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evaluate_CNN_test.py
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evaluate_CNN_test.py
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import numpy as np
import glob
import time
import cPickle as pickle
from keras.models import Model, load_model
from sklearn.metrics import mean_squared_error as MSE
from sklearn.metrics import mean_absolute_error as MAE
from sklearn.metrics import explained_variance_score
from sklearn.metrics import roc_curve, auc
# NOTE: during this project I've changed my coding style
# and was too lazy to edit the old code to match the new style
# so please ignore any style related wierdness
# thanks for not being petty about unimportant shit
# ALSO NOTE: prints are for logging purposes
#%% helper functions
def dict2bin(row_inds_spike_times_map, num_segments, sim_duration_ms):
bin_spikes_matrix = np.zeros((num_segments, sim_duration_ms), dtype='bool')
for row_ind in row_inds_spike_times_map.keys():
for spike_time in row_inds_spike_times_map[row_ind]:
bin_spikes_matrix[row_ind,spike_time] = 1.0
return bin_spikes_matrix
def parse_sim_experiment_file(sim_experiment_file):
print('-----------------------------------------------------------------')
print("loading file: '" + sim_experiment_file.split("\\")[-1] + "'")
loading_start_time = time.time()
experiment_dict = pickle.load(open(sim_experiment_file, "rb" ))
# gather params
num_simulations = len(experiment_dict['Results']['listOfSingleSimulationDicts'])
num_segments = len(experiment_dict['Params']['allSegmentsType'])
sim_duration_ms = experiment_dict['Params']['totalSimDurationInSec'] * 1000
num_ex_synapses = num_segments
num_inh_synapses = num_segments
num_synapses = num_ex_synapses + num_inh_synapses
# collect X, y_spike, y_soma
X = np.zeros((num_synapses,sim_duration_ms,num_simulations), dtype='bool')
y_spike = np.zeros((sim_duration_ms,num_simulations))
y_soma = np.zeros((sim_duration_ms,num_simulations))
for k, sim_dict in enumerate(experiment_dict['Results']['listOfSingleSimulationDicts']):
X_ex = dict2bin(sim_dict['exInputSpikeTimes'] , num_segments, sim_duration_ms)
X_inh = dict2bin(sim_dict['inhInputSpikeTimes'], num_segments, sim_duration_ms)
X[:,:,k] = np.vstack((X_ex,X_inh))
spike_times = (sim_dict['outputSpikeTimes'].astype(float) - 0.5).astype(int)
y_spike[spike_times,k] = 1.0
y_soma[:,k] = sim_dict['somaVoltageLowRes']
loading_duration_sec = time.time() - loading_start_time
print('loading took %.3f seconds' %(loading_duration_sec))
print('-----------------------------------------------------------------')
return X, y_spike, y_soma
def parse_multiple_sim_experiment_files(sim_experiment_files):
for k, sim_experiment_file in enumerate(sim_experiment_files):
X_curr, y_spike_curr, y_soma_curr = parse_sim_experiment_file(sim_experiment_file)
if k == 0:
X = X_curr
y_spike = y_spike_curr
y_soma = y_soma_curr
else:
X = np.dstack((X,X_curr))
y_spike = np.hstack((y_spike,y_spike_curr))
y_soma = np.hstack((y_soma,y_soma_curr))
return X, y_spike, y_soma
def calc_AUC_at_desired_FP(y_test, y_test_hat, desired_false_positive_rate=0.01):
fpr, tpr, thresholds = roc_curve(y_test.ravel(), y_test_hat.ravel())
linear_spaced_FPR = np.linspace(0,1,num=20000)
linear_spaced_TPR = np.interp(linear_spaced_FPR, fpr, tpr)
desired_fp_ind = min(max(1, np.argmin(abs(linear_spaced_FPR - desired_false_positive_rate))), linear_spaced_TPR.shape[0] - 1)
return linear_spaced_TPR[:desired_fp_ind].mean()
def calc_TP_at_desired_FP(y_test, y_test_hat, desired_false_positive_rate=0.0025):
fpr, tpr, thresholds = roc_curve(y_test.ravel(), y_test_hat.ravel())
desired_fp_ind = np.argmin(abs(fpr - desired_false_positive_rate))
if desired_fp_ind == 0:
desired_fp_ind = 1
return tpr[desired_fp_ind]
def exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat, desired_FP_list=[0.0025,0.0100]):
# evaluate the model and save the results
# evaluation_start_time = time.time()
# store results in the hyper param dict and return it
evaluations_results_dict = {}
for desired_FP in desired_FP_list:
TP_at_desired_FP = calc_TP_at_desired_FP(y_spikes_GT, y_spikes_hat, desired_false_positive_rate=desired_FP)
AUC_at_desired_FP = calc_AUC_at_desired_FP(y_spikes_GT, y_spikes_hat, desired_false_positive_rate=desired_FP)
TP_key_string = 'TP @ %.4f FP' %(desired_FP)
