def plot_sep(opt):
opt.set_params()
opt.opdict['fig_path'] = os.path.join(opt.opdict['outdir'],'figures')
from do_classification import classifier
### LINEAR SVM ###
opt.opdict['method'] = 'svm'
classifier(opt)
#opt.plot_PDFs()
out_svm = opt.out
print "SVM", out_svm['thetas']
x_train = opt.train_x
x_test = opt.x
y_train = opt.train_y
y_test = opt.y
# *** Plot ***
plot_2f_synthetics(out_svm,x_train,x_test,y_test,y_train=y_train)
#plt.savefig('%s/Test_%dc_%s_SVM.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
### LOGISTIC REGRESSION ###
opt.opdict['method'] = 'lr'
out_lr = {}
for b in range(1):
opt.opdict['learn_file'] = os.path.join(opt.opdict['libdir'],'LR_%d'%b)
#os.remove(opt.opdict['learn_file'])
classifier(opt)
out_lr[b] = opt.out
print "LR", out_lr[0]['thetas']
# *** Plot ***
if b == 0:
print sorted(out_lr[0])
plot_2f_synthetics(out_lr[0],x_train,x_test,y_test,y_train=y_train)
#plt.savefig('%s/Test_%dc_%s_LR.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
else:
plot_2f_synth_var(out_lr,x_train,x_test,y_test,opt.NB_test)
#plt.savefig('%s/Test_%dc_LR_%s.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
if opt.opdict['plot_prec_rec']:
plot_2f_synth_var(out_lr,x_train,x_test,y_test,opt.NB_test)
#plt.savefig('%s/Test_%dc_bad_threshold.png'%(opt.opdict['fig_path'],len(opt.types)))
plt.show()
### NON LINEAR SVM ###
opt.opdict['method'] = 'svm_nl'
classifier(opt)
out_svm_nl = opt.out
plot_2f_nonlinear(out_svm_nl,x_train,x_test,y_test,y_train=y_train,synth=True)
#plt.savefig('%s/Test_%dc_%s_SVM_NL.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
### COMPARE ALL 3 METHODS ON THE SAME PLOT ###
plot_2f_synthetics(out_lr[0],x_train,x_test,y_test,out_comp=out_svm,y_train=y_train,map_nl=out_svm_nl)
#plt.savefig('%s/Test_%dc_%s.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
def plot_sep(opt):
opt.set_params()
opt.opdict['fig_path'] = os.path.join(opt.opdict['outdir'], 'figures')
from do_classification import classifier
### LINEAR SVM ###
opt.opdict['method'] = 'svm'
classifier(opt)
#opt.plot_PDFs()
out_svm = opt.out
print "SVM", out_svm['thetas']
x_train = opt.train_x
x_test = opt.x
y_train = opt.train_y
y_test = opt.y
# *** Plot ***
plot_2f_synthetics(out_svm, x_train, x_test, y_test, y_train=y_train)
#plt.savefig('%s/Test_%dc_%s_SVM.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
### LOGISTIC REGRESSION ###
opt.opdict['method'] = 'lr'
out_lr = {}
for b in range(1):
opt.opdict['learn_file'] = os.path.join(opt.opdict['libdir'],
'LR_%d' % b)
#os.remove(opt.opdict['learn_file'])
classifier(opt)
out_lr[b] = opt.out
print "LR", out_lr[0]['thetas']
# *** Plot ***
if b == 0:
print sorted(out_lr[0])
plot_2f_synthetics(out_lr[0], x_train, x_test, y_test, y_train=y_train)
#plt.savefig('%s/Test_%dc_%s_LR.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
else:
plot_2f_synth_var(out_lr, x_train, x_test, y_test, opt.NB_test)
#plt.savefig('%s/Test_%dc_LR_%s.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
if opt.opdict['plot_prec_rec']:
plot_2f_synth_var(out_lr, x_train, x_test, y_test, opt.NB_test)
#plt.savefig('%s/Test_%dc_bad_threshold.png'%(opt.opdict['fig_path'],len(opt.types)))
plt.show()
### NON LINEAR SVM ###
opt.opdict['method'] = 'svm_nl'
classifier(opt)
out_svm_nl = opt.out
plot_2f_nonlinear(out_svm_nl,
x_train,
x_test,
y_test,
y_train=y_train,
synth=True)
#plt.savefig('%s/Test_%dc_%s_SVM_NL.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
### COMPARE ALL 3 METHODS ON THE SAME PLOT ###
plot_2f_synthetics(out_lr[0],
x_train,
x_test,
y_test,
out_comp=out_svm,
y_train=y_train,
map_nl=out_svm_nl)
#plt.savefig('%s/Test_%dc_%s.png'%(opt.opdict['fig_path'],len(opt.types),opt.sep))
plt.show()
def classifier(opt):
"""
Classification of the different types of events.
