def csv_import(task_id): # pragma: no cover
task = ImportTask.objects.get(pk=task_id)
log = StringIO()
task.task_id = csv_import.request.id
task.log("Started import at %s" % timezone.now())
task.log("--------------------------------")
task.save()
try:
with transaction.atomic():
model = class_from_string(task.model_class)
records = model.import_csv(task, log)
task.save()
task.log(log.getvalue())
task.log("Import finished at %s" % timezone.now())
task.log("%d record(s) added." % len(records))
except Exception as e:
import traceback
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
task.log(log.getvalue())
raise e
return task
def download_album(user_id, community_id, album_id, task_id):
logger.info(user_id, community_id, album_id, task_id)
try:
user = Users.objects.get(id=user_id)
except (DoesNotExist, ValidationError):
raise Exception('User does not exist')
api = API(user.access_token, v=5.95)
response = api.photos.get(owner_id=f'-{community_id}',
album_id=album_id,
count=50)
items = response['items']
count = response['count']
folder = generate_uuid1()
photo_album = PhotoAlbum(folder)
photo_album.add(items)
path = photo_album.make_archive()
try:
archive = open(path, 'rb')
task = Tasks.objects.get(id=task_id)
task.archive.put(archive, content_type='application/zip')
task.save()
finally:
archive.close()
return
def create_task_and_maps(task_parameters, include_heatmap=True):
'''
task_parameters:
'basemap_ending_year': (int, "ending_year"),
'basemap_sample_size': (int, "sample_size"),
'basemap_starting_year': (int, "starting_year"),
'number_of_terms': int,
'ranking_algorithm': int,
'similarity_algorithm': int,
'filtering_algorithm': int,
'basemap_author': (str, 'author'),
'basemap_institution': (str, 'institution'),
'basemap_term_type': (int, 'term_type'),
if include_heatmap then also pass the following:
'heatmap_starting_year': (int, "starting_year"),
'heatmap_ending_year': (int, "ending_year"),
'heatmap_sample_size': (int, "sample_size"),
'heatmap_author': (str, 'author'),
'heatmap_institution': (str, 'institution'),
'heatmap_term_type': (int, 'term_type'),
)
'''
# set up new objects
basemap = Basemap(finished=False, **filter_basemap_args(task_parameters))
basemap.save()
if include_heatmap:
heatmap = Heatmap(finished=False, **filter_heatmap_args(task_parameters))
heatmap.save()
task = Task(basemap=basemap, heatmap=heatmap)
else:
task = Task(basemap=basemap)
task.save()
return task
def setup_task_ispaid(booking):
global notpaid_manager
event_date = booking.selection_set.all().first().datetime_init
diff = (event_date - datetime.now()).days
task_date = (datetime.now() +
timedelta(hours=24)) if diff >= 1 else (event_date -
timedelta(hours=1))
schedule, _ = CrontabSchedule.objects.get_or_create(
minute=task_date.minute,
hour=task_date.hour,
day_of_week=get_cron_weekday(task_date.strftime("%A")),
day_of_month=task_date.day,
month_of_year=task_date.month,
timezone=pytz.timezone('Europe/Madrid'))
task = PeriodicTask.objects.create(
crontab=schedule,
name="Check after 24h if " + str(booking.id) + " is_paid",
task='trainWellApp.tasks.booking_notpaid',
args=json.dumps([booking.id]),
)
notpaid_manager[booking.id] = task.id
task.kwargs = json.dumps({'id': task.id})
task.save()
def process_band_math(self, chunk, task_id=None, num_scn_per_chk=None):
"""Apply some band math to a chunk and return the args
Opens the chunk dataset and applys some band math defined by _apply_band_math(dataset)
_apply_band_math creates some product using the bands already present in the dataset and
returns the dataarray. The data array is then appended under 'band_math', then saves the
result to disk in the same path as the nc file already exists.
Args:
chunk: The return from the recombine_time_chunks function - path, metadata, and {chunk ids}
num_scn_per_chk: The number of scenes per chunk. Used to determine task progress.
"""
task = FractionalCoverTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
def _apply_band_math(dataset):
clear_mask = task.satellite.get_clean_mask_func()(dataset)
# mask out water manually. Necessary for frac. cover.
wofs = wofs_classify(dataset, clean_mask=clear_mask, mosaic=True)
clear_mask[wofs.wofs.values == 1] = False
return frac_coverage_classify(dataset,
clean_mask=clear_mask,
no_data=task.satellite.no_data_value)
if chunk is None:
return None
dataset = xr.open_dataset(chunk[0]).load()
dataset = xr.merge([dataset, _apply_band_math(dataset)])
#remove previous nc and write band math to disk
os.remove(chunk[0])
dataset.to_netcdf(chunk[0])
task.scenes_processed = F('scenes_processed') + num_scn_per_chk
task.save(update_fields=['scenes_processed'])
return chunk
def start_chunk_processing(self, chunk_details, task_id=None):
"""Create a fully asyncrhonous processing pipeline from paramters and a list of chunks.
The most efficient way to do this is to create a group of time chunks for each geographic chunk,
recombine over the time index, then combine geographic last.
If we create an animation, this needs to be reversed - e.g. group of geographic for each time,
recombine over geographic, then recombine time last.
The full processing pipeline is completed, then the create_output_products task is triggered, completing the task.
"""
if chunk_details is None:
return None
parameters = chunk_details.get('parameters')
geographic_chunks = chunk_details.get('geographic_chunks')
time_chunks = chunk_details.get('time_chunks')
task = FractionalCoverTask.objects.get(pk=task_id)
# Get an estimate of the amount of work to be done: the number of scenes
# to process, also considering intermediate chunks to be combined.
num_scenes = len(geographic_chunks) * sum([len(time_chunk) for time_chunk in time_chunks])
# recombine_time_chunks() and process_band_math() scenes:
# num_scn_per_chk * len(time_chunks) * len(geographic_chunks)
num_scn_per_chk = round(num_scenes / (len(time_chunks) * len(geographic_chunks)))
# recombine_geographic_chunks() and create_output_products() scenes:
# num_scn_per_chk_geo * len(geographic_chunks)
num_scn_per_chk_geo = round(num_scenes / len(geographic_chunks))
# Scene processing progress is tracked in: processing_task(), recombine_time_chunks(),
# and process_band_math(). Scenes in process_band_math() are counted twice
# for the sake of tracking progress because it takes so long to run. So 1 + 1 + 2 = 4.
task.total_scenes = 4 * num_scenes
task.scenes_processed = 0
task.save(update_fields=['total_scenes', 'scenes_processed'])
if check_cancel_task(self, task): return
task.update_status("WAIT", "Starting processing.")
