def fnIsotonicRegression(self, year, avgTemp, predictYear):
feature_train, feature_test, target_train, target_test = train_test_split(
year, avgTemp, test_size=0.1, random_state=42)
isoReg = IsotonicRegression()
isoReg.fit(feature_train, target_train)
return (isoReg.score(feature_test,
target_test), isoReg.predict(predictYear))
#timePoly = stopPoly - startPoly
timeIso = stopIso - startIso
timeRid = stopRid - startRid
print('%.6f seconds' % time)
# #############################################################################
#print('Logistic regression score: %.3f' % logreg.score(X_test,y_test))
print("Linear regression score: %.3f\n Mean squared error: %.4f\n Time: %.6f" %
(svr_lin.score(X_test, y_test), mean_squared_error(y_test,
y_lin), timeLin))
print(
"Radial basis function score: %.3f\n Mean squared error: %.4f\n Time: %.6f"
% (svr_rbf.score(X_test, y_test), mean_squared_error(y_test,
y_rbf), timeRbf))
#print('Polynomial score: %.3f\n Mean squared error: %.4f\n Time: %.6f' % (svr_poly.score(X_test,y_test), mean_squared_error(y_test, y_poly), timePoly))
print(
'Isotonic score: %.3f\n Mean squared error: %.4f\n Time: %.6f' % (ir.score(
X_test[:, 0], y_test), mean_squared_error(y_test, y_iso), timeIso))
print('Ridge score: %.3f\n Mean squared error: %.4f\n Time: %.6f' %
(rid.score(X_test, y_test), mean_squared_error(y_test, y_rid), timeRid))
# Look at the results
lw = 2
plt.scatter(X_test[:, 0], y_test, color='darkorange', label='data')
plt.plot(X_test, y_rbf, color='navy', lw=lw, label='RBF model')
plt.plot(X_test, y_lin, color='c', lw=lw, label='Linear model')
plt.plot(X_test, y_iso, color='cornflowerblue', lw=lw, label='Isotonic model')
plt.plot(X_test, y_rid, color='yellow', lw=lw, label='Ridge model')
#plt.plot(X_test, y_poly, color='cornflowerblue', lw=lw, label='Polynomial model')
#plt.plot(X_test, y_log, color='red', lw=lw, label='Logistic regression')
plt.xlabel('data')
plt.ylabel('target')
plt.title('Support Vector Regression')
dsim_x = np.asarray(dsim['disp'])
dsim_y = np.asarray(dsim['mpg'])
#View scatter plot of x and mpg
plt.scatter(dsim['disp'], dsim['mpg'])
plt.xlabel('disp')
plt.ylabel('mpg')
plt.title('Scatterplot of x and y')
plt.show()
#Fit isotonic regression
iso_reg = IsotonicRegression()
print(iso_reg.get_params())
iso_fitted_values = iso_reg.fit_transform(dsim_x, dsim_y)
iso_predictions = iso_reg.predict(dsim_x)
print('R squared:', iso_reg.score(dsim_x, dsim_y))
#Plot the fitted line
order = dsim['disp'].sort_values().index.tolist()
plt.scatter(dsim['disp'], dsim['mpg'])
plt.plot(dsim['disp'][order], iso_fitted_values[order], color='brown')
plt.xlabel('disp')
plt.ylabel('mpg')
plt.title('Isotonic Regression')
plt.show()
'''
-------------------------------------------------------------------------------
--------------------------------Smoothing--------------------------------------
-------------------------------------------------------------------------------
'''
def palatability_identity_calculations(rec_dir, pal_ranks=None,
unit_type=None, params=None,
shell=False):
dat = dataset.load_dataset(rec_dir)
dim = dat.dig_in_mapping
if pal_ranks is None:
dim = get_palatability_ranks(dim, shell=shell)
elif 'palatability_rank' in dim.columns:
pass
else:
dim['palatability_rank'] = dim['name'].map(pal_ranks)
dim = dim.dropna(subset=['palatability_rank'])
dim = dim.reset_index(drop=True)
num_tastes = len(dim)
taste_names = dim.name.to_list()
trial_list = dat.dig_in_trials.copy()
trial_list = trial_list[[True if x in taste_names else False
for x in trial_list.name]]
num_trials = trial_list.groupby('channel').count()['name'].unique()
if len(num_trials) > 1:
raise ValueError('Unequal number of trials for tastes to used')
else:
num_trials = num_trials[0]
dim['num_trials'] = num_trials
