def test_habitat_quality_nodata(self):
"""Habitat Quality: on missing base and future LULC rasters."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'workspace_dir': self.workspace_dir,
}
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
args['lulc_cur_path'] = os.path.join(args['workspace_dir'],
'lc_samp_cur_b.tif')
make_lulc_raster(args['lulc_cur_path'], 2)
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
habitat_quality.execute(args)
# Reasonable to just check quality out in this case
assert_array_sum(
os.path.join(args['workspace_dir'], 'output', 'quality_c.tif'),
5951.2827)
def test_habitat_quality_nodata_small_fut(self):
"""Habitat Quality: small test with future raster only."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant':
'0.5',
'landuse_cur_uri':
os.path.join(REGRESSION_DATA, 'small_lulc_base.tif'),
'landuse_bas_uri':
os.path.join(REGRESSION_DATA, 'small_lulc_base.tif'),
'sensitivity_uri':
os.path.join(REGRESSION_DATA, 'small_sensitivity_samp.csv'),
'threat_raster_folder':
os.path.join(REGRESSION_DATA),
'threats_uri':
os.path.join(REGRESSION_DATA, 'small_threats_samp.csv'),
u'workspace_dir':
self.workspace_dir,
}
habitat_quality.execute(args)
HabitatQualityTests._test_same_files(
os.path.join(REGRESSION_DATA, 'file_list_small_nodata_fut.txt'),
args['workspace_dir'])
# reasonable to just check quality out in this case
natcap.invest.pygeoprocessing_0_3_3.testing.assert_rasters_equal(
os.path.join(REGRESSION_DATA, 'small_quality_out_c.tif'),
os.path.join(self.workspace_dir, 'output', 'quality_out_c.tif'),
1e-6)
def test_habitat_quality_missing_threat(self):
"""Habitat Quality: expected ValueError on missing threat raster."""
from natcap.invest import habitat_quality
args = {
'access_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality', 'access_samp.shp'),
'half_saturation_constant':
'0.5',
'landuse_cur_uri':
os.path.join(REGRESSION_DATA, 'small_lulc_base.tif'),
'sensitivity_uri':
os.path.join(REGRESSION_DATA,
'small_sensitivity_samp_missing_threat.csv'),
'threat_raster_folder':
os.path.join(REGRESSION_DATA),
'threats_uri':
os.path.join(REGRESSION_DATA,
'small_threats_samp_missing_threat.csv'),
u'workspace_dir':
self.workspace_dir,
}
with self.assertRaises(ValueError):
habitat_quality.execute(args)
def test_habitat_quality_nodata_fut(self):
"""Habitat Quality: on missing future LULC raster."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'workspace_dir': self.workspace_dir,
}
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
scenarios = ['_bas_', '_cur_'] # Missing '_fut_'
for lulc_val, scenario in enumerate(scenarios, start=1):
args['lulc' + scenario + 'path'] = os.path.join(
args['workspace_dir'], 'lc_samp' + scenario + 'b.tif')
make_lulc_raster(args['lulc' + scenario + 'path'], lulc_val)
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
habitat_quality.execute(args)
# Reasonable to just check quality out in this case
assert_array_sum(
os.path.join(args['workspace_dir'], 'output', 'quality_c.tif'),
5951.2827)
def test_habitat_quality_invalid_decay_type(self):
"""Habitat Quality: expected ValueError on invalid decay type."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'workspace_dir': self.workspace_dir,
}
args['access_vector_path'] = os.path.join(args['workspace_dir'],
'access_samp.shp')
make_access_shp(args['access_vector_path'])
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
args['lulc_cur_path'] = os.path.join(args['workspace_dir'],
'lc_samp_cur_b.tif')
make_lulc_raster(args['lulc_cur_path'], 2)
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'])
# Include an invalid decay function name to the threats csv table.
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'],
include_invalid_decay=True)
with self.assertRaises(ValueError):
habitat_quality.execute(args)
def test_habitat_quality_bad_rasters(self):
"""Habitat Quality: on threats that aren't real rasters."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'workspace_dir': self.workspace_dir,
}
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
args['lulc_cur_path'] = os.path.join(args['workspace_dir'],
'lc_samp_cur_b.tif')
make_lulc_raster(args['lulc_cur_path'], 2)