logger.info("START_CHUNK_PROCESSING")
processing_pipeline = (group([
group([
processing_task.s(
task_id=task_id,
geo_chunk_id=geo_index,
time_chunk_id=time_index,
geographic_chunk=geographic_chunk,
time_chunk=time_chunk,
**parameters) for time_index, time_chunk in enumerate(time_chunks)
]) | recombine_time_chunks.s(task_id=task_id, num_scn_per_chk=num_scn_per_chk)
| process_band_math.s(task_id=task_id, num_scn_per_chk=2*num_scn_per_chk_geo)
for geo_index, geographic_chunk in enumerate(geographic_chunks)
]) | recombine_geographic_chunks.s(task_id=task_id)
| create_output_products.s(task_id=task_id)
| task_clean_up.si(task_id=task_id, task_model='FractionalCoverTask')).apply_async()
return True
def csv_import(task_id): #pragma: no cover
from django.db import transaction
# there is a possible race condition between this task starting
# so we have a bit of loop here to fetch the task
tries = 0
task = None
while tries < 5 and not task:
try:
task = ImportTask.objects.get(pk=task_id)
except Exception as e:
# this object just doesn't exist yet, sleep a bit then try again
tries+=1
if tries >= 5:
raise e
else:
sleep(1)
transaction.enter_transaction_management()
transaction.managed()
log = StringIO.StringIO()
try:
task.task_id = csv_import.request.id
task.log("Started import at %s" % timezone.now())
task.log("--------------------------------")
task.save()
transaction.commit()
model = class_from_string(task.model_class)
records = model.import_csv(task, log)
task.log(log.getvalue())
task.log("Import finished at %s" % timezone.now())
task.log("%d record(s) added." % len(records))
transaction.commit()
except Exception as e:
transaction.rollback()
import traceback
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
task.log(log.getvalue())
transaction.commit()
raise e
finally:
transaction.leave_transaction_management()
return task
def recombine_time_chunks(self, chunks, task_id=None, num_scn_per_chk=None):
"""Recombine processed chunks over the time index.
Open time chunked processed datasets and recombine them using the same function
that was used to process them. This assumes an iterative algorithm - if it is not, then it will
simply return the data again.
Args:
chunks: list of the return from the processing_task function - path, metadata, and {chunk ids}
num_scn_per_chk: The number of scenes per chunk. Used to determine task progress.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
task = FractionalCoverTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
#sorting based on time id - earlier processed first as they're incremented e.g. 0, 1, 2..
chunks = chunks if isinstance(chunks, list) else [chunks]
chunks = [chunk for chunk in chunks if chunk is not None]
if len(chunks) == 0:
return None
total_chunks = sorted(chunks, key=lambda x: x[0])
geo_chunk_id = total_chunks[0][2]['geo_chunk_id']
time_chunk_id = total_chunks[0][2]['time_chunk_id']
metadata = {}
combined_data = None
for index, chunk in enumerate(total_chunks):
metadata.update(chunk[1])
data = xr.open_dataset(chunk[0])
if combined_data is None:
combined_data = data
task.scenes_processed = F('scenes_processed') + num_scn_per_chk
task.save(update_fields=['scenes_processed'])
continue
#give time an indice to keep mosaicking from breaking.
data = xr.concat([data], 'time')
data['time'] = [0]
clear_mask = task.satellite.get_clean_mask_func()(data)
combined_data = task.get_processing_method()(data,
clean_mask=clear_mask,
intermediate_product=combined_data,
no_data=task.satellite.no_data_value,
reverse_time=task.get_reverse_time())
if check_cancel_task(self, task): return
task.scenes_processed = F('scenes_processed') + num_scn_per_chk
task.save(update_fields=['scenes_processed'])
if combined_data is None:
return None
path = os.path.join(task.get_temp_path(), "recombined_time_{}.nc".format(geo_chunk_id))
export_xarray_to_netcdf(combined_data, path)
logger.info("Done combining time chunks for geo: " + str(geo_chunk_id))
return path, metadata, {'geo_chunk_id': geo_chunk_id, 'time_chunk_id': time_chunk_id}
def start_chunk_processing(self, chunk_details, task_id=None):
"""Create a fully asyncrhonous processing pipeline from paramters and a list of chunks.
The most efficient way to do this is to create a group of time chunks for each geographic chunk,
recombine over the time index, then combine geographic last.
If we create an animation, this needs to be reversed - e.g. group of geographic for each time,
recombine over geographic, then recombine time last.
The full processing pipeline is completed, then the create_output_products task is triggered, completing the task.
"""
if chunk_details is None:
return None
parameters = chunk_details.get('parameters')
geographic_chunks = chunk_details.get('geographic_chunks')
time_chunks = chunk_details.get('time_chunks')
task = SpectralIndicesTask.objects.get(pk=task_id)
# Track task progress.
num_scenes = len(geographic_chunks) * sum(
[len(time_chunk) for time_chunk in time_chunks])
# Scene processing progress is tracked in processing_task().
task.total_scenes = num_scenes
task.scenes_processed = 0
task.save(update_fields=['total_scenes', 'scenes_processed'])
if check_cancel_task(self, task): return
task.update_status("WAIT", "Starting processing.")
logger.info("START_CHUNK_PROCESSING")
processing_pipeline = (
group([
group([
processing_task.s(task_id=task_id,
geo_chunk_id=geo_index,
time_chunk_id=time_index,
geographic_chunk=geographic_chunk,
time_chunk=time_chunk,
**parameters)
for time_index, time_chunk in enumerate(time_chunks)
]) | recombine_time_chunks.s(task_id=task_id)
| process_band_math.s(task_id=task_id)
for geo_index, geographic_chunk in enumerate(geographic_chunks)
]) | recombine_geographic_chunks.s(task_id=task_id)
| create_output_products.s(task_id=task_id)
| task_clean_up.si(task_id=task_id,
task_model='SpectralIndicesTask')).apply_async()
return True
def recombine_geographic_chunks(self, chunks, task_id=None, num_scn_per_chk=None):
"""Recombine processed data over the geographic indices
For each geographic chunk process spawned by the main task, open the resulting dataset
and combine it into a single dataset. Combine metadata as well, writing to disk.
Args:
chunks: list of the return from the processing_task function - path, metadata, and {chunk ids}
num_scn_per_chk: The number of scenes per chunk. Used to determine task progress.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
task = TsmTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
total_chunks = [chunks] if not isinstance(chunks, list) else chunks
total_chunks = [chunk for chunk in total_chunks if chunk is not None]
if len(total_chunks) == 0:
return None
geo_chunk_id = total_chunks[0][2]['geo_chunk_id']
time_chunk_id = total_chunks[0][2]['time_chunk_id']
metadata = {}
chunk_data = []
for index, chunk in enumerate(total_chunks):
metadata = task.combine_metadata(metadata, chunk[1])
chunk_data.append(xr.open_dataset(chunk[0]))
task.scenes_processed = F('scenes_processed') + num_scn_per_chk
task.save(update_fields=['scenes_processed'])
combined_data = combine_geographic_chunks(chunk_data)
if task.animated_product.animation_id != "none":
base_index = (task.get_chunk_size()['time'] if task.get_chunk_size()['time'] is not None else 1) * time_chunk_id
for index in range((task.get_chunk_size()['time'] if task.get_chunk_size()['time'] is not None else 1)):
animated_data = []
for chunk in total_chunks:
geo_chunk_index = chunk[2]['geo_chunk_id']
