add refratory period to fitting, add burstiness error
This commit is contained in:
alexanderott
parent
44c9024f1f
commit
2a55078894
51
Baseline.py
51
Baseline.py
@ -27,6 +27,53 @@ class Baseline:
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def get_coefficient_of_variation(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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def get_burstiness(self):
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isis = np.array(self.get_interspike_intervals()) * 1000 # change unit to ms
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if len(isis) <= 10:
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return 0
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step = 0.1
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bins = np.arange(0, min(isis) * 3, step)
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num_spikes_per_bin = np.zeros(bins.shape)
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for i, bin in enumerate(bins):
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num_of_spikes = np.sum(isis[(isis >= bin) & (isis < bin + step)])
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num_spikes_per_bin[i] = num_of_spikes
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max_found = -1
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end_of_peak = -1
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if max(num_spikes_per_bin) < 10:
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return 0
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for i, num in enumerate(num_spikes_per_bin):
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if i + 1 >= len(num_spikes_per_bin):
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return 0
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if max_found == -1:
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if num_spikes_per_bin[i+1] > num:
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continue
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elif num > 10:
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max_found = i
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else:
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if num_spikes_per_bin[i + 1] > num:
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end_of_peak = i +1
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break
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burstiness = sum(num_spikes_per_bin[:end_of_peak]) / len(isis)
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# bins = np.arange(0, max(isis) * 1.01, 0.1)
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#
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# plt.title('Baseline ISIs - burstiness {:.2f}'.format(burstiness))
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# plt.xlabel('ISI in ms')
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# plt.ylabel('Count')
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# plt.hist(isis, bins=bins)
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# plt.plot((0.5*step, bins[end_of_peak-1] + 0.5*step,), (0, 0), 'o')
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# plt.show()
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return burstiness
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def get_interspike_intervals(self):
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raise NotImplementedError("NOT YET OVERRIDDEN FROM ABSTRACT CLASS")
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@ -298,12 +345,12 @@ class BaselineModel(Baseline):
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save_path, position, time_length)
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def get_baseline_class(data, eod_freq=None) -> Baseline:
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def get_baseline_class(data, eod_freq=None, trials=1) -> Baseline:
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if isinstance(data, CellData):
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return BaselineCellData(data)
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if isinstance(data, LifacNoiseModel):
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if eod_freq is None:
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raise ValueError("The EOD frequency is needed for the BaselineModel Class.")
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return BaselineModel(data, eod_freq)
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return BaselineModel(data, eod_freq, trials=trials)
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raise ValueError("Unknown type: Cannot find corresponding Baseline class. data was type:" + str(type(data)))
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@ -10,7 +10,14 @@ def icelldata_of_dir(base_path):
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item_path = base_path + item
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try:
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yield CellData(item_path)
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data = CellData(item_path)
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trace = data.get_base_traces(trace_type=data.V1)
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if len(trace) == 0:
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print("NO V1 TRACE FOUND: ", item_path)
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continue
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else:
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yield data
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except TypeError as e:
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warn_msg = str(e)
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warn(warn_msg)
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@ -456,12 +456,12 @@ class FICurveModel(FICurve):
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plt.close()
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def get_fi_curve_class(data, stimulus_values, eod_freq=None) -> FICurve:
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def get_fi_curve_class(data, stimulus_values, eod_freq=None, trials=5) -> FICurve:
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if isinstance(data, CellData):
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return FICurveCellData(data, stimulus_values)
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if isinstance(data, LifacNoiseModel):
