def test__init__(self):
self.oh = Occurrences(self.root)
self.assertEqual(self.oh.root, self.root)
self.assertEqual(self.oh.length, 0)
self.assertEqual(self.oh.path, [])
self.assertEqual(self.oh.name, [])
self.assertEqual(self.oh.spec_dict, {})
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 test_validate_occurrences(self):
self.oh = Occurrences(self.root)
self.oh.validate_occurrences()
self.assertEqual(self.oh.length, 2)
self.assertEqual(self.oh.path, [
self.root + '/occurrences/arachis_duranensis.csv',
self.root + '/occurrences/solanum_bukasovii.csv'
])
self.assertEqual(self.oh.name,
['arachis_duranensis', 'solanum_bukasovii'])
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_species_dictionary(self):
self.oh = Occurrences(self.root)
self.oh.validate_occurrences()
self.oh.species_dictionary()
self.assertIsInstance(self.oh.spec_dict, dict)
self.assertEqual(list(self.oh.spec_dict.keys()),
['arachis_duranensis', 'solanum_bukasovii'])
self.assertEqual(list(self.oh.spec_dict['arachis_duranensis']),
['dLon', 'dLat'])
spec_dict_truth = pd.read_csv(self.root +
'/occurrences/solanum_bukasovii.csv')[[
'decimalLongitude', 'decimalLatitude'
]]
self.assertEqual(
self.oh.spec_dict['solanum_bukasovii'].values.tolist(),
spec_dict_truth.to_numpy().tolist())
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)