# if we're animating, combine it all and save to disk.
path = os.path.join(task.get_temp_path(),
"animation_{}_{}.nc".format(str(geo_chunk_index), str(base_index + index)))
if os.path.exists(path):
animated_data.append(xr.open_dataset(path))
path = os.path.join(task.get_temp_path(), "animation_{}.nc".format(base_index + index))
if len(animated_data) > 0:
combine_geographic_chunks(animated_data).to_netcdf(path)
path = os.path.join(task.get_temp_path(), "recombined_geo_{}.nc".format(time_chunk_id))
combined_data.to_netcdf(path)
logger.info("Done combining geographic chunks for time: " + str(time_chunk_id))
return path, metadata, {'geo_chunk_id': geo_chunk_id, 'time_chunk_id': time_chunk_id}
def generateOutput(output_task_id):
task = OutputTask.objects.get(id=output_task_id)
search_data = cPickle.loads(task.search_form.encode('utf-8'))
experiments = find(search_data)
return_data = search_data['out']['data']
if return_data == 'I':
pass
elif return_data == 'P':
pass
elif return_data == 'S':
pass
elif return_data == 'A':
pass
else:
task.is_finished = True
task.save()
return
# TODO -- write the results of the search
# create the temporary directory to store the script results
tmp_dir = tempfile.mkdtemp()
out_dir = os.path.join(os.path.dirname(__file__), 'site_media', 'tasks')
# TODO -- run the script
script_name = 'test.sh'
script = os.path.join(settings.TASK_SCRIPT_DIR, script_name)
subprocess.call(script, shell=True, cwd=tmp_dir)
# collect all files and zip them
result_files = os.listdir(tmp_dir)
tmp_tar = tempfile.NamedTemporaryFile(delete=False)
t = tarfile.open(fileobj=tmp_tar, mode='w:bz2')
for f in result_files:
filename = os.path.join(tmp_dir, f)
t.add(filename, arcname=f)
t.close()
tmp_tar.close()
# move the results to a django-accessible directory
shutil.move(tmp_tar.name, task.output_abs_path())
# delete all files (and temp_dir)
shutil.rmtree(tmp_dir)
# mark the task as finished
task.is_finished = True
task.save()
def create_task_with_existing_basemap(basemap_id, heatmap_task_parameters):
"""heatmap_task_parameters:
'heatmap_starting_year': (int, "starting_year"),
'heatmap_ending_year': (int, "ending_year"),
'heatmap_sample_size': (int, "sample_size"),
'heatmap_author': (str, 'author'),
'heatmap_conference': (str, 'conference'),
'heatmap_journal': (str, 'journal'),
'heatmap_term_type': (int, 'term_type'),
"""
basemap = Basemap.objects.get(id=basemap_id)
heatmap = Heatmap(finished=False, **filter_heatmap_args(heatmap_task_parameters))
heatmap.save()
task = Task(basemap=basemap, heatmap=heatmap)
task.save()
return task
def start_chunk_processing(self, chunk_details, task_id=None):
"""Create a fully asyncrhonous processing pipeline from paramters and a list of chunks.
The most efficient way to do this is to create a group of time chunks for each geographic chunk,
recombine over the time index, then combine geographic last.
If we create an animation, this needs to be reversed - e.g. group of geographic for each time,
recombine over geographic, then recombine time last.
The full processing pipeline is completed, then the create_output_products task is triggered, completing the task.
"""
if chunk_details is None:
return None
parameters = chunk_details.get('parameters')
geographic_chunks = chunk_details.get('geographic_chunks')
time_chunks = chunk_details.get('time_chunks')
task = CoastalChangeTask.objects.get(pk=task_id)
# This calculation does not account for time chunking because this app
# does not support time chunking.
num_times_fst_lst_yrs = len(time_chunks[0][0]) + len(time_chunks[0][1])
task.total_scenes = len(geographic_chunks) * len(
time_chunks) * num_times_fst_lst_yrs
task.scenes_processed = 0
task.save()
if check_cancel_task(self, task): return
task.update_status("WAIT", "Starting processing.")
logger.info("START_CHUNK_PROCESSING")
processing_pipeline = (group([
group([
processing_task.s(
task_id=task_id,
geo_chunk_id=geo_index,
time_chunk_id=time_index,
geographic_chunk=geographic_chunk,
time_chunk=time_chunk,
**parameters) for geo_index, geographic_chunk in enumerate(geographic_chunks)
]) | recombine_geographic_chunks.s(task_id=task_id) for time_index, time_chunk in enumerate(time_chunks)
]) | recombine_time_chunks.s(task_id=task_id) | create_output_products.s(task_id=task_id)\
| task_clean_up.si(task_id=task_id, task_model='CoastalChangeTask')).apply_async()
return True
def delay_task(*args, **kwargs):
"""
Run task at time
args = PeriodicTask.id
"""
try:
task_id = args[0]
print 'task id = %s' % task_id
task = PeriodicTask.objects.get(task='w3af_webui.tasks.delay_task',
name='delay_%s' % task_id,
)
task.interval = None
task.enabled = False
task.save()
scan_create_start(task_id)
except Exception, e:
logger.error("delay task exception %s" % e)
raise Exception, e
def delay_task(*args, **kwargs):
"""
Run task at time
args = PeriodicTask.id
"""
try:
task_id = args[0]
print 'task id = %s' % task_id
task = PeriodicTask.objects.get(
task='w3af_webui.tasks.delay_task',
name='delay_%s' % task_id,
)
task.interval = None
task.enabled = False
task.save()
scan_create_start(task_id)
except Exception, e:
logger.error("delay task exception %s" % e)
raise Exception, e
def csv_import(task): #pragma: no cover
from django.db import transaction
transaction.enter_transaction_management()
transaction.managed()
log = StringIO.StringIO()
try:
task.task_id = csv_import.request.id
task.log("Started import at %s" % datetime.now())
task.log("--------------------------------")
task.save()
transaction.commit()
model = class_from_string(task.model_class)
records = model.import_csv(task.csv_file.file, task.created_by, log)
task.log(log.getvalue())
task.log("Import finished at %s" % datetime.now())
task.log("%d record(s) added." % len(records))
transaction.commit()
except Exception as e:
transaction.rollback()
import traceback
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
task.log(log.getvalue())
transaction.commit()
raise e
finally:
transaction.leave_transaction_management()
return task
def csv_import(task): #pragma: no cover
from django.db import transaction
transaction.enter_transaction_management()
transaction.managed()
log = StringIO.StringIO()
try:
task.task_id = csv_import.request.id
task.log("Started import at %s" % datetime.now())
task.log("--------------------------------")
task.save()
transaction.commit()
model = class_from_string(task.model_class)
records = model.import_csv(task.csv_file.file, task.created_by, log)
task.log(log.getvalue())
task.log("Import finished at %s" % datetime.now())
task.log("%d record(s) added." % len(records))
transaction.commit()
except Exception as e:
transaction.rollback()
import traceback
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
task.log(log.getvalue())
transaction.commit()
raise e
finally:
transaction.leave_transaction_management()
return task
def monthly_task(*args, **kwargs):
try:
task_id = args[0]
task = PeriodicTask.objects.get(task='w3af_webui.tasks.monthly_task',
name=task_id,
)
now = datetime.now()
next_time = now + relativedelta(months=+1)
delta = next_time - now
interval = IntervalSchedule.from_schedule(schedule(delta))
interval.save()
logger.info('set interval %s for celery task %s' % (
interval,
task.name,
))
task.interval = interval
task.save()
scan_create_start(task_id)
except Exception, e:
logger.error("monthly task exception %s" % e)
raise Exception, e
def monthly_task(*args, **kwargs):
try:
task_id = args[0]
task = PeriodicTask.objects.get(
task='w3af_webui.tasks.monthly_task',
name=task_id,
)
now = datetime.now()
next_time = now + relativedelta(months=+1)
delta = next_time - now
interval = IntervalSchedule.from_schedule(schedule(delta))
interval.save()
logger.info('set interval %s for celery task %s' % (
interval,
task.name,
))
task.interval = interval
task.save()
scan_create_start(task_id)
except Exception, e:
logger.error("monthly task exception %s" % e)
raise Exception, e
def expire_tasks():
"""Find any tasks that are past their expiration date and unassign them.
We currently run this once per day (at 7 AM server time).
