def do_me(self, mdig_model):
# TODO move this to roc module
if "linux" not in sys.platform:
print "ROC analysis not supported on platforms other than Linux"
sys.exit(1)
from mdig.roc import ROCAnalysis
self.ROC = ROCAnalysis(self.model_names, self.options)
self.ROC.run()
def do_me(self,mdig_model):
# TODO move this to roc module
if "linux" not in sys.platform:
print "ROC analysis not supported on platforms other than Linux"
sys.exit(1)
from mdig.roc import ROCAnalysis
self.ROC = ROCAnalysis(self.model_names,self.options)
self.ROC.run()
class ROCAction(Action):
description = "Create Receiver Operating Characteristic curves for " + \
"occupancy envelopes and calculate AUC."
def __init__(self):
super(ROCAction, self).__init__()
self.parser = OptionParser(
version=mdig.version_string,
description=self.description,
usage="%prog roc [options] <model_name1> <model_name2> ...")
# Can theoretically run on any number of models
self.model_limit = None
self.preload = False
self.add_options()
def add_options(self):
super(ROCAction, self).add_options()
self.parser.add_option("-o",
"--overwrite",
help="Overwrite existing files",
action="store_true",
dest="overwrite_flag")
self.parser.add_option(
"-b",
"--bootstraps",
help="Number of resamplings to use for creating statistics",
action="store",
dest="bootstraps")
self.parser.add_option("-V",
"--vuc",
help="Calculate Volume Under the Curve",
action="store_true",
dest="calc_vuc")
self.parser.add_option("-a",
"--auc",
help="Calculate Area Under the Curve",
action="store_true",
dest="calc_auc")
self.parser.add_option("--graph-auc",
help="Graph the change in AUC over time",
action="store_true",
dest="graph_auc")
self.parser.add_option(
"--graph-roc",
help=
"Graph yearly ROC curves (creates one for each year and replicate)",
action="store_true",
dest="graph_roc")
self.parser.add_option("-x",
"--start",
help="Start time to calculate ROC/AUC for",
action="store",
type="int",
dest="start_time")
self.parser.add_option("-y",
"--end",
help="End time to calculate ROC/AUC for",
action="store",
type="int",
dest="end_time")
self.parser.add_option(
"-s",
"--sites",
help="The vector that will contain the sites to compare " +
"performance with (required).",
action="store",
dest="sites_vector",
type="string")
self.parser.add_option(
"-m",
"--mask",
help="The raster map used as the limit for where random " +
"absences can go and used for the total area to compare to.",
action="store",
dest="area_mask",
type="string")
self.parser.add_option(
"-l",
"--lifestage",
help="Lifestage to analyse (lifestage name or default='all')",
action="store",
dest="lifestage",
type="string")
self.parser.add_option(
"-d",
"--dir",
help="Base directory to save output in (don't use repository)",
action="store",
dest="output_dir",
type="string")
self.parser.add_option(
"-t",
"--tags",
help=
"List of comma separated tags for labelling each model within graph legends",
action="store",
dest="model_tags",
type="string")
def act_on_options(self, options):
super(ROCAction, self).act_on_options(self, options)
config.get_config().overwrite_flag = self.options.overwrite_flag
if self.options.lifestage is None:
self.options.lifestage = "all"
if self.options.sites_vector is None:
self.log.error("No sites vector provided.")
sys.exit(mdig.mdig_exit_codes["cmdline_error"])
if self.options.area_mask is None:
self.log.error("No area mask specified.")
sys.exit(mdig.mdig_exit_codes["cmdline_error"])
if self.options.output_dir is not None:
if not os.path.isdir(options.output_dir):
self.log.info(
"Directory %s doesn't exist, attemping to" + " create\n",
options.output_dir)
utils.make_path(options.output_dir)
else:
self.options.output_dir = "."
if self.options.model_tags is not None:
tags = self.options.model_tags.split(",")
if len(tags) != len(self.model_names):
self.log.error("Number of tags given not the same as number "+\
" of models.")