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if eod_freq is None:
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raise ValueError("The FiCurveModel needs the eod variable to work")
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return FICurveModel(data, stimulus_values, eod_freq)
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return FICurveModel(data, stimulus_values, eod_freq, trials=trials)
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raise ValueError("Unknown type: Cannot find corresponding Baseline class. Data was type:" + str(type(data)))
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274
Fitter.py
274
Fitter.py
@ -1,208 +1,13 @@
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from models.LIFACnoise import LifacNoiseModel
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from stimuli.SinusoidalStepStimulus import SinusoidalStepStimulus
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from CellData import CellData, icelldata_of_dir
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from CellData import CellData
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from Baseline import get_baseline_class
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from FiCurve import get_fi_curve_class
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from AdaptionCurrent import Adaption
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import numpy as np
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from warnings import warn
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from scipy.optimize import minimize
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import time
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import os
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SAVE_PATH_PREFIX = ""
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FIT_ROUTINE = ""
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def main():
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# fitter = Fitter()
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# run_with_real_data(fitter, fitter.fit_routine_3)
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test_fit_routines()
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def test_fit_routines():
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fitter = Fitter()
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names = ("routine_1", "routine_2", "routine_3")
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global FIT_ROUTINE
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for i, routine in enumerate([fitter.fit_routine_1, fitter.fit_routine_2, fitter.fit_routine_3]):
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FIT_ROUTINE = names[i]
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run_with_real_data(fitter, routine)
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best = []
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cells = sorted(os.listdir("test_routines/" + names[0] + "/"))
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for name in names:
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save_path = "test_routines/" + name + "/"
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cell_best = []
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for directory in sorted(os.listdir(save_path)):
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path = os.path.join(save_path, directory)
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if os.path.isdir(path):
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cell_best.append(find_best_run(path))
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best.append(cell_best)
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with open("test_routines/comparision.csv", "w") as res_file:
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res_file.write("routine")
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for cell in cells:
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res_file.write("," + cell)
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for i, routine_results in enumerate(best):
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res_file.write(names[i])
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for cell_best in routine_results:
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res_file.write("," + str(cell_best))
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def find_best_run(cell_path):
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values = []
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for directory in sorted(os.listdir(cell_path)):
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start_par_path = os.path.join(cell_path, directory)
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if os.path.isdir(start_par_path):
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values.append(float(start_par_path.split("_")[-1]))
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return min(values)
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def iget_start_parameters():
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# mem_tau, input_scaling, noise_strength, dend_tau,
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# expand by tau_a, delta_a ?
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mem_tau_list = [0.01]
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input_scaling_list = [40, 60]
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noise_strength_list = [0.03] # [0.02, 0.06]
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dend_tau_list = [0.001, 0.002]
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delta_a_list = [0.035, 0.065]
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for mem_tau in mem_tau_list:
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for input_scaling in input_scaling_list:
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for noise_strength in noise_strength_list:
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for dend_tau in dend_tau_list:
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for delta_a in delta_a_list:
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yield {"mem_tau": mem_tau, "input_scaling": input_scaling,
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"noise_strength": noise_strength, "dend_tau": dend_tau,
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"delta_a": delta_a}
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def run_with_real_data(fitter, fit_routine_func, parallel=False):
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count = 0