"""
from teams.models import Task
expired_tasks = Task.objects.incomplete().filter(
expiration_date__isnull=False,
expiration_date__lt=datetime.now(),
)
for task in expired_tasks:
task.assignee = task.expiration_date = None
# run each inside a try/except so that one
# rotten apple doesn't make a huge mess
try:
task.save()
except Exception as e:
logger.error('Error on expiring tasks', extra={
'task': task,
'exception': e,
})
def save_failed_task(self, exc, task_id, args, kwargs, traceback):
"""
:type exc: Exception
"""
task = FailedTask()
task.celery_task_id = task_id
task.full_name = self.name
task.name = self.name.split('.')[-1]
task.exception_class = exc.__class__.__name__
task.exception_msg = unicode(exc).strip()
task.traceback = unicode(traceback).strip()
task.updated_at = timezone.now()
if args:
task.args = json.dumps(list(args))
if kwargs:
task.kwargs = json.dumps(kwargs)
# Find if task with same args, name and exception already exists
# If it do, update failures count and last updated_at
#: :type: FailedTask
existing_task = FailedTask.objects.filter(
args=task.args,
kwargs=task.kwargs,
full_name=task.full_name,
exception_class=task.exception_class,
exception_msg=task.exception_msg,
)
if len(existing_task):
existing_task = existing_task[0]
existing_task.failures += 1
existing_task.updated_at = task.updated_at
existing_task.save(force_update=True,
update_fields=('updated_at', 'failures'))
else:
task.save(force_insert=True)
def save_failed_task(self, exc, task_id, args, kwargs, traceback):
"""
:type exc: Exception
"""
task = FailedTask()
task.celery_task_id = task_id
task.full_name = self.name
task.name = self.name.split('.')[-1]
task.exception_class = exc.__class__.__name__
task.exception_msg = unicode(exc).strip()
task.traceback = unicode(traceback).strip()
task.updated_at = timezone.now()
if args:
task.args = json.dumps(list(args))
if kwargs:
task.kwargs = json.dumps(kwargs)
# Find if task with same args, name and exception already exists
# If it do, update failures count and last updated_at
#: :type: FailedTask
existing_task = FailedTask.objects.filter(
args=task.args,
kwargs=task.kwargs,
full_name=task.full_name,
exception_class=task.exception_class,
exception_msg=task.exception_msg,
)
if len(existing_task):
existing_task = existing_task[0]
existing_task.failures += 1
existing_task.updated_at = task.updated_at
existing_task.save(force_update=True,
update_fields=('updated_at', 'failures'))
else:
task.save(force_insert=True)
def setup_task_event_done(booking):
global events_done_manager
event_date = booking.selection_set.all().last()
task_date = event_date.datetime_init + timedelta(hours=1)
schedule, _ = CrontabSchedule.objects.get_or_create(
minute=task_date.minute,
hour=task_date.hour,
day_of_week=get_cron_weekday(task_date.strftime("%A")),
day_of_month=task_date.day,
month_of_year=task_date.month,
timezone=pytz.timezone('Europe/Madrid'))
task = PeriodicTask.objects.create(
crontab=schedule,
name="Booking " + str(booking.id) + " happened",
task='trainWellApp.tasks.event_done',
args=json.dumps([booking.id]),
)
events_done_manager[booking.id] = task.id
task.kwargs = json.dumps({'id': task.id})
task.save()
def setup_task_invoice(invoice):
global invoices_manager
curr_year = datetime.now().year
task_date = datetime.now().replace(year=curr_year + 2) # By law 2 years.
schedule, _ = CrontabSchedule.objects.get_or_create(
minute=task_date.minute,
hour=task_date.hour,
day_of_week=get_cron_weekday(task_date.strftime("%A")),
day_of_month=task_date.day,
month_of_year=task_date.month,
timezone=pytz.timezone('Europe/Madrid'))
task = PeriodicTask.objects.create(
crontab=schedule,
name="Invoice " + str(invoice.id) + " deleted",
task='trainWellApp.tasks.invoice_timeout',
args=json.dumps([invoice.id]),
)
invoices_manager[invoice.id] = task.id
task.kwargs = json.dumps({'id': task.id})
task.save()
def processing_task(self,
task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = SpectralIndicesTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
metadata = {}
times = list(
map(_get_datetime_range_containing, time_chunk) if task.get_iterative(
) else [_get_datetime_range_containing(time_chunk[0], time_chunk[-1])])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
iteration_data = None
for time_index, time in enumerate(times):
updated_params.update({'time': time})
data = dc.get_dataset_by_extent(**updated_params)
if check_cancel_task(self, task): return
if data is None:
logger.info("Empty chunk.")
continue
if 'time' not in data:
logger.info("Invalid chunk.")
continue
clear_mask = task.satellite.get_clean_mask_func()(data)
add_timestamp_data_to_xr(data)
metadata = task.metadata_from_dataset(metadata, data, clear_mask,
updated_params)
iteration_data = task.get_processing_method()(
data,
clean_mask=clear_mask,
intermediate_product=iteration_data,
no_data=task.satellite.no_data_value,
reverse_time=task.get_reverse_time())
if check_cancel_task(self, task): return
task.scenes_processed = F('scenes_processed') + 1
task.save(update_fields=['scenes_processed'])
if iteration_data is None:
return None
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
export_xarray_to_netcdf(iteration_data, path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def processing_task(self,
task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = NdviAnomalyTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
metadata = {}
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1),
max(time_ranges) + timedelta(microseconds=1))
base_scene_time_range = parameters['time']
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
# Generate the baseline data - one time slice at a time
full_dataset = []
for time_index, time in enumerate(time_chunk):
updated_params.update({'time': _get_datetime_range_containing(time)})
data = dc.get_dataset_by_extent(**updated_params)
if check_cancel_task(self, task): return
if data is None or 'time' not in data:
logger.info("Invalid chunk.")
continue
full_dataset.append(data.copy(deep=True))
# load selected scene and mosaic just in case we got two scenes (handles scene boundaries/overlapping data)
updated_params.update({'time': base_scene_time_range})
selected_scene = dc.get_dataset_by_extent(**updated_params)
if check_cancel_task(self, task): return
if len(full_dataset) == 0 or 'time' not in selected_scene:
return None
#concat individual slices over time, compute metadata + mosaic
baseline_data = xr.concat(full_dataset, 'time')
baseline_clear_mask = task.satellite.get_clean_mask_func()(baseline_data)
metadata = task.metadata_from_dataset(metadata, baseline_data,
baseline_clear_mask, parameters)
selected_scene_clear_mask = task.satellite.get_clean_mask_func()(
selected_scene)
metadata = task.metadata_from_dataset(metadata, selected_scene,
selected_scene_clear_mask,
parameters)
selected_scene = task.get_processing_method()(
selected_scene,
clean_mask=selected_scene_clear_mask,
intermediate_product=None,
no_data=task.satellite.no_data_value)
# we need to re generate the clear mask using the mosaic now.
selected_scene_clear_mask = task.satellite.get_clean_mask_func()(
selected_scene)
if check_cancel_task(self, task): return
ndvi_products = compute_ndvi_anomaly(
baseline_data,
selected_scene,
baseline_clear_mask=baseline_clear_mask,
selected_scene_clear_mask=selected_scene_clear_mask,
no_data=task.satellite.no_data_value)
full_product = xr.merge([ndvi_products, selected_scene])
task.scenes_processed = F('scenes_processed') + 1
task.save(update_fields=['scenes_processed'])
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
full_product.to_netcdf(path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def processing_task(self,
task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = CustomMosaicToolTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
iteration_data = None
metadata = {}
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1),
max(time_ranges) + timedelta(microseconds=1))
times = list(
map(_get_datetime_range_containing, time_chunk) if task.get_iterative(
) else [_get_datetime_range_containing(time_chunk[0], time_chunk[-1])])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
#updated_params.update({'products': parameters['']})
iteration_data = None
base_index = (task.get_chunk_size()['time'] if task.get_chunk_size()
['time'] is not None else 1) * time_chunk_id
for time_index, time in enumerate(times):
updated_params.update({'time': time})
data = dc.get_stacked_datasets_by_extent(**updated_params)
if check_cancel_task(self, task): return
if data is None or 'time' not in data:
logger.info("Invalid chunk.")
