def run_benchmark(self, output_file_path):
"""
Run benchmark for all learners on every dataset provided.
The result will be output to the provided file.
"""
dataloader = DataLoader()
f = open(output_file_path,'w')
# score, learner_1_name, learner_2_name, ..., learner_n_name
f.write("dataset")
for learner in self.learners:
f.write(", " + learner.name())
# write scores for all data sets
for dataset_id in self.dataset_ids:
print "Benchmarking dataset: " + str(dataset_id)
f.write("\n" + str(dataset_id))
train_data = dataloader.load_sequences_from_file("../data/" + str(dataset_id) + ".pautomac" + ".train")
test_data = dataloader.load_sequences_from_file("../data/" + str(dataset_id) + ".pautomac" + ".test")
solution_data = dataloader.load_probabilities_from_file("../data/" + str(dataset_id) + ".pautomac_solution" + ".txt")
for learner in self.learners:
print "Training learner: " + learner.name()
learner.train(train_data, test_data)
print "Evaluating learner: " + learner.name()
score = learner.evaluate(test_data, solution_data)
print "Achieved score: " + str(score)
str_score = " {0:.1f}".format(score)
while len(str_score) < 8:
str_score = " " + str_score
f.write(", " + str_score)
f.close()
def extractData():
parser = OptionParser()
parser.add_option("--inputDir", dest="inputDir", help="Input directory", metavar="DIRECTORY")
parser.add_option("--mrc_number", dest="mrc_number", help="Number of mrc files to be trained.", metavar="VALUE", default=-1)
parser.add_option("--coordinate_symbol", dest="coordinate_symbol", help="The symbol of the coordinate file, like '_manualPick'", metavar="STRING")
parser.add_option("--particle_size", dest="particle_size", help="the size of the particle.", metavar="VALUE", default=-1)
parser.add_option("--save_dir", dest="save_dir", help="save the training samples to this directory", metavar="DIRECTORY", default="../trained_model")
parser.add_option("--save_file", dest="save_file", help="save the training samples to file", metavar="FILE")
(opt, args) = parser.parse_args()
inputDir = opt.inputDir
particle_size = int(opt.particle_size)
coordinate_symbol = opt.coordinate_symbol
mrc_number = int(opt.mrc_number)
output_dir = opt.save_dir
output_filename = opt.save_file
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
if particle_size == -1:
print("particle size should be a positive value!")
return
output_filename = os.path.join(output_dir, output_filename)
DataLoader.extractData(inputDir, particle_size, coordinate_symbol, mrc_number, output_filename)
def load_data(filePath: str,
label_txt_filePath: str,
shuffle: bool = True,
seq_length: int = 3000,
batch_size: int = 64,
training: bool = True):
voc = Vocab()
dataLoader = DataLoader()
# 全部数据
dataLoader.sequences = dataLoader.read_fasta_file(fasta_file_path=filePath)
# 训练集
dataLoader.train_seq = dataLoader.sequences[:900]
# 测试集
dataLoader.test_seq = dataLoader.sequences[900:1000]
# 标签，0/1
dataLoader.labels = dataLoader.read_label_txt(
label_file_path=label_txt_filePath)
# 训练集的向量表示
dataLoader.train_vectorized_seq = voc.sequences_to_ids(
dataLoader.train_seq)
# 测试集的向量表示
dataLoader.test_vectorized_seq = voc.sequences_to_ids(dataLoader.test_seq)
# print(dataLoader.train_vectorized_seq)
# print(dataLoader.test_vectorized_seq)
# x_batch, y_batch = dataLoader.get_batch(shuffle=shuffle, seq_length=seq_length, batch_size=batch_size, training=training)
# print("x_batch.shape={}, y_batch.shape={}".format(x_batch.shape, y_batch.shape))
# print("x_batch[0]:{}".format(x_batch[0]))
# print("y_batch[0]:{}".format(y_batch[0]))
return voc, dataLoader
def _reading_data():
print(config.USER)
# step2 the way to load_data
# load data contains :
# the way to load data
# the way to preprocess with data
# doing some special data cleaning process
trainFilepath = os.path.join(os.getcwd(), "data", config.FILENAME)
trainDataLoader = DataLoader(trainFilepath)
train_data = trainDataLoader.load_data(useSpark=False, interactive=False)
train_data.save_data(os.getcwd())
def main():
ranker = SVMRank()
file_name = 'input/BioASQ-trainingDataset6b.json'
data = DataLoader(file_name)
