.start_with(False))
mouse = MouseInput.input(self)
# noinspection PyTypeChecker
self.active = self.on_mouse_down.pipe(
ops.filter(lambda e: e.button == MouseButton.LEFT),
ops.map(lambda _: rx.concat(rx.of(True), mouse.on_button_release(MouseButton.LEFT).pipe(
ops.take(1),
ops.map(lambda _: False)))),
ops.exclusive(),
ops.start_with(False))
def initialize_regulators(config, kafka_feedback):
regulators = {}
for regulator in config:
control = kafka_feedback.pipe(
trace_observable("regulator feedback"),
ops.filter(lambda i: i[0] == regulator['feedback']),
ops.map(lambda i: i[1] / 1000),
pid(rx.concat(rx.just(1.0), rx.never()),
-0.001, -0.001, 0.0),
#ops.map(lambda i: 1/i if i != 0 else 1.0),
ops.map(lambda i: max(min(i, 0.01), 0.0)),
trace_observable("regulator"),
)
regulators[regulator['control']] = control
return regulators
def makinage(aio_scheduler, sources):
def on_error(e):
raise e
config, read_request, http_request = read_config_from_args(
sources.argv.argv,
sources.file.response,
sources.http.response,
scheduler=aio_scheduler
)
first_config = rx.concat(config.pipe(ops.take(1),), rx.never())
kafka_source = sources.kafka.response.pipe(
trace_observable("kafka source1"),
ops.replay(),
ops.ref_count(),
trace_observable("kafka source2"),
)
kafka_source.subscribe(on_error=on_error)
kafka_request = first_config.pipe(
ops.flat_map(lambda i: create_operators(
i, config,
kafka_source,
sources.kafka.feedback.pipe(ops.share()),
)),
ops.subscribe_on(aio_scheduler),
trace_observable("makinage"),
)
'''
config.pipe(ops.subscribe_on(aio_scheduler)).subscribe(
on_next=print,
on_error=print,
)
'''
return MakiNageSink(
file=file.Sink(request=read_request),
http=http.Sink(request=http_request),
kafka=kafka.Sink(request=kafka_request),
)
def _export_and_download_stack(stack, export_description, year_dir):
stack_drive_description = 'stack_' + export_description
stack_drive_folder = '{}-{}'.format(stack_drive_description,
str(uuid.uuid4()))
stack_drive_path = '{}/{}'.format(drive_folder_path,
stack_drive_folder)
create_stack_drive_folder = create_folder_with_path(
credentials, stack_drive_path).pipe(flat_map(lambda _: empty()))
export_stack = _export_stack(stack, stack_drive_description,
stack_drive_folder).pipe(
flat_map(lambda _: empty()))
download_stack_from_drive = _download_from_drive(
path=stack_drive_path, destination=year_dir).pipe(
map(lambda p: {'stack_bytes': p.downloaded_bytes}))
return concat(
create_stack_drive_folder,
export_stack,
of({'exported': 1}),
download_stack_from_drive,
of({'downloaded': 1}),
)
def _export_year(geometry, year_start, year_end, export_description,
year_dir):
stack = _create_stack(geometry, year_start, year_end)
ee.InitializeThread(credentials)
if not stack.bandNames().size().getInfo():
logging.info('No data between {} and {}'.format(
year_start, year_end))
return of({
'exported': 1,
'downloaded': 1,
'downloaded_bytes': 0,
'processed': 1
})
initial_progress = of({
'exported': 0,
'stack_bytes': 0,
'dates_bytes': 0,
'downloaded': 0,
'processed': 0
})
def aggregate_downloaded_bytes(p):
return {
'exported': p['exported'],
'downloaded': p['downloaded'],
'downloaded_bytes': p['stack_bytes'] + p['dates_bytes'],
'processed': p['processed']
}
return concat(
initial_progress,
merge(
_export_and_download_stack(stack, export_description,
year_dir),
_export_and_download_dates(stack, export_description,
year_dir)), _process_year(year_dir),
of({'processed': 1})).pipe(scan(lambda acc, p: {
**acc,
**p
}, {}), map(aggregate_downloaded_bytes))
def repeat(source: Observable) -> Observable:
"""Repeats the observable sequence a specified number of times.
If the repeat count is not specified, the sequence repeats
indefinitely.
Examples:
>>> repeated = source.repeat()
>>> repeated = source.repeat(42)
Args:
source: The observable source to repeat.
