def test_simplevsfull_plot(self):
config = 'tests/small_simple.yaml'
simple = niche_vlaanderen.Niche()
simple.run_config_file(config)
config_full = "tests/small.yaml"
full = niche_vlaanderen.Niche()
full.run_config_file(config_full)
delta = niche_vlaanderen.NicheDelta(simple, full)
# as the full model always contains less than the simple model,
# we can use this in a test
df = delta.table
self.assertEqual(0, df[df.presence == "only in model 2"].area_ha.sum())
import matplotlib as mpl
mpl.use('agg')
import matplotlib.pyplot as plt
plt.show = lambda: None
delta.plot(5)
delta.name = "vergelijking"
delta.plot(5)
def test_mxw_validation_yml(self):
myniche = niche_vlaanderen.Niche()
# should not raise
myniche.run_config_file("tests/small_nostrict.yml")
n2 = niche_vlaanderen.Niche()
n2.read_config_file("tests/small_nostrict.yml")
with pytest.raises(NicheException):
n2.run()
def test_combine(self):
fp = nv.Flooding()
myniche = nv.Niche()
input = "testcase/dijle/"
myniche.set_input("soil_code", input + "bodemv.asc")
myniche.set_input("msw", input + "gvg_0_cm.asc")
myniche.set_input("mlw", input + "glg_0_cm.asc")
myniche.set_input("mhw", input + "ghg_0_cm.asc")
myniche.set_input("seepage", input + "kwel_mm_dag.asc")
myniche.set_input("management", input + "beheer_int.asc")
myniche.set_input("nitrogen_atmospheric", input + "depositie_def.asc")
myniche.set_input("nitrogen_animal", input + "bemest_dier.asc")
myniche.set_input("nitrogen_fertilizer", input + "bemest_kunst.asc")
myniche.set_input("inundation_vegetation", input + "overstr_veg.asc")
myniche.set_input("inundation_acidity", input + "ovrstr_t10_50.asc")
myniche.set_input("inundation_nutrient", input + "ovrstr_t10_50.asc")
myniche.set_input("minerality", input + "minerality.asc")
myniche.set_input("rainwater", input + "nulgrid.asc")
with pytest.raises(FloodingException):
# niche model not yet run
fp.combine(myniche)
myniche.run()
with pytest.raises(FloodingException):
# floodplain model not yet run
fp.combine(myniche)
fp.calculate("testcase/flooding/ff_bt_t10_h.asc",
"T10",
period="winter",
duration=1)
small = nv.Niche()
small.run_config_file("tests/small.yaml")
with pytest.raises(FloodingException):
# floodplain has different spatial extent than niche
fp.combine(small)
result = fp.combine(myniche)
# get unique values for every vegtype
unique = []
for i in result._veg:
unique.append(np.unique(result._veg[i]))
unique = np.unique(np.hstack(unique))
expected = np.array([-99, -1, 1, 2, 3])
np.testing.assert_equal(expected, unique)
def test_run_configuration_abiotic(self):
config = 'tests/small_abiotic.yaml'
myniche = niche_vlaanderen.Niche()
myniche.run_config_file(config)
config = 'tests/small_abiotic_extra.yaml'
myniche = niche_vlaanderen.Niche()
myniche.run_config_file(config)
# rerun with a file with missing abiotic values
config = 'tests/small_abiotic_invalid.yaml'
myniche = niche_vlaanderen.Niche()
with pytest.raises(NicheException):
myniche.run_config_file(config)
def test_differentvegsize(self):
myniche = niche_vlaanderen.Niche(
ct_vegetation="tests/data/bad_ct/one_vegetation.csv")
myniche.set_input("mhw", "tests/data/small/mhw.asc")
myniche.set_input("mlw", "tests/data/small/mlw.asc")
myniche.set_input("soil_code", "tests/data/small/soil_code.asc")
myniche.run(full_model=False)
small = niche_vlaanderen.Niche()
small.run_config_file("tests/small.yaml")
# we try to compare but both elements have different vegetations
with pytest.raises(NicheException):
niche_vlaanderen.NicheDelta(small, myniche)
def test_rereadoutput(self):
"""
This tests checks if the output written by the model is a valid input
for a new run
"""
config = 'tests/small_simple.yaml'
myniche = niche_vlaanderen.Niche()
myniche.run_config_file(config)
myniche = niche_vlaanderen.Niche()
shutil.copy('_output/log.txt', 'log.txt')
config = 'log.txt'
myniche2 = niche_vlaanderen.Niche()
myniche2.run_config_file(config)
def test_overwrite_codetable_nojoin(self):
# test should generate a warning
myniche = niche_vlaanderen.Niche(
ct_vegetation="tests/data/bad_ct/vegetation_noinnerjoin.csv")
