def main():
# get paths to all SpatialML files of required format
all_files = os.listdir(config.SPATIALML_CORPUS_DIR)
files_wanted = [file for file in all_files if file.endswith(config.SPATIALML_FILE_SUFFIX)]
# TESTING
# files_wanted = [files_wanted[4]]
# for each file strip unwanted tags and write result to a file with the same name in the simple SpatialML directory
for filename in files_wanted:
# parse as xml
content = utilities.read_from_file(config.SPATIALML_CORPUS_DIR + filename)
soup = BeautifulSoup(content, 'xml')
# unwrap all unneeded tags (replace with contents)
for tag in soup.find_all('LINK') + soup.find_all(('RLINK')) + soup.find_all('SIGNAL'):
tag.unwrap()
# unwrap nominal place tags (= tags of nominal references eg. 'city')
for tag in soup.find_all('PLACE', attrs={'form': 'NOM'}):
tag.unwrap()
# unwrap predicative place tags (= tags of e.g. 'Japanese' rather than 'Japan')
for tag in soup.find_all('PLACE', attrs={'predicative': 'true'}):
tag.unwrap()
# write to file with same name in simple SpatialML directory
utilities.write_to_file(config.SPATIALML_SIMPLE_DIR + filename, str(soup))
def main():
# get paths to all SpatialML files of required format
all_files = os.listdir(config.SPATIALML_CORPUS_DIR)
files_wanted = [file for file in all_files if file.endswith(config.SPATIALML_FILE_SUFFIX)]
# for each file obtain just the text and write this to a file with the same name in the raw SpatialML directory
for filename in files_wanted:
content = utilities.read_from_file(config.SPATIALML_CORPUS_DIR + filename)
soup = BeautifulSoup(content, "xml")
text = soup.get_text()
utilities.write_to_file(config.SPATIALML_RAW_DIR + filename, text)
def test_write_to_file():
file_name = 'test_write_to_file.wav'
audio_bytes = b'test_write_to_file.wav'
file_path = write_to_file(file_name, audio_bytes)
assert os.path.exists(file_path)
os.remove(file_path)
assert not os.path.exists(file_path)
assert file_path == os.path.join(os.getcwd(), file_name)
def create_train2id_100000e():
train2id_path = "./FB15K/test2id.txt"
train2id_100000 = read_data2id_partly(train2id_path)
print(len(train2id_100000))
print(train2id_100000[0])
write_to_file('./FB15K/test2id_10000.txt', train2id_100000)
def get_word_bag(train2id, relation2id, entity_description_obj):
print("get_triples_description - begin ... \n")
"""
重要，不要删除
train2id : the index of train data
relation2id: the index of relation
entity_description_obj : entity object which contains id, symbol, name, description, neighbours.
word_bag : the number of words of relation and entity
pre_word_embedding: the word-vector of all words
return: pre-description embedding.
"""
# number_of_entity = len(entity_description_obj)
# print(number_of_entity)
# all_entity_description_list = []
# for i in range(number_of_entity):
# tmp_en = entity_description_obj[i]
#
# entity_str = tmp_en.id + '\t' + tmp_en.symb + '\t' + tmp_en.label + '\t' + tmp_en.description
# print(entity_str)
#
# en_des_word_list = tmp_en.get_entity_description()
#
# all_entity_description_list.append(en_des_word_list)
word_list = ["NULL"]
head_description_list = []
# relation_description_list = []
# tail_description_list = []
for i in range(len(train2id)):
print(i)