Returns:
The observable sequence producing the elements of the given
sequence repeatedly.
"""
if repeat_count is None:
gen = infinite()
else:
gen = range(repeat_count)
return rx.defer(lambda _: rx.concat(source for _ in gen))
def time_series_to_sepal(
credentials,
description: str,
download_dir: str,
image_collection_factory,
start_date: Union[int, str, date],
end_date: Union[int, str, date],
region: Union[ee.Geometry, ee.Feature, ee.FeatureCollection],
dimensions=None,
scale: int = None,
crs: str = None,
crs_transform: str = None,
max_pixels: Union[int, float] = None,
file_dimensions=None,
skip_empty_tiles=None,
file_format: str = None,
format_options: str = None,
precision: str = None,
nodata_value: int = None,
retries: int = 0
):
start_date = to_date(start_date)
end_date = to_date(end_date)
year_ranges = split_range_by_year(start_date, end_date)
drive_folder_path = '_'.join(['Sepal', description, str(uuid.uuid4())])
def _create_drive_folder():
return concat(
progress(
default_message='Creating Google Drive download folder...',
message_key='tasks.retrieve.time_series_to_sepal.creating_drive_folder'
),
create_folder_with_path(credentials, drive_folder_path).pipe(
flat_map(lambda _: empty())
)
)
def _export_geometries():
def aggregate_progress(progresses, count):
p = _sum_dicts(progresses.values(), excluded_keys=['geometry'])
exported = round(100 * p['exported'] / count)
downloaded = round(100 * p['downloaded'] / count)
downloaded_bytes = format_bytes(p['downloaded_bytes'])
processed = round(100 * p['processed'] / count)
return progress(
default_message='Exported {}%, Downloaded {}% ({}), Processed {}%'.format(
exported, downloaded, downloaded_bytes, processed
),
message_key='tasks.retrieve.time_series_to_sepal.progress',
exported=exported,
downloaded=downloaded,
downloaded_bytes=downloaded_bytes,
processed=processed
)
features_collection = _to_features_collection(region)
def export_geometry(geometry, i, geometry_count):
geometry_description = str(i + 1).zfill(len(str(geometry_count)))
return defer(
lambda _: _export_geometry(
geometry,
geometry_description=geometry_description
)
)
return concat(
progress(
default_message='Tiling AOI...',
message_key='tasks.retrieve.time_series_to_sepal.tiling'
),
_extract_feature_indexes(features_collection).pipe(
flat_map(
lambda feature_indexes: _to_geometries(features_collection, feature_indexes).pipe(
flat_map(
lambda geometries: concat(
*[
export_geometry(geometry, i, len(feature_indexes))
for i, geometry in enumerate(geometries)
]
)
),
scan(lambda acc, p: {**acc, p['geometry']: p}, {}),
flat_map(lambda progresses: aggregate_progress(
progresses,
count=len(feature_indexes) * len(year_ranges)
))
)
)
)
)
def _export_geometry(geometry, geometry_description):
export_years = combine_latest(
*[_export_year(
geometry=geometry,
year_start=year_range[0],
year_end=year_range[1],
export_description='{}_{}_{}'.format(geometry_description, year_range[0].year, description),
year_dir='/'.join([download_dir, description, geometry_description, str(year_range[0].year)])
) for year_range in year_ranges]
).pipe(
map(lambda progresses: _sum_dicts(progresses)),
map(lambda p: {**p, 'geometry': geometry_description})
)
process_geometry = _process_geometry('/'.join([download_dir, description, geometry_description]))
return concat(
export_years,
process_geometry
)
def _to_features_collection(r) -> ee.FeatureCollection:
return tile(r, TILE_SIZE_IN_DEGREES)
def _extract_feature_indexes(_feature_collection):
def action():
return _feature_collection.aggregate_array('system:index').getInfo()
return execute(credentials, action, description='Feature indexes from FeatureCollection')
def _to_geometries(_feature_collection, feature_indexes) -> Observable:
def action():
return [
ee.Feature(
_feature_collection