# Get which units to use
unit_table = h5io.get_unit_table(rec_dir)
unit_types = ['Single', 'Multi', 'All', 'Custom']
if unit_type is None:
q = userIO.ask_user('Which units do you want to use for taste '
'discrimination and palatability analysis?',
choices=unit_types,
shell=shell)
unit_type = unit_types[q]
if unit_type == 'Single':
chosen_units = unit_table.loc[unit_table['single_unit'],
'unit_num'].to_list()
elif unit_type == 'Multi':
chosen_units = unit_table.loc[unit_table['single_unit'] == False,
'unit_num'].to_list()
elif unit_type == 'All':
chosen_units = unit_table['unit_num'].to_list()
else:
selection = userIO.select_from_list('Select units to use:',
unit_table['unit_num'],
'Select Units',
multi_select=True)
chosen_units = list(map(int, selection))
num_units = len(chosen_units)
unit_table = unit_table.loc[chosen_units]
# Enter Parameters
if params is None or params.keys() != default_pal_id_params.keys():
params = {'window_size': 250, 'window_step': 25,
'num_comparison_bins': 5, 'comparison_bin_size': 250,
'discrim_p': 0.01, 'pal_deduce_start_time': 700,
'pal_deduce_end_time': 1200}
params = userIO.confirm_parameter_dict(params,
('Palatability/Identity '
'Calculation Parameters'
'\nTimes in ms'), shell=shell)
win_size = params['window_size']
win_step = params['window_step']
print('Running palatability/identity calculations with parameters:\n%s' %
dp.print_dict(params))
with tables.open_file(dat.h5_file, 'r+') as hf5:
trains_dig_in = hf5.list_nodes('/spike_trains')
time = trains_dig_in[0].array_time[:]
bin_times = np.arange(time[0], time[-1] - win_size + win_step,
win_step)
num_bins = len(bin_times)
palatability = np.empty((num_bins, num_units, num_tastes*num_trials),
dtype=int)
identity = np.empty((num_bins, num_units, num_tastes*num_trials),
dtype=int)
unscaled_response = np.empty((num_bins, num_units, num_tastes*num_trials),
dtype=np.dtype('float64'))
response = np.empty((num_bins, num_units, num_tastes*num_trials),
dtype=np.dtype('float64'))
laser = np.empty((num_bins, num_units, num_tastes*num_trials, 2),
dtype=float)
# Fill arrays with data
print('Filling data arrays...')
onesies = np.ones((num_bins, num_units, num_trials))
for i, row in dim.iterrows():
idx = range(num_trials*i, num_trials*(i+1))
palatability[:, :, idx] = row.palatability_rank * onesies
identity[:, :, idx] = row.dig_in * onesies
for j, u in enumerate(chosen_units):
for k,t in enumerate(bin_times):
t_idx = np.where((time >= t) & (time <= t+win_size))[0]
unscaled_response[k, j, idx] = \
np.mean(trains_dig_in[i].spike_array[:, u, t_idx],
axis=1)
try:
lasers[k, j, idx] = \
np.vstack((trains_dig_in[i].laser_durations[:],
trains_dig_in[i].laser_onset_lag[:]))
except:
laser[k, j, idx] = np.zeros((num_trials, 2))
# Scaling was not done, so:
response = unscaled_response.copy()
# Make ancillary_analysis node and put in arrays
if '/ancillary_analysis' in hf5:
hf5.remove_node('/ancillary_analysis', recursive=True)
hf5.create_group('/', 'ancillary_analysis')
hf5.create_array('/ancillary_analysis', 'palatability', palatability)
hf5.create_array('/ancillary_analysis', 'identity', identity)
hf5.create_array('/ancillary_analysis', 'laser', laser)
hf5.create_array('/ancillary_analysis', 'scaled_neural_response',
response)
hf5.create_array('/ancillary_analysis', 'window_params',
np.array([win_size, win_step]))
hf5.create_array('/ancillary_analysis', 'bin_times', bin_times)
hf5.create_array('/ancillary_analysis', 'unscaled_neural_response',
unscaled_response)
# for backwards compatibility
hf5.create_array('/ancillary_analysis', 'params',
np.array([win_size, win_step]))
hf5.create_array('/ancillary_analysis', 'pre_stim', np.array(time[0]))
hf5.flush()
# Get unique laser (duration, lag) combinations
print('Organizing trial data...')