# head_description_list = []
# print(i," --> ",train2id[i],"\n")
# if i == 10:
# print("i = 10 break !")
# break
head_index = int(train2id[i][0])
tail_index = int(train2id[i][1])
relation_index = int(train2id[i][2])
head_obj = entity_description_obj[head_index]
tail_obj = entity_description_obj[tail_index]
rela_des = relation2id[relation_index][0]
# head_description = head_obj.get_des()
relation_description = str(
rela_des) + ', ' + 'which is between ' + head_obj.symb + ' and ' + tail_obj.symb + ';' \
+ head_obj.get_random_neighbour() + ';' + tail_obj.get_random_neighbour()
# tail_description = tail_obj.get_des()
# text_process(head_description)
# print(head_description,"\n")
# print(relation_description,"\n")
# print(tail_description,"\n")
# print("===================")
"""
obtain entity and relation description represented by word
"""
# head_description_word_list = entity_text_process(head_description)
# relation_description_word_list = relation_text_process(relation_description)
# tail_description_word_list = entity_text_process(tail_description)
#
head_description_word_list = head_obj.get_entity_description()
relation_description_word_list = relation_text_process(
relation_description)
tail_description_word_list = tail_obj.get_entity_description()
""" create word-bag , I have obtain word list , and obtain each word embedding using glove"""
word_list += head_description_word_list
word_list += relation_description_word_list
word_list += tail_description_word_list
word_list = list(set(word_list))
""" next , all words become vector using World2vector
将获取的head_description_word_list，relation_description_word_list，tail_description_word_list
通过word词模型，变成向量,然后使用LSTM进行编码
from get_word2vector import get_word2vec
"""
# print("\n head description pre-vector... \n")
# print(head_description_word_list)
# print(np.array(pre_word_embedding[[word_bag[x] for x in head_description_word_list]]))
#
# print("\n relation description pre-vector... \n")
# print(relation_description_word_list)
# print(np.array(pre_word_embedding[[word_bag[x] for x in relation_description_word_list]]))
#
# print("\n tail description pre-vector... \n")
# print(tail_description_word_list)
# print(np.array(pre_word_embedding[[word_bag[x] for x in tail_description_word_list]]))
# get sentence embedding
head_description_list.append(head_description_word_list)
# relation_description_list.append(relation_description_word_list)
# tail_description_list.append(tail_description_word_list)
# print("head_description_list",head_description_list)
# get_sentence_init_embedding(pre_word_embedding,word_list,head_description_list)
write_to_file("./FB15K/word_bag_2.txt", word_list)
def naive_implementation_shelve(input_file: str,
output_file: str = None) -> str:
if not os.path.exists(input_file):
raise FileNotFoundError
if not output_file:
output_file = generate_output_file_path(input_file, 'naive_shelve')
tmp_dir = RunningConstants.TMP_DIR.value
if os.path.exists(tmp_dir):
shutil.rmtree(tmp_dir)
os.makedirs(tmp_dir)
dict_file_path = os.path.join(tmp_dir, 'shelve_naive_dict')
activities_map = shelve.open(dict_file_path, writeback=True)
task_start_time = time.time()
with open(input_file, mode='r', encoding='utf-8') as file:
with mmap.mmap(file.fileno(), length=0,
access=mmap.ACCESS_READ) as mmap_obj:
try:
chunks = mmap_obj.read().decode() + '\n'
idx = 0
line = ''
while idx < len(chunks):
if not (chunks[idx] == '\n'):
line += chunks[idx]
else:
if 'Driver' in line:
activities_map[line[7:]] = (0, 0)
elif 'Trip' in line:
driver_name, start_time, end_time, distance = line[
5:].split()
time_spent = get_time_spent(start_time, end_time)
distance = float(distance)
current_trip_speed = (distance * 3600) / time_spent
if 5 <= current_trip_speed <= 100:
if driver_name not in activities_map:
activities_map[driver_name] = (0, 0)
prev_distance, prev_time = activities_map[
driver_name]
activities_map[driver_name] = (prev_distance +
distance,
prev_time +
time_spent)
line = ''
idx += 1
except ZeroDivisionError as zde:
print('Time-Spent maybe zero: ' + str(time_spent))
print("Error: ", ex)
except KeyError as ke:
print('Driver Name may not be in the central dictionary: ')
print("Error: ", ex)
except IOError as ioe:
print('I/O Error({0}): {1}'.format(ioe.errno, ioe.strerror))
print("Error: ", ex)
except Exception as ex:
print("Error: ", ex)
task_total_time = time.time() - task_start_time
# Preparing the final dataset and completing the output file
write_to_file(output_file, activities_map)
log_appender({
'input_file': input_file,
'output_file': output_file,
'time_taken': task_total_time
})
# clean up of shelve, tmp directories
activities_map.close()
shutil.rmtree(tmp_dir)
return output_file
def multiprocessing_implementation_shelve(input_file: str, output_file: str=None,
tmp_dir:str = None, chunk_size: int = None) -> str:
"""Implementation using python's multiprocessing library and shelve
This module is distinguished from the naive implementation in that it
exploits the available CPU cores to parallely read the file chunks in an
attempt to speedup the data-wrangling tasks. And, it's distinguished from the
multiprocessing_implementation.py file in that it uses Python's shelve over
Counter as persistent, dynamic key-value store. For detailed analysis refer to
the Readme.md file.
