def main(ctx, ndvi_threshold, ndwi_threshold, pre_event, post_event):
dump(ctx)
os.environ["PREFIX"] = "/opt/anaconda/envs/env_burned_area"
os.environ["PROJ_LIB"] = os.path.join(os.environ["PREFIX"], "share/proj")
os.environ["GDAL_DATA"] = os.path.join(os.environ["PREFIX"], "share/gdal")
burned_area_item = burned(
pre_item=get_item(os.path.join(pre_event, "catalog.json")),
post_item=get_item(os.path.join(post_event, "catalog.json")),
ndvi_threshold=ndvi_threshold,
ndwi_threshold=ndwi_threshold,
)
logging.info("Output catalog")
catalog = Catalog(id="catalog", description="Results")
catalog.clear_items()
catalog.clear_children()
catalog.add_items([burned_area_item])
catalog.describe()
catalog.normalize_and_save(root_href="./",
catalog_type=CatalogType.SELF_CONTAINED)
def test_clear_children_sets_parent_and_root_to_None(self):
catalog = Catalog(id='test', description='test')
subcat1 = Catalog(id='subcat', description='test')
subcat2 = Catalog(id='subcat2', description='test2')
catalog.add_children([subcat1, subcat2])
self.assertIsNotNone(subcat1.get_parent())
self.assertIsNotNone(subcat2.get_parent())
self.assertIsNotNone(subcat1.get_root())
self.assertIsNotNone(subcat2.get_root())
children = list(catalog.get_children())
self.assertEqual(len(children), 2)
catalog.clear_children()
self.assertIsNone(subcat1.get_parent())
self.assertIsNone(subcat2.get_parent())
self.assertIsNone(subcat1.get_root())
self.assertIsNone(subcat2.get_root())
def test_clear_children_removes_from_cache(self):
catalog = Catalog(id='test', description='test')
subcat = Catalog(id='subcat', description='test')
catalog.add_child(subcat)
children = list(catalog.get_children())
self.assertEqual(len(children), 1)
self.assertEqual(children[0].description, 'test')
catalog.clear_children()
subcat = Catalog(id='subcat', description='test2')
catalog.add_child(subcat)
children = list(catalog.get_children())
self.assertEqual(len(children), 1)
self.assertEqual(children[0].description, 'test2')
catalog.remove_child('subcat')
subcat = Catalog(id='subcat', description='test3')
catalog.add_child(subcat)
children = list(catalog.get_children())
self.assertEqual(len(children), 1)
self.assertEqual(children[0].description, 'test3')
def main(ndvi_threshold, ndwi_threshold, pre_event, post_event):
os.environ['PREFIX']='/opt/anaconda/envs/env_burned_area'
os.environ['PROJ_LIB'] = os.path.join(os.environ['PREFIX'], 'share/proj')
os.environ['GDAL_DATA'] = os.path.join(os.environ['PREFIX'], 'share/gdal')
s2_item_pre = S2_stac_item(pre_event['value'])
s2_item_post = S2_stac_item(post_event['value'])
s2_items = dict()
s2_items['pre-event'] = S2_stac_item(pre_event['value'])
s2_items['post-event'] = S2_stac_item(post_event['value'])
dates = []
bboxes = []
for index, item in enumerate([s2_item_pre.item, s2_item_post.item]):
dates.append(item.datetime)
bboxes.append(shape(item.geometry).bounds)
logging.info('Stacking bands for input {}'.format(item.id))
vrt_bands = []
for band in ['B04', 'B08', 'B11', 'SCL']:
vrt_bands.append('/vsicurl/{}'.format(item.assets[band].get_absolute_href()))
vrt = '{}.vrt'.format('pre_event' if index == 0 else 'post_event')
