def link_exp_hol(expressions,holders, knaf_obj,threshold_hol,use_dependencies=True,use_tokens=True,use_lemmas=True):
assigned_holders = [] # (expression_type, exp_ids,
if len(holders) == 0:
for exp_ids in expressions:
assigned_holders.append([])
else:
feat_index_filename = config_manager.get_index_features_exp_hol_filename()
feat_index = Cfeature_index()
feat_index.load_from_file(feat_index_filename)
examples_file = NamedTemporaryFile(delete=False)
for exp_ids in expressions:
for hol_ids in holders:
feats = extract_feats_exp_hol(exp_ids,hol_ids,knaf_obj, use_dependencies=use_dependencies,use_tokens=use_tokens,use_lemmas=use_lemmas)
feat_index.encode_example_for_classification(feats,examples_file,my_class='0')
examples_file.close()
## In examples_file.name we can find the examples file
## The format in the example file will be:
# exp1 --> hol1
# exp1 --> hol2
# exp1 --> hol3
# exp2 --> hol1
# exp2 --> hol2
# exp2 --> hol3
model_file = config_manager.get_filename_model_exp_hol()
results = run_svm_classify(examples_file.name, model_file)
idx = 0 # This idx will iterate from 0 to num_exp X num_tar
selected = [] # will stor for each exp --> (best_tar_idx, best_svm_val)
for exp in expressions:
#Selecting the best for this exp
best_value = -1
best_idx = -1
for num_hol , hol in enumerate(holders):
#This is the probably of exp to be related with the target num_tar
value = results[idx]
#We select the best among the targets for the exp processed
if value > best_value:
best_value = value
best_idx = num_hol
idx += 1
selected.append((best_idx,best_value))
#print selected
for best_hol_idx, best_value in selected:
if best_value >= threshold_hol:
assigned_holders.append(holders[best_hol_idx])
else:
assigned_holders.append([])
os.remove(examples_file.name)
return assigned_holders
def classify(kaf_obj,term_ids,index_filename,model_filename, svm_path):
index_features = Cfeature_index()
index_features.load_from_file(index_filename)
test_file = NamedTemporaryFile(delete=False)
tokens = get_tokens_for_terms(kaf_obj,term_ids)
features = extract_features_polarity_classifier_from_tokens(tokens)
index_features.encode_example_for_classification(features,test_file)
test_file.close()
results = run_svm_classify(svm_path, test_file.name,model_filename)
os.remove(test_file.name)
if results[0] >= 0:
return 'positive'
else:
return 'negative'
def link_exp_tar_all(expressions,targets, knaf_obj,threshold, use_dependencies=True,use_tokens=True, use_lemmas=True):
pairs = []
if len(targets) == 0:
for exp_ids, exp_type in expressions:
pairs.append((exp_ids,exp_type,[]))
else:
feat_index_filename = config_manager.get_index_features_exp_tar_filename()
feat_index = Cfeature_index()
feat_index.load_from_file(feat_index_filename)
examples_file = NamedTemporaryFile(delete=False)
T = 0
for exp_ids, exp_type in expressions:
#print>>sys.stderr,exp_ids, T, 'of', len(expressions)
T = T+1
for tar_ids in targets:
#print>>sys.stderr,'\t',tar_ids
feats = extract_feats_exp_tar(exp_ids,tar_ids,knaf_obj, use_dependencies=use_dependencies,use_tokens=use_tokens,use_lemmas=use_lemmas)
feat_index.encode_example_for_classification(feats, examples_file,my_class='0')
examples_file.close()
model_file = config_manager.get_filename_model_exp_tar()
results = run_svm_classify(examples_file.name, model_file)
os.remove(examples_file.name)
#threshold = -0.75
idx = 0
for exp,exp_type in expressions:
at_least_one = False
for num_tar, tar in enumerate(targets):