continue
clear_mask = task.satellite.get_clean_mask_func()(data)
add_timestamp_data_to_xr(data)
metadata = task.metadata_from_dataset(metadata, data, clear_mask,
updated_params)
iteration_data = task.get_processing_method()(
data,
clean_mask=clear_mask,
intermediate_product=iteration_data,
no_data=task.satellite.no_data_value,
reverse_time=task.get_reverse_time())
if check_cancel_task(self, task): return
if task.animated_product.animation_id != "none":
path = os.path.join(
task.get_temp_path(),
"animation_{}_{}.nc".format(str(geo_chunk_id),
str(base_index + time_index)))
if task.animated_product.animation_id == "scene":
#need to clear out all the metadata..
clear_attrs(data)
#can't reindex on time - weird?
export_xarray_to_netcdf(data.isel(time=0).drop('time'), path)
elif task.animated_product.animation_id == "cumulative":
export_xarray_to_netcdf(iteration_data, path)
task.scenes_processed = F('scenes_processed') + 1
# Avoid overwriting the task's status if it is cancelled.
task.save(update_fields=['scenes_processed'])
if iteration_data is None:
return None
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
export_xarray_to_netcdf(iteration_data, path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def faq_csv_import(org_id, task_id): # pragma: no cover
task = ImportTask.objects.get(id=task_id)
org = Org.objects.get(id=org_id)
task.task_id = faq_csv_import.request.id
task.log("Started import at %s" % timezone.now())
task.log("--------------------------------")
task.save()
try:
with transaction.atomic() and open(
task.csv_file.path
) as csv_file: # transaction prevents partial csv import
# Load csv into Dict
records = csv.DictReader(csv_file)
lines = 0
for line in records:
lines += 1
# Get or create parent Language object
parent_lang = line["Parent Language"]
# Get label objects
labels = get_labels(task, org, line["Labels"])
# Create parent FAQ
parent_faq = FAQ.create(org, line["Parent Question"],
line["Parent Answer"], parent_lang,
None, labels)
# Start creation of translation FAQs
# get a list of the csv keys
keys = list(line)
# remove non-translation keys
parent_keys = [
"Parent Question", "Parent Language", "Parent Answer",
"Parent ID", "Labels"
]
[keys.remove(parent_key) for parent_key in parent_keys]
# get a set of unique translation language codes
lang_codes = set()
for key in keys:
lang_code, name = key.split(" ")
lang_codes.add(lang_code)
# Loop through for each translation
for lang_code in lang_codes:
# Create translation FAQ
FAQ.create(
org,
line["%s Question" % lang_code],
line["%s Answer" % lang_code],
lang_code,
parent_faq,
labels,
)
task.save()
task.log("Import finished at %s" % timezone.now())
task.log("%d FAQ(s) added." % lines)
except Exception as e:
if not settings.TESTING:
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
raise e
return task
def perform_sync_task(task):
"""
Run sync_task
TODO: move to SyncTask object
"""
logger.info('start with sync of server %s' % task.server.name)
data_set = task.data_set
if task.server.is_local_server:
path_and_parameters = task.server.url.split('?')
path = path_and_parameters[0]
regex = r'^' + path + r'/?$'
external_server = ServerMapping.objects.get(
relative_path__regex=regex,
).external_server
if len(path_and_parameters) > 1:
parameters = path_and_parameters[1]
service_url = external_server + '?' + parameters
else:
service_url = external_server
else:
service_url = task.server.url
password = task.server.password
username = task.server.username
wms = WebMapService(
service_url,
version='1.1.1',
password=password,
username=username,
)
if task.tag:
tag, new = task.tag, False
else:
tag, new = Tag.objects.get_or_create(
slug='server_%s' % task.server.name)
# layers = Layer.objects.filter(server=task.server)
layers = Layer.objects.filter(source_ident=task.source_ident)
layer_dict = dict(layers.values_list('layers', 'id'))
#update server info
task.server.title = wms.identification.title
task.server.abstract = wms.identification.abstract
task.server.save()
new = 0
new_names = []
removed = 0
removed_names = []
updated = 0
for wmslayer in wms.contents:
if wmslayer in layer_dict:
layer = layers.get(pk=layer_dict[wmslayer])
del layer_dict[wmslayer]
updated += 1
else:
layer = Layer()
layer.server = task.server
layer.layers = wmslayer
layer.name = wms[wmslayer].title
layer.slug = slugify(layer.name)
layer.save()
layer.tags.add(tag)
new += 1
new_names.append(layer.name)
layer.data_set = data_set
layer.is_local_server = task.server.is_local_server
layer.is_clickable = task.server.is_clickable
if not layer.js_popup_class and task.server.js_popup_class:
layer.js_popup_class = task.server.js_popup_class
layer.valid = True
if data_set:
layer.owner_type = Layer.OWNER_TYPE_DATASET
else:
layer.owner_type = Layer.OWNER_TYPE_PUBLIC
layer.source_ident = task.source_ident
layer.save()
#nog iets met styles?
for name, id in layer_dict.items():
layer = layers.get(pk=id)
layer.valid = False
layer.save()
removed += 1
removed_names.append(layer.name)
logger.info('%i new layers: %s.' % (new, str(', '.join(new_names))))
logger.info('%i updated layers.' % (updated))
logger.info('%i removed layers: %s.' % (
removed, str(', '.join(removed_names))))
task.last_sync = datetime.datetime.now()
task.last_result = '%i new, %i updated, %i removed' % (
new, updated, removed)
task.save()
def processing_task(self,
task_id=None,
geo_chunk_id=None,
geographic_chunk=None,
num_scn_per_chk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
num_scn_per_chk: A dictionary of the number of scenes per chunk for the baseline
and analysis extents. Used to determine task progress.
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = str(geo_chunk_id)
task = SpectralAnomalyTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
if not os.path.exists(task.get_temp_path()):
