def algorithm_serialization(args, options):
nat_env_file = args[0]
nat_env_name = args[1]
alg_id = args[2]
occ_file = args[3]
spp_name = args[4]
if not omtest.checkArguments(options, "algorithm", alg_id):
return ('skip', None)
coordSys = "GEOGCS[\"WGS84\", DATUM[\"WGS84\", SPHEROID[\"WGS84\", 6378137.0, 298.257223563]], PRIMEM[\"Greenwich\", 0.0], UNIT[\"degree\", 0.017453292519943295], AXIS[\"Longitude\",EAST], AXIS[\"Latitude\",NORTH]]"
(nat_env_list, nat_env_mask) = omtest.get_env_list(nat_env_file,
nat_env_name, "../data")
(presences, absences) = omtest.get_occurrences(occ_file, spp_name,
coordSys, 0, 1, 2, None)
alg_params = omtest.get_alg_default_params(alg_id)
filename_prefix = "ser_%s_%s" % (alg_id, spp_name.replace(" ", "_"))
bmp_filename = filename_prefix + "_projection.bmp"
xml_filename = filename_prefix + ".xml"
expected_filename = filename_prefix + "_expected.bmp"
mod = om.OpenModeller()
mod.setOccurrences(presences, absences)
mod.setEnvironment([], nat_env_list, nat_env_mask)
mod.setAlgorithm(alg_id, alg_params)
mod.run()
cfg = mod.getModelConfiguration()
om.Configuration.writeXml(cfg, xml_filename)
# write native projection (to be used as expected map)
mf = om.MapFormat()
mf.setFormat(om.MapFormat.GreyBMP)
mod.projectNativeRange(expected_filename, mf)
# now load it all from xml and try to project again
mod2 = om.OpenModeller()
cfg2 = om.Configuration.readXml(xml_filename)
mod2.setModelConfiguration(cfg2)
mf2 = om.MapFormat()
mf2.setFormat(om.MapFormat.GreyBMP)
mod2.projectNativeRange(bmp_filename, mf2)
result = omtest.get_map_results_obj(mod, None, presences, absences,
"algs/" + bmp_filename,
"algs/" + expected_filename,
"algs/" + xml_filename)
return ('success', result)
def algorithm_absences(args, options):
nat_env_file = args[0]
nat_env_name = args[1]
alg_id = args[2]
uses_absences = args[3]
occ_file = args[4]
spp_name = args[5]
# disregar whether the alg uses absences or not
# test whether alg runs if absence points are present
#if not uses_absences:
# return ('skip', None)
if not omtest.checkArguments(options, "algorithm", alg_id):
return ('skip', None)
coordSys = "GEOGCS[\"WGS84\", DATUM[\"WGS84\", SPHEROID[\"WGS84\", 6378137.0, 298.257223563]], PRIMEM[\"Greenwich\", 0.0], UNIT[\"degree\", 0.017453292519943295], AXIS[\"Longitude\",EAST], AXIS[\"Latitude\",NORTH]]"
(nat_env_list, nat_env_mask) = omtest.get_env_list(nat_env_file,
nat_env_name, "../data")
(presences, absences) = omtest.get_occurrences(occ_file, spp_name,
coordSys, 0, 1, 2, 3)
alg_params = omtest.get_alg_default_params(alg_id)
filename_prefix = "abs_%s_%s" % (alg_id, spp_name)
bmp_filename = filename_prefix + ".bmp"
xml_filename = filename_prefix + ".xml"
expected_filename = filename_prefix + "_expected.bmp"
mod = om.OpenModeller()
mod.setOccurrences(presences, absences)
mod.setEnvironment([], nat_env_list, nat_env_mask)
mod.setAlgorithm(alg_id, alg_params)
mod.run()
cfg = mod.getModelConfiguration()
om.Configuration.writeXml(cfg, xml_filename)
mf = om.MapFormat()
mf.setFormat(om.MapFormat.GreyBMP)
mod.projectNativeRange(bmp_filename, mf)
result = omtest.get_map_results_obj(mod, None, presences, absences,
"algs/" + bmp_filename,
"algs/" + expected_filename,
"algs/" + xml_filename)
return ('success', result)
def check_algorithm(args, options):
alg_id = args
if not omtest.checkArguments(options, "algorithm", alg_id):
return ('skip', None)
mod = om.OpenModeller()
try:
algMetadata = mod.algorithmMetadata(alg_id)
return ('success', None)
except:
return ('fail', None)
def matrix_input(args, options):
nat_env_file = args[0]
nat_env_name = args[1]
alg_id = args[2]
occ_file = args[3]
spp_name = args[4]
if not omtest.checkArguments(options, "algorithm", alg_id):
return ('skip', None)
coordSys = "GEOGCS[\"WGS84\", DATUM[\"WGS84\", SPHEROID[\"WGS84\", 6378137.0, 298.257223563]], PRIMEM[\"Greenwich\", 0.0], UNIT[\"degree\", 0.017453292519943295], AXIS[\"Longitude\",EAST], AXIS[\"Latitude\",NORTH]]"
(nat_env_list, nat_env_mask) = omtest.get_env_list(nat_env_file,
nat_env_name, "../data")
(presences, absences) = omtest.get_occurrences(occ_file, spp_name,
coordSys, 0, 1, 2, 3)
# sample environment at presence and points
natEnv = om.makeEnvironment([], nat_env_list, nat_env_mask)
presences.setEnvironment(natEnv)
absences.setEnvironment(natEnv)
alg_params = omtest.get_alg_default_params(alg_id)
filename_prefix = "matrix_input_%s_%s" % (alg_id, spp_name.replace(
" ", "_"))
bmp_filename = filename_prefix + ".bmp"
xml_filename = filename_prefix + ".xml"
expected_filename = filename_prefix + "_expected.bmp"
mod = om.OpenModeller()
mod.setOccurrences(presences, absences)
mod.setAlgorithm(alg_id, alg_params)
mod.run()
cfg = mod.getModelConfiguration()
om.Configuration.writeXml(cfg, xml_filename)
mf = om.MapFormat()
mf.setFormat(om.MapFormat.GreyBMP)
mod.createMap(natEnv, bmp_filename, mf)
result = omtest.get_map_results_obj(mod, natEnv, presences, absences,
"algs/" + bmp_filename,
"algs/" + expected_filename,
"algs/" + xml_filename)
return ('success', result)
def sample_dummy_skip(args, options):
# you can test the command line arguments like that:
if not omtest.checkArguments(options, "algorithm", "bioclim"):
return ('success', None)
else:
return ('skip', None)