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for cell_data in icelldata_of_dir("./data/"):
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count += 1
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if count < 7:
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pass
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#continue
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print("cell:", cell_data.get_data_path())
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trace = cell_data.get_base_traces(trace_type=cell_data.V1)
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if len(trace) == 0:
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print("NO V1 TRACE FOUND")
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continue
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global FIT_ROUTINE
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# results_path = "results/" + os.path.split(cell_data.get_data_path())[-1] + "/"
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results_path = "test_routines/" + FIT_ROUTINE + "/" + os.path.split(cell_data.get_data_path())[-1] + "/"
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print("results at:", results_path)
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if not os.path.exists(results_path):
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os.makedirs(results_path)
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# plot cell images:
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cell_save_path = results_path + "cell/"
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if not os.path.exists(cell_save_path):
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os.makedirs(cell_save_path)
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data_baseline = get_baseline_class(cell_data)
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data_baseline.plot_baseline(cell_save_path)
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data_baseline.plot_interspike_interval_histogram(cell_save_path)
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data_baseline.plot_serial_correlation(6, cell_save_path)
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data_fi_curve = get_fi_curve_class(cell_data, cell_data.get_fi_contrasts())
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data_fi_curve.plot_fi_curve(cell_save_path)
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start_par_count = 0
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for start_parameters in iget_start_parameters():
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start_par_count += 1
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print("START PARAMETERS:", start_par_count)
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start_time = time.time()
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# fitter = Fitter()
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fmin, parameters = fitter.fit_model_to_data(cell_data, start_parameters, fit_routine_func)
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print(fmin)
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print(parameters)
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end_time = time.time()
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parameter_set_path = results_path + "start_par_set_{}_fmin_{:.2f}".format(start_par_count, fmin["fun"]) + "/"
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if not os.path.exists(parameter_set_path):
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os.makedirs(parameter_set_path)
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with open(parameter_set_path + "parameters_info.txt".format(start_par_count), "w") as file:
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file.writelines(["start_parameters:\t" + str(start_parameters),
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"\nfinal_parameters:\t" + str(parameters),
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"\nfinal_fmin:\t" + str(fmin)])
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print('Fitting of cell took function took {:.3f} s'.format((end_time - start_time)))
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# print(results_path)
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print_comparision_cell_model(cell_data, data_baseline, data_fi_curve, parameters,
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plot=True, save_path=parameter_set_path)
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# from Sounds import play_finished_sound
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# play_finished_sound()
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pass
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def print_comparision_cell_model(cell_data, data_baseline, data_fi_curve, parameters, plot=False, save_path=None):
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model = LifacNoiseModel(parameters)
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eod_frequency = cell_data.get_eod_frequency()
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model_baseline = get_baseline_class(model, eod_frequency)
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m_bf = model_baseline.get_baseline_frequency()
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m_vs = model_baseline.get_vector_strength()
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m_sc = model_baseline.get_serial_correlation(1)
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m_cv = model_baseline.get_coefficient_of_variation()
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model_ficurve = get_fi_curve_class(model, cell_data.get_fi_contrasts(), eod_frequency)
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m_f_infinities = model_ficurve.get_f_inf_frequencies()
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m_f_zeros = model_ficurve.get_f_zero_frequencies()
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m_f_infinities_slope = model_ficurve.get_f_inf_slope()
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m_f_zero_slope = model_ficurve.get_f_zero_fit_slope_at_straight()
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c_bf = data_baseline.get_baseline_frequency()
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c_vs = data_baseline.get_vector_strength()
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c_sc = data_baseline.get_serial_correlation(1)
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c_cv = data_baseline.get_coefficient_of_variation()