data.load_ner_entities()
questions = data.get_questions_of_type(C.FACTOID_TYPE)[:419]
for i, question in enumerate(questions):
ranked_sentences = question.ranked_sentences()
X, y = get_features(question, ranked_sentences)
ranker.feed(X, y, i)
ranker.train_from_feed()
ranker.save('weights_2')
def main():
file_name = 'input/BioASQ-task6bPhaseB-testset3.json'
file_name = 'input/BioASQ-trainingDataset6b.json'
file_name = 'input/BioASQ-trainingDataset5b.json'
file_name = 'input/phaseB_5b_05.json'
save_model_file_name = 'weights_2'
ranker = SVMRank(save_model_file_name)
data = DataLoader(file_name)
data.load_ner_entities()
ans_file = 'output/factoid_list_%s.json' % data.name
questions = data.get_questions_of_type(C.FACTOID_TYPE)
for i, question in enumerate(tqdm(questions)):
ranked_sentences = question.ranked_sentences()
X, candidates = get_only_features(question, ranked_sentences)
top_answers = ranker.classify_from_feed(X, candidates, i)
question.exact_answer = [[answer] for answer in top_answers[:5]]
# question.exact_answer = [answer for answer in top_answers]
# print question.exact_answer_ref
# print '\n'
# print top5
# print '\n'
# print '\n\n\n'
questions = data.get_questions_of_type(C.LIST_TYPE)
for i, question in enumerate(tqdm(questions)):
ranked_sentences = question.ranked_sentences()
X, candidates = get_only_features(question, ranked_sentences)
top_answers = ranker.classify_from_feed(X, candidates, i)
question.exact_answer = [[answer] for answer in top_answers[:10]]
data.save_factoid_list_answers(ans_file)
def run_cv(fold_iterator, logger, params_dict, upsample=True):
for traindirs, testdirs in fold_iterator:
# TRAIN LOCAL PREDICTION MODEL
# Generators
logger.info('############ FOLD #############')
logger.info('Training folders are {}'.format(traindirs))
training_generator = DataLoader(data_dir,
traindirs,
32,
width_template=params_dict['width'],
upsample=upsample)
validation_generator = DataLoader(data_dir,
testdirs,
32,
width_template=params_dict['width'],
type='val',
upsample=upsample)
# Design model
model = create_model(params_dict['width'] + 1,
params_dict['h1'],
params_dict['h2'],
params_dict['h3'],
embed_size=params_dict['embed_size'],
drop_out_rate=params_dict['dropout_rate'],
use_batch_norm=params_dict['use_batchnorm'])
# Train model on training dataset
'''
model.fit_generator(generator=training_generator,
validation_data=validation_generator,
use_multiprocessing=True,
epochs=params_dict['n_epochs'],
workers=6)
'''
try:
model.load_weights(os.path.join(checkpoint_dir, 'model22.h5'))
except OSError:
print('here')
model.fit_generator(generator=training_generator,
validation_data=validation_generator,
use_multiprocessing=True,
epochs=params_dict['n_epochs'],
workers=4,
max_queue_size=20)
model.save_weights(os.path.join(checkpoint_dir, 'model.h5'))
metrics = model.evaluate_generator(generator=validation_generator,
workers=4,
max_queue_size=20)
logger.info(metrics)
def extractData():
parser = OptionParser()
parser.add_option("--inputDir",
dest="inputDir",
help="Input directory",
metavar="DIRECTORY")
parser.add_option("--mrc_number",
dest="mrc_number",
help="Number of mrc files to be trained.",
metavar="VALUE",
default=-1)
parser.add_option(
"--coordinate_symbol",
dest="coordinate_symbol",
help="The symbol of the coordinate file, like '_manualPick'",
metavar="STRING")
parser.add_option("--particle_size",
dest="particle_size",
help="the size of the particle.",
metavar="VALUE",
default=-1)
parser.add_option("--save_dir",
dest="save_dir",
help="save the training samples to this directory",
metavar="DIRECTORY",
default="../trained_model")
parser.add_option("--save_file",
dest="save_file",
help="save the training samples to file",
metavar="FILE")
(opt, args) = parser.parse_args()
inputDir = opt.inputDir
particle_size = int(opt.particle_size)
coordinate_symbol = opt.coordinate_symbol
mrc_number = int(opt.mrc_number)
output_dir = opt.save_dir
output_filename = opt.save_file
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
if particle_size == -1:
print("particle size should be a positive value!")