opt is an object of the class Options()
"""
list_attr = opt.__dict__.keys()
if not 'x' in list_attr:
opt.do_tri()
X = opt.x
Y = opt.y
list_attr = opt.__dict__.keys()
if 'train_x' in list_attr:
X_TRAIN = opt.train_x
Y_TRAIN = opt.train_y
dic_results = {}
for isc in sorted(opt.xs):
print "==========",opt.trad[isc],"=========="
subdic = {}
if isc > 0:
if opt.trad[isc][0] == sta_prev:
marker_sta = 1
else:
marker_sta = 0
sta_prev = opt.trad[isc][0]
else:
marker_sta = 0
sta_prev = opt.trad[isc][0]
if len(opt.xs[isc]) == 0:
continue
# About the training set
if len(opt.opdict['stations']) == 1 and opt.opdict['boot'] > 1 and 'train_x' not in list_attr:
if os.path.exists(opt.opdict['train_file']):
print opt.opdict['train_file']
TRAIN_Y = read_binary_file(opt.opdict['train_file'])
else:
TRAIN_Y = {}
for tir in range(opt.opdict['boot']):
TRAIN_Y[tir] = {}
elif 'train_x' in list_attr:
opt.x = opt.xs_train[isc]
opt.y = opt.ys_train[isc]
if opt.opdict['plot_pdf']:
opt.compute_pdfs()
g_train = opt.gaussians
del opt.gaussians
opt.classname2number()
x_ref_train = opt.x
y_ref_train = opt.y
# About the test set
opt.x = opt.xs[isc]
opt.y = opt.ys[isc]
if opt.opdict['plot_pdf']:
opt.compute_pdfs()
set = pd.DataFrame(index=opt.ys[isc].index,columns=['Otime'])
set['Otime'] = opt.xs[isc].index
opt.classname2number()
x_test = opt.x
y_ref = opt.y
x_ref = opt.x
if opt.opdict['plot_dataset']:
opt.composition_dataset()
#K = len(opt.types)
### ITERATE OVER TRAINING SET DRAWS ###
for b in range(opt.opdict['boot']):
print "\n-------------------- # iter: %d --------------------\n"%(b+1)
subsubdic = {}
print "WHOLE SET", x_ref.shape, y_ref.shape
### if there is no pre-defined training set ###
if 'train_x' not in list_attr:
x_train = x_test.copy()
if len(opt.opdict['stations']) == 1 and opt.opdict['boot'] > 1:
if len(TRAIN_Y[b]) > 0:
y_train = y_ref.reindex(index=TRAIN_Y[b]['training_set'])
y_train = y_train.dropna(how='any')
y_cv = y_ref.reindex(index=TRAIN_Y[b]['cv_set'])
y_cv = y_cv.dropna(how='any')
y_test = y_ref.reindex(index=TRAIN_Y[b]['test_set'])
y_test = y_test.dropna(how='any')
else:
y_train, y_cv, y_test = generate_datasets(opt.opdict['proportions'],opt.numt,y_ref)
TRAIN_Y[b]['training_set'] = map(int,list(y_train.index))
TRAIN_Y[b]['cv_set'] = map(int,list(y_cv.index))
TRAIN_Y[b]['test_set'] = map(int,list(y_test.index))
### multi-stations case ###
else:
if marker_sta == 0:
y_train, y_cv, y_test = generate_datasets(opt.opdict['proportions'],opt.numt,y_ref)
list_ev_train = y_train.index
list_ev_cv = y_cv.index
list_ev_test = y_test.index
else:
y_train = y_ref.reindex(index=list_ev_train)
y_train = y_train.dropna(how='any')
y_cv = y_ref.reindex(index=list_ev_cv)
y_cv = y_cv.dropna(how='any')
y_test = y_ref.reindex(index=list_ev_test)
y_test = y_test.dropna(how='any')
x_train = x_ref.reindex(index=y_train.index)
### if a training set was pre-defined ###
else:
x_train = x_ref_train.copy()
y_train = y_ref_train.copy()
y_train, y_cv, y_test = generate_datasets(opt.opdict['proportions'],opt.numt,y_ref,y_train=y_train)
x_cv = x_ref.reindex(index=y_cv.index)
x_test = x_ref.reindex(index=y_test.index)
i_train = y_train.index
x_train.index = range(x_train.shape[0])