unique_lasers = np.vstack(list({tuple(row) for row in laser[0, 0, :, :]}))
unique_lasers = unique_lasers[unique_lasers[:, 1].argsort(), :]
num_conditions = unique_lasers.shape[0]
trials = []
for row in unique_lasers:
tmp_trials = [j for j in range(num_trials * num_tastes)
if np.array_equal(laser[0, 0, j, :], row)]
trials.append(tmp_trials)
trials_per_condition = [len(x) for x in trials]
if not all(x == trials_per_condition[0] for x in trials_per_condition):
raise ValueError('Different number of trials for each laser condition')
trials_per_condition = int(trials_per_condition[0] / num_tastes) #assumes same number of trials per taste per condition
print('Detected:\n %i tastes\n %i laser conditions\n'
' %i trials per condition per taste' %
(num_tastes, num_conditions, trials_per_condition))
trials = np.array(trials)
# Store laser conditions and indices of trials per condition in trial x
# taste space
hf5.create_array('/ancillary_analysis', 'trials', trials)
hf5.create_array('/ancillary_analysis', 'laser_combination_d_l',
unique_lasers)
hf5.flush()
# Taste Similarity Calculation
neural_response_laser = np.empty((num_conditions, num_bins,
num_tastes, num_units,
trials_per_condition),
dtype=np.dtype('float64'))
taste_cosine_similarity = np.empty((num_conditions, num_bins,
num_tastes, num_tastes),
dtype=np.dtype('float64'))
taste_euclidean_distance = np.empty((num_conditions, num_bins,
num_tastes, num_tastes),
dtype=np.dtype('float64'))
# Re-format neural responses from bin x unit x (trial*taste) to
# laser_condition x bin x taste x unit x trial
print('Reformatting data arrays...')
for i, trial in enumerate(trials):
for j, _ in enumerate(bin_times):
for k, _ in dim.iterrows():
idx = np.where((trial >= num_trials*k) &
(trial < num_trials*(k+1)))[0]
neural_response_laser[i, j, k, :, :] = \
response[j, :, trial[idx]].T
# Compute taste cosine similarity and euclidean distances
print('Computing taste cosine similarity and euclidean distances...')
for i, _ in enumerate(trials):
for j, _ in enumerate(bin_times):
for k, _ in dim.iterrows():
for l, _ in dim.iterrows():
taste_cosine_similarity[i, j, k, l] = \
np.mean(cosine_similarity(
neural_response_laser[i, j, k, :, :].T,
neural_response_laser[i, j, l, :, :].T))
taste_euclidean_distance[i, j, k, l] = \
np.mean(cdist(
neural_response_laser[i, j, k, :, :].T,
neural_response_laser[i, j, l, :, :].T,
metric='euclidean'))
hf5.create_array('/ancillary_analysis', 'taste_cosine_similarity',
taste_cosine_similarity)
hf5.create_array('/ancillary_analysis', 'taste_euclidean_distance',
taste_euclidean_distance)
hf5.flush()
# Taste Responsiveness calculations
bin_params = [params['num_comparison_bins'],
params['comparison_bin_size']]
discrim_p = params['discrim_p']
responsive_neurons = []
discriminating_neurons = []
taste_responsiveness = np.zeros((bin_params[0], num_units, 2))
new_bin_times = np.arange(0, np.prod(bin_params), bin_params[1])
baseline = np.where(bin_times < 0)[0]
print('Computing taste responsiveness and taste discrimination...')