evaluations_results_dict[TP_key_string] = TP_at_desired_FP
AUC_key_string = 'AUC @ %.4f FP' %(desired_FP)
evaluations_results_dict[AUC_key_string] = AUC_at_desired_FP
# print('--------------------------------------------------')
fpr, tpr, thresholds = roc_curve(y_spikes_GT.ravel(), y_spikes_hat.ravel())
AUC_score = auc(fpr, tpr)
# print('AUC = %.4f' %(AUC_score))
soma_explained_variance_percent = 100.0 * explained_variance_score(y_soma_GT.ravel(),y_soma_hat.ravel())
soma_RMSE = np.sqrt(MSE(y_soma_GT.ravel(),y_soma_hat.ravel()))
soma_MAE = MAE(y_soma_GT.ravel(),y_soma_hat.ravel())
# print('soma explained variance percent = %.2f%s' %(soma_explained_variance_percent, '%'))
# print('--------------------------------------------------')
evaluations_results_dict['AUC'] = AUC_score
evaluations_results_dict['soma_explained_variance_percent'] = soma_explained_variance_percent
evaluations_results_dict['soma_RMSE'] = soma_RMSE
evaluations_results_dict['soma_MAE'] = soma_MAE
# evaluation_duration_min = (time.time() - evaluation_start_time)/60
# print('finished evaluation. time took to evaluate results is %.2f minutes' %(evaluation_duration_min))
# print('----------------------------------------------------------------------------------------------------')
return evaluations_results_dict
def filter_and_exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat, desired_FP_list=[0.0025,0.0100],
ignore_time_at_start_ms=500, num_spikes_per_sim=[0,24]):
time_points_to_eval = np.arange(y_spikes_GT.shape[1]) >= ignore_time_at_start_ms
simulations_to_eval = np.logical_and((y_spikes_GT.sum(axis=1) >= num_spikes_per_sim[0]),(y_spikes_GT.sum(axis=1) <= num_spikes_per_sim[1]))
print('----------------------------------------------------------------------------------------------------')
print('total amount of simualtions is %d (percent of simulations kept = %.2f%s)' %(y_spikes_GT.shape[0], 100 * simulations_to_eval.mean(),'%'))
y_spikes_GT_to_eval = y_spikes_GT[simulations_to_eval,:][:,time_points_to_eval]
y_spikes_hat_to_eval = y_spikes_hat[simulations_to_eval,:][:,time_points_to_eval]
y_soma_GT_to_eval = y_soma_GT[simulations_to_eval,:][:,time_points_to_eval]
y_soma_hat_to_eval = y_soma_hat[simulations_to_eval,:][:,time_points_to_eval]
return exctract_key_results(y_spikes_GT_to_eval, y_spikes_hat_to_eval, y_soma_GT_to_eval, y_soma_hat_to_eval, desired_FP_list=desired_FP_list)
#%% evel scrip params
synapse_type = 'NMDA'
#synapse_type = 'AMPA'
# synapse_type = 'AMPA_SK'
best_models_dir = '/Reseach/Single_Neuron_InOut/models/best_models/'
if synapse_type == 'NMDA':
valid_data_dir = '/Reseach/Single_Neuron_InOut/data/L5PC_NMDA_valid/'
test_data_dir = '/Reseach/Single_Neuron_InOut/data/L5PC_NMDA_test/'
models_to_evalulate = glob.glob(best_models_dir + '/*/NMDA*_model.h5')
elif synapse_type == 'AMPA':
valid_data_dir = '/Reseach/Single_Neuron_InOut/data/L5PC_AMPA_valid/'
test_data_dir = '/Reseach/Single_Neuron_InOut/data/L5PC_AMPA_test/'
models_to_evalulate = glob.glob(best_models_dir + '/*/AMPA*_model.h5')
models_to_ignore = glob.glob(best_models_dir + '/*/AMPA_SK*_model.h5')
models_to_evalulate = list(set(models_to_evalulate).difference(set(models_to_ignore)))
elif synapse_type == 'AMPA_SK':
valid_data_dir = '/Reseach/Single_Neuron_InOut/data/L5PC_AMPA_SK_valid/'
test_data_dir = '/Reseach/Single_Neuron_InOut/data/L5PC_AMPA_SK_test/'
models_to_evalulate = glob.glob(best_models_dir + '/*/AMPA_SK*_model.h5')
print('-----------------------------------------------')
print('finding data')
print('-----------------------------------------------')
valid_files = glob.glob(valid_data_dir + '*_128_simulationRuns*_6_secDuration_*')
test_files = glob.glob(test_data_dir + '*_128_simulationRuns*_6_secDuration_*')
print('number of validation files is %d' %(len(valid_files)))
print('number of test files is %d' %(len(test_files)))
print('number of models to evaluate is %d' %(len(models_to_evalulate)))
print('-----------------------------------------------')
print('models that will be evaluated are:')
for k, curr_model_name in enumerate(models_to_evalulate):
print('%d: %s' %(k + 1, curr_model_name))
print('-----------------------------------------------')
#%% load valid and test datasets
print('----------------------------------------------------------------------------------------')
print('loading testing files...')