y_train.index = range(y_train.shape[0])
print "TRAINING SET", x_train.shape, y_train.shape
if x_train.shape[0] != y_train.shape[0]:
print "Training set: Incoherence in x and y dimensions"
sys.exit()
i_cv = y_cv.index
x_cv.index = range(x_cv.shape[0])
y_cv.index = range(y_cv.shape[0])
print "CROSS-VALIDATION SET", x_cv.shape, y_cv.shape
if x_cv.shape[0] != y_cv.shape[0]:
print "Cross-validation set: Incoherence in x and y dimensions"
sys.exit()
subsubdic['list_ev'] = np.array(y_test.index)
i_test = y_test.index
x_test.index = range(x_test.shape[0])
y_test.index = range(y_test.shape[0])
print "TEST SET", x_test.shape, y_test.shape
if x_test.shape[0] != y_test.shape[0]:
print "Test set: Incoherence in x and y dimensions"
sys.exit()
opt.train_x = x_train
opt.x = x_test
opt.train_y = y_train
opt.y = y_test
if opt.opdict['plot_pdf']:
opt.plot_all_pdfs(save=opt.opdict['save_pdf'])
if 'train_x' in list_attr:
opt.plot_superposed_pdfs(g_train,save=opt.opdict['save_pdf'])
else:
opt.plot_all_pdfs(save=opt.opdict['save_pdf'])
if opt.opdict['method'] == '1b1':
# EXTRACTEURS
print "********** EXTRACTION 1-BY-1 **********"
opt.opdict['boot'] = 1
one_by_one(opt,x_ref,y_ref,set['Otime'],boot=10,method='svm')
continue
elif opt.opdict['method'] == 'ova':
print "********** EXTRACTION 1-VS-ALL **********"
opt.opdict['boot'] = 1
one_vs_all(opt,x_ref,y_ref,set['Otime'],boot=10,method='svm')
continue
elif opt.opdict['method'] in ['svm','svm_nl']:
# SVM
print "********** SVM **********"
if opt.opdict['method'] == 'svm':
kern = 'Lin'
else:
kern = 'NonLin'
out = implement_svm(x_train,x_test,y_train,y_test,opt.types,opt.opdict,kern=kern,proba=opt.opdict['probas'])
if 'map' in sorted(out):
opt.map = out['map']
if 'thetas' in sorted(out):
theta_vec = out['thetas']
theta,threshold = {},{}
for it in range(len(theta_vec)):
theta[it+1] = np.append(theta_vec[it][-1],theta_vec[it][:-1])
threshold[it+1] = 0.5
out['thetas'] = theta
out['threshold'] = threshold
elif opt.opdict['method'] == 'lrsk':
# LOGISTIC REGRESSION (scikit learn)
print "********* Logistic regression (sklearn) **********"
out = implement_lr_sklearn(x_train,x_test,y_train,y_test)
threshold, theta = {},{}
for it in range(len(out['thetas'])):
threshold[it+1] = 0.5
theta[it+1] = np.append(out['thetas'][it][-1],out['thetas'][it][:-1])
out['threshold'] = threshold
out['thetas'] = theta
elif opt.opdict['method'] == 'lr':
# LOGISTIC REGRESSION
print "********* Logistic regression **********"
from LR_functions import do_all_logistic_regression
out = do_all_logistic_regression(x_train,x_test,x_cv,y_train,y_test,y_cv)
theta = out['thetas']
threshold = out['threshold']
if 'learn_file' in sorted(opt.opdict):
learn_filename = opt.opdict['learn_file']
if not os.path.exists(learn_filename):
wtr = write_binary_file(learn_filename,i_train)
CLASS_test = out['label_test']
CLASS_train = out['label_train']
# TRAINING SET
print "\t *TRAINING SET"
y_train_np = y_train.NumType.values.ravel()
from sklearn.metrics import confusion_matrix
cmat_train = confusion_matrix(y_train_np,CLASS_train)
p_tr = dic_percent(cmat_train,opt.types,verbose=True)
out['rate_train'] = p_tr
print " Global : %.2f%%"%p_tr['global']