for i, t in enumerate(new_bin_times):
places = np.where((bin_times >= t) &
(bin_times <= t+bin_params[1]))[0]
for j, u in enumerate(chosen_units):
# Check taste responsiveness
f, p = f_oneway(np.mean(response[places, j, :], axis=0),
np.mean(response[baseline, j, :], axis=0))
if np.isnan(f):
f = 0.0
p = 1.0
if p <= discrim_p and u not in responsive_neurons:
responsive_neurons.append(u)
taste_responsiveness[i, j, 0] = 1
# Check taste discrimination
taste_idx = [np.arange(num_trials*k, num_trials*(k+1))
for k in range(num_tastes)]
taste_responses = [np.mean(response[places, j, :][:, k], axis=0)
for k in taste_idx]
f, p = f_oneway(*taste_responses)
if np.isnan(f):
f = 0.0
p = 1.0
if p <= discrim_p and u not in discriminating_neurons:
discriminating_neurons.append(u)
responsive_neurons = np.sort(responsive_neurons)
discriminating_neurons = np.sort(discriminating_neurons)
# Write taste responsive and taste discriminating units to text file
save_file = os.path.join(rec_dir, 'discriminative_responsive_neurons.txt')
with open(save_file, 'w') as f:
print('Taste discriminative neurons', file=f)
for u in discriminating_neurons:
print(u, file=f)
print('Taste responsive neurons', file=f)
for u in responsive_neurons:
print(u, file=f)
hf5.create_array('/ancillary_analysis', 'taste_disciminating_neurons',
discriminating_neurons)
hf5.create_array('/ancillary_analysis', 'taste_responsive_neurons',
responsive_neurons)
hf5.create_array('/ancillary_analysis', 'taste_responsiveness',
taste_responsiveness)
hf5.flush()
# Get time course of taste discrimibility
print('Getting taste discrimination time course...')
p_discrim = np.empty((num_conditions, num_bins, num_tastes, num_tastes,
num_units), dtype=np.dtype('float64'))
for i in range(num_conditions):
for j, t in enumerate(bin_times):
for k in range(num_tastes):
for l in range(num_tastes):
for m in range(num_units):
_, p = ttest_ind(neural_response_laser[i, j, k, m, :],
neural_response_laser[i, j, l, m, :],
equal_var = False)
if np.isnan(p):
p = 1.0
p_discrim[i, j, k, l, m] = p
hf5.create_array('/ancillary_analysis', 'p_discriminability',
p_discrim)
hf5.flush()
# Palatability Rank Order calculation (if > 2 tastes)
t_start = params['pal_deduce_start_time']
t_end = params['pal_deduce_end_time']
if num_tastes > 2:
print('Deducing palatability rank order...')
palatability_rank_order_deduction(rec_dir, neural_response_laser,
unique_lasers,
bin_times, [t_start, t_end])
# Palatability calculation
r_spearman = np.zeros((num_conditions, num_bins, num_units))
p_spearman = np.ones((num_conditions, num_bins, num_units))
r_pearson = np.zeros((num_conditions, num_bins, num_units))
p_pearson = np.ones((num_conditions, num_bins, num_units))
f_identity = np.ones((num_conditions, num_bins, num_units))
p_identity = np.ones((num_conditions, num_bins, num_units))
lda_palatability = np.zeros((num_conditions, num_bins))
lda_identity = np.zeros((num_conditions, num_bins))
r_isotonic = np.zeros((num_conditions, num_bins, num_units))
id_pal_regress = np.zeros((num_conditions, num_bins, num_units, 2))
pairwise_identity = np.zeros((num_conditions, num_bins, num_tastes, num_tastes))
print('Computing palatability metrics...')