return None
metadata = {}
# For both the baseline and analysis time ranges for this
# geographic chunk, load, calculate the spectral index, composite,
# and filter the data according to user-supplied parameters -
# recording where the data was out of the filter's range so we can
# create the output product (an image).
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
spectral_index = task.query_type.result_id
composites = {}
composites_out_of_range = {}
no_data_value = task.satellite.no_data_value
for composite_name in ['baseline', 'analysis']:
if check_cancel_task(self, task): return
# Use the corresponding time range for the baseline and analysis data.
updated_params['time'] = \
updated_params['baseline_time' if composite_name == 'baseline' else 'analysis_time']
time_column_data = dc.get_dataset_by_extent(**updated_params)
# If this geographic chunk is outside the data extents, return None.
if len(time_column_data.dims) == 0: return None
# Obtain the clean mask for the satellite.
time_column_clean_mask = task.satellite.get_clean_mask_func()(
time_column_data)
measurements_list = task.satellite.measurements.replace(" ",
"").split(",")
# Obtain the mask for valid Landsat values.
time_column_invalid_mask = landsat_clean_mask_invalid(\
time_column_data, platform=task.satellite.platform,
collection=task.satellite.collection, level=task.satellite.level).values
# Also exclude data points with the no_data value.
no_data_mask = time_column_data[
measurements_list[0]].values != no_data_value
# Combine the clean masks.
time_column_clean_mask = time_column_clean_mask | time_column_invalid_mask | no_data_mask
# Obtain the composite.
composite = task.get_processing_method()(
time_column_data,
clean_mask=time_column_clean_mask,
no_data=task.satellite.no_data_value)
# Obtain the mask for valid Landsat values.
composite_invalid_mask = landsat_clean_mask_invalid(\
composite, platform=task.satellite.platform,
collection=task.satellite.collection, level=task.satellite.level).values
# Also exclude data points with the no_data value via the compositing mask.
composite_no_data_mask = composite[
measurements_list[0]].values != no_data_value
composite_clean_mask = composite_invalid_mask | composite_no_data_mask
# Compute the spectral index for the composite.
spec_ind_params = dict()
if spectral_index == 'fractional_cover':
spec_ind_params = dict(clean_mask=composite_clean_mask,
no_data=no_data_value)
spec_ind_result = spectral_indices_function_map[spectral_index](
composite, **spec_ind_params)
if spectral_index in ['ndvi', 'ndbi', 'ndwi', 'evi']:
composite[spectral_index] = spec_ind_result
else: # Fractional Cover
composite = xr.merge([composite, spec_ind_result])
# Fractional Cover is supposed to have a range of [0, 100], with its bands -
# 'bs', 'pv', and 'npv' - summing to 100. However, the function we use
# can have the sum of those bands as high as 106.
# frac_cov_min, frac_cov_max = spectral_indices_range_map[spectral_index]
frac_cov_min, frac_cov_max = 0, 106
for band in ['bs', 'pv', 'npv']:
composite[band].values = \
np.interp(composite[band].values, (frac_cov_min, frac_cov_max),
spectral_indices_range_map[spectral_index])
composites[composite_name] = composite
# Determine where the composite is out of range.
# We rename the resulting xarray.DataArray because calling to_netcdf()
# on it at the end of this function will save it as a Dataset
# with one data variable with the same name as the DataArray.
if spectral_index in ['ndvi', 'ndbi', 'ndwi', 'evi']:
composites_out_of_range[composite_name] = \
xr_or(composite[spectral_index] < task.composite_threshold_min,
task.composite_threshold_max < composite[spectral_index]).rename(spectral_index)
else: # Fractional Cover
# For fractional cover, a composite pixel is out of range if any of its
# fractional cover bands are out of range.
composites_out_of_range[composite_name] = xr_or(
xr_or(
xr_or(composite['bs'] < task.composite_threshold_min,
task.composite_threshold_max < composite['bs']),
xr_or(composite['pv'] < task.composite_threshold_min,
task.composite_threshold_max < composite['pv'])),
xr_or(composite['npv'] < task.composite_threshold_min,
task.composite_threshold_max <
composite['npv'])).rename(spectral_index)
# Update the metadata with the current data (baseline or analysis).
metadata = task.metadata_from_dataset(metadata, time_column_data,
time_column_clean_mask,
parameters)
# Record task progress (baseline or analysis composite data obtained).
task.scenes_processed = F(
'scenes_processed') + num_scn_per_chk[composite_name]
task.save(update_fields=['scenes_processed'])
dc.close()
if check_cancel_task(self, task): return
# Create a difference composite.
diff_composite = composites['analysis'] - composites['baseline']
# Find where either the baseline or analysis composite was out of range for a pixel.
composite_out_of_range = xr_or(*composites_out_of_range.values())
# Find where either the baseline or analysis composite was no_data.
if spectral_index in ['ndvi', 'ndbi', 'ndwi', 'evi']:
composite_no_data = xr_or(
composites['baseline'][measurements_list[0]] == no_data_value,
composites['analysis'][measurements_list[0]] == no_data_value)
if spectral_index == 'evi': # EVI returns no_data for values outside [-1,1].
composite_no_data = xr_or(
composite_no_data,
xr_or(composites['baseline'][spectral_index] == no_data_value,
composites['analysis'][spectral_index] == no_data_value))
else: # Fractional Cover
composite_no_data = xr_or(
xr_or(
xr_or(composites['baseline']['bs'] == no_data_value,
composites['baseline']['pv'] == no_data_value),
composites['baseline']['npv'] == no_data_value),
xr_or(
xr_or(composites['baseline']['bs'] == no_data_value,
composites['baseline']['pv'] == no_data_value),
composites['baseline']['npv'] == no_data_value))
composite_no_data = composite_no_data.rename(spectral_index)
# Drop unneeded data variables.
diff_composite = diff_composite.drop(measurements_list)
if check_cancel_task(self, task): return
composite_path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
export_xarray_to_netcdf(diff_composite, composite_path)
composite_out_of_range_path = os.path.join(task.get_temp_path(),
chunk_id + "_out_of_range.nc")
logger.info("composite_out_of_range:" + str(composite_out_of_range))
export_xarray_to_netcdf(composite_out_of_range,
composite_out_of_range_path)
composite_no_data_path = os.path.join(task.get_temp_path(),
chunk_id + "_no_data.nc")
export_xarray_to_netcdf(composite_no_data, composite_no_data_path)
return composite_path, composite_out_of_range_path, composite_no_data_path, \
metadata, {'geo_chunk_id': geo_chunk_id}
def processing_task(task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Computes a single SLIP baseline comparison - returns a slip mask and mosaic.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = SlipTask.objects.get(pk=task_id)
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
metadata = {}
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1), max(time_ranges) + timedelta(microseconds=1))
time_range = _get_datetime_range_containing(time_chunk[0], time_chunk[-1])
dc = DataAccessApi(config=task.config_path)
updated_params = {**parameters}
updated_params.update(geographic_chunk)
updated_params.update({'time': time_range})
data = dc.get_dataset_by_extent(**updated_params)
#grab dem data as well
dem_parameters = {**updated_params}
dem_parameters.update({'product': 'terra_aster_gdm_' + task.area_id, 'platform': 'TERRA'})
dem_parameters.pop('time')
dem_parameters.pop('measurements')
dem_data = dc.get_dataset_by_extent(**dem_parameters)
if 'time' not in data or 'time' not in dem_data:
return None
#target data is most recent, with the baseline being everything else.
target_data = xr.concat([data.isel(time=-1)], 'time')
baseline_data = data.isel(time=slice(None, -1))
target_clear_mask = task.satellite.get_clean_mask_func()(target_data)
baseline_clear_mask = task.satellite.get_clean_mask_func()(baseline_data)
combined_baseline = task.get_processing_method()(baseline_data,
clean_mask=baseline_clear_mask,
no_data=task.satellite.no_data_value,
reverse_time=task.get_reverse_time())
target_data = create_mosaic(
target_data,
clean_mask=target_clear_mask,
no_data=task.satellite.no_data_value,
reverse_time=task.get_reverse_time())
slip_data = compute_slip(combined_baseline, target_data, dem_data, no_data=task.satellite.no_data_value)
target_data['slip'] = slip_data
metadata = task.metadata_from_dataset(
metadata, target_data, target_clear_mask, updated_params, time=data.time.values.astype('M8[ms]').tolist()[-1])
task.scenes_processed = F('scenes_processed') + 1
task.save()
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
clear_attrs(target_data)
target_data.to_netcdf(path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {'geo_chunk_id': geo_chunk_id, 'time_chunk_id': time_chunk_id}
def processing_task(task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = CoastalChangeTask.objects.get(pk=task_id)
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
iteration_data = None
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1),
max(time_ranges) + timedelta(microseconds=1))
starting_year = _get_datetime_range_containing(*time_chunk[0])
comparison_year = _get_datetime_range_containing(*time_chunk[1])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
def _compute_mosaic(time):
updated_params.update({'time': time})
data = dc.get_dataset_by_extent(**updated_params)
if data is None or 'time' not in data:
logger.info("Invalid chunk.")