if opt.opdict['plot_confusion'] or opt.opdict['save_confusion']:
plot_confusion_mat(cmat_train,opt.types,'Training',opt.opdict['method'].upper())
if opt.opdict['save_confusion']:
savefig = '%s/training_%s.png'%(opt.opdict['fig_path'],opt.opdict['result_file'])
print "Confusion matrix saved in %s"%savefig
plt.savefig(savefig)
# TEST SET
print "\t *TEST SET"
y_test_np = y_test.NumType.values.ravel()
cmat_test = confusion_matrix(y_test_np,CLASS_test)
p_test = dic_percent(cmat_test,opt.types,verbose=True)
out['rate_test'] = p_test
print " Global : %.2f%%"%p_test['global']
if opt.opdict['plot_confusion'] or opt.opdict['save_confusion']:
plot_confusion_mat(cmat_test,opt.types,'Test',opt.opdict['method'].upper())
if opt.opdict['save_confusion']:
savefig = '%s/test_%s.png'%(opt.opdict['fig_path'],opt.opdict['result_file'])
print "Confusion matrix saved in %s"%savefig
plt.savefig(savefig)
if opt.opdict['plot_confusion']:
plt.show()
else:
plt.close()
# PLOT PRECISION AND RECALL
if opt.opdict['plot_prec_rec']:
from LR_functions import normalize,plot_precision_recall
x_train, x_test = normalize(x_train,x_test)
plot_precision_recall(x_train,y_train.NumType,x_test,y_test.NumType,theta)
pourcentages = (p_tr['global'],p_test['global'])
out['method'] = opt.opdict['method']
out['types'] = opt.types
opt.out = out
# PLOT DECISION BOUNDARIES
n_feat = x_train.shape[1] # number of features
if n_feat < 4:
if opt.opdict['plot_sep'] or opt.opdict['save_sep']:
print "\nPLOTTING"
print "Theta values:",theta
print "Threshold:", threshold
# COMPARE AND PLOT LR AND SVM RESULTS
out_svm, out_nl = {},{}
dir = '%s_SEP'%opt.opdict['method'].upper()
if opt.opdict['method']=='lr' and opt.opdict['compare']:
dir = 'LR_SVM_SEP'
out_svm = implement_svm(x_train,x_test,y_train,y_test,opt.types,opt.opdict,kern='Lin')
cmat_svm_tr = confusion_matrix(y_train_np,out_svm['label_train'])
cmat_svm_test = confusion_matrix(y_test_np,out_svm['label_test'])
svm_ptr = dic_percent(cmat_svm_tr,opt.types)
svm_pt = dic_percent(cmat_svm_test,opt.types)
theta_svm,t_svm = {},{}
for it in range(len(out_svm['thetas'])):
theta_svm[it+1] = np.append(out_svm['thetas'][it][-1],out_svm['thetas'][it][:-1])
t_svm[it+1] = 0.5
out_svm['thetas'] = theta_svm
out_svm['threshold'] = t_svm
out_svm['rate_test'] = svm_pt
out_svm['rate_train'] = svm_ptr
out_svm['method'] = 'SVM'
if opt.opdict['method'] in ['lr','svm'] and opt.opdict['compare_nl']:
dir = '%s_NL_SEP'%opt.opdict['method'].upper()
out_nl = implement_svm(x_train,x_test,y_train,y_test,opt.types,opt.opdict,kern='NonLin')
cmat_svm_tr = confusion_matrix(y_train_np,out_nl['label_train'])
cmat_svm_test = confusion_matrix(y_test_np,out_nl['label_test'])
svm_ptr = dic_percent(cmat_svm_tr,opt.types)
svm_pt = dic_percent(cmat_svm_test,opt.types)
out_nl['rate_test'] = svm_pt
out_nl['rate_train'] = svm_ptr
out_nl['method'] = 'SVM_NL'
save_dir = os.path.join(opt.opdict['fig_path'],dir)
opt.verify_and_create(save_dir)
from LR_functions import normalize
x_train, x_test = normalize(x_train,x_test)
x_train_good = x_train.reindex(index=y_train[y_train.NumType.values==CLASS_train].index)
x_train_bad = x_train.reindex(index=y_train[y_train.NumType.values!=CLASS_train].index)