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c_f_inf_slope = data_fi_curve.get_f_inf_slope()
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c_f_inf_values = data_fi_curve.f_inf_frequencies
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c_f_zero_slope = data_fi_curve.get_f_zero_fit_slope_at_straight()
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c_f_zero_values = data_fi_curve.f_zero_frequencies
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print("EOD-frequency: {:.2f}".format(cell_data.get_eod_frequency()))
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print("bf: cell - {:.2f} vs model {:.2f}".format(c_bf, m_bf))
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print("vs: cell - {:.2f} vs model {:.2f}".format(c_vs, m_vs))
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print("sc: cell - {:.2f} vs model {:.2f}".format(c_sc[0], m_sc[0]))
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print("cv: cell - {:.2f} vs model {:.2f}".format(c_cv, m_cv))
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print("f_inf_slope: cell - {:.2f} vs model {:.2f}".format(c_f_inf_slope, m_f_infinities_slope))
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print("f infinity values:\n cell -", c_f_inf_values, "\n model -", m_f_infinities)
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print("f_zero_slope: cell - {:.2f} vs model {:.2f}".format(c_f_zero_slope, m_f_zero_slope))
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print("f zero values:\n cell -", c_f_zero_values, "\n model -", m_f_zeros)
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if save_path is not None:
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with open(save_path + "value_comparision.tsv", 'w') as value_file:
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value_file.write("Variable\tCell\tModel\n")
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value_file.write("baseline_frequency\t{:.2f}\t{:.2f}\n".format(c_bf, m_bf))
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value_file.write("vector_strength\t{:.2f}\t{:.2f}\n".format(c_vs, m_vs))
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value_file.write("serial_correlation\t{:.2f}\t{:.2f}\n".format(c_sc[0], m_sc[0]))
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value_file.write("coefficient_of_variation\t{:.2f}\t{:.2f}\n".format(c_cv, m_cv))
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value_file.write("f_inf_slope\t{:.2f}\t{:.2f}\n".format(c_f_inf_slope, m_f_infinities_slope))
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value_file.write("f_zero_slope\t{:.2f}\t{:.2f}\n".format(c_f_zero_slope, m_f_zero_slope))
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if plot:
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# plot model images
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model_baseline.plot_baseline(save_path)
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model_baseline.plot_interspike_interval_histogram(save_path)
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model_baseline.plot_serial_correlation(6, save_path)
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model_ficurve.plot_fi_curve(save_path)
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model_ficurve.plot_fi_curve_comparision(data_fi_curve, model_ficurve, save_path)
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class Fitter:
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@ -219,13 +24,14 @@ class Fitter:
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self.fi_contrasts = []
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self.eod_freq = 0
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self.sc_max_lag = 1
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self.sc_max_lag = 2
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# values to be replicated:
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self.baseline_freq = 0
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self.vector_strength = -1
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self.serial_correlation = []
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self.coefficient_of_variation = 0
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self.burstiness = -1
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self.f_inf_values = []
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self.f_inf_slope = 0
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@ -249,6 +55,7 @@ class Fitter:
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self.vector_strength = data_baseline.get_vector_strength()
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self.serial_correlation = data_baseline.get_serial_correlation(self.sc_max_lag)
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self.coefficient_of_variation = data_baseline.get_coefficient_of_variation()
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self.burstiness = data_baseline.get_burstiness()
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fi_curve = get_fi_curve_class(cell_data, cell_data.get_fi_contrasts())
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self.fi_contrasts = fi_curve.stimulus_values
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@ -277,54 +84,27 @@ class Fitter:
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x0 = np.array([start_parameters["mem_tau"], start_parameters["noise_strength"],
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start_parameters["input_scaling"], self.tau_a, start_parameters["delta_a"],
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start_parameters["dend_tau"]])
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start_parameters["dend_tau"], start_parameters["refractory_period"]])
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initial_simplex = create_init_simples(x0, search_scale=2)
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# error_list = [error_bf, error_vs, error_sc, error_cv,
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# error_f_inf, error_f_inf_slope, error_f_zero, error_f_zero_slope]
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error_weights = (0, 1, 1, 1, 1, 1, 1, 1)
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error_weights = (0, 1, 1, 1, 1, 1, 1, 1, 1)
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fmin = minimize(fun=self.cost_function_all,
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args=(error_weights,), x0=x0, method="Nelder-Mead",
