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 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 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 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 get_alg_default_params(alg_id):
mod = om.OpenModeller()
#algParams = mod.algorithmMetadata(alg_id).getParameterList();
algParamList = []
algList = mod.availableAlgorithms()
for i in range(0, len(algList)):
if algList[i].id == alg_id:
algParams = algList[i].getParameterList()
for param in algParams:
algParamList.append([param.id, param.typical])
return algParamList
return None
import om
# You'll need this instance for sure...
mod = om.OpenModeller()
# Some basic information
print "\nWelcome to the openModeller Python Binding test\n"
print "openModeller version", mod.getVersion()
# Loop over algorithms to collect their names
algList = mod.availableAlgorithms()
strAlgList = ""
for i in range(0, len(algList)):
alg = algList[i]
if i > 0:
strAlgList += ", "
strAlgList += alg.name
print "\n", mod.numAvailableAlgorithms(), "algorithm(s) available: ", strAlgList
# Display all metadata for a particular algorithm
algId = 'GARP'
print "\nMetadata of a particular algorithm:\n"
alg = mod.algorithmMetadata(algId)
acceptsCategoricalMaps = "no"
def summarize():
global success_counter, failure_counter, blow_counter, skip_counter
global cur_name
global report_entry_set, map_stats_entry_set
print
print 'Test Script: %s' % cur_name
print 'Succeeded: %d' % success_counter
print 'Failed: %d (%d blew exceptions)' \
% (failure_counter+blow_counter, blow_counter)
print 'Skipped: %d' % skip_counter
print
# find whether we are in test root dir or one level up
if os.path.exists(os.path.join("..", "SummaryReport.tmpl")):
os.chdir("..")
elif not os.path.exists("SummaryReport.tmpl"):
raise "Could not find HTML template files."
# Compile or load already precompiled template.
template = TemplateManager().prepare("SummaryReport.tmpl")
tproc = TemplateProcessor()
# Set the title.
mod = om.OpenModeller()
tproc.set("om_version", mod.getVersion())
tproc.set("om_num_algs", mod.numAvailableAlgorithms())
# htmltmpl requires var name starting with uppercase (!?!)
Entries = report_entry_set
tproc.set("Entries", Entries)
# get list of algorithms
Algorithms = []
algList = mod.availableAlgorithms()
for i in range(0, len(algList)):
alg = {}
alg["class"] = "a"
alg["id"] = algList[i].id
alg["name"] = algList[i].name
Algorithms.append(alg)
tproc.set("Algorithms", Algorithms)
# write the processed template to disk
summary_file = file("index.html", "w")
summary_file.write(tproc.process(template))
summary_file.close()
# Compile or load already precompiled template.
template = TemplateManager().prepare("MapReport.tmpl")
tproc = TemplateProcessor()
# htmltmpl requires var name starting with uppercase (!?!)
Mapstats = map_stats_entry_set
tproc.set("Mapstats", Mapstats)
# write the processed template to disk
map_file = file("MapReport.html", "w")
map_file.write(tproc.process(template))
map_file.close()