test_file_loading_start_time = time.time()
v_threshold = -55
# load test data
X_test , y_spike_test , y_soma_test = parse_multiple_sim_experiment_files(test_files)
y_soma_test[y_soma_test > v_threshold] = v_threshold
test_file_loading_duration_min = (time.time() - test_file_loading_start_time) / 60
print('time took to load data is %.3f minutes' %(test_file_loading_duration_min))
print('----------------------------------------------------------------------------------------')
#%% loop through all models files, make prediction on valid set, evaluate perfomrance and store
for k, model_filename in enumerate(models_to_evalulate):
print('------------------------------')
print('starting evaluating model %d' %(k + 1))
print('------------------------------')
print('----------------------------------------------------------------------------------------')
print('loading model "%s"' %(model_filename.split('/')[-1]))
model_loading_start_time = time.time()
temporal_conv_net = load_model(model_filename)
temporal_conv_net.summary()
input_window_size = temporal_conv_net.input_shape[1]
# load pickle file
model_metadata_filename = model_filename.split('_model.h5')[0] + '_training.pickle'
model_metadata_dict = pickle.load(open(model_metadata_filename, "rb" ))
architecture_dict = model_metadata_dict['architecture_dict']
time_window_T = (np.array(architecture_dict['filter_sizes_per_layer']) - 1).sum() + 1
overlap_size = min(max(time_window_T + 1, min(150, input_window_size - 50)), 250)
print('overlap_size = %d' %(overlap_size))
print('time_window_T = %d' %(time_window_T))
model_loading_duration_min = (time.time() - model_loading_start_time) / 60
print('time took to load model is %.3f minutes' %(model_loading_duration_min))
print('----------------------------------------------------------------------------------------')
# create spike predictions on test set
print('----------------------------------------------------------------------------------------')
print('predicting using model...')
prediction_start_time = time.time()
y_train_soma_bias = -67.7
X_test_for_keras = np.transpose(X_test,axes=[2,1,0])
y1_test_for_keras = y_spike_test.T[:,:,np.newaxis]
y2_test_for_keras = y_soma_test.T[:,:,np.newaxis] - y_train_soma_bias
y1_test_for_keras_hat = np.zeros(y1_test_for_keras.shape)
y2_test_for_keras_hat = np.zeros(y2_test_for_keras.shape)
num_test_splits = 2 + (X_test_for_keras.shape[1] - input_window_size) / (input_window_size - overlap_size)
for k in range(num_test_splits):
start_time_ind = k * (input_window_size - overlap_size)
end_time_ind = start_time_ind + input_window_size
curr_X_test_for_keras = X_test_for_keras[:,start_time_ind:end_time_ind,:]
if curr_X_test_for_keras.shape[1] < input_window_size:
padding_size = input_window_size - curr_X_test_for_keras.shape[1]
X_pad = np.zeros((curr_X_test_for_keras.shape[0],padding_size,curr_X_test_for_keras.shape[2]))
curr_X_test_for_keras = np.hstack((curr_X_test_for_keras,X_pad))
curr_y1_test_for_keras, curr_y2_test_for_keras, _ = temporal_conv_net.predict(curr_X_test_for_keras)
if k == 0:
y1_test_for_keras_hat[:,:end_time_ind,:] = curr_y1_test_for_keras
y2_test_for_keras_hat[:,:end_time_ind,:] = curr_y2_test_for_keras
elif k == (num_test_splits - 1):
t0 = start_time_ind + overlap_size
duration_to_fill = y1_test_for_keras_hat.shape[1] - t0
y1_test_for_keras_hat[:,t0:,:] = curr_y1_test_for_keras[:,overlap_size:(overlap_size + duration_to_fill),:]
y2_test_for_keras_hat[:,t0:,:] = curr_y2_test_for_keras[:,overlap_size:(overlap_size + duration_to_fill),:]
else:
t0 = start_time_ind + overlap_size
y1_test_for_keras_hat[:,t0:end_time_ind,:] = curr_y1_test_for_keras[:,overlap_size:,:]
y2_test_for_keras_hat[:,t0:end_time_ind,:] = curr_y2_test_for_keras[:,overlap_size:,:]
# zero score the prediction and align it with the actual test
s_dst = y2_test_for_keras.std()
m_dst = y2_test_for_keras.mean()
s_src = y2_test_for_keras_hat.std()
m_src = y2_test_for_keras_hat.mean()
y2_test_for_keras_hat = (y2_test_for_keras_hat - m_src) / s_src
y2_test_for_keras_hat = s_dst * y2_test_for_keras_hat + m_dst
y_test = y_spike_test
y_test_hat = y1_test_for_keras_hat[:,:,0].T
# convert to simple (num_sims X num_time_points) format
y_spikes_GT = y_test.T
y_spikes_hat = y_test_hat.T
y_soma_GT = y2_test_for_keras[:,:,0]
y_soma_hat = y2_test_for_keras_hat[:,:,0]
prediction_duration_min = (time.time() - prediction_start_time) / 60
print('finished prediction. time took to predict is %.2f minutes' %(prediction_duration_min))
print('----------------------------------------------------------------------------------------')
total_num_samples = y_spikes_GT.shape[0]
# evaluate the model and save the results on the full dataset
print('----------------------------------------------------------------------------------------------------------------')
print('----------------------------------------------------------------------------------------------------------------')
print('----------------------------------------------------------------------------------------------------------------')
print('calculating and saving key results for entire data...')