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options={"initial_simplex": initial_simplex, "xatol": 0.001, "maxfev": 200, "maxiter": 400})
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return fmin, self.base_model.get_parameters()
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# similar results to fit routine 1
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def fit_routine_2(self, start_parameters):
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self.counter = 0
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# fit only v_offset, mem_tau, input_scaling, dend_tau
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x0 = np.array([start_parameters["mem_tau"], start_parameters["noise_strength"],
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start_parameters["input_scaling"], self.tau_a, start_parameters["delta_a"],
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start_parameters["dend_tau"]])
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initial_simplex = create_init_simples(x0, search_scale=2)
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# error_list = [error_bf, error_vs, error_sc, error_cv,
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# error_f_inf, error_f_inf_slope, error_f_zero, error_f_zero_slope]
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error_weights = (0, 2, 2, 2, 1, 1, 1, 1)
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fmin = minimize(fun=self.cost_function_all,
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args=(error_weights,), x0=x0, method="Nelder-Mead",
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options={"initial_simplex": initial_simplex, "xatol": 0.001, "maxfev": 100, "maxiter": 400})
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best_pars = fmin.x
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x0 = np.array([best_pars[0], best_pars[2], # mem_tau, input_scaling
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best_pars[4], best_pars[5]]) # delta_a, dend_tau
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initial_simplex = create_init_simples(x0, search_scale=2)
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error_weights = (0, 1, 1, 1, 3, 2, 3, 2)
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fmin = minimize(fun=self.cost_function_only_adaption,
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args=(error_weights,), x0=x0, method="Nelder-Mead",
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options={"initial_simplex": initial_simplex, "xatol": 0.001, "maxfev": 100, "maxiter": 400})
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return fmin, self.base_model.get_parameters()
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def fit_routine_3(self, start_parameters):
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self.counter = 0
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x0 = np.array([start_parameters["mem_tau"], start_parameters["input_scaling"], # mem_tau, input_scaling
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start_parameters["delta_a"], start_parameters["dend_tau"]]) # delta_a, dend_tau
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initial_simplex = create_init_simples(x0, search_scale=2)
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error_weights = (0, 1, 1, 1, 3, 2, 3, 2)
|
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error_weights = (0, 1, 1, 1, 1, 3, 2, 3, 2)
|
||||
fmin = minimize(fun=self.cost_function_only_adaption,
|
||||
args=(error_weights,), x0=x0, method="Nelder-Mead",
|
||||
options={"initial_simplex": initial_simplex, "xatol": 0.001, "maxfev": 100, "maxiter": 400})
|
||||
@ -335,7 +115,7 @@ class Fitter:
|
||||
initial_simplex = create_init_simples(x0, search_scale=2)
|
||||
# error_list = [error_bf, error_vs, error_sc, error_cv,
|
||||
# error_f_inf, error_f_inf_slope, error_f_zero, error_f_zero_slope]
|
||||
error_weights = (0, 2, 2, 2, 1, 1, 1, 1)
|
||||
error_weights = (0, 2, 2, 2, 2, 1, 1, 1, 1)
|
||||
fmin = minimize(fun=self.cost_function_all,
|
||||
args=(error_weights,), x0=x0, method="Nelder-Mead",
|
||||
options={"initial_simplex": initial_simplex, "xatol": 0.001, "maxfev": 100, "maxiter": 400})
|
||||
@ -349,6 +129,7 @@ class Fitter:
|
||||
self.base_model.set_variable("tau_a", X[3])
|
||||
self.base_model.set_variable("delta_a", X[4])
|
||||
self.base_model.set_variable("dend_tau", X[5])
|
||||
self.base_model.set_variable("refractory_period", X[6])
|
||||
|
||||
base_stimulus = SinusoidalStepStimulus(self.eod_freq, 0)
|
||||
# find right v-offset
|
||||
@ -471,6 +252,8 @@ class Fitter:
|
||||
vector_strength = model_baseline.get_vector_strength()
|
||||
serial_correlation = model_baseline.get_serial_correlation(self.sc_max_lag)
|
||||
coefficient_of_variation = model_baseline.get_coefficient_of_variation()
|
||||
burstiness = model_baseline.get_burstiness()
|
||||
|
||||
|
||||
fi_curve_model = get_fi_curve_class(model, self.fi_contrasts, self.eod_freq)
|
||||
f_zeros = fi_curve_model.get_f_zero_frequencies()
|
||||
@ -483,11 +266,14 @@ class Fitter:
|
||||
error_bf = abs((baseline_freq - self.baseline_freq) / self.baseline_freq)
|
||||
error_vs = abs((vector_strength - self.vector_strength) / 0.1)
|
||||
error_cv = abs((coefficient_of_variation - self.coefficient_of_variation) / 0.1)
|
||||
error_bursty = (abs(burstiness - self.burstiness) / 0.02)
|
||||
|
||||
error_sc = 0
|
||||
for i in range(self.sc_max_lag):
|
||||
error_sc = abs((serial_correlation[i] - self.serial_correlation[i]) / 0.1)
|
||||
error_sc = error_sc / self.sc_max_lag
|
||||
error_sc += abs((serial_correlation[i] - self.serial_correlation[i]) / 0.1)
|
||||
# error_sc = error_sc / self.sc_max_lag
|
||||
|
||||
|
||||
|
||||
error_f_inf_slope = abs((f_infinities_slope - self.f_inf_slope) / (self.f_inf_slope/20))
|
||||
error_f_inf = calculate_list_error(f_infinities, self.f_inf_values)
|
||||
@ -497,7 +283,7 @@ class Fitter:
|
||||
/ (self.f_zero_slope_at_straight / 10)
|
||||
error_f_zero = calculate_list_error(f_zeros, self.f_zero_values)
|
||||
|
||||
error_list = [error_bf, error_vs, error_sc, error_cv,
|
||||
error_list = [error_bf, error_vs, error_sc, error_cv, error_bursty,
|
||||
error_f_inf, error_f_inf_slope, error_f_zero, error_f_zero_slope_at_straight]
|
||||
|
||||
if error_weights is not None and len(error_weights) == len(error_list):
|
||||
@ -506,28 +292,6 @@ class Fitter:
|
||||
elif error_weights is not None:
|
||||
warn("Error: weights had different length than errors and were ignored!")