return
output_filename = os.path.join(output_dir, output_filename)
DataLoader.extractData(inputDir, particle_size, coordinate_symbol,
mrc_number, output_filename)
def get_data_loaders(data_root, speaker_id, test_shuffle=True):
data_loaders = {}
local_conditioning = hparams.cin_channels > 0
for phase in ["train", "test"]:
train = phase == "train"
X = FileSourceDataset(
RawAudioDataSource(data_root,
speaker_id=speaker_id,
train=train,
test_size=hparams.test_size,
test_num_samples=hparams.test_num_samples,
random_state=hparams.random_state))
if local_conditioning:
Mel = FileSourceDataset(
MelSpecDataSource(data_root,
speaker_id=speaker_id,
train=train,
test_size=hparams.test_size,
test_num_samples=hparams.test_num_samples,
random_state=hparams.random_state))
assert len(X) == len(Mel)
print("Local conditioning enabled. Shape of a sample: {}.".format(
Mel[0].shape))
else:
Mel = None
print("[{}]: length of the dataset is {}".format(phase, len(X)))
if train:
lengths = np.array(X.file_data_source.lengths)
# Prepare sampler
sampler = PartialyRandomizedSimilarTimeLengthSampler(
lengths, batch_size=hparams.batch_size)
shuffle = False
else:
sampler = None
shuffle = test_shuffle
dataset = PyTorchDataset(X, Mel)
data_loader = DataLoader(dataset,
batch_size=hparams.batch_size,
num_workers=hparams.num_workers,
sampler=sampler,
shuffle=shuffle,
collate_fn=collate_fn,
pin_memory=hparams.pin_memory)
speaker_ids = {}
for idx, (x, c, g) in enumerate(dataset):
if g is not None:
try:
speaker_ids[g] += 1
except KeyError:
speaker_ids[g] = 1
if len(speaker_ids) > 0:
print("Speaker stats:", speaker_ids)
data_loaders[phase] = data_loader
return data_loaders
def _build_data(self, data_dir='train_dir', num_classes=10, mode='train'):
loader = DataLoader(data_dir=data_dir, num_classes=num_classes,
mode=mode, height=self.height, width=self.width)
dataset = tf.data.Dataset.from_generator(generator=loader.generator,
output_types=(tf.float32,
tf.int32),
output_shapes=(tf.TensorShape([self.height, self.width, 3]),
tf.TensorShape([self.num_classes])))
return dataset
def prepare_data_loader_train_10_splits(texture_train_data_set_path,
texture_train_label_set_path,
texture_val_data_set_path,
texture_val_label_set_path,
texture_batch_size, num_workers,
device):
data_loader_list = []
for i in range(10):
idx = i + 1
print("Split: {0}".format(idx))
texture_train_data_set_path = texture_train_data_set_path.format(idx)
texture_train_label_set_path = texture_train_label_set_path.format(idx)
texture_val_data_set_path = texture_val_data_set_path.format(idx)
texture_val_label_set_path = texture_val_label_set_path.format(idx)
dL = DataLoader()
texture_train_set, train_set_size = dL.get_tensor_set(
texture_train_data_set_path, texture_train_label_set_path, device)
texture_val_set, val_set_size = dL.get_tensor_set(
texture_val_data_set_path, texture_val_label_set_path, device)
print("Train set size: {0}".format(train_set_size))
print("Val set size: {0}".format(val_set_size))
texture_train_data_loader = torch.utils.data.DataLoader(
texture_train_set,
batch_size=texture_batch_size,
shuffle=True,
num_workers=num_workers)
texture_val_data_loader = torch.utils.data.DataLoader(texture_val_set,
num_workers=1,
shuffle=False,
pin_memory=True)
data_loader_dict = {
"train": texture_train_data_loader,
"val": texture_val_data_loader
}
data_loader_list.append(data_loader_dict)
return data_loader_list
def starcraft_sp_test():
# Create DataLoader instance to load and format data
dataLoader = DataLoader()
logging.info("Program started")
logging.info("Loading starcraft data")
# Read skillcraft dataset, the class index is the second column
dataLoader.read(filename="data/SkillCraft1_Dataset.csv",
classIndex=1,
numOfFeatures=15)
# Normalize data values from 0 - 1
#dataLoader.normalize()
# Create new labels to fit into binary classification
dataLoader.scaleToBinary(5)
# Spectral Clustering
# Binary
clustering(dataLoader.x_train,
dataLoader.y_train,
writer_starcraft,
'starcraft-binary',
multiple=True,
binary=True)
# Multiclass
#clustering(dataLoader.x_train, dataLoader.multi_y_train, writer_starcraft, 'starcraft-multiclass', multiple=True, binary=False)
# Write all the results
writer_starcraft.save()
def prepare_data_loader_test_10_splits(texture_test_data_set_path,
texture_test_label_set_path, device):
data_loader_list = []
for i in range(10):
idx = i + 1
print("Split: {0}".format(idx))
texture_test_data_set_path = texture_test_data_set_path.format(idx)
texture_test_label_set_path = texture_test_label_set_path.format(idx)
dL = DataLoader()
texture_test_set, test_set_size = dL.get_tensor_set(
texture_test_data_set_path, texture_test_label_set_path, device)
print("Test set size: {0}".format(test_set_size))
test_data_loader = torch.utils.data.DataLoader(texture_test_set,
num_workers=1,
shuffle=False,
pin_memory=True)
data_loader_list.append(test_data_loader)
return data_loader_list
def test_real_dataset(create_obj_func,
src_name=None,
trg_name=None,
show=False,
block_figure_on_end=False):
print('Running {} ...'.format(os.path.basename(__file__)))
if src_name is None:
if len(sys.argv) > 2:
src_name = sys.argv[2]
else:
raise Exception('Not specify source dataset')
if trg_name is None:
if len(sys.argv) > 3:
trg_name = sys.argv[3]
else:
raise Exception('Not specify trgget dataset')
np.random.seed(random_seed())
tf.set_random_seed(random_seed())
tf.reset_default_graph()
print("========== Test on real data ==========")
users_params = dict()
users_params = parse_arguments(users_params)
data_format = 'mat'
if 'format' in users_params:
data_format, users_params = extract_param('format', data_format,
users_params)
data_loader = DataLoader(src_domain=src_name,
trg_domain=trg_name,
data_path=data_dir(),
data_format=data_format,
cast_data=users_params['cast_data'])
assert users_params['batch_size'] % data_loader.num_src_domain == 0
print('users_params:', users_params)
learner = create_obj_func(users_params)
learner.dim_src = data_loader.data_shape
learner.dim_trg = data_loader.data_shape
learner.x_trg_test = data_loader.trg_test[0][0]
learner.y_trg_test = data_loader.trg_test[0][1]
learner._init(data_loader)
learner._build_model()
learner._fit_loop()
def test(self,
data_dir='test_b',
model_dir=None,
output_dir=None,
threshold=0.5):
print("testing starts.")
