def process_file(file):
"""Read and process one file and write the results
to disc in the same format as the input file.
:param file: the file to process
:type file: str
:param config: the config namespace from the command
line parser
:type config: argparse.Namespace
"""
# read data
data, profile = floodfill.read_data(file)
# process data
data = floodfill.isolate_burned_pixels(data, config.upper_value,
config.lower_value)
fire_ids, burn_dates = floodfill.floodfill(data, config.cut_off)
# write data
fname, ext = os.path.splitext(os.path.basename(file))
# save burndates if required
if config.save_bd:
out_path_bds = os.path.join(config.output_folder,
f"{fname}-floodfill_burndates{ext}")
floodfill.write_data(out_path_bds, burn_dates, profile)
# save patch ids
out_path_ids = os.path.join(config.output_folder,
f"{fname}-floodfill_ids{ext}")
floodfill.write_data(out_path_ids, fire_ids, profile)
def process_file(file, config):
"""Read and process one file and write the results
to disc in the same format as the input file.
:param file: the file to process
:type file: str
:param config: the config namespace from the command
line parser
:type config: argparse.Namespace
"""
# read data
data, profile = floodfill.read_data(file)
# process data
data = floodfill.isolate_burned_pixels(data, config.upper_value,
config.lower_value)
fire_ids, burn_dates = floodfill.run_algo(name=config.algorithm,
raster=data,
cut_off=config.cut_off)
# save burndates if required
if config.save_bd:
out_path_bds = _get_filename(config.output_folder, file,
'floodfill_burndates')
floodfill.write_data(out_path_bds, burn_dates, profile)
# save patch ids
out_path_ids = _get_filename(config.output_folder, file, 'floodfill_ids')
floodfill.write_data(out_path_ids, fire_ids, profile)
def test_writing(self):
with tempfile.TemporaryDirectory() as tmp:
file_name = os.path.join(tmp, 'test.tif')
floodfill.write_data(file_name, self.data, self.profile)
self.assertTrue(os.path.isfile(file_name))
# read data again and check if it is the same
data_tmp, profile_tmp = floodfill.read_data(file_name)
self.assertTrue(numpy.all(data_tmp == self.data))
def test_floodfill(self):
"""Test the floodfill algorithm itself.
"""
data, _ = floodfill.read_data(TEST_FILE)
data = floodfill.isolate_burned_pixels(data, 366, 1)
ids, burn_dates = nogueira_etal.run(data, 3)
self.assertEqual(ids.max(), 929) # correct number of fires found?
# are the burn dates still the same as in the input?
self.assertTrue(numpy.all(burn_dates == data))
def test_process_file(self):
data, _ = floodfill.read_data(TEST_FILE)
with tempfile.TemporaryDirectory() as tmp:
config = __main__.parse_command_line(
[f'--input={TEST_FILE}', f'--output-folder={tmp}', '-b'])
__main__.process_file(config.input, config=config)
# construct file names
bd_file = __main__._get_filename(config.output_folder,
config.input,
'floodfill_burndates')
id_file = __main__._get_filename(config.output_folder,
config.input,
'floodfill_ids')
self.assertTrue(os.path.isfile(bd_file))
self.assertTrue(os.path.isfile(id_file))
# read data again and check if it is the same
burn_dates, _ = floodfill.read_data(bd_file)
self.assertTrue(numpy.all(burn_dates == data))
def test_cleaning(self):
"""Check if data cleaning works as intended.
"""
data, _ = floodfill.read_data(TEST_FILE)
lower = 1 # lower fire value bound
upper = 366 # upper fire value bound
data[0, 0] = -1 # create lower outlier
data[0, 1] = 10000 # create upper outlier
data = floodfill.isolate_burned_pixels(data, upper, lower)
self.assertLessEqual(data.max(), upper)
min_burned = data[data != 0].min()
self.assertGreaterEqual(min_burned, lower)
def setUp(self):
self.data, self.profile = floodfill.read_data(TEST_FILE)