sys.exit(mdig.mdig_exit_codes["cmdline_error"])
self.options.model_tags = tags
def do_me(self, mdig_model):
# TODO move this to roc module
if "linux" not in sys.platform:
print "ROC analysis not supported on platforms other than Linux"
sys.exit(1)
from mdig.roc import ROCAnalysis
self.ROC = ROCAnalysis(self.model_names, self.options)
self.ROC.run()
class ROCAction(Action):
description = "Create Receiver Operating Characteristic curves for " + \
"occupancy envelopes and calculate AUC."
def __init__(self):
super(ROCAction, self).__init__()
self.parser = OptionParser(version=mdig.version_string,
description = self.description,
usage = "%prog roc [options] <model_name1> <model_name2> ...")
# Can theoretically run on any number of models
self.model_limit = None
self.preload = False
self.add_options()
def add_options(self):
super(ROCAction, self).add_options()
self.parser.add_option("-o","--overwrite",
help="Overwrite existing files",
action="store_true",
dest="overwrite_flag")
self.parser.add_option("-b","--bootstraps",
help="Number of resamplings to use for creating statistics",
action="store",
dest="bootstraps")
self.parser.add_option("-V","--vuc",
help="Calculate Volume Under the Curve",
action="store_true",
dest="calc_vuc")
self.parser.add_option("-a","--auc",
help="Calculate Area Under the Curve",
action="store_true",
dest="calc_auc")
self.parser.add_option("--graph-auc",
help="Graph the change in AUC over time",
action="store_true",
dest="graph_auc")
self.parser.add_option("--graph-roc",
help="Graph yearly ROC curves (creates one for each year and replicate)",
action="store_true",
dest="graph_roc")
self.parser.add_option("-x","--start",
help="Start time to calculate ROC/AUC for",
action="store",
type="int",
dest="start_time")
self.parser.add_option("-y","--end",
help="End time to calculate ROC/AUC for",
action="store",
type="int",
dest="end_time")
self.parser.add_option("-s","--sites",
help="The vector that will contain the sites to compare " +
"performance with (required).",
action="store",
dest="sites_vector",
type="string")
self.parser.add_option("-m","--mask",
help="The raster map used as the limit for where random " +
"absences can go and used for the total area to compare to.",
action="store",
dest="area_mask",
type="string")
self.parser.add_option("-l","--lifestage",
help="Lifestage to analyse (lifestage name or default='all')",
action="store",
dest="lifestage",
type="string")
self.parser.add_option("-d","--dir",
help="Base directory to save output in (don't use repository)",
action="store",
dest="output_dir",
type="string")
self.parser.add_option("-t","--tags",
help="List of comma separated tags for labelling each model within graph legends",
action="store",
dest="model_tags",
type="string")
def act_on_options(self,options):
super(ROCAction, self).act_on_options(self, options)
config.get_config().overwrite_flag = self.options.overwrite_flag
if self.options.lifestage is None:
self.options.lifestage = "all"
if self.options.sites_vector is None:
self.log.error("No sites vector provided.")
sys.exit(mdig.mdig_exit_codes["cmdline_error"])
if self.options.area_mask is None:
self.log.error("No area mask specified.")
sys.exit(mdig.mdig_exit_codes["cmdline_error"])
if self.options.output_dir is not None:
if not os.path.isdir(options.output_dir):
self.log.info("Directory %s doesn't exist, attemping to" +
" create\n",options.output_dir)
utils.make_path(options.output_dir)
else:
self.options.output_dir = "."
if self.options.model_tags is not None:
tags = self.options.model_tags.split(",")
if len(tags) != len(self.model_names):
self.log.error("Number of tags given not the same as number "+\
" of models.")
sys.exit(mdig.mdig_exit_codes["cmdline_error"])
self.options.model_tags = tags
def do_me(self,mdig_model):
# TODO move this to roc module
if "linux" not in sys.platform:
print "ROC analysis not supported on platforms other than Linux"
sys.exit(1)
from mdig.roc import ROCAnalysis
self.ROC = ROCAnalysis(self.model_names,self.options)
self.ROC.run()