saving_start_time = time.time()
desired_FP_list = [0.0001, 0.0005, 0.0010, 0.0015, 0.0020, 0.0025, 0.0050, 0.0100, 0.0200, 0.0300, 0.0400, 0.0500, 0.1000]
evaluations_results_dict = {}
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,18]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
evaluations_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [1,24]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
evaluations_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,24]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s": (<|========|>)' %(filter_string))
evaluations_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,30]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
evaluations_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,90]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
evaluations_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT, y_spikes_hat, y_soma_GT, y_soma_hat,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
model_metadata_dict['evaluations_results_dict'] = evaluations_results_dict
# create 50 random subsamples of 50% of the dataset for estimating variance due to random training sets
print('-----------------------------------------------------------------------')
print('calculating results for different subsample subsets...')
print('-----------------------------------------------------------------------')
num_random_subsamples = 12
num_simulations_per_subsample = int(0.67 * total_num_samples)
list_of_eval_results_dict = []
for subsample_ind in range(num_random_subsamples):
print('----------------------')
print('subset %d:' %(subsample_ind))
print('----------------------')
samples_subset = np.random.choice(total_num_samples, size=num_simulations_per_subsample, replace=False)
y_spikes_GT_sub = y_spikes_GT[samples_subset]
y_spikes_hat_sub = y_spikes_hat[samples_subset]
y_soma_GT_sub = y_soma_GT[samples_subset]
y_soma_hat_sub = y_soma_hat[samples_subset]
eval_subset_results_dict = {}
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,18]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
eval_subset_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT_sub, y_spikes_hat_sub, y_soma_GT_sub, y_soma_hat_sub,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [1,24]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
eval_subset_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT_sub, y_spikes_hat_sub, y_soma_GT_sub, y_soma_hat_sub,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,24]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s": (<|========|>)' %(filter_string))
eval_subset_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT_sub, y_spikes_hat_sub, y_soma_GT_sub, y_soma_hat_sub,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,30]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
eval_subset_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT_sub, y_spikes_hat_sub, y_soma_GT_sub, y_soma_hat_sub,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
ignore_time_at_start_ms = 500
num_spikes_per_sim = [0,90]
filter_string = 'starting_at_%dms_spikes_in_[%d,%d]_range' %(ignore_time_at_start_ms, num_spikes_per_sim[0], num_spikes_per_sim[1])
print('"%s":' %(filter_string))
eval_subset_results_dict[filter_string] = filter_and_exctract_key_results(y_spikes_GT_sub, y_spikes_hat_sub, y_soma_GT_sub, y_soma_hat_sub,
desired_FP_list=desired_FP_list,
ignore_time_at_start_ms=ignore_time_at_start_ms,
num_spikes_per_sim=num_spikes_per_sim)
list_of_eval_results_dict.append(eval_subset_results_dict)
print('----------------------')
model_metadata_dict['list_of_subset_eval_results_dict'] = list_of_eval_results_dict
print('-----------------------------------------------------------------------')
print('finished calculating results for different subsample subsets')
print('-----------------------------------------------------------------------')
metadata_evaluation_filename = model_filename.split('_model.h5')[0] + '_evaluation_test.pickle'
print('saving: "%s"' %(metadata_evaluation_filename))
pickle.dump(model_metadata_dict, open(metadata_evaluation_filename, "wb"), protocol=2)
saving_duration_min = (time.time() - saving_start_time) / 60
print('time took to evaluate and save results is %.3f minutes' %(saving_duration_min))
print('----------------------------------------------------------------------------------------------------------------')
print('----------------------------------------------------------------------------------------------------------------')
print('----------------------------------------------------------------------------------------------------------------')
#%%
print('finihsed evaluation script')