def run_command_on_occupancy_envelopes(self, cmd_string, ls, times=None):
""" Runs a command across occupancy envelopes
cmd_string is the command to run, with %0 for current map, %1 for
previous saved map, etc.
ls is a list of lifestages to run command on
times is a list of times to run command on, -ve values are interpreted
as indices from the end of the array e.g. -1 == last map.
"""
mdig_config = config.get_config()
if not self.is_complete():
self.log.error("Incomplete instance [%s]" % self)
raise InstanceIncompleteException()
ac = AnalysisCommand(cmd_string)
self.set_region()
envelopes = self.get_occupancy_envelopes()
for ls_id in ls:
e_times = [int(t) for t in envelopes[ls_id].keys()]
ac.init_output_file(self)
ac.set_times(self.experiment.get_period(), e_times, times)
ac.run_command(envelopes[ls_id])
if mdig_config.analysis_add_to_xml:
# add the analysis result to xml filename
# under instance...
self.add_analysis_result(ls_id, ac)
def run_command_on_occupancy_envelopes(self, cmd_string, ls, times=None):
""" Runs a command across occupancy envelopes
cmd_string is the command to run, with %0 for current map, %1 for
previous saved map, etc.
ls is a list of lifestages to run command on
times is a list of times to run command on, -ve values are interpreted
as indices from the end of the array e.g. -1 == last map.
"""
mdig_config = config.get_config()
if not self.is_complete():
self.log.error("Incomplete instance [%s]" % self)
raise InstanceIncompleteException()
ac = AnalysisCommand(cmd_string)
self.set_region()
envelopes = self.get_occupancy_envelopes()
for ls_id in ls:
e_times = [ int(t) for t in envelopes[ls_id].keys() ]
ac.init_output_file(self)
ac.set_times(self.experiment.get_period(), e_times, times)
ac.run_command(envelopes[ls_id])
if mdig_config.analysis_add_to_xml:
# add the analysis result to xml filename
# under instance...
self.add_analysis_result(ls_id, ac)
def run_command_on_replicates(self, cmd_string, ls, times=None):
""" Run a command across all replicate maps.
cmd_string is the command to run, with %0 for current map, %1 for
previous saved map, etc.
ls is a list of lifestages to run command on.
times is a list of times to run command on, -ve values are interpreted
as indices from the end of the array e.g. -1 == last map.
"""
self.set_region()
if not self.is_complete():
self.log.warning(
"Instance [%s] is incomplete, but will continue anyway" % self)
ac = AnalysisCommand(cmd_string)
for r in self.replicates:
for ls_id in ls:
saved_maps = r.get_saved_maps(ls_id)
r_times = [int(t) for t in saved_maps.keys()]
ac.init_output_file(self, r)
ac.set_times(self.experiment.get_period(), r_times, times)
ac.run_command(saved_maps)
if config.get_config().analysis_add_to_xml:
# add the analysis result to xml filename
# under instance...
r.add_analysis_result(ls_id, ac)
def run_command_on_replicates(self, cmd_string, ls, times=None):
""" Run a command across all replicate maps.
cmd_string is the command to run, with %0 for current map, %1 for
previous saved map, etc.
ls is a list of lifestages to run command on.
times is a list of times to run command on, -ve values are interpreted
as indices from the end of the array e.g. -1 == last map.
"""
self.set_region()
if not self.is_complete():
self.log.warning(
"Instance [%s] is incomplete, but will continue anyway" % self)
ac = AnalysisCommand(cmd_string)
for r in self.replicates:
for ls_id in ls:
saved_maps = r.get_saved_maps(ls_id)
r_times = [ int(t) for t in saved_maps.keys() ]
ac.init_output_file(self, r)
ac.set_times(self.experiment.get_period(),r_times,times)
ac.run_command(saved_maps)
if config.get_config().analysis_add_to_xml:
# add the analysis result to xml filename
# under instance...
r.add_analysis_result(ls_id, ac)