# Make an empty threat raster in the workspace folder.
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'],
make_empty_raster=True)
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
with self.assertRaises(ValueError):
habitat_quality.execute(args)
def test_habitat_quality_missing_sensitivity_threat(self):
"""Habitat Quality: ValueError w/ missing threat in sensitivity."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'workspace_dir': self.workspace_dir,
}
args['access_vector_path'] = os.path.join(args['workspace_dir'],
'access_samp.shp')
make_access_shp(args['access_vector_path'])
# Include a missing threat to the sensitivity csv table
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'],
include_threat=False)
args['lulc_cur_path'] = os.path.join(args['workspace_dir'],
'lc_samp_cur_b.tif')
make_lulc_raster(args['lulc_cur_path'], 2)
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
with self.assertRaises(ValueError):
habitat_quality.execute(args)
def test_habitat_quality_numeric_threats(self):
"""Habitat Quality: regression test on numeric threat names."""
from natcap.invest import habitat_quality
threat_array = numpy.zeros((100, 100), dtype=numpy.int8)
threatnames = ['1111', '2222']
threats_folder = os.path.join(self.workspace_dir, 'threats')
os.makedirs(threats_folder)
for suffix in ['_c', '_f']:
for i, threat in enumerate(threatnames):
raster_path = os.path.join(threats_folder,
threat + suffix + '.tif')
threat_array[100//(i+1):, :] = 1 # making variations among threats
make_raster_from_array(threat_array, raster_path)
threat_csv_path = os.path.join(self.workspace_dir, 'threats.csv')
with open(threat_csv_path, 'w') as open_table:
open_table.write('MAX_DIST,WEIGHT,THREAT,DECAY\n')
open_table.write('0.9,0.7,%s,linear\n' % threatnames[0])
open_table.write('0.5,1.0,%s,exponential\n' % threatnames[1])
args = {
'half_saturation_constant': '0.5',
'results_suffix': 'regression',
'threats_table_path': threat_csv_path,
'workspace_dir': os.path.join(self.workspace_dir, 'workspace'),
'threat_raster_folder': threats_folder,
'sensitivity_table_path': os.path.join(self.workspace_dir,
'sensitivity_samp.csv'),
'access_vector_path': os.path.join(self.workspace_dir,
'access_samp.shp')
}
make_access_shp(args['access_vector_path'])
scenarios = ['_bas_', '_cur_', '_fut_']
for lulc_val, scenario in enumerate(scenarios, start=1):
args['lulc' + scenario + 'path'] = os.path.join(
self.workspace_dir, 'lc_samp' + scenario + 'b.tif')
make_lulc_raster(args['lulc' + scenario + 'path'], lulc_val)
with open(args['sensitivity_table_path'], 'w') as open_table:
open_table.write('LULC,NAME,HABITAT,L_%s,L_%s\n' % tuple(threatnames))
open_table.write('1,"lulc 1",1,1,1\n')
open_table.write('2,"lulc 2",0.5,0.5,1\n')
open_table.write('3,"lulc 3",0,0.3,1\n')
habitat_quality.execute(args)
# Assert values were obtained by summing each output raster.
for output_filename, assert_value in {
'deg_sum_c_regression.tif': 1792.8088,
'deg_sum_f_regression.tif': 2308.9636,
'quality_c_regression.tif': 6928.5293,
'quality_f_regression.tif': 4916.338,
'rarity_c_regression.tif': 2500.0000000,
'rarity_f_regression.tif': 2500.0000000
}.items():
assert_array_sum(
os.path.join(args['workspace_dir'], 'output', output_filename),
assert_value)
def test_habitat_quality_lulc_bbox(self):
"""Habitat Quality: regression test for bbox sizes."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'results_suffix': 'regression',
'workspace_dir': self.workspace_dir,
}
args['access_vector_path'] = os.path.join(args['workspace_dir'],
'access_samp.shp')
make_access_shp(args['access_vector_path'])
scenarios = ['_bas_', '_cur_', '_fut_']
for lulc_val, scenario in enumerate(scenarios, start=1):
args['lulc' + scenario + 'path'] = os.path.join(
args['workspace_dir'], 'lc_samp' + scenario + 'b.tif')
make_lulc_raster(args['lulc' + scenario + 'path'], lulc_val)
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'],
side_length=50,
threat_values=[1, 1])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
habitat_quality.execute(args)
base_lulc_bbox = pygeoprocessing.get_raster_info(
args['lulc_bas_path'])['bounding_box']
