Alexander/P-unit_model
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tried to make parrallel fitting not need more and more ram

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a.ott 2020-06-04 17:13:09 +02:00
parent 7077c5b8e6
commit c5d580512e
1 changed files with 23 additions and 13 deletions
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36
run_Fitter.py
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@ -49,16 +49,14 @@ def fit_cell_base(parameter):
"\n error: {:.2f}".format(sum(error))) "\n error: {:.2f}".format(sum(error)))
def fit_all_cells_parallel_sync(cells, start_parameters, results_base_folder): def fit_all_cells_parallel_sync(cells, start_parameters, thread_pool, results_base_folder):
parameter = [] parameter = []
for cell in cells: for cell in cells:
for i, s_pars in enumerate(start_parameters): for i, s_pars in enumerate(start_parameters):
parameter.append((cell, i, s_pars, results_base_folder)) parameter.append((cell, i, s_pars, results_base_folder))
core_count = mp.cpu_count()
pool = mp.Pool(core_count - 1)
time1 = time.time() time1 = time.time()
pool.map(fit_cell_base, parameter) thread_pool.map(fit_cell_base, parameter)
time2 = time.time() time2 = time.time()
print("Time taken for all cells and start parameters ({:}): {:.2f}s".format(len(parameter), time2 - time1)) print("Time taken for all cells and start parameters ({:}): {:.2f}s".format(len(parameter), time2 - time1))
@ -273,17 +271,29 @@ def save_fitting_run_info(cell_data, parameters, start_parameters, plot=False, s
def test_effect_of_refractory_period(): def test_effect_of_refractory_period():
ref_periods = np.arange(0.0006, 0.001, 0.0015) ref_periods = [0.0006, 0.001, 0.0015]
counter = 0
core_count = mp.cpu_count()
pool = mp.Pool(core_count - 1)
for cell in icelldata_of_dir("./data/"):
counter += 1
if counter < 10:
continue
elif counter >= 14:
return
start_parameters_base = [p for p in iget_start_parameters()]
for ref_period in ref_periods:
print(cell.get_data_path())
print("ref period: {:.4f}".format(ref_period))
results_base_folder = "./test_routines/ref_period_{:.4f}/".format(ref_period)
all_start_parameters = copy.deepcopy(start_parameters_base)
for par_set in all_start_parameters:
par_set["refractory_period"] = ref_period
fit_all_cells_parallel_sync([cell], all_start_parameters, pool, results_base_folder)
cells = [c for c in icelldata_of_dir("./data/")] del cell
start_parameters_base = [p for p in iget_start_parameters()]
for ref_period in ref_periods:
results_base_folder = "./test_routines/ref_period_{:.3f}/".format(ref_period)
all_start_parameters = copy.deepcopy(start_parameters_base)
for par_set in all_start_parameters:
par_set["refractory_period"] = ref_period
fit_all_cells_parallel_sync(cells, all_start_parameters, results_base_folder)
if __name__ == '__main__': if __name__ == '__main__':
main() main()