return None, None
clear_mask = task.satellite.get_clean_mask_func()(data)
metadata = task.metadata_from_dataset({}, data, clear_mask,
updated_params)
return task.get_processing_method()(
data, clean_mask=clear_mask,
no_data=task.satellite.no_data_value), metadata
old_mosaic, old_metadata = _compute_mosaic(starting_year)
new_mosaic, new_metadata = _compute_mosaic(comparison_year)
if old_mosaic is None or new_mosaic is None:
return None
metadata = {**old_metadata, **new_metadata}
output_product = compute_coastal_change(
old_mosaic, new_mosaic, no_data=task.satellite.no_data_value)
task.scenes_processed = F('scenes_processed') + 1
task.save()
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
output_product.to_netcdf(path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def processing_task(self,
task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = TsmTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
metadata = {}
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1), max(time_ranges) + timedelta(microseconds=1))
times = list(
map(_get_datetime_range_containing, time_chunk)
if task.get_iterative() else [_get_datetime_range_containing(time_chunk[0], time_chunk[-1])])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
#updated_params.update({'products': parameters['']})
water_analysis = None
tsm_analysis = None
combined_data = None
base_index = (task.get_chunk_size()['time'] if task.get_chunk_size()['time'] is not None else 1) * time_chunk_id
for time_index, time in enumerate(times):
updated_params.update({'time': time})
data = dc.get_stacked_datasets_by_extent(**updated_params)
if check_cancel_task(self, task): return
if data is None or 'time' not in data:
logger.info("Invalid chunk.")
continue
clear_mask = task.satellite.get_clean_mask_func()(data)
wofs_data = task.get_processing_method()(data,
clean_mask=clear_mask,
enforce_float64=True,
no_data=task.satellite.no_data_value)
water_analysis = perform_timeseries_analysis(
wofs_data, 'wofs', intermediate_product=water_analysis, no_data=task.satellite.no_data_value)
clear_mask[(data.swir2.values > 100) | (wofs_data.wofs.values == 0)] = False
tsm_data = tsm(data, clean_mask=clear_mask, no_data=task.satellite.no_data_value)
tsm_analysis = perform_timeseries_analysis(
tsm_data, 'tsm', intermediate_product=tsm_analysis, no_data=task.satellite.no_data_value)
if check_cancel_task(self, task): return
combined_data = tsm_analysis
combined_data['wofs'] = water_analysis.total_data
combined_data['wofs_total_clean'] = water_analysis.total_clean
metadata = task.metadata_from_dataset(metadata, tsm_data, clear_mask, updated_params)
if task.animated_product.animation_id != "none":
path = os.path.join(task.get_temp_path(),
"animation_{}_{}.nc".format(str(geo_chunk_id), str(base_index + time_index)))
animated_data = tsm_data.isel(
time=0, drop=True) if task.animated_product.animation_id == "scene" else combined_data
animated_data.to_netcdf(path)
task.scenes_processed = F('scenes_processed') + 1
task.save(update_fields=['scenes_processed'])
if combined_data is None:
return None
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
combined_data.to_netcdf(path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {'geo_chunk_id': geo_chunk_id, 'time_chunk_id': time_chunk_id}
def processing_task(task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = FractionalCoverTask.objects.get(pk=task_id)
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
iteration_data = None
metadata = {}
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1),
max(time_ranges) + timedelta(microseconds=1))
times = list(
map(_get_datetime_range_containing, time_chunk) if task.get_iterative(
) else [_get_datetime_range_containing(time_chunk[0], time_chunk[-1])])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
#updated_params.update({'products': parameters['']})
iteration_data = None
base_index = (task.get_chunk_size()['time'] if task.get_chunk_size()
['time'] is not None else 1) * time_chunk_id
for time_index, time in enumerate(times):
updated_params.update({'time': time})
data = dc.get_stacked_datasets_by_extent(**updated_params)
if data is None or 'time' not in data:
logger.info("Invalid chunk.")
continue
clear_mask = create_cfmask_clean_mask(
data.cf_mask) if 'cf_mask' in data else create_bit_mask(
data.pixel_qa, [1, 2])
add_timestamp_data_to_xr(data)
metadata = task.metadata_from_dataset(metadata, data, clear_mask,
updated_params)
iteration_data = task.get_processing_method()(
data, clean_mask=clear_mask, intermediate_product=iteration_data)
task.scenes_processed = F('scenes_processed') + 1
task.save()
if iteration_data is None:
return None
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
iteration_data.to_netcdf(path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def processing_task(task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = AppNameTask.objects.get(pk=task_id)
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
iteration_data = None
metadata = {}
def _get_datetime_range_containing(*time_ranges):
return (min(time_ranges) - timedelta(microseconds=1),
max(time_ranges) + timedelta(microseconds=1))
times = list(
map(_get_datetime_range_containing, time_chunk) if task.get_iterative(
) else [_get_datetime_range_containing(time_chunk[0], time_chunk[-1])])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
#updated_params.update({'products': parameters['']})
iteration_data = None
base_index = (task.get_chunk_size()['time'] if task.get_chunk_size()
['time'] is not None else 1) * time_chunk_id
for time_index, time in enumerate(times):
updated_params.update({'time': time})
# TODO: If this is not a multisensory app replace get_stacked_datasets_by_extent with get_dataset_by_extent
data = dc.get_stacked_datasets_by_extent(**updated_params)
if data is None or 'time' not in data:
logger.info("Invalid chunk.")
continue
# TODO: Replace anything here with your processing - do you need to create additional masks? Apply bandmaths? etc.
clear_mask = create_cfmask_clean_mask(
data.cf_mask) if 'cf_mask' in data else create_bit_mask(
data.pixel_qa, [1, 2])
add_timestamp_data_to_xr(data)
metadata = task.metadata_from_dataset(metadata, data, clear_mask,
updated_params)
# TODO: Make sure you're producing everything required for your algorithm.
iteration_data = task.get_processing_method()(
data, clean_mask=clear_mask, intermediate_product=iteration_data)
# TODO: If there is no animation you can remove this block. Otherwise, save off the data that you need.
if task.animated_product.animation_id != "none":
path = os.path.join(
task.get_temp_path(),
"animation_{}_{}.nc".format(str(geo_chunk_id),
str(base_index + time_index)))
if task.animated_product.animation_id == "scene":
#need to clear out all the metadata..
clear_attrs(data)
#can't reindex on time - weird?
data.isel(time=0).drop('time').to_netcdf(path)
elif task.animated_product.animation_id == "cumulative":
iteration_data.to_netcdf(path)
task.scenes_processed = F('scenes_processed') + 1
task.save()
if iteration_data is None:
return None
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
iteration_data.to_netcdf(path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def start_chunk_processing(self, chunk_details, task_id=None):
"""Create a fully asyncrhonous processing pipeline from paramters and a list of chunks.
The most efficient way to do this is to create a group of time chunks for each geographic chunk,
recombine over the time index, then combine geographic last.
