def test_validate_gis(self):
self.gh = GIS(self.root)
self.gh.validate_gis()
self.assertEqual(self.gh.gis, self.root + '/gis')
self.assertEqual(self.gh.scaled, self.gh.root + '/gis/layers/scaled')
self.assertEqual(self.gh.non_scaled,
self.gh.root + '/gis/layers/non-scaled')
self.assertEqual(self.gh.world_locations_to_predict,
self.root + '/gis/world_locations_to_predict.csv')
self.assertEqual(self.gh.empty_map,
self.root + '/gis/layers/empty_land_map.tif')
with self.assertRaises(IOError):
self.gh = GIS(self.root + '/scaled')
self.gh.validate_gis()
def test_validate_tif(self):
self.gh = GIS(self.root)
self.gh.validate_gis()
self.gh.validate_tif()
f1, n1 = self.gh.variables_list(self.root + '/gis/layers/scaled')
f2, n2 = self.gh.variables_list(self.root + '/gis/layers/non-scaled')
variables_truth = sorted(f1) + sorted(f2)
names_truth = sorted(n1) + sorted(n2)
self.assertEqual(self.gh.variables, variables_truth)
self.assertEqual(self.gh.names, names_truth)
self.assertEqual(self.gh.length, 6)
self.assertEqual(self.gh.scaled_len, 4)
with self.assertRaises(IOError):
self.gh = GIS(self.root + '/scaled')
self.gh.validate_gis()
def __init__(self, root, dat_root='/data', occ_root='/data/occurrences'):
"""sdmdl object initiation."""
self.root = root
self.occ_root = self.root + occ_root if occ_root == '/data/occurrences' else occ_root
self.dat_root = self.root + dat_root if dat_root == '/data' else dat_root
self.oh = Occurrences(self.occ_root)
self.oh.validate_occurrences()
self.oh.species_dictionary()
self.gh = GIS(self.dat_root)
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.ch = Config(self.dat_root, self.oh, self.gh)
self.ch.search_config()
self.ch.read_yaml()
self.verbose = self.ch.verbose
if not self.verbose:
# used to silence tensorflow backend deprecation warnings.
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
logging.getLogger("tensorflow").setLevel(logging.ERROR)
def setUp(self):
self.root = os.path.abspath(os.path.join(
os.path.dirname(__file__))) + '/test_data'
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.verbose = False
self.cbm = BandStatistics(self.gh, self.verbose)
def setUp(self):
self.root = (os.path.abspath(os.path.join(os.path.dirname(__file__))) +
'/test_data').replace('\\', '/')
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.verbose = False
self.crs = RasterStack(self.gh, self.verbose)
def setUp(self):
self.root = os.path.abspath(os.path.join(
os.path.dirname(__file__))) + '/test_data'
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.verbose = False
self.cpd = PredictionData(self.gh, self.verbose)
def test_define_output(self):
self.gh = GIS(self.root)
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.assertEqual(self.gh.presence, (self.gh.non_scaled + '/presence'))
self.assertEqual(self.gh.stack, (self.gh.gis + '/stack'))
self.assertEqual(self.gh.stack_clip, (self.gh.gis + '/stack_clip'))
self.assertEqual(self.gh.spec_ppa, (self.gh.root + '/spec_ppa'))
self.assertEqual(self.gh.spec_ppa_env,
(self.gh.root + '/spec_ppa_env'))
def setUp(self):
self.root = (os.path.abspath(os.path.join(os.path.dirname(__file__))) +
'/test_data').replace('\\', '/')
self.oh = Occurrences(self.root + '/root')
self.oh.validate_occurrences()
self.oh.species_dictionary()
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.ch = Config(self.root + '/root', self.oh, self.gh)
def setUp(self):
self.root = os.path.abspath(os.path.join(
os.path.dirname(__file__))) + '/test_data'
self.oh = Occurrences(self.root + '/root')
self.oh.validate_occurrences()
self.oh.species_dictionary()
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.verbose = False
self.cpm = PresenceMap(self.oh, self.gh, self.verbose)
def setUp(self):
self.root = os.path.abspath(os.path.join(os.path.dirname(__file__))) + '/test_data'
self.oh = Occurrences(self.root + '/root')
self.oh.validate_occurrences()
self.oh.species_dictionary()
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.ch = Config(self.root + '/root', self.oh, self.gh)
self.ch.search_config()
self.ch.read_yaml()
self.verbose = False
self.t = Trainer(self.oh, self.gh, self.ch, self.verbose)
def test_validate_list(self):
self.gh = GIS(self.root)
self.gh.validate_gis()
test_root = self.root + '/gis/layers/scaled'
f, n, = self.gh.variables_list(test_root)
f_truth = []
n_truth = []
for a, b, c in sorted(os.walk(test_root)):
for file in c:
file_ext = file.split('.')[-1]
fx = file_ext.lower()
if fx == 'tif' or fx == 'tiff':
f_truth += [a.replace('\\', '/') + '/' + file]
n_truth += [file.replace('.%s' % file_ext, '')]
self.assertEqual(f, f_truth)
self.assertEqual(n, n_truth)
def test__init__(self):
self.gh = GIS(self.root)
self.assertEqual(self.gh.root, self.root)
self.assertEqual(self.gh.scaled, '')
self.assertEqual(self.gh.non_scaled, '')
self.assertEqual(self.gh.gis, '')
self.assertEqual(self.gh.world_locations_to_predict, '')
self.assertEqual(self.gh.empty_map, '')
self.assertEqual(self.gh.variables, [])
self.assertEqual(self.gh.names, [])
self.assertEqual(self.gh.length, 0)
self.assertEqual(self.gh.scaled_len, 0)
self.assertEqual(self.gh.presence, '')
self.assertEqual(self.gh.stack, '')
self.assertEqual(self.gh.stack_clip, '')
self.assertEqual(self.gh.spec_ppa, '')
self.assertEqual(self.gh.spec_ppa_env, '')
def setUp(self):
self.root = (os.path.abspath(os.path.join(os.path.dirname(__file__))) +
'/test_data').replace('\\', '/')
self.oh = Occurrences(self.root + '/root')
self.oh.validate_occurrences()
self.oh.species_dictionary()
self.gh = GIS(self.root + '/root')
self.gh.validate_gis()
self.gh.validate_tif()
self.gh.define_output()
self.ch = Config(self.root, self.oh, self.gh)
self.ch.search_config()
self.ch.read_yaml()
self.ch.random_seed = 1
self.verbose = False
self.ppa = PresencePseudoAbsence(self.oh, self.gh, self.ch,
self.verbose)