myniche.read_config_file("tests/small.yaml")
with pytest.warns(UserWarning):
myniche.run()
def test_incomplete_model(self):
myniche = niche_vlaanderen.Niche()
myniche.set_input("mhw", "tests/data/small/msw.asc")
with pytest.raises(NicheException):
myniche.run() # incomplete, keys are missing
with pytest.raises(NicheException):
myniche.write("_temp") # should raise, no calculation done
def test_overwrite_codetable(self):
myniche = niche_vlaanderen.Niche(
ct_vegetation="tests/data/bad_ct/one_vegetation_limited.csv",
ct_acidity="tests/data/bad_ct/acidity_limited.csv",
lnk_acidity="tests/data/bad_ct/lnk_acidity_limited.csv",
ct_nutrient_level="tests/data/bad_ct/nutrient_level.csv")
myniche.read_config_file("tests/small.yaml")
myniche.run()
def test_uint(self):
myniche = niche_vlaanderen.Niche()
myniche.set_input("mhw", "tests/data/small/mhw.asc")
myniche.set_input("mlw", "tests/data/small/mlw.asc")
myniche.set_input("soil_code", "tests/data/tif/soil_code.tif")
myniche.run(full_model=False)
# this dataset should contain one nodata cell
df = myniche.table
assert np.all(df[df.presence == "no data"]["area_ha"] == 0.0625)
def test_simplevsfull_write(self):
config = 'tests/small_simple.yaml'
simple = niche_vlaanderen.Niche()
simple.run_config_file(config)
config_full = "tests/small.yaml"
full = niche_vlaanderen.Niche()
full.run_config_file(config_full)
delta = niche_vlaanderen.NicheDelta(simple, full)
tmpdir = tempfile.mkdtemp()
tmpsubdir = tmpdir + "/new"
delta.write(tmpsubdir)
# check tempdir contains the vegetation and the abiotic files
expected_files = [
'D1.tif', 'D2.tif', 'D3.tif', 'D4.tif', 'D5.tif', 'D6.tif',
'D7.tif', 'D8.tif', 'D9.tif', 'D10.tif', 'D11.tif', 'D12.tif',
'D13.tif', 'D14.tif', 'D15.tif', 'D16.tif', 'D17.tif', 'D18.tif',
'D19.tif', 'D20.tif', 'D21.tif', 'D22.tif', 'D23.tif', 'D24.tif',
'D25.tif', 'D26.tif', 'D27.tif', 'D28.tif', 'legend_delta.csv',
'delta_summary.csv'
]
dir = os.listdir(tmpsubdir)
if sys.version_info < (3, 2):
self.assertItemsEqual(expected_files, dir)
else:
self.assertCountEqual(expected_files, dir)
delta.name = "vgl"
delta.write(tmpsubdir)
dir = os.listdir(tmpsubdir)
assert 60 == len(dir)
assert 30 == sum(f.startswith("vgl_") for f in dir)
shutil.rmtree(tmpdir)
def testinvalidDelta(self):
small = niche_vlaanderen.Niche()
with pytest.raises(NicheException):
# should fail as there is no extent yet
niche_vlaanderen.NicheDelta(small, small)
small.read_config_file("tests/small_simple.yaml")
with pytest.raises(NicheException):
# should fail as the model has not yet been run
niche_vlaanderen.NicheDelta(small, small)
zwb = TestNiche.create_zwarte_beek_niche()
zwb.run()
small.run(full_model=False)
# should fail due to different extent
with pytest.raises(NicheException):
niche_vlaanderen.NicheDelta(zwb, small)
def create_zwarte_beek_niche():
myniche = niche_vlaanderen.Niche()
input_dir = "testcase/zwarte_beek/input/"
myniche.set_input("soil_code", input_dir + "soil_code.asc")
myniche.set_input("mhw", input_dir + "mhw.asc")
myniche.set_input("mlw", input_dir + "mlw.asc")
myniche.set_input("msw", input_dir + "msw.asc")
myniche.set_input("minerality", input_dir + "minerality.asc")
myniche.set_input("nitrogen_atmospheric",
input_dir + "nitrogen_atmospheric.asc")
myniche.set_input("nitrogen_animal", 0)
myniche.set_input("nitrogen_fertilizer", 0)
myniche.set_input("management", input_dir + "management.asc")
myniche.set_input("inundation_nutrient", input_dir + "inundation.asc")
myniche.set_input("inundation_acidity", input_dir + "inundation.asc")
myniche.set_input("seepage", input_dir + "seepage.asc")
myniche.set_input("rainwater", input_dir + "rainwater.asc")
return myniche
def cli(ctx, config, example, version):
"""Command line interface to the NICHE vegetation model
"""
if example:
ex = resource_filename(
"niche_vlaanderen",
"system_tables/example.yaml")
with open(ex) as f:
print(f.read())
if config is not None:
n = niche_vlaanderen.Niche()
n.run_config_file(config, overwrite_ct=True)
click.echo(n)
if config is None and not example:
# we should really find a neater way to show --help here by default.
print("No config file added. Use --help for more info")
if version:
print("niche_vlaanderen version: " + niche_vlaanderen.__version__)
def test_overwrite_code_table(self):
myniche = niche_vlaanderen.Niche(
ct_vegetation="tests/data/bad_ct/one_vegetation.csv")
myniche.set_input("mhw", "tests/data/small/mhw.asc")
myniche.set_input("mlw", "tests/data/small/mlw.asc")
myniche.set_input("soil_code", "tests/data/small/soil_code.asc")
myniche.run(full_model=False)
# we expect only one vegetation type, as the codetable has only one
self.assertEqual(1, len(myniche.occurrence))
# we try to overwrite using a non existing key
with pytest.raises(NicheException):
myniche._set_ct("bla", "tests/data/bad_ct/one_vegetation.csv")
# we try to overwrite using a non existing codetable
with pytest.raises(NicheException):
myniche._set_ct("ct_vegetation", "nonexisting")
assert myniche._vegcode2name(1) == "Sphagno-Betuletum"
def test_testcase_simple(self):
"""
This tests runs the data from the testcase/zwarte_beek.
Note: validation is done in the vegetation tests - not here.
"""
myniche = niche_vlaanderen.Niche()
input_dir = "testcase/zwarte_beek/input/"
myniche.set_input("soil_code", input_dir + "soil_code.asc")
myniche.set_input("mhw", input_dir + "mhw.asc")
myniche.set_input("mlw", input_dir + "mlw.asc")
myniche.name = "simple"
myniche.run(full_model=False)
tmpdir = tempfile.mkdtemp()
myniche.write(tmpdir)
# check tempdir contains the vegetation files
expected_files = [
'V01.tif', 'V02.tif', 'V03.tif', 'V04.tif', 'V05.tif', 'V06.tif',
'V07.tif', 'V08.tif', 'V09.tif', 'V10.tif', 'V11.tif', 'V12.tif',
'V13.tif', 'V14.tif', 'V15.tif', 'V16.tif', 'V17.tif', 'V18.tif',
'V19.tif', 'V20.tif', 'V21.tif', 'V22.tif', 'V23.tif', 'V24.tif',
'V25.tif', 'V26.tif', 'V27.tif', 'V28.tif', 'log.txt',
'summary.csv'
]
expected_files = ["simple_" + i for i in expected_files]
dir = os.listdir(tmpdir)
if sys.version_info < (3, 2):
self.assertItemsEqual(expected_files, dir)
else:
self.assertCountEqual(expected_files, dir)
shutil.rmtree(tmpdir)
def test_invalidfile(self):
n = niche_vlaanderen.Niche()
with pytest.raises(RasterioIOError):
n.set_input("msw", "nonexistingfile")
def test_run_configuration(self):
config = 'tests/small_simple.yaml'
myniche = niche_vlaanderen.Niche()
myniche.run_config_file(config)
def test_run_configuration_numeric(self):
config = 'tests/small_ct.yaml'
myniche = niche_vlaanderen.Niche()
myniche.run_config_file(config)
def test_invalid_input_type(self):
n = niche_vlaanderen.Niche()
with pytest.raises(NicheException):
n.set_input("bla", "testcase/zwarte_beek/input/soil_code.asc")
def create_small():
myniche = niche_vlaanderen.Niche()
myniche.read_config_file("tests/small.yaml")
return myniche
def test_overwrite_codetable_nonexisting(self):
# assume error - file does not exist
with pytest.raises(NicheException):
niche_vlaanderen.Niche(ct_vegetation="nonexisting file")
def test_read_configuration(self):
config = 'tests/small_simple.yaml'
myniche = niche_vlaanderen.Niche()
myniche.read_config_file(config)
myniche.run(full_model=False)