loader = DataLoader(data_dir=data_dir,
mode='test',
height=self.height,
width=self.width,
label_value=self.label_values)
testset = tf.data.Dataset.from_generator(
generator=loader.generator,
output_types=(tf.string, tf.int32, tf.float32),
output_shapes=(tf.TensorShape([]), tf.TensorShape([2]),
tf.TensorShape([self.height, self.width, 3])))
testset = testset.batch(1)
testset = testset.prefetch(10)
test_init = self.it.make_initializer(testset)
saver = tf.train.Saver()
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
with tf.Session(config=config) as sess:
saver.restore(sess, model_dir)
sess.run(test_init)
queue = multiprocessing.Queue(maxsize=30)
writer_process = multiprocessing.Process(
target=writer,
args=[output_dir, self.label_values, queue, 'stop'])
writer_process.start()
print('writing predictions...')
try:
while True:
img, path, size, output_image = sess.run(
[self.img, self.path, self.size, self.logits])
queue.put(('continue', path, size, img, output_image))
except tf.errors.OutOfRangeError:
queue.put(('stop', None, None, None, None))
print('testing finished.')
def test(self, data_dir='test', model_dir=None, output_dir='result', batch_size=10):
print("testing starts.")
if not os.path.exists(output_dir):
os.mkdir(output_dir)
# load test data
loader = DataLoader(data_dir=data_dir, num_classes=self.num_classes,
mode='test', height=self.height, width=self.width)
testset = tf.data.Dataset.from_generator(generator=loader.generator,
output_types=(tf.string,
tf.float32),
output_shapes=(tf.TensorShape([]),
tf.TensorShape([self.height, self.width, 3])))
testset = testset.shuffle(100)
testset = testset.batch(batch_size)
testset = testset.prefetch(20)
test_init = self.it.make_initializer(testset)
saver = tf.train.Saver()
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
with tf.Session(config=config) as sess:
saver.restore(sess, model_dir)
sess.run(test_init)
queue = multiprocessing.Queue(maxsize=30)
writer_process = multiprocessing.Process(target=writer, args=[output_dir, batch_size, queue, 'stop'])
writer_process.start()
print('writing predictions...')
try:
while True:
img_name, pre_label = sess.run([self.img_name, self.prediction_value])
queue.put(('continue', img_name, pre_label))
except tf.errors.OutOfRangeError:
queue.put(('stop', None, None))
print('testing finished.')
def pick(self, mrc_filename):
"""Do the picking job through tensorflow.
This function read the micrograph data information based on the given filename of micrograph.
Then do the auto picking based on pre-trained CNN model.
Args:
mrc_filename: string, it is the filename of the target micrograph.
Returns:
return list_coordinate
list_coordinate: a list, the length of this list stands for the number of picked particles.
Each element in the list is also a list, the length is 4, the first one is y-axis,
the second one is x-axis, the third one is the predicted score, the fourth is the micrograph filename.