.filterMetadata('system:index', 'equals', feature_index)
.first()
).geometry()
for feature_index in feature_indexes
]
return execute(credentials, action, description='FeatureCollection to geometries')
def _export_year(geometry, year_start, year_end, export_description, year_dir):
stack = _create_stack(geometry, year_start, year_end)
ee.InitializeThread(credentials)
if not stack.bandNames().size().getInfo():
logging.info('No data between {} and {}'.format(year_start, year_end))
return of({
'exported': 1,
'downloaded': 1,
'downloaded_bytes': 0,
'processed': 1
})
initial_progress = of({
'exported': 0,
'stack_bytes': 0,
'dates_bytes': 0,
'downloaded': 0,
'processed': 0
})
def aggregate_downloaded_bytes(p):
return {
'exported': p['exported'],
'downloaded': p['downloaded'],
'downloaded_bytes': p['stack_bytes'] + p['dates_bytes'],
'processed': p['processed']
}
return concat(
initial_progress,
merge(
_export_and_download_stack(stack, export_description, year_dir),
_export_and_download_dates(stack, export_description, year_dir)
),
_process_year(year_dir),
of({'processed': 1})
).pipe(
scan(lambda acc, p: {**acc, **p}, {}),
map(aggregate_downloaded_bytes)
)
def _create_stack(geometry, start, end):
def to_daily_mosaic(image):
return ee.ImageCollection(ee.List(image.get('images'))) \
.median() \
.rename(ee.Image(image).getString('date'))
image_collection = image_collection_factory(geometry, start, end) \
.map(lambda image: image.set('date', image.date().format('yyyy-MM-dd')))
distinct_date_images = image_collection.distinct('date')
daily_mosaics = ee.ImageCollection(
ee.Join.saveAll('images').apply(
primary=distinct_date_images,
secondary=image_collection,
condition=ee.Filter.equals(leftField='date', rightField='date')
).map(to_daily_mosaic)
)
stack = daily_mosaics \
.toBands() \
.regexpRename('.*(.{10})', '$1') \
.clip(geometry)
return set_precision(stack, precision) if precision else stack
def _export_and_download_stack(stack, export_description, year_dir):
stack_drive_description = 'stack_' + export_description
stack_drive_folder = '{}-{}'.format(stack_drive_description, str(uuid.uuid4()))
stack_drive_path = '{}/{}'.format(drive_folder_path, stack_drive_folder)
create_stack_drive_folder = create_folder_with_path(credentials, stack_drive_path).pipe(
flat_map(lambda _: empty())
)
export_stack = _export_stack(stack, stack_drive_description, stack_drive_folder).pipe(
flat_map(lambda _: empty())
)
download_stack_from_drive = _download_from_drive(
path=stack_drive_path,
destination=year_dir
).pipe(
map(lambda p: {'stack_bytes': p.downloaded_bytes})
)
return concat(
create_stack_drive_folder,
export_stack,
of({'exported': 1}),
download_stack_from_drive,
of({'downloaded': 1}),
)
def _export_stack(stack, drive_description, folder):
return export_image_to_drive(
credentials,
stack,
description=drive_description,
folder=folder,
dimensions=dimensions,
scale=scale,
crs=crs,
crs_transform=crs_transform,
max_pixels=max_pixels,
file_dimensions=file_dimensions,
skip_empty_tiles=skip_empty_tiles,
file_format=file_format,
format_options=format_options,
retries=retries,
)
def _export_and_download_dates(stack, export_description, year_dir):
table_drive_description = 'dates_' + export_description
dates_drive_folder = '{}-{}'.format(table_drive_description, str(uuid.uuid4()))
dates_drive_path = '{}/{}'.format(drive_folder_path, dates_drive_folder)
create_dates_drive_folder = create_folder_with_path(credentials, dates_drive_path).pipe(
flat_map(lambda _: empty())
)
export_dates = _export_dates(stack.bandNames(), table_drive_description, dates_drive_folder)
download_dates_from_drive = _download_from_drive(
path=dates_drive_path,
destination=year_dir
).pipe(
map(lambda p: {'dates_bytes': p.downloaded_bytes})
)
return concat(
create_dates_drive_folder,
export_dates,