# Assert values were obtained by summing each output raster.
for output_filename in [
'deg_sum_c_regression.tif', 'deg_sum_f_regression.tif',
'quality_c_regression.tif', 'quality_f_regression.tif',
'rarity_c_regression.tif', 'rarity_f_regression.tif'
]:
raster_path = os.path.join(args['workspace_dir'], 'output',
output_filename)
# Check that the output raster has the same bounding box as the
# LULC rasters.
raster_info = pygeoprocessing.get_raster_info(raster_path)
raster_bbox = raster_info['bounding_box']
numpy.testing.assert_allclose(raster_bbox,
base_lulc_bbox,
rtol=0,
atol=1e-6)
def test_habitat_quality_missing_lucodes_in_table(self):
"""Habitat Quality: on missing lucodes in the sensitivity table."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'workspace_dir': self.workspace_dir,
}
args['access_vector_path'] = os.path.join(args['workspace_dir'],
'access_samp.shp')
make_access_shp(args['access_vector_path'])
scenarios = ['_bas_', '_cur_', '_fut_']
for lulc_val, scenario in enumerate(scenarios, start=1):
path = os.path.join(args['workspace_dir'],
'lc_samp' + scenario + 'b.tif')
args['lulc' + scenario + 'path'] = path
make_lulc_raster(path, lulc_val)
# Add a nodata value to this raster to make sure we don't include
# the nodata value in the error message.
raster = gdal.OpenEx(path, gdal.OF_RASTER | gdal.GA_Update)
band = raster.GetRasterBand(1)
band_nodata = 255
band.SetNoDataValue(band_nodata) # band nodata before this is -1
current_array = band.ReadAsArray()
current_array[49][49] = band_nodata
band.WriteArray(current_array)
band = None
raster = None
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'],
missing_lines=True)
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
with self.assertRaises(ValueError) as cm:
habitat_quality.execute(args)
actual_message = str(cm.exception)
self.assertTrue(
'The following land cover codes were found in ' in actual_message,
actual_message)
# 2, 3 are the missing landcover codes.
# Raster nodata is 255 and should NOT appear in this list.
self.assertTrue(': 2, 3.' in actual_message, actual_message)
def test_habitat_quality_regression(self):
"""Habitat Quality: base regression test with simplified data."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'results_suffix': 'regression',
'workspace_dir': self.workspace_dir,
}
args['access_vector_path'] = os.path.join(args['workspace_dir'],
'access_samp.shp')
make_access_shp(args['access_vector_path'])
scenarios = ['_bas_', '_cur_', '_fut_']
for lulc_val, scenario in enumerate(scenarios, start=1):
args['lulc' + scenario + 'path'] = os.path.join(
args['workspace_dir'], 'lc_samp' + scenario + 'b.tif')
make_lulc_raster(args['lulc' + scenario + 'path'], lulc_val)
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'],
threat_values=[0.5, 6.6])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
habitat_quality.execute(args)
# Assert values were obtained by summing each output raster.
for output_filename, assert_value in {
'deg_sum_c_regression.tif': 1792.8088,
'deg_sum_f_regression.tif': 2308.9636,
'quality_c_regression.tif': 6928.5293,
'quality_f_regression.tif': 4916.338,
'rarity_c_regression.tif': 2500.0000000,
'rarity_f_regression.tif': 2500.0000000
}.items():
raster_path = os.path.join(args['workspace_dir'], 'output',
output_filename)
