def set_up_population(self, detail_level):
grid_length = self.side_length * detail_level
cells_file = self.get_detail_level_results(detail_level)
# If cells_file.events is empty then the detail level directory has
# probably only just been created, and this file does not yet exist.
if cells_file.events == []:
cells_file.set_space_parameters(wrapping=self.wrapping,
is_3d=self.is_3d, side_length=self.side_length)
bio_array_path = os.path.join(self.detail_level_dir, 'bio_array')
self.bio_array = numpy.ones((grid_length,)*2, dtype=numpy.int)
last_path = os.path.join(self.root_dir, 'lastIter',
'event_location_last.xml')
last_file = SimulationResultsFile(path=last_path, read_only=True)
cells_file.copy_event_list(last_file)
cells_file.set_up_population(detail_level, grid_length,
self.wrapping, self.bio_array)
toolbox_basic.save_array(self.bio_array, bio_array_path)
self.make_mesh_files(self.bio_array, detail_level)
# Finally, update and save the 'cell_locations.xml' file.
head = 'mark,x,i_min,i_max,y,j_min,j_max'
if self.is_3d: head += ',z,k_min,k_max'
cells_file.set_event_list_header(head)
cells_file.write()
else:
cells_file.setup_ranges(grid_length, self.wrapping)
return cells_file
def get_concn_array(self, detail_level, sif_name):
self.get_run_dir(detail_level, sif_name)
grid_length = detail_level * self.side_length
array_path = os.path.join(self.run_dir, 'concn_array')
if os.path.isfile(array_path):
concn_array = toolbox_basic.load_array(array_path)
else:
result_file_path = os.path.join(self.run_dir, 'case.result')
result_file_path = toolbox_basic.check_path(result_file_path)
# This isn't quite correct! Without wrapping, Elmer skips some nodes
num_nodes = (grid_length + 1)**2
array_shape = (grid_length + 1,)*2
with open(result_file_path, 'Ur') as f:
last_lines = f.readlines()[-num_nodes:]
concn_array = numpy.array([float(line) for line in last_lines])
concn_array = numpy.reshape(concn_array, array_shape)
toolbox_basic.save_array(concn_array, array_path)
return concn_array
def get_run_results(self, detail_level, sif_name, read_only=False):
self.get_run_dir(detail_level, sif_name)
rates_path = os.path.join(self.run_dir, 'cell_rates.xml')
rates_file = SimulationResultsFile(path=rates_path, read_only=read_only)
if rates_file.events == []:
grid_length = self.side_length * detail_level
rates_file = self.get_detail_level_results(detail_level)
rates_file.path = rates_path
rates_file.setup_ranges(grid_length, self.wrapping)
rate_array = numpy.zeros((grid_length,)*2, dtype=numpy.float)
concn_array = self.get_concn_array(detail_level, sif_name)
consume_rate, produce_rate = \
self.get_consume_produce_functions(detail_level, sif_name)
rates_file.calc_rates_from_concn_array(concn_array, consume_rate,
produce_rate, rate_array=rate_array)
array_path = os.path.join(self.run_dir, 'rate_array')
toolbox_basic.save_array(rate_array, array_path)
head = 'mark,x,y'
if self.is_3d: head += ',z'
head += ',rate,amean_surf_concn'
rates_file.set_event_list_header(head)
rates_file.set_concn_rate_results(concn_array, rate_array)
rates_file.write()
return rates_file