"""
# read the micrograph image data
print(mrc_filename)
header, body = DataLoader.readMrcFile(mrc_filename)
num_col = header[0]
num_row = header[1]
body_2d = np.array(body, dtype = np.float32).reshape(num_row, num_col)
# do process to micrograph
body_2d, bin_size = DataLoader.preprocess_micrograph(body_2d)
# Edge detection to get the ice noise mask
# a binary matrix, 1 stands for the ice noise site
# mask = edge_detection_ice(body_2d)
step_size = 4
candidate_patches = None
candidate_patches_exist = False
num_total_patch = 0
patch_size = int(self.particle_size/bin_size)
# the size to do peak detection
local_window_size = int(0.6*patch_size/step_size)
#print("image_col:", body_2d.shape[0])
#print("particle_size:", patch_size)
#print("step_size:", step_size)
map_col = int((body_2d.shape[0]-patch_size)/step_size)
map_row = int((body_2d.shape[1]-patch_size)/step_size)
#prediction = np.zeros((map_col, map_row), dtype = float)
time1 = time.time()
particle_candidate_all = []
map_index_col = 0
for col in range(0, body_2d.shape[0]-patch_size+1, step_size):
for row in range(0, body_2d.shape[1]-patch_size+1, step_size):
# extract the particle patch
patch = np.copy(body_2d[col:(col+patch_size), row:(row+patch_size)])
# do preprocess to the particle
patch = DataLoader.preprocess_particle(patch, self.model_input_size)
particle_candidate_all.append(patch)
num_total_patch = num_total_patch + 1
map_index_col = map_index_col + 1
map_index_row = map_index_col-map_col+map_row
#print("map_col:",map_col)
#print("map_row:",map_row)
#print(len(particle_candidate_all))
#print("map_index_col:",map_index_col)
#print("map_index_row:",map_index_row)
#print("col*row:",map_index_col*map_index_row)
# reshape it to fit the input format of the model
particle_candidate_all = np.array(particle_candidate_all).reshape(num_total_patch, self.model_input_size[1], self.model_input_size[2], 1)
# predict
predictions = self.deepModel.evaluation(particle_candidate_all, self.sess)
predictions = predictions[:, 1:2]
predictions = predictions.reshape(map_index_col, map_index_row)
time_cost = time.time() - time1
print("time cost: %d s"%time_cost)
#display.save_image(prediction, "prediction.png")
# get the prediction value to be a positive sample, it is a value between 0~1
# the following code not tested
# do a connected component analysis
# prediction = detete_large_component(prediction)
# do a local peak detection to get the best coordinate
# list_coordinate is a 2D list of shape (number_particle, 3)
# element in list_coordinate is [x_coordinate, y_coordinate, prediction_value]
list_coordinate = self.peak_detection(predictions, local_window_size)
# add the mrc filename to the list of each coordinate
for i in range(len(list_coordinate)):
list_coordinate[i].append(mrc_filename)
# transform the coordinates to the original size
list_coordinate[i][0] = (list_coordinate[i][0]*step_size+patch_size/2)*bin_size
list_coordinate[i][1] = (list_coordinate[i][1]*step_size+patch_size/2)*bin_size
return list_coordinate
from dataLoader import DataLoader
loader = DataLoader()
loader.loadAll()
fileobj = open("csv/subjectAreaDump.csv", 'w')
for id, paper in loader.papers.iteritems():
if paper.accepted:
fileobj.write("%s|%d|%s" %
(paper.primarySpecificSubjectArea, id, paper.title))
for subj in paper.specificSubjectAreas:
fileobj.write("|" + subj)
fileobj.write("\n")
fileobj.close()
from pathlib import Path
from flask import Flask, render_template, make_response, jsonify, request, send_from_directory
import configurations
from analyzeResults import AnalyzeResults
from dataLoader import DataLoader
from hitCounter import HitCounter
import numpy as np
from vistDataset import VistDataset
import base64
import time
app = Flask(__name__)
data_loader = DataLoader(root_path=configurations.root_data)
hit_counter = HitCounter(root_path=configurations.root_data,
story_max_hits=configurations.max_story_submit)
vist_dataset = VistDataset(root_path=configurations.root_data,
hit_counter=hit_counter,
samples_num=configurations.samples)
analyze_results = AnalyzeResults(data_root=configurations.root_data,
data_loader=data_loader,
vist_dataset=vist_dataset)
@app.route('/api/images/<image_id>', methods=['GET'])
def serve_image(image_id):
print("Requested image file: {}".format(image_id))
image_path = data_loader._find_file(image_id)
if image_path is None:
from myModel import MyModel
from dataLoader import DataLoader
if __name__ == '__main__':
ENABLE_SAVE_MODEL = True
MODEL_NAME = 'mini'
# 4 mnist
# H, W, C = 28, 28, 1
# (x_train, y_train), (x_test, y_test) = tf.keras.datasets.mnist.load_data()
# 4 ukiyoe
DATA_PATH = './data/'
H, W, C = 224, 224, 3
RH, RW = 224, 224
x_train, y_train, x_test, y_test = DataLoader(0.2).load(DATA_PATH)
if C == 1:
x_train = np.sum(x_train, axis=-1) / 3
x_test = np.sum(x_test, axis=-1) / 3
x_train = x_train.astype('float32') / 255
x_test = x_test.astype('float32') / 255
x_train = x_train.reshape(x_train.shape[0], H, W, C)
x_test = x_test.reshape(x_test.shape[0], H, W, C)
model = MyModel()