for i, t in enumerate(trials):
for j in range(num_bins):
for k in range(num_units):
ranks = rankdata(response[j, k, t])
r_spearman[i, j, k], p_spearman[i, j, k] = \
spearmanr(ranks, palatability[j, k, t])
r_pearson[i, j, k], p_pearson[i, j, k] = \
pearsonr(response[j, k, t], palatability[j, k, t])
if np.isnan(r_spearman[i, j, k]):
r_spearman[i, j, k] = 0.0
p_spearman[i, j, k] = 1.0
if np.isnan(r_pearson[i, j, k]):
r_pearson[i, j, k] = 0.0
p_pearson[i, j, k] = 1.0
# Isotonic regression of firing against palatability
model = IsotonicRegression(increasing = 'auto')
model.fit(palatability[j, k, t], response[j, k, t])
r_isotonic[i, j, k] = model.score(palatability[j, k, t],
response[j, k, t])
# Multiple Regression of firing rate against palatability and identity
# Regress palatability on identity
tmp_id = identity[j, k, t].reshape(-1, 1)
tmp_pal = palatability[j, k, t].reshape(-1, 1)
tmp_resp = response[j, k, t].reshape(-1, 1)
model_pi = LinearRegression()
model_pi.fit(tmp_id, tmp_pal)
pi_residuals = tmp_pal - model_pi.predict(tmp_id)
# Regress identity on palatability
model_ip = LinearRegression()
model_ip.fit(tmp_pal, tmp_id)
ip_residuals = tmp_id - model_ip.predict(tmp_pal)
# Regress firing on identity
model_fi = LinearRegression()
model_fi.fit(tmp_id, tmp_resp)
fi_residuals = tmp_resp - model_fi.predict(tmp_id)
# Regress firing on palatability
model_fp = LinearRegression()
model_fp.fit(tmp_pal, tmp_resp)
fp_residuals = tmp_resp - model_fp.predict(tmp_pal)
# Get partial correlation coefficient of response with identity
idp_reg0, p = pearsonr(fp_residuals, ip_residuals)
if np.isnan(idp_reg0):
idp_reg0 = 0.0
idp_reg1, p = pearsonr(fi_residuals, pi_residuals)
if np.isnan(idp_reg1):
idp_reg1 = 0.0
id_pal_regress[i, j, k, 0] = idp_reg0
id_pal_regress[i, j, k, 1] = idp_reg1
# Identity Calculation
samples = []
for _, row in dim.iterrows():
taste = row.dig_in
samples.append([trial for trial in t
if identity[j, k, trial] == taste])
tmp_resp = [response[j, k, sample] for sample in samples]
f_identity[i, j, k], p_identity[i, j, k] = f_oneway(*tmp_resp)
if np.isnan(f_identity[i, j, k]):
f_identity[i, j, k] = 0.0
p_identity[i, j, k] = 1.0
# Linear Discriminant analysis for palatability
X = response[j, :, t]
Y = palatability[j, 0, t]
test_results = []
c_validator = LeavePOut(1)
for train, test in c_validator.split(X, Y):
model = LDA()
model.fit(X[train, :], Y[train])
tmp = np.mean(model.predict(X[test]) == Y[test])
test_results.append(tmp)
lda_palatability[i, j] = np.mean(test_results)
# Linear Discriminant analysis for identity
Y = identity[j, 0, t]
test_results = []
c_validator = LeavePOut(1)
for train, test in c_validator.split(X, Y):
model = LDA()
model.fit(X[train, :], Y[train])
tmp = np.mean(model.predict(X[test]) == Y[test])
test_results.append(tmp)
lda_identity[i, j] = np.mean(test_results)
# Pairwise Identity Calculation
for _, r1 in dim.iterrows():
for _, r2 in dim.iterrows():
t1 = r1.dig_in
t2 = r2.dig_in
tmp_trials = np.where((identity[j, 0, :] == t1) |
(identity[j, 0, :] == t2))[0]
idx = [trial for trial in t if trial in tmp_trials]
X = response[j, :, idx]
Y = identity[j, 0, idx]
test_results = []
c_validator = StratifiedShuffleSplit(n_splits=10,
test_size=0.25,
random_state=0)
for train, test in c_validator.split(X, Y):
model = GaussianNB()
model.fit(X[train, :], Y[train])
tmp_score = model.score(X[test, :], Y[test])
test_results.append(tmp_score)
pairwise_identity[i, j, t1, t2] = np.mean(test_results)
hf5.create_array('/ancillary_analysis', 'r_pearson', r_pearson)
hf5.create_array('/ancillary_analysis', 'r_spearman', r_spearman)
hf5.create_array('/ancillary_analysis', 'p_pearson', p_pearson)
hf5.create_array('/ancillary_analysis', 'p_spearman', p_spearman)
hf5.create_array('/ancillary_analysis', 'lda_palatability', lda_palatability)
hf5.create_array('/ancillary_analysis', 'lda_identity', lda_identity)
hf5.create_array('/ancillary_analysis', 'r_isotonic', r_isotonic)