# Check that the raster's computed values are what we expect.
# In this case, the LULC and threat rasters should have been
# expanded to be beyond the bounds of the original threat values,
# so we should exclude those new nodata pixel values.
assert_array_sum(raster_path, assert_value, include_nodata=False)
def test_habitat_quality_regression(self):
"""Habitat Quality: base regression test with simplified data."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant': '0.5',
'suffix': 'regression',
u'workspace_dir': self.workspace_dir,
}
args['access_vector_path'] = os.path.join(args['workspace_dir'],
'access_samp.shp')
make_access_shp(args['access_vector_path'])
scenarios = ['_bas_', '_cur_', '_fut_']
for lulc_val, scenario in enumerate(scenarios):
args['lulc' + scenario + 'path'] = os.path.join(
args['workspace_dir'], 'lc_samp' + scenario + 'b.tif')
make_lulc_raster(args['lulc' + scenario + 'path'], lulc_val)
args['sensitivity_table_path'] = os.path.join(args['workspace_dir'],
'sensitivity_samp.csv')
make_sensitivity_samp_csv(args['sensitivity_table_path'])
args['threat_raster_folder'] = args['workspace_dir']
make_threats_raster(args['threat_raster_folder'])
args['threats_table_path'] = os.path.join(args['workspace_dir'],
'threats_samp.csv')
make_threats_csv(args['threats_table_path'])
habitat_quality.execute(args)
# Assert values were obtained by summing each output raster.
for output_filename, assert_value in {
'deg_sum_c_regression.tif': 10.728817,
'deg_sum_f_regression.tif': 16.461340,
'quality_c_regression.tif': 7499.9975586,
'quality_f_regression.tif': 4999.9995117,
'rarity_c_regression.tif': 2500.0000000,
'rarity_f_regression.tif': 2500.0000000
}.iteritems():
assert_array_sum(
os.path.join(args['workspace_dir'], 'output', output_filename),
assert_value)
def test_habitat_quality_regression(self):
"""Habitat Quality: base regression test."""
from natcap.invest import habitat_quality
args = {
'access_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality', 'access_samp.shp'),
'half_saturation_constant':
'0.5',
'landuse_bas_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality', 'lc_samp_bse_b.tif'),
'landuse_cur_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality', 'lc_samp_cur_b.tif'),
'landuse_fut_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality', 'lc_samp_fut_b.tif'),
'sensitivity_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality',
'sensitivity_samp.csv'),
'suffix':
'regression',
'threat_raster_folder':
os.path.join(SAMPLE_DATA, 'HabitatQuality'),
'threats_uri':
os.path.join(SAMPLE_DATA, 'HabitatQuality', 'threats_samp.csv'),
u'workspace_dir':
self.workspace_dir,
}
habitat_quality.execute(args)
HabitatQualityTests._test_same_files(
os.path.join(REGRESSION_DATA, 'file_list_regression.txt'),
args['workspace_dir'])
for output_filename in [
'rarity_f_regression.tif', 'deg_sum_out_c_regression.tif',
'deg_sum_out_f_regression.tif', 'quality_out_c_regression.tif',
'quality_out_f_regression.tif', 'rarity_c_regression.tif'
]:
natcap.invest.pygeoprocessing_0_3_3.testing.assert_rasters_equal(
os.path.join(REGRESSION_DATA, output_filename),
os.path.join(self.workspace_dir, 'output', output_filename),
1e-6)
def test_habitat_quality_bad_rasters(self):
"""Habitat Quality: on threats that aren't real rasters."""
from natcap.invest import habitat_quality
args = {
'half_saturation_constant':
'0.5',
'landuse_cur_uri':
os.path.join(REGRESSION_DATA, 'small_lulc_base.tif'),
'sensitivity_uri':
os.path.join(REGRESSION_DATA, 'small_sensitivity_samp.csv'),
'threat_raster_folder':
os.path.join(REGRESSION_DATA, 'bad_rasters'),
'threats_uri':
os.path.join(REGRESSION_DATA, 'small_threats_samp.csv'),
u'workspace_dir':
self.workspace_dir,
}
with self.assertRaises(ValueError):
habitat_quality.execute(args)