|
||||
|
||||
|
||||
# error = sum(error_list)
|
||||
# self.counter += 1
|
||||
# if self.counter % 200 == 0: # and False:
|
||||
# print("\nCost function run times: {:}\n".format(self.counter),
|
||||
# "Total weighted error: {:.4f}\n".format(error),
|
||||
# "Baseline frequency - expected: {:.0f}, current: {:.0f}, error: {:.3f}\n".format(
|
||||
# self.baseline_freq, baseline_freq, error_bf),
|
||||
# "Vector strength - expected: {:.2f}, current: {:.2f}, error: {:.3f}\n".format(
|
||||
# self.vector_strength, vector_strength, error_vs),
|
||||
# "Serial correlation - expected: {:.2f}, current: {:.2f}, error: {:.3f}\n".format(
|
||||
# self.serial_correlation[0], serial_correlation[0], error_sc),
|
||||
# "Coefficient of variation - expected: {:.2f}, current: {:.2f}, error: {:.3f}\n".format(
|
||||
# self.coefficient_of_variation, coefficient_of_variation, error_cv),
|
||||
# "f-infinity slope - expected: {:.0f}, current: {:.0f}, error: {:.3f}\n".format(
|
||||
# self.f_inf_slope, f_infinities_slope, error_f_inf_slope),
|
||||
# "f-infinity values:\nexpected:", np.around(self.f_inf_values), "\ncurrent: ", np.around(f_infinities),
|
||||
# "\nerror: {:.3f}\n".format(error_f_inf),
|
||||
# "f-zero slope - expected: {:.0f}, current: {:.0f}, error: {:.3f}\n".format(
|
||||
# self.f_zero_slope_at_straight, f_zero_slope_at_straight, error_f_zero_slope_at_straight),
|
||||
# "f-zero values:\nexpected:", np.around(self.f_zero_values), "\ncurrent: ", np.around(f_zeros),
|
||||
# "\nerror: {:.3f}".format(error_f_zero))
|
||||
return error_list
|
||||
|
||||
|
||||
@ -559,4 +323,4 @@ def create_init_simples(x0, search_scale=3.):
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
print("use run_fitter.py to run the Fitter.")
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
|
||||
from models.LIFACnoise import LifacNoiseModel
|
||||
from CellData import CellData, icelldata_of_dir
|
||||
from CellData import icelldata_of_dir
|
||||
from Baseline import get_baseline_class
|
||||
from FiCurve import get_fi_curve_class
|
||||
from Fitter import Fitter
|
||||
@ -11,24 +11,25 @@ import os
|
||||
import multiprocessing as mp
|
||||
|
||||
|
||||
SAVE_PATH_PREFIX = ""
|
||||
FIT_ROUTINE = ""
|
||||
|
||||
def main():
|
||||
count = 0
|
||||
for data in icelldata_of_dir("./data/"):
|
||||
count += 1
|
||||
if count <= 3:
|
||||
continue
|
||||
trace = data.get_base_traces(trace_type=data.V1)
|
||||
if len(trace) == 0:
|
||||
print("NO V1 TRACE FOUND")
|
||||
continue
|
||||
# if count <= 3:
|
||||
# continue
|
||||
|
||||
fit_cell_parrallel(data, [p for p in iget_start_parameters()])
|
||||
break
|
||||
|
||||
|
||||
def fit_cell_parrallel(cell_data, start_parameters):
|
||||
cell_path = os.path.basename(cell_data.get_data_path())
|
||||
print(cell_path)
|
||||
core_count = mp.cpu_count()
|
||||
pool = mp.Pool(core_count - 3)
|
||||
pool = mp.Pool(core_count - 1)
|
||||
|
||||
fitter = Fitter()
|
||||
fitter.set_data_reference_values(cell_data)
|
||||
@ -38,14 +39,16 @@ def fit_cell_parrallel(cell_data, start_parameters):
|
||||
print("Time taken for all start parameters ({:}): {:.2f}s".format(len(start_parameters), time2-time1))
|
||||
for i, (fmin, fin_pars) in enumerate(outputs):
|
||||
error = fitter.calculate_errors(model=LifacNoiseModel(fin_pars))
|
||||