tif = '{}.tif'.format('pre_event' if index == 0 else 'post_event')
logging.info('Build vrt for {}'.format(item.id))
ds = gdal.BuildVRT(vrt,
vrt_bands,
srcNodata=0,
xRes=10,
yRes=10,
separate=True)
ds.FlushCache()
logging.info('Translate {}'.format(item.id))
gdal.Translate(tif,
vrt,
outputType=gdal.GDT_UInt16)
os.remove(vrt)
ds = gdal.Open('pre_event.tif')
pre_b04 = ds.GetRasterBand(1).ReadAsArray()
pre_b08 = ds.GetRasterBand(2).ReadAsArray()
pre_b11 = ds.GetRasterBand(3).ReadAsArray()
pre_scl = ds.GetRasterBand(4).ReadAsArray()
ds = None
os.remove('pre_event.tif')
ds = gdal.Open('post_event.tif')
post_b04 = ds.GetRasterBand(1).ReadAsArray()
post_b08 = ds.GetRasterBand(2).ReadAsArray()
post_b11 = ds.GetRasterBand(3).ReadAsArray()
post_scl = ds.GetRasterBand(4).ReadAsArray()
width = ds.RasterXSize
height = ds.RasterYSize
input_geotransform = ds.GetGeoTransform()
input_georef = ds.GetProjectionRef()
ds = None
os.remove('post_event.tif')
gain = 10000
pre_ndwi2 = (pre_b08 / gain - pre_b11 / gain) / (pre_b08 / gain + pre_b11 / gain)
post_ndwi2 = (post_b08 / gain - post_b11 / gain) / (post_b08 / gain + post_b11 / gain)
pre_b11 = None
post_b11 = None
pre_ndvi = (pre_b08 / gain - pre_b04 / gain) / (pre_b08 / gain + pre_b04 / gain)
post_ndvi = (post_b08 / gain - post_b04 / gain) / (post_b08 / gain + post_b04 / gain)
pre_b04 = None
post_b04 = None
pre_b08 = None
post_b08 = None
conditions = (((post_ndwi2 - pre_ndwi2) > float(ndwi_threshold['value'])) & ((post_ndvi - pre_ndvi) > float(ndvi_threshold['value'])) & (pre_scl == 4) | (post_scl == 4))
burned = np.zeros((height, width), dtype=np.uint8)
burned[conditions] = 1
pre_ndwi2 = None
post_ndwi2 = None
pre_ndvi = None
post_ndvi = None
burned[np.where((pre_scl == 0) | (post_scl == 0) | (pre_scl == 1) | (post_scl == 1) | (pre_scl == 5) | (post_scl == 5) | (pre_scl == 6) | (post_scl == 6) | (pre_scl == 7) | (post_scl == 7) | (pre_scl == 8) | (post_scl == 8) | (pre_scl == 9) | (post_scl == 9))] = 2
logging.info('Write output product')
output_name = 'S2_BURNED_AREA_{}'.format('_'.join([d.strftime("%Y%m%d") for d in dates]))
write_tif(burned, '{}.tif'.format(output_name), width, height, input_geotransform, input_georef)
logging.info('Output catalog')
catalog = Catalog(id='catalog', description='Results')
catalog.clear_items()
catalog.clear_children()
result_titles = dict()
result_titles[output_name] = {'title': 'Burned area analysis from Sentinel-2',
'media_type': MediaType.COG}
items = []
for key, value in result_titles.items():
result_item = Item(id=key,
geometry=s2_items['pre-event'].item.geometry,
bbox=s2_items['pre-event'].item.bbox,
datetime=s2_items['pre-event'].item.datetime,
properties={})
result_item.add_asset(key='data',
asset=Asset(href='./{}.tif'.format(key),
media_type=value['media_type'],
title=value['title']))
items.append(result_item)
#collection.add_items(items)
catalog.add_items(items)
catalog.describe()
catalog.normalize_and_save(root_href='./',
catalog_type=CatalogType.SELF_CONTAINED)
shutil.move('{}.tif'.format(output_name),
os.path.join('./',
output_name,
'{}.tif'.format(output_name)))