loss_object = tf.keras.losses.SparseCategoricalCrossentropy()
optimizer = tf.keras.optimizers.Adam()
train_loss = tf.keras.metrics.Mean(name='train_loss')
from numpy import *
from decimal import *
from sys import *
from learner import Learner
from decimal import *
from sys import *
from utilities import *
from dataLoader import DataLoader
import time
list1 = [[1, 2], [3, 4], [5, 6]]
list2 = [2, 3]
#for x in xrange(0, len(list1), 2):
# print list1[x]
dataloader = DataLoader()
train_data = dataloader.load_sequences_from_file("../data/" + "1" + ".pautomac" + ".test")
#comps = collect_unique_symbol_compositions(train_data, 2)
MathiasLearner.train(train_data)
#print comps.index([1, 1])
def train():
parser = OptionParser()
parser.add_option("--train_inputDir", dest="train_inputDir", help="Input directory", metavar="DIRECTORY")
parser.add_option("--train_inputFile", dest="train_inputFile", help="Input file", metavar="FILE")
parser.add_option("--train_type", dest="train_type", help="Training type, 1|2|3|4.", metavar="VALUE", default=2)
parser.add_option("--particle_number", dest="train_number", help="Number of positive samples to train.", metavar="VALUE", default=-1)
parser.add_option("--mrc_number", dest="mrc_number", help="Number of mrc files to be trained.", metavar="VALUE", default=-1)
parser.add_option("--coordinate_symbol", dest="coordinate_symbol", help="The symbol of the coordinate file, like '_manualPick'", metavar="STRING")
parser.add_option("--particle_size", dest="particle_size", help="the size of the particle.", metavar="VALUE", default=-1)
parser.add_option("--validation_ratio", dest="validation_ratio", help="the ratio.", metavar="VALUE", default=0.1)
parser.add_option("--model_retrain", action="store_true", dest="model_retrain", help="train the model using the pre-trained model as parameters initialization .", default=False)
parser.add_option("--model_load_file", dest="model_load_file", help="pre-trained model", metavar="FILE")
parser.add_option("--model_save_dir", dest="model_save_dir", help="save the model to this directory", metavar="DIRECTORY", default="../trained_model")
parser.add_option("--model_save_file", dest="model_save_file", help="save the model to file", metavar="FILE")
(opt, args) = parser.parse_args()
# set the tensoflow seed
tf.set_random_seed(1234)
# set the numpy seed
np.random.seed(1234)
# define the input size of the model
model_input_size = [100, 64, 64, 1]
num_class = 2 # the number of the class
batch_size = model_input_size[0]
# define input parameters
train_type = int(opt.train_type)
train_inputDir = opt.train_inputDir
train_inputFile = opt.train_inputFile
train_number = float(opt.train_number)
mrc_number = int(opt.mrc_number)
coordinate_symbol = opt.coordinate_symbol
debug_dir = '../train_output' # output dir
particle_size = int(opt.particle_size)
validation_ratio = float(opt.validation_ratio)
# define the save model
model_retrain = opt.model_retrain
model_load_file = opt.model_load_file
model_save_dir = opt.model_save_dir
model_save_file = os.path.join(model_save_dir, opt.model_save_file)
if not os.access(model_save_dir, os.F_OK):
os.mkdir(model_save_dir)
if not os.access(debug_dir, os.F_OK):
os.mkdir(debug_dir)
# define the learning rate decay parameters
# more information about this, refer to function tf.train.exponential_decay()
learning_rate = 0.01
learning_rate_decay_factor = 0.95
# the value will be changed base on the train_size and batch size
learning_rate_decay_steps = 400
learning_rate_staircase = True
# momentum
momentum = 0.9
# load training dataset
dataLoader = DataLoader()
if train_type == 1:
# load train data from mrc file dir
train_number = int(train_number)
train_data, train_label, eval_data, eval_label = dataLoader.load_trainData_From_mrcFileDir(train_inputDir, particle_size, model_input_size, validation_ratio, coordinate_symbol, mrc_number, train_number)
elif train_type == 2:
# load train data from numpy data struct
train_number = int(train_number)
train_data, train_label, eval_data, eval_label = dataLoader.load_trainData_From_ExtractedDataFile(train_inputDir, train_inputFile, model_input_size, validation_ratio, train_number)
elif train_type == 3:
# load train data from relion .star file
train_number = int(train_number)
train_data, train_label, eval_data, eval_label = dataLoader.load_trainData_From_RelionStarFile(train_inputFile, particle_size, model_input_size, validation_ratio, train_number)
elif train_type == 4:
# load train data from prepicked results
train_data, train_label, eval_data, eval_label = dataLoader.load_trainData_From_PrePickedResults(train_inputDir, train_inputFile, particle_size, model_input_size, validation_ratio, train_number)
else:
print("ERROR: invalid value of train_type:", train_type)
display.show_particle(train_data, os.path.join(debug_dir, 'positive.png'))
# test whether train_data exist
try:
train_data
except NameError:
print("ERROR: in function load.loadInputTrainData.")
return None
else:
print("Load training data successfully!")