For usage pattern and motivating examples, refer to the test folder.
Parameters
----------
input_file*: Support both relative, absolute references to the input file location.
output_file: Support both relative, absolute references to the output file location.
chunk_size: Hyperparameter (supporting tradeoff) controling block size read by each core.
(* - Required parameters)
Returns
-------
output file location (for sharing with downstream tasks, if needed).
"""
# Returning error should the supplied file be missing
if not os.path.exists(input_file):
raise FileNotFoundError
if not output_file:
output_file = generate_output_file_path(input_file, 'mproc')
# Making use of the existing cpu cores
cores = mp.cpu_count()
pool = mp.Pool(cores)
task_splits = []
task_queues = mp.Manager().Queue()
dict_file_path = os.path.join(tmp_dir, 'shelve_dict')
if os.path.exists(tmp_dir):
shutil.rmtree(tmp_dir)
os.makedirs(tmp_dir)
# Registering the shelve in the working directory
chunk_activities = shelve.open(dict_file_path)
task_start_time = time.time()
# Job Splitter: Processing chunked file-splits
for chunk_start, chunkSize in extract_chunk_info(input_file, chunk_size):
task_splits += pool.apply_async(master_node, (chunk_start, chunkSize, input_file, task_queues)),
# Job Merge: Catching up with the yet-to-finish processes
while len(task_splits) > 0:
task_splits.pop(0).get()
task_queues.put(RunningConstants.QUEUE_END_FLAG.value)
# Processing the returned key-values across splits
for split_dict in iter(task_queues.get, RunningConstants.QUEUE_END_FLAG.value):
if len(split_dict):
for driver_name, (distance, time_spent) in iter(split_dict.items()):
if driver_name not in chunk_activities:
chunk_activities[driver_name] = (distance, time_spent)
else:
prev_distance, prev_time = chunk_activities[driver_name]
chunk_activities[driver_name] = (prev_distance+distance,
prev_time + time_spent)
task_total_time = time.time() - task_start_time
# Preparing the final dataset and completing the output file
write_to_file(output_file, chunk_activities)
log_appender({'input_file': input_file, 'output_file': output_file,
'time_taken': task_total_time})
# clean up of pool, shelve, tmp directories
pool.close()
chunk_activities.close()
shutil.rmtree(tmp_dir)
return output_file
innerf2.append(f1_score(y_v,ipred))
#compute the average
RFinnerscore.append(sum(innerf2)/len(innerf2))
best_n_estimator = n_estimatorsvalues[np.argmax(RFinnerscore)]
#predict the labels for the test set using best c parameter
labels_predictions =random_forest_gini(features_train,labels_train,features_test,best_n_estimator)
#calculating the performance
rf_accuracy = accuracy_score(labels_test,labels_predictions)
rf_f1 = f1_score(labels_test,labels_predictions)
rf_auc_roc = roc_auc_score(labels_test,labels_predictions)
rf_ave_preci = average_precision_score(labels_test,labels_predictions)
#appending the results to the list for computing the average performance of SVM
accuracy_RF.append(rf_accuracy)
f1_RF.append(rf_f1)
auc_roc_RF.append(rf_auc_roc)
#Record per fold performance results in a file
write_to_file("rf",accuracy_RF,f1_RF,auc_roc_RF)
#compute Average performance measure For GaussianNaiveBayes
print "\n##Average performance measure for SVM with a RBF kernel##\n"
print "\tAverage Accuracy: = "+ average_performance_metric(accuracy_RF)
print "\tAverage F1 Score: = "+ average_performance_metric(f1_RF)
print "\tAverage AUC ROC: = "+ average_performance_metric(auc_roc_RF)
print
def naive_implementation(input_file: str, output_file: str = None) -> str:
"""Naive implementation
This module implements naively the task of generating the report comprised
of the total driven miles and the average speed. All numerical data reported
have been rounded to the nearest integer.