hf5.create_array('/ancillary_analysis', 'id_pal_regress', id_pal_regress)
hf5.create_array('/ancillary_analysis', 'f_identity', f_identity)
hf5.create_array('/ancillary_analysis', 'p_identity', p_identity)
hf5.create_array('/ancillary_analysis', 'pairwise_NB_identity', pairwise_identity)
hf5.flush()
#error
from sklearn.cross_validation import train_test_split
from sklearn.neighbors import KNeighborsClassifier
from sklearn import metrics
from sklearn.svm import SVC
import numpy as np
import pandas as pd
from sklearn.isotonic import IsotonicRegression
df=pd.read_csv('newtest.csv')
df1=pd.read_csv('newtest1.csv')
x=df.drop(['tag'],axis=1)
y=df.drop(['kx','ky','kz','wa','wb','wc','wd','we','wf'],axis=1)
X=df1.drop(['tag'],axis=1)
Y=df1.drop(['kx','ky','kz','wa','wb','wc','wd','we','wf'],axis=1)
X_train , X_test , Y_train , Y_test = train_test_split(x,y , random_state=5)
ir=IsotonicRegression()
ir.fit(X_train,Y_train)
print ir.score(X_test,Y_test)
from sklearn.utils import check_random_state
main = pd.read_csv('/Users/Theo/Google Drive/College/Senior Thesis/Materials Science/data/isotonic/lasam.csv', sep=',',names = ['Time','G'])
mainx_data = main.Time[1:60]
mainx_target = main.G[1:60]
###############################################################################
# Fit Isotonic Regression model
###############################################################################
ir = IsotonicRegression()
lr = LinearRegression()
y_ = ir.fit_transform(mainx_data, mainx_target)
predictions = ir.predict([10])
print predictions
print ir.score(mainx_data, mainx_target)
#print("RSS: %.2f"
# % np.mean((ir.predict(mainx_target) - mainy_target) ** 2))
###############################################################################
# Plot result
###############################################################################
fig = plt.figure()
plt.plot(mainx_data, mainx_target, 'r.', markersize=12)
plt.plot(mainx_data, y_, 'g.-', markersize=12)
plt.legend(('Data', 'Isotonic Fit', 'Linear Fit'), loc='lower right')
plt.title('Isotonic regression')
plt.show()
n = 12
x = np.arange(n)
rs = check_random_state(0)
y = np.append([],java)
###############################################################################
# Fit IsotonicRegression and LinearRegression models
ir = IsotonicRegression()
y_ = ir.fit_transform(x, y)
lr = LinearRegression()
lr.fit(x[:, np.newaxis], y) # x needs to be 2d for LinearRegression
print ir.score(x,y)
###############################################################################
# plot result
segments = [[[i, y[i]], [i, y_[i]]] for i in range(n)]
lc = LineCollection(segments, zorder=0)
lc.set_array(np.ones(len(y)))
lc.set_linewidths(0.5 * np.ones(n))
fig = plt.figure()
plt.plot(x, y, 'r.', markersize=12)
plt.plot(x, y_, 'g.-', markersize=12)
plt.plot(x, lr.predict(x[:, np.newaxis]), 'b-')
plt.gca().add_collection(lc)
plt.legend(('Data', 'Isotonic Fit', 'Linear Fit'), loc='lower right')
plt.title('Isotonic regression')
n = 12
x = np.arange(n)
rs = check_random_state(0)
y = np.append([], java)
###############################################################################
# Fit IsotonicRegression and LinearRegression models
ir = IsotonicRegression()
y_ = ir.fit_transform(x, y)
lr = LinearRegression()
lr.fit(x[:, np.newaxis], y) # x needs to be 2d for LinearRegression
print ir.score(x, y)
###############################################################################
# plot result
segments = [[[i, y[i]], [i, y_[i]]] for i in range(n)]
lc = LineCollection(segments, zorder=0)
lc.set_array(np.ones(len(y)))
lc.set_linewidths(0.5 * np.ones(n))
fig = plt.figure()
plt.plot(x, y, 'r.', markersize=12)
plt.plot(x, y_, 'g.-', markersize=12)
plt.plot(x, lr.predict(x[:, np.newaxis]), 'b-')
plt.gca().add_collection(lc)
plt.legend(('Data', 'Isotonic Fit', 'Linear Fit'), loc='lower right')
plt.title('Isotonic regression')