If we create an animation, this needs to be reversed - e.g. group of geographic for each time,
recombine over geographic, then recombine time last.
The full processing pipeline is completed, then the create_output_products task is triggered, completing the task.
"""
if chunk_details is None:
return None
parameters = chunk_details.get('parameters')
geographic_chunks = chunk_details.get('geographic_chunks')
task = SpectralAnomalyTask.objects.get(pk=task_id)
api = DataAccessApi(config=task.config_path)
# Get an estimate of the amount of work to be done: the number of scenes
# to process, also considering intermediate chunks to be combined.
# Determine the number of scenes for the baseline and analysis extents.
num_scenes = {}
params_temp = parameters.copy()
for composite_name in ['baseline', 'analysis']:
num_scenes[composite_name] = 0
for geographic_chunk in geographic_chunks:
params_temp.update(geographic_chunk)
params_temp['measurements'] = []
# Use the corresponding time range for the baseline and analysis data.
params_temp['time'] = \
params_temp['baseline_time' if composite_name == 'baseline' else 'analysis_time']
params_temp_clean = params_temp.copy()
del params_temp_clean['baseline_time'], params_temp_clean['analysis_time'], \
params_temp_clean['composite_range'], params_temp_clean['change_range']
data = api.dc.load(**params_temp_clean)
if 'time' in data.coords:
num_scenes[composite_name] += len(data.time)
# The number of scenes per geographic chunk for baseline and analysis extents.
num_scn_per_chk_geo = {
k: round(v / len(geographic_chunks))
for k, v in num_scenes.items()
}
# Scene processing progress is tracked in processing_task().
task.total_scenes = sum(num_scenes.values())
task.scenes_processed = 0
task.save(update_fields=['total_scenes', 'scenes_processed'])
if check_cancel_task(self, task): return
task.update_status("WAIT", "Starting processing.")
processing_pipeline = (group([
processing_task.s(
task_id=task_id,
geo_chunk_id=geo_index,
geographic_chunk=geographic_chunk,
num_scn_per_chk=num_scn_per_chk_geo,
**parameters) for geo_index, geographic_chunk in enumerate(geographic_chunks)
]) | recombine_geographic_chunks.s(task_id=task_id) | create_output_products.s(task_id=task_id) \
| task_clean_up.si(task_id=task_id, task_model='SpectralAnomalyTask')).apply_async()
return True
def processing_task(self,
task_id=None,
geo_chunk_id=None,
time_chunk_id=None,
geographic_chunk=None,
time_chunk=None,
**parameters):
"""Process a parameter set and save the results to disk.
Uses the geographic and time chunk id to identify output products.
**params is updated with time and geographic ranges then used to load data.
the task model holds the iterative property that signifies whether the algorithm
is iterative or if all data needs to be loaded at once.
Args:
task_id, geo_chunk_id, time_chunk_id: identification for the main task and what chunk this is processing
geographic_chunk: range of latitude and longitude to load - dict with keys latitude, longitude
time_chunk: list of acquisition dates
parameters: all required kwargs to load data.
Returns:
path to the output product, metadata dict, and a dict containing the geo/time ids
"""
chunk_id = "_".join([str(geo_chunk_id), str(time_chunk_id)])
task = WaterDetectionTask.objects.get(pk=task_id)
if check_cancel_task(self, task): return
logger.info("Starting chunk: " + chunk_id)
if not os.path.exists(task.get_temp_path()):
return None
metadata = {}
times = list(
map(_get_datetime_range_containing, time_chunk) if task.get_iterative(
) else [_get_datetime_range_containing(time_chunk[0], time_chunk[-1])])
dc = DataAccessApi(config=task.config_path)
updated_params = parameters
updated_params.update(geographic_chunk)
water_analysis = None
base_index = (task.get_chunk_size()['time'] if task.get_chunk_size()
['time'] is not None else 1) * time_chunk_id
for time_index, time in enumerate(times):
updated_params.update({'time': time})
data = dc.get_stacked_datasets_by_extent(**updated_params)
if check_cancel_task(self, task): return
if data is None:
logger.info("Empty chunk.")
continue
if 'time' not in data:
logger.info("Invalid chunk.")
continue
clear_mask = task.satellite.get_clean_mask_func()(data)
# Ensure data variables have the range of Landsat 7 Collection 1 Level 2
# since the color scales are tailored for that dataset.
platform = task.satellite.platform
collection = task.satellite.collection
level = task.satellite.level
if (platform, collection) != ('LANDSAT_7', 'c1'):
data = \
convert_range(data, from_platform=platform,
from_collection=collection, from_level=level,
to_platform='LANDSAT_7', to_collection='c1', to_level='l2')
wofs_data = task.get_processing_method()(
data, clean_mask=clear_mask, no_data=task.satellite.no_data_value)
water_analysis = perform_timeseries_analysis(
wofs_data,
'wofs',
intermediate_product=water_analysis,
no_data=task.satellite.no_data_value)
metadata = task.metadata_from_dataset(metadata, wofs_data,
clear_mask.data, updated_params)
if task.animated_product.animation_id != "none":
path = os.path.join(
task.get_temp_path(),
"animation_{}_{}.nc".format(str(geo_chunk_id),
str(base_index + time_index)))
animated_data = wofs_data.isel(
time=0, drop=True
) if task.animated_product.animation_id == "scene" else water_analysis
export_xarray_to_netcdf(animated_data, path)
if check_cancel_task(self, task): return
task.scenes_processed = F('scenes_processed') + 1
task.save(update_fields=['scenes_processed'])
if water_analysis is None:
return None
path = os.path.join(task.get_temp_path(), chunk_id + ".nc")
export_xarray_to_netcdf(water_analysis, path)
dc.close()
logger.info("Done with chunk: " + chunk_id)
return path, metadata, {
'geo_chunk_id': geo_chunk_id,
'time_chunk_id': time_chunk_id
}
def csv_import(task_id): # pragma: no cover
from django.db import transaction
# there is a possible race condition between this task starting
# so we have a bit of loop here to fetch the task
tries = 0
task = None
while tries < 5 and not task:
try:
task = ImportTask.objects.get(pk=task_id)
except Exception as e:
# this object just doesn't exist yet, sleep a bit then try again
tries += 1
if tries >= 5:
raise e
else:
sleep(1)
log = StringIO()
if StrictVersion(django.get_version()) < StrictVersion('1.6'):
transaction.enter_transaction_management()
transaction.managed()
try:
task.task_id = csv_import.request.id
task.log("Started import at %s" % timezone.now())
task.log("--------------------------------")
task.save()
transaction.commit()
model = class_from_string(task.model_class)
records = model.import_csv(task, log)
task.save()
task.log(log.getvalue())
task.log("Import finished at %s" % timezone.now())
task.log("%d record(s) added." % len(records))
transaction.commit()
except Exception as e:
transaction.rollback()
import traceback
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
task.log(log.getvalue())
transaction.commit()
raise e
finally:
transaction.leave_transaction_management()
else:
task.task_id = csv_import.request.id
task.log("Started import at %s" % timezone.now())
task.log("--------------------------------")
task.save()
try:
with transaction.atomic():
model = class_from_string(task.model_class)
records = model.import_csv(task, log)
task.save()
task.log(log.getvalue())
task.log("Import finished at %s" % timezone.now())
task.log("%d record(s) added." % len(records))
except Exception as e:
import traceback
traceback.print_exc(e)
task.log("\nError: %s\n" % e)
task.log(log.getvalue())
raise e
return task