print_comparision_cell_model(cell_data, fin_pars, plot=True, save_path="./test_routines/" + cell_path + "/start_parameter_{:}_err_{:.2f}/".format(i+1, sum(error)))
|
||||
save_path = "./test_routines/" + cell_path + "/start_parameter_{:}_err_{:.2f}/".format(i+1, sum(error))
|
||||
save_fitting_run_info(cell_data, fin_pars, start_parameters[i],
|
||||
plot=True, save_path=save_path)
|
||||
|
||||
|
||||
def test_fit_routines():
|
||||
fitter = Fitter()
|
||||
names = ("routine_1", "routine_2", "routine_3")
|
||||
names = ("routine_1", "routine_2")
|
||||
global FIT_ROUTINE
|
||||
for i, routine in enumerate([fitter.fit_routine_1, fitter.fit_routine_2, fitter.fit_routine_3]):
|
||||
for i, routine in enumerate([fitter.fit_routine_1, fitter.fit_routine_2]):
|
||||
FIT_ROUTINE = names[i]
|
||||
run_with_real_data(fitter, routine)
|
||||
|
||||
@ -91,15 +94,17 @@ def iget_start_parameters():
|
||||
noise_strength_list = [0.03] # [0.02, 0.06]
|
||||
dend_tau_list = [0.001, 0.002]
|
||||
delta_a_list = [0.035, 0.065]
|
||||
ref_time_list = [0.00065]
|
||||
|
||||
for mem_tau in mem_tau_list:
|
||||
for input_scaling in input_scaling_list:
|
||||
for noise_strength in noise_strength_list:
|
||||
for dend_tau in dend_tau_list:
|
||||
for delta_a in delta_a_list:
|
||||
yield {"mem_tau": mem_tau, "input_scaling": input_scaling,
|
||||
"noise_strength": noise_strength, "dend_tau": dend_tau,
|
||||
"delta_a": delta_a}
|
||||
for ref_time in ref_time_list:
|
||||
yield {"mem_tau": mem_tau, "input_scaling": input_scaling,
|
||||
"noise_strength": noise_strength, "dend_tau": dend_tau,
|
||||
"delta_a": delta_a, "refractory_period": ref_time}
|
||||
|
||||
|
||||
def run_with_real_data(fitter, fit_routine_func, parallel=False):
|
||||
@ -149,27 +154,26 @@ def run_with_real_data(fitter, fit_routine_func, parallel=False):
|
||||
print(parameters)
|
||||
end_time = time.time()
|
||||
parameter_set_path = results_path + "start_par_set_{}_fmin_{:.2f}".format(start_par_count, fmin["fun"]) + "/"
|
||||
if not os.path.exists(parameter_set_path):
|
||||
os.makedirs(parameter_set_path)
|
||||
with open(parameter_set_path + "parameters_info.txt".format(start_par_count), "w") as file:
|
||||
file.writelines(["start_parameters:\t" + str(start_parameters),
|
||||
"\nfinal_parameters:\t" + str(parameters),
|
||||
"\nfinal_fmin:\t" + str(fmin)])
|
||||
|
||||
print('Fitting of cell took function took {:.3f} s'.format((end_time - start_time)))
|
||||
# print(results_path)
|
||||
print_comparision_cell_model(cell_data, parameters,
|
||||
plot=True, save_path=parameter_set_path)
|
||||
save_fitting_run_info(cell_data, parameters, start_parameters,
|
||||
plot=True, save_path=parameter_set_path)
|
||||
|
||||
# from Sounds import play_finished_sound
|
||||
# play_finished_sound()
|
||||
pass
|
||||
|
||||
|
||||
def print_comparision_cell_model(cell_data, parameters, plot=False, save_path=None):
|
||||
def save_fitting_run_info(cell_data, parameters, start_parameters, plot=False, save_path=None):
|
||||
if save_path is not None:
|
||||
if not os.path.exists(save_path):
|
||||
os.makedirs(save_path)
|
||||
|
||||
with open(save_path + "parameters_info.txt", "w") as file:
|
||||
file.writelines(["start_parameters:\t" + str(start_parameters),
|
||||
"\nfinal_parameters:\t" + str(parameters)])
|
||||
|
||||
model = LifacNoiseModel(parameters)