value = results[idx]
idx += 1
if value >= threshold:
pairs.append((exp,exp_type,tar))
at_least_one = True
if not at_least_one:
pairs.append((exp,exp_type,[]))
return pairs
def link_exp_tar_all(expressions,targets, knaf_obj,threshold, use_dependencies=True,use_tokens=True, use_lemmas=True):
pairs = []
if len(targets) == 0:
for exp_ids, exp_type in expressions:
pairs.append((exp_ids,exp_type,[]))
else:
feat_index_filename = config_manager.get_index_features_exp_tar_filename()
feat_index = Cfeature_index()
feat_index.load_from_file(feat_index_filename)
examples_file = NamedTemporaryFile(delete=False)
for exp_ids, exp_type in expressions:
for tar_ids in targets:
feats = extract_feats_exp_tar(exp_ids,tar_ids,knaf_obj, use_dependencies=use_dependencies,use_tokens=use_tokens,use_lemmas=use_lemmas)
feat_index.encode_example_for_classification(feats, examples_file,my_class='0')
examples_file.close()
model_file = config_manager.get_filename_model_exp_tar()
results = run_svm_classify(examples_file.name, model_file)
threshold = -0.75
idx = 0
for exp,exp_type in expressions:
at_least_one = False
for num_tar, tar in enumerate(targets):
value = results[idx]
idx += 1
if value >= threshold:
pairs.append((exp,exp_type,tar))
at_least_one = True
if not at_least_one:
pairs.append((exp,exp_type,[]))
os.remove(examples_file.name)
return pairs
def link_exp_tar(expressions,targets, knaf_obj,use_dependencies=True,use_tokens=True, use_lemmas=True):
assigned_targets = [] # (expression_type, exp_ids,
if len(targets) == 0:
for exp_ids in expressions:
assigned_targets.append([])
elif len(targets) == 1:
for exp_ids in expressions:
assigned_targets.append(targets[0])
else:
feat_index_filename = config_manager.get_index_features_exp_tar_filename()
feat_index = Cfeature_index()
feat_index.load_from_file(feat_index_filename)
examples_file = NamedTemporaryFile(delete=False)
for exp_ids in expressions:
for tar_ids in targets:
feats = extract_feats_exp_tar(exp_ids,tar_ids,knaf_obj, use_dependencies=use_dependencies,use_tokens=use_tokens,use_lemmas=use_lemmas)
feat_index.encode_example_for_classification(feats, examples_file,my_class='0')
examples_file.close()
## In examples_file.name we can find the examples file
## The format in the example file will be:
# exp1 --> tar1
# exp1 --> tar2
# exp1 --> tar3
# exp2 --> tar1
# exp2 --> tar2
# exp2 --> tar3
model_file = config_manager.get_filename_model_exp_tar()
results = run_svm_classify(examples_file.name, model_file)
idx = 0 # This idx will iterate from 0 to num_exp X num_tar
selected = [] # will stor for each exp --> (best_tar_idx, best_svm_val)
for exp in expressions:
#Selecting the best for this exp
best_value = -100
best_idx = -100
#print>>sys.stderr,' Exp:', exp
for num_tar , tar in enumerate(targets):
#This is the probably of exp to be related with the target num_tar
value = results[idx]
#print>>sys.stderr,' Target:',tar
#print>>sys.stderr,' Value:', value
#print>>sys.stderr, exp
#print>>sys.stderr, tar
#print>>sys.stderr, num_tar, value
#print
#We select the best among the targets for the exp processed
if value > best_value:
best_value = value
best_idx = num_tar
idx += 1
selected.append((best_idx,best_value))
#print>>sys.stderr,' Selected:', targets[best_idx]
#print selected
for best_tar_idx, best_value in selected:
assigned_targets.append(targets[best_tar_idx])
#print>>sys.stderr, 'SELECTED',best_tar_idx,targets[best_tar_idx]
os.remove(examples_file.name)
return assigned_targets