download_dates_from_drive
)
def _export_dates(dates, drive_description, folder):
date_table = ee.FeatureCollection(
dates.map(lambda d: ee.Feature(None, {'date': d}))
)
return export_table_to_drive(
credentials,
date_table,
description=drive_description,
folder=folder,
file_format='CSV'
).pipe(
flat_map(lambda _: empty())
)
def _download_from_drive(path, destination):
return download_path(
credentials,
path=path,
destination=destination,
delete_after_download=True,
retries=2
)
def _process_year(year_dir):
def action():
parent_dir = join(year_dir, pardir)
tif_names = [f for f in listdir(year_dir) if f.endswith('.tif')]
tile_pattern = re.compile('.*-(\d{10}-\d{10}).tif')
for tif_name in tif_names:
tile_name = tile_pattern.match(tif_name).group(1) \
if tile_pattern.match(tif_name) else '0000000000-0000000000'
tile_dir = abspath(join(parent_dir, tile_name))
subprocess.check_call(['mkdir', '-p', tile_dir])
subprocess.check_call(
'mv {0} {1}'.format(abspath(join(year_dir, tif_name)), abspath(join(tile_dir, tif_name))),
shell=True)
subprocess.check_call('mv {0} {1}'.format(join(year_dir, '*.csv'), parent_dir), shell=True)
subprocess.check_call('rm -rf {0}'.format(year_dir).split(' '))
return from_callable(action).pipe(
flat_map(lambda _: empty())
)
def _process_geometry(geometry_dir):
def action():
dates = create_dates_csv()
if dates:
tiles_to_vrts(dates)
def create_dates_csv():
dates_path = join(geometry_dir, 'dates.csv')
csv_paths = sorted(glob(join(geometry_dir, '*.csv')))
if dates_path in csv_paths:
csv_paths.remove(dates_path)
if not csv_paths:
return None
with open(dates_path, 'w') as dates_file:
for csv_path in csv_paths:
with open(csv_path, 'r') as csv_file:
for row in csv.DictReader(csv_file):
if row['date']:
dates_file.write(row['date'] + '\n')
subprocess.check_call('rm -rf {0}'.format(csv_path).split(' '))
dates_file.flush()
os.fsync(dates_file.fileno())
return [d.rstrip('\n') for d in open(dates_path)]
def tiles_to_vrts(dates):
tile_dirs = sorted([d for d in glob(join(geometry_dir, '*')) if isdir(d)])
for tile_dir in tile_dirs:
tile_to_vrt(tile_dir)
gdal.SetConfigOption('VRT_SHARED_SOURCE', '0')
vrt = gdal.BuildVRT(
geometry_dir + '/stack.vrt', sorted(glob(join(geometry_dir, '*.vrt'))),
VRTNodata=nodata_value
)
if vrt:
vrt.FlushCache()
set_band_metadata('DATE', dates, [geometry_dir + '/*.vrt'])
def tile_to_vrt(tile_dir):
tif_paths = sorted(glob(join(tile_dir, '*.tif')))
for tif_path in tif_paths:
tif_file = gdal.Open(tif_path)
tif_path_no_extension = os.path.splitext(tif_path)[0]
if tif_file:
for band_index in range(1, tif_file.RasterCount + 1):
tif_vrt_path = '{0}_{1}.vrt'.format(tif_path_no_extension, str(band_index).zfill(10))
gdal.SetConfigOption('VRT_SHARED_SOURCE', '0')
vrt = gdal.BuildVRT(
tif_vrt_path, tif_path,
bandList=[band_index],
VRTNodata=nodata_value)
if vrt:
vrt.FlushCache()
stack_vrt_path = tile_dir + '_stack.vrt'
vrt_paths = sorted(glob(join(tile_dir, '*.vrt')))
gdal.SetConfigOption('VRT_SHARED_SOURCE', '0')
vrt = gdal.BuildVRT(
stack_vrt_path, vrt_paths,
separate=True,
VRTNodata=0)
if vrt:
vrt.FlushCache()
return from_callable(action).pipe(
flat_map(lambda _: empty())
)
def _delete_drive_folder():
return concat(
progress(
default_message='Deleting Google Drive download folder...',
message_key='tasks.retrieve.time_series_to_sepal.deleting_drive_folder'
),
delete_file_with_path(
credentials,
path=drive_folder_path
).pipe(
flat_map(lambda _: empty())
)
)
def _sum_dicts(dicts: list, excluded_keys: list = ()):
keys = reduce(lambda acc, d: acc.union(set(d)), dicts, set())
keys = [key for key in keys if key not in excluded_keys]
return {key: sum([d.get(key, 0) for d in dicts]) for key in keys}
return concat(
_create_drive_folder(),
_export_geometries(),
_delete_drive_folder()
).pipe(
merge_finalize(_delete_drive_folder)
)