def run(self):
"""Run a gridsearch trial.
"""
# Update logging if module is invoked from the command line
if __name__ == "__main__":
# Create stdout log handler
self._logger.addHandler(crf_util.get_StreamHandler(self.verbosity))
self._logger.debug("Logging stream handler to sys.stdout added.")
super().run()
def run(self):
"""Run a gridsearch trial.
"""
if __name__ == "__main__":
# Create stdout log handler if module is invoked from the command line
self._logger.addHandler(crf_util.get_StreamHandler(self.verbosity))
self._logger.debug("Logging stream handler to sys.stdout added.")
self.setup_exec_train_model()
# Wait for train CRF to be done and run merge and save_best
crf_util.wait_and_run(self.test_train_CRFs,
self.merge_save_train_models)
best_params_path = os.path.join(self._expt_dir, self._experiment,
"results", "best_parameters.txt")
self._logger.info("Grid search complete. Best parameters in {}".format(
best_params_path) + " in the following order:\n{}\n".format(
self.__class__._PARAMS_TO_EXTRACT))
def run(self):
"""Run a shuffled controls trial.
"""
if __name__ == "__main__":
# Create stdout log handler if module is invoked from the command line
self._logger.addHandler(crf_util.get_StreamHandler(self.verbosity))
self._logger.debug("Logging stream handler to sys.stdout added.")
# Create bare-bones shuffle folder and create shuffled datasets
self.setup_shuffle_model()
# Get best params
best_params = GridsearchTrial.get_best_parameters(
os.path.join(self._expt_dir, self._experiment, "results"))
self._logger.info("Parameters for {} collected.\n".format(
self.condition_name))
# create shuffle configs with best params (write and run write_configs_for_loopy.m)
self.create_shuffle_configs(best_params)
# Wait for all shuffled datasets to be created and run shuffle/start_jobs.sh
crf_util.wait_and_run(self.simple_test_shuffle_datasets,
self.train_controls)
# Wait for shuffle CRFs to be done and run merge and save_shuffle
crf_util.wait_and_run(self.test_shuffle_CRFs,
self.exec_merge_shuffle_CRFs)
shuffles.exec_merge_shuffle_CRFs)
# Extract ensemble neuron IDs. Write to disk?
if __name__ == "__main__":
start_time = time.time()
try:
condition = sys.argv[1]
except IndexError:
raise TypeError("A condition name must be passed on the command line.")
logger = logging.getLogger("top")
logger.setLevel(logging.DEBUG)
init_log_handler = logging.StreamHandler(stream=sys.stdout)
init_log_handler.setLevel(logging.INFO)
logger.addHandler(init_log_handler)
if len(sys.argv) > 2:
ini_fname = sys.argv[2]
logger.info("Using custom settings filename: {}".format(ini_fname))
shuffles = ShuffledControlsTrial(condition, ini_fname=ini_fname)
gridsearch = GridsearchTrial(condition, ini_fname=ini_fname)
else:
shuffles = ShuffledControlsTrial(condition)
gridsearch = GridsearchTrial(condition)
logger.addHandler(crf_util.get_StreamHandler(gridsearch.verbosity))
logger.removeHandler(init_log_handler)
main(gridsearch, shuffles, logger)
print("Total run time: {0:.2f} seconds".format(time.time() - start_time))