For usage pattern and motivating examples, refer to the test folder.
Parameters
----------
input_file*: Support both relative, absolute references to the input file location.
output_file: Support both relative, absolute references to the output file location.
(* - Required parameters)
Returns
-------
output file location (for sharing with downstream tasks, if needed).
"""
# Returning error should the supplied file be missing
if not os.path.exists(input_file):
raise FileNotFoundError
if not output_file:
output_file = generate_output_file_path(input_file, 'naive')
activities_map = Counter() # Registering the chunk counter
task_start_time = time.time()
with open(input_file, mode='r', encoding='utf-8') as file:
with mmap.mmap(file.fileno(), length=0,
access=mmap.ACCESS_READ) as mmap_obj:
try:
chunks = mmap_obj.read().decode() + '\n'
idx = 0
line = ''
while idx < len(chunks):
if not (chunks[idx] == '\n'):
line += chunks[idx]
else:
if 'Driver' in line:
activities_map[line[7:]] = (0, 0)
elif 'Trip' in line:
driver_name, start_time, end_time, distance = line[
5:].split()
time_spent = get_time_spent(start_time, end_time)
distance = float(distance)
current_trip_speed = (distance * 3600) / time_spent
if 5 <= current_trip_speed <= 100:
if driver_name not in activities_map:
activities_map[driver_name] = (0, 0)
# Processing the key-values
prev_distance, prev_time = activities_map[
driver_name]
activities_map[driver_name] = (prev_distance +
distance,
prev_time +
time_spent)
line = ''
idx += 1
except ZeroDivisionError as zde:
print('Time-Spent maybe zero: ' + str(time_spent))
print("Error: ", ex)
except KeyError as ke:
print('Driver Name may not be in the central dictionary: ')
print("Error: ", ex)
except IOError as ioe:
print('I/O Error({0}): {1}'.format(ioe.errno, ioe.strerror))
print("Error: ", ex)
except Exception as ex:
print("Error: ", ex)
task_total_time = time.time() - task_start_time
# Preparing the final dataset and completing the output file
write_to_file(output_file, activities_map)
log_appender({
'input_file': input_file,
'output_file': output_file,
'time_taken': task_total_time
})
return output_file
features_train = dataset[0][train_index]
labels_train = dataset[1][train_index]
features_test = dataset[0][test_index]
labels_test = dataset[1][test_index]
# Training the model, using the Gaussian Navie Bayes classifier
labels_predictions = gaussian_naive_bayes(features_train,labels_train,features_test)
# Evaluate the performance of the learned model
gnb_Accuracy= accuracy_score(labels_test, labels_predictions)
gnb_f1 = f1_score(labels_test,labels_predictions)
gnb_auc_roc = roc_auc_score(labels_test,labels_predictions)
#Store the result for averaged computation
accuracy_GNB.append(gnb_Accuracy)
f1_GNB.append(gnb_f1)
auc_roc_GNB.append(gnb_auc_roc)
#Record per fold performance results in a file
write_to_file("gnb",accuracy_GNB,f1_GNB,auc_roc_GNB)
#compute Average performance measure For GaussianNaiveBayes
print "\n##Average performance measure For GaussianNaiveBayes##\n"
print "\tAverage Accuracy: = "+ average_performance_metric(accuracy_GNB)
print "\tAverage F1 Score: = "+ average_performance_metric(f1_GNB)
print "\tAverage AUC ROC: = "+ average_performance_metric(auc_roc_GNB)
print
from node import Node
import utilities
import time
import depth_first