|
||||
eod_frequency = cell_data.get_eod_frequency()
|
||||
|
||||
@ -178,6 +182,7 @@ def print_comparision_cell_model(cell_data, parameters, plot=False, save_path=No
|
||||
m_vs = model_baseline.get_vector_strength()
|
||||
m_sc = model_baseline.get_serial_correlation(1)
|
||||
m_cv = model_baseline.get_coefficient_of_variation()
|
||||
m_burst = model_baseline.get_burstiness()
|
||||
|
||||
model_ficurve = get_fi_curve_class(model, cell_data.get_fi_contrasts(), eod_frequency)
|
||||
m_f_infinities = model_ficurve.get_f_inf_frequencies()
|
||||
@ -190,6 +195,7 @@ def print_comparision_cell_model(cell_data, parameters, plot=False, save_path=No
|
||||
c_vs = data_baseline.get_vector_strength()
|
||||
c_sc = data_baseline.get_serial_correlation(1)
|
||||
c_cv = data_baseline.get_coefficient_of_variation()
|
||||
c_burst = data_baseline.get_burstiness()
|
||||
|
||||
data_fi_curve = get_fi_curve_class(cell_data, cell_data.get_fi_contrasts())
|
||||
c_f_inf_slope = data_fi_curve.get_f_inf_slope()
|
||||
@ -213,6 +219,7 @@ def print_comparision_cell_model(cell_data, parameters, plot=False, save_path=No
|
||||
value_file.write("baseline_frequency\t{:.2f}\t{:.2f}\n".format(c_bf, m_bf))
|
||||
value_file.write("vector_strength\t{:.2f}\t{:.2f}\n".format(c_vs, m_vs))
|
||||
value_file.write("serial_correlation\t{:.2f}\t{:.2f}\n".format(c_sc[0], m_sc[0]))
|
||||
value_file.write("Burstiness\t{:.2f}\t{:.2f}\n".format(c_burst, m_burst))
|
||||
value_file.write("coefficient_of_variation\t{:.2f}\t{:.2f}\n".format(c_cv, m_cv))
|
||||
value_file.write("f_inf_slope\t{:.2f}\t{:.2f}\n".format(c_f_inf_slope, m_f_infinities_slope))
|
||||
value_file.write("f_zero_slope\t{:.2f}\t{:.2f}\n".format(c_f_zero_slope, m_f_zero_slope))
|
||||
|
||||
@ -3,17 +3,25 @@ import matplotlib.pyplot as plt
|
||||
import numpy as np
|
||||
from DataParserFactory import get_parser
|
||||
import pprint
|
||||
from Baseline import get_baseline_class
|
||||
from FiCurve import get_fi_curve_class
|
||||
from CellData import icelldata_of_dir
|
||||
from models.LIFACnoise import LifacNoiseModel
|
||||
|
||||
parameter_bursty_model = {'step_size': 5e-05, 'mem_tau': 0.0066693150193490695, 'v_base': 0, 'v_zero': 0,
|
||||
'threshold': 1, 'v_offset': -45.703125, 'input_scaling': 172.13861987237314,
|
||||
'delta_a': 0.06148215166012024, 'tau_a': 0.03391674075000068, 'a_zero': 2,
|
||||
'noise_strength': 0.0684136549210377, 'dend_tau': 0.0013694103932013805,
|
||||
'refractory_period': 0.001}
|
||||
eod = 752
|
||||
model = LifacNoiseModel(parameter_bursty_model)
|
||||
baseline_model = get_baseline_class(model, 752, trials=2)
|
||||
baseline_model.get_burstiness()
|
||||
|
||||
base_path = "../data/2012-06-27-an-invivo-1"
|
||||
fi_file = base_path + "/fispikes1.dat"
|
||||
baseline_file = base_path + "/basespikes1.dat"
|
||||
sam_file = base_path + "/samallspikes1.dat"
|
||||
stimuli_file = base_path + "/stimuli.dat"
|
||||
quit()
|
||||
|
||||
parser = get_parser(base_path)
|
||||
|
||||
spiketimes, contrasts, delta_fs, eod_freqs, durations, trans_amplitudes = parser.__get_sam_spiketimes__()
|
||||
for cell_data in icelldata_of_dir("../data/"):
|
||||
baseline = get_baseline_class(cell_data)
|
||||
|
||||
|
||||
print(eod_freqs)
|
||||
baseline.get_burstiness()
|
||||
Loading…
Reference in New Issue
Block a user