# shuffle the training data
train_data, train_label = shuffle_in_unison_inplace(train_data, train_label)
eval_data, eval_label = shuffle_in_unison_inplace(eval_data, eval_label)
train_size = train_data.shape[0]
eval_size = eval_data.shape[0]
# initalize the decay_steps based on train_size and batch size.
# change the learning rate each 2 epochs
learning_rate_decay_steps = 10*(train_size // batch_size)
# initialize the parameters of deepModel
deepModel = DeepModel(particle_size, model_input_size, num_class)
deepModel.init_learning_rate(learning_rate = learning_rate, learning_rate_decay_factor = learning_rate_decay_factor,
decay_steps = learning_rate_decay_steps, staircase = learning_rate_staircase)
deepModel.init_momentum(momentum = momentum)
# initialize the model
# define the computation procedure of optimizer, loss, lr, prediction, eval_prediction
deepModel.init_model_graph_train()
saver = tf.train.Saver(tf.all_variables())
start_time = time.time()
init = tf.initialize_all_variables()
with tf.Session(config=tf.ConfigProto(log_device_placement=False)) as sess:
# initialize all the parameters
sess.run(init)
max_epochs = 200 # the max number of epoch to train the model
best_eval_error_rate = 100
toleration_patience = 10
toleration_patience_flag = 0
eval_frequency = train_size // batch_size # the frequency to evaluate the evaluation dataset
for step in xrange(int(max_epochs * train_size) // batch_size):
# get the batch training data
offset = (step * batch_size) % (train_size - batch_size)
batch_data = train_data[offset:(offset+batch_size), ...]
batch_label = train_label[offset:(offset+batch_size)]
# online augmentation
#batch_data = DataLoader.preprocess_particle_online(batch_data)
loss_value, lr, train_prediction = deepModel.train_batch(batch_data, batch_label,sess)
# do the computation
if step % eval_frequency == 0:
stop_time = time.time() - start_time
start_time = time.time()
eval_prediction = deepModel.evaluation(eval_data, sess)
eval_error_rate = error_rate(eval_prediction, eval_label)
print('epoch: %.2f , %.2f ms' % (step * batch_size /train_size, 1000 * stop_time / eval_frequency))
print('train loss: %.6f,\t learning rate: %.6f' % (loss_value, lr))
print('train error: %.6f%%,\t valid error: %.6f%%' % (error_rate(train_prediction, batch_label), eval_error_rate))
if eval_error_rate < best_eval_error_rate:
best_eval_error_rate = eval_error_rate
toleration_patience = 10
else:
toleration_patience = toleration_patience - 1
if toleration_patience == 0:
saver.save(sess, model_save_file)
break
def test_my_own_png(self):
# load the mnist test data CSV file into a list
test_data_list = DataLoader.load_my_data()
self.__test_png(self.n, test_data_list)
args = get_args()
setup_seed(args.seed)
device = args.device
checkpoint_dir = args.checkpoint_dir
if not os.path.exists(checkpoint_dir):
os.makedirs(checkpoint_dir)
data = np.load(args.dataset_path)
model = net().to(device)
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
dataLoader = DataLoader(data['X'],
data['Y'],
train_val_split=[0.7, 0.15, 0.15],
batch_size=args.batch_size,
device=device)
loader_train, loader_val, loader_test = dataLoader.get_loader()
trainer = Trainer(model, optimizer)
loss_fn = torch.nn.functional.cross_entropy
trainer.train_with_val(loss_fn,
loader_train=loader_train,
loader_val=loader_val,
epochs=args.epochs,
save_path=checkpoint_dir + 'model.pth',
save_best_only=True,
monitor_on='acc')
trainer.test(loader_test, loss_fn, info='Test ')
def learn_test(expr):
loader = DataLoader()
dataset = loader.loadData(
dataset=expr) # dataset options: electricity, traffic, BLE
pastObserve = pastObserves[expr]
o_columns = dataset.columns
predCol = o_columns[-1]
lenAll = len(dataset)
lenx = int(lenAll * .75)
test_orig = []
mean_errors = []
error_stds = []
all_errors = []
all_predictions = []
values = dataset.values
origData = values
# normalize
parameters = dataset.values.shape[1]
scaler = MinMaxScaler(feature_range=(0, 1))
scaled = scaler.fit_transform(values)
reframed = series_to_supervised(scaled, pastObserve, 1)
# drop columns we don't want to predict
droppings = []
for i in range(1, pastObserve + 1):
x = [a for a in range(parameters * (i - 1), parameters * i - 1)]