# Take puzzle in as input from user
# Split input by spaces and convert all elements to int
puzzle = [int(x) for x in input().split()]
root_node = Node(puzzle, None, '0', 0)
#DFS
start_time = time.time()
goal_node = depth_first.search(root_node)
solution_path = utilities.find_solution_path(goal_node)
utilities.write_to_file(solution_path, 'puzzleDFS.txt')
print("Time to finish DFS: {}".format(time.time() - start_time))
# 0 2 3 4 1 6 7 8 5 9 10 11 <- solved instantaneously
# 0 2 3 4 1 5 7 8 6 9 10 11 <- solved instantaneously
# 9 0 6 1 3 10 8 11 2 5 7 4 <- solved instantaneously
# 1 0 3 7 5 2 6 4 9 10 11 8 <- puzzle from handout
#print ("Is puzzle valid? "+str(utilities.valid(root_node)))
#print ("Is puzzle in goal state? "+str(utilities.goal(root_node)))
#print ("Manhattan distance: "+str(heuristics.manhattan_distance(root_node)))
#print ("SPI: "+str(heuristics.sum_of_permutation_inversion(root_node)))
#print ("Hamming distance: "+str(heuristics.hamming_distance(root_node)))
#BFS
#HD
start_time = time.time()
goal_node = best_first.searchHD(root_node)
solution_path = utilities.find_solution_path(goal_node)
utilities.write_to_file(solution_path, 'puzzleBFS-h1.txt')
print("Time to finish BFS hamming distance: {}".format(time.time() -
start_time))
#MD
start_time = time.time()
goal_node = best_first.searchMD(root_node)
solution_path = utilities.find_solution_path(goal_node)
utilities.write_to_file(solution_path, 'puzzleBFS-h2.txt')
print("Time to finish BFS Manhattan distance: {}".format(time.time() -
start_time))
#A*
#SPI
#start_time = time.time()
#goal_node = a_star.searchSPI(root_node)
#solution_path = utilities.find_solution_path(goal_node)
#utilities.write_to_file(solution_path, 'puzzleAs-h1.txt')
#compute the average
innerscore.append(sum(innerf1)/len(innerf1))
#pick C that give the best f1
bestC=C[np.argmax(innerscore)]
print ""
#predict the labels for the test set using best c parameter
labels_predictions =svm_rbf(features_train,labels_train,features_test,bestC)
#calculating the performance
svm_accuracy = accuracy_score(labels_test,labels_predictions)
svm_f1 = f1_score(labels_test,labels_predictions)
svm_auc_roc = roc_auc_score(labels_test,labels_predictions)
svm_ave_preci = average_precision_score(labels_test,labels_predictions)
#appending the results to the list for computing the average performance of SVM
accuracy_SVM.append(svm_accuracy)
f1_SVM.append(svm_f1)
auc_roc_SVM.append(svm_auc_roc)
#Record per fold performance results in a file
write_to_file("svm",accuracy_SVM,f1_SVM,auc_roc_SVM)
#compute Average performance measure For GaussianNaiveBayes
print "\n##Average performance measure for SVM with a RBF kernel##\n"
print "\tAverage Accuracy: = "+ average_performance_metric(accuracy_SVM)
print "\tAverage F1 Score: = "+ average_performance_metric(f1_SVM)
print "\tAverage AUC ROC: = "+ average_performance_metric(auc_roc_SVM)
print
def map_locations(url=None, file=None, display_map=False):
""" Main logic of program, perform entire pipeline on the text indicated by the command line arguments given,
writing each stage of the pipeline to files in the results directory. """
# exit if neither url nor file given
if url is None and file is None:
print("A url or file must be given to read content to process from, see help (-h or --help option) for more "
"information.")