good_train = y_train.reindex(index=x_train_good.index)
x_test_good = x_test.reindex(index=y_test[y_test.NumType.values==CLASS_test].index)
x_test_bad = x_test.reindex(index=y_test[y_test.NumType.values!=CLASS_test].index)
# PLOT FOR 1 ATTRIBUTE AND 2 CLASSES
if n_feat == 1 and len(opt.opdict['types']) == 2:
name = opt.opdict['feat_list'][0]
from plot_functions import plot_hyp_func_1f, histo_pdfs
if opt.opdict['method']=='lr' and opt.opdict['compare']:
plot_hyp_func_1f(x_train,y_train,theta,opt.opdict['method'],threshold=threshold,x_ok=x_test_good,x_bad=x_test_bad,th_comp=theta_svm,cmat_test=cmat_test,cmat_svm=cmat_svm_test,cmat_train=cmat_train)
else:
#histo_pdfs(x_test,y_test,x_train=x_train,y_train=y_train)
plot_hyp_func_1f(x_train,y_train,theta,opt.opdict['method'],threshold=threshold,x_ok=x_test_good,x_bad=x_test_bad,cmat_test=cmat_test,cmat_train=cmat_train)
# PLOT FOR 2 ATTRIBUTES AND 2 to 3 CLASSES
elif n_feat == 2:
name = '%s_%s'%(opt.opdict['feat_list'][0],opt.opdict['feat_list'][1])
if opt.opdict['method'] in ['lr','svm']:
from plot_2features import plot_2f_all
plot_2f_all(out,x_train,y_train,x_test,y_test,x_test_bad)
elif opt.opdict['method']=='lr' and opt.opdict['compare']:
from plot_2features import plot_2f_all
plot_2f_all(out,x_train,y_train,x_test,y_test,x_test_bad,out_comp=out_svm,map_nl=out_nl)
elif opt.opdict['method'] == 'svm_nl':
from plot_2features import plot_2f_nonlinear
plot_2f_nonlinear(out,x_train,y_train,x_test,y_test,y_train=y_train)
# PLOT FOR 3 ATTRIBUTES
elif n_feat == 3:
from plot_functions import plot_db_3d
plot_db_3d(x_train,y_train.NumType,theta[1],title='Training set')
plot_db_3d(x_test,y_test.NumType,theta[1],title='Test set')
name = '%s_%s_%s'%(opt.opdict['feat_list'][0],opt.opdict['feat_list'][1],opt.opdict['feat_list'][2])
if opt.opdict['save_sep']:
savename = '%s/CL_sep_%s.png'%(save_dir,name)
print "Figure saved in %s"%savename
plt.savefig(savename)
if opt.opdict['plot_sep']:
plt.show()
else:
plt.close()
# WRITE RESULTS INTO A DICTIONARY
subsubdic['%'] = pourcentages
trad_CLASS_test = []
for i in CLASS_test:
i = int(i)
trad_CLASS_test.append(opt.types[i])
subsubdic['classification'] = trad_CLASS_test
if opt.opdict['probas']:
subsubdic['proba'] = out['probas']
if opt.opdict['plot_var']:
subsubdic['out'] = out
subdic[b] = subsubdic
if opt.opdict['plot_var'] and opt.opdict['method'] in ['lr','svm','lrsk'] and n_feat==2 and len(opt.opdict['types'])==2:
from plot_2features import plot_2f_variability
plot_2f_variability(subdic,x_train,y_train,x_test,y_test)
plt.savefig('%s/%s_variability_pas.png'%(opt.opdict['fig_path'],opt.opdict['method'].upper()))
plt.show()
dic_results[opt.trad[isc]] = subdic
dic_results['header'] = {}
dic_results['header']['features'] = opt.opdict['feat_list']
dic_results['header']['types'] = opt.opdict['types']
dic_results['header']['catalog'] = opt.opdict['label_test']
if opt.opdict['method'] in ['lr','lrsk','svm','svm_nl']:
print "Save results in file %s"%opt.opdict['result_path']
write_binary_file(opt.opdict['result_path'],dic_results)
if 'train_file' in sorted(opt.opdict):
if not os.path.exists(opt.opdict['train_file']) and opt.opdict['boot'] > 1:
write_binary_file(opt.opdict['train_file'],TRAIN_Y)