exit(1)
# starting message
loc = url if file is None else file
print("Starting map_locations for {}...".format(loc))
# obtain the content to process
if file is not None:
# read content from file
print("Reading article from file...")
title = file
content = utilities.read_from_file(file)
elif url is not None:
# make request to Readability API for url
print("Obtaining article from url...")
readability_response = readability_interface.readability_request(url)
title = readability_response['title']
html_content = readability_response['content']
content = BeautifulSoup(html_content).get_text()
# form results directory for article
print("Forming results directory for article...")
results_dir = make_results_dir(title)
# store content of article
print("Writing article content to file...")
content_file = results_dir + '01_content.txt'
utilities.write_to_file(content_file, content)
# tag file using Stanford CoreNLP server
print("Tagging named entities in article...")
try:
corenlp_tagged_text = corenlp_interface.corenlp_tag_text(content)
except ConnectionRefusedError as ex:
# print (most likely) reason for error, trace, and quit
print("Stanford CoreNLP server must be run to tag named entities! (settings in config.py)")
ex.with_traceback()
# store tagged article
print("Writing tagged article to file...")
corenlp_tagged_file = results_dir + '02_corenlp_tagged.xml'
utilities.write_to_file(corenlp_tagged_file, corenlp_tagged_text)
# disambiguate identified locations to find most likely candidate (candidates written to files in disambiguate())
print("Disambiguating identified locations...")
identified_locations = identification.identify(corenlp_tagged_text, results_dir)
# print("\n********************", identified_locs_to_xml(identified_locations, corenlp_tagged_text), "*******************\n")
# form kml for identified locations
print("Creating kml for article locations...")
kml = kml_generation.create_kml(identified_locations)
print("Writing kml to file...")
relative_kml_file = '04_kml.kml'
kml_file = results_dir + relative_kml_file
utilities.write_to_file(kml_file, kml)
print("Creating html files for map...")
# map html file
with open(config.CONTEXT_DIR + config.MAP_VIEW_TEMPLATE) as template_file:
template = string.Template(template_file.read())
html = template.substitute(kml_file=relative_kml_file, title=title)
map_html_file = results_dir + '05_map_view.html'
utilities.write_to_file(map_html_file, html)
# article html file
with open(config.CONTEXT_DIR + config.ARTICLE_TEMPLATE) as template_file:
template = string.Template(template_file.read())
# Form article content html, adding bold tags around identified locations.
# find positions of all ided locs and add bold tags in reverse order so positions don't shift
content_html_list = list(content)
positions = {}
for ided_loc in identified_locations:
positions[ided_loc.start] = ided_loc.stop
start_positions = reversed(sorted(positions.keys()))
for start_pos in start_positions:
stop_pos = positions[start_pos]
content_html_list.insert(stop_pos-1, '</b>')
content_html_list.insert(start_pos-1, '<b>')
# replace newlines with paragraphs
for index, el in enumerate(content_html_list):
if el == '\n':
content_html_list[index] = '<p>'
content_html = ''.join(content_html_list)
# create and save the html
html = template.substitute(article_title=title, article_content=content_html)
article_html_file = results_dir + '06_identified_locs.html'
utilities.write_to_file(article_html_file, html)
if display_map:
print("Opening map...")
# webbrowser.open_new_tab(article_html_file)
webbrowser.open_new_tab(map_html_file)
print("Map: file://" + map_html_file)
print("map_locations successfully completed for {}.\n".format(loc))