droppings.extend(x)
reframed.drop(reframed.columns[droppings], axis=1, inplace=True)
valuesTrans = reframed.values
test = valuesTrans
# split into input and outputs
train_X_all, train_y_all = valuesTrans[:, :-1], valuesTrans[:, -1]
test_X, test_y = test[:, :-1], test[:, -1]
trainingModels = []
for i in range(modelsNo):
deepModel = create_model(parameters, pastObserve)
trainingModels.append(deepModel)
dy = 0
sparsity = 3
for model in trainingModels:
# fit network
partsLen = int(len(train_X_all) / sparsity) * sparsity
a = np.arange(partsLen)
a = a.reshape(sparsity, int(partsLen / sparsity))
ixs = []
# just consider part of dataset not all of that
for t in range(sparsity):
if (t == dy):
ixs.append(a[t])
# ixs.append(a[t+1]) # for considering 40% sparsity
# ixs.append(a[t+2]) # for considering 60% sparsity
ixs = np.array(ixs)
train_ixs = ixs.flatten()
train_X, train_y = train_X_all[train_ixs], train_y_all[train_ixs]
model.fit(train_X, train_y, epochs=20, batch_size=20, verbose=2)
dy += 1
# calculate predictions
predictions = model.predict(test_X)
predictions = predictions.reshape((len(predictions), 1))
pads = np.zeros(len(test_y) * (parameters - 1))
pads = pads.reshape(len(test_y), parameters - 1)
inv_yhat = concatenate((pads, predictions), axis=1)
inv_yhat = scaler.inverse_transform(inv_yhat)
inv_yhat = inv_yhat[:, -1]
inv_yhat = np.around(inv_yhat, decimals=2)
# invert scaling for actual
test_y = test_y.reshape((len(test_y), 1))
inv_test = concatenate((test_X[:, pastObserve:], test_y), axis=1)
test_orig = scaler.inverse_transform(inv_test)
origY = test_orig[:, -1]
meanErr, std, errors = report_errors(origY, inv_yhat, errorType[expr])
mean_errors.append(meanErr)
error_stds.append(std)
all_errors.append(errors)
all_predictions.append(inv_yhat)
print(min(origY), max(origY))
print(min(inv_yhat), max(inv_yhat))
print('Test Mean Error: %.3f ' % meanErr)
p_cols = []
df = DataFrame(test_orig, columns=o_columns)
for k in range(len(all_predictions)):
colName = 'predict_' + str(k + 1)
p_cols.append(colName)
df[colName] = all_predictions[k]
for k in range(len(all_predictions)):
errName = 'error_' + str(k + 1)
df[errName] = all_errors[k]
print(errorType[expr])
print(mean_errors)
if not os.path.exists(models_output_folder):
os.makedirs(models_output_folder)
outDetails_filename = models_output_folder + 'predictions_details_%s.csv' % expr
out_filename = models_output_folder + 'predictions_output_%s.csv' % expr
df.to_csv(outDetails_filename, index=False)
models_prediction_cols = p_cols
models_prediction_cols.append(predCol)
df_modelOutput = df[models_prediction_cols]
df_modelOutput.to_csv(out_filename, index=False)
def starcraft_svm_test():
# Create DataLoader instance to load and format data
dataLoader = DataLoader()
logging.info("Program started")
logging.info("Loading starcraft data")
# Read skillcraft dataset, the class index is the second column
dataLoader.read(filename="data/SkillCraft1_Dataset.csv",
classIndex=1,
numOfFeatures=15)
multi_label_count = dataLoader.labelCount(8)
# Creates plots for a few of the data features
# dataLoader.visualize()
# Normalize data values from 0 - 1
#dataLoader.normalize()
# Create new labels to fit into binary classification
dataLoader.scaleToBinary(5)
label_count = dataLoader.binaryLabelCount(5)
logging.info("Number of examples per class")
logging.info("Casual - (1): " + str(label_count[0]))
logging.info("Hardcore - (-1): " + str(label_count[1]))
label_count = dataLoader.labelCount(8)
logDataCount(label_count)
"""
# Create SVM
svm = SVM()
# Train and predict for binary svm
logging.info("Running SVM for binary classification")
# Train for binary single run with these objects
logging.info("Single binary SVM")
svm.train(dataLoader.x_train, dataLoader.y_train, dataLoader.x_test, dataLoader.y_test)
# Train and test binary svm multiple times for all available binary variables
logging.info("Multiple runs with different parameters - binary SVM")
svm.train(dataLoader.x_train, dataLoader.y_train, dataLoader.x_test, dataLoader.y_test, iterate=True)
# Save binary results to excel sheet
logging.info("Saving binary SVM results")
svm.results.to_excel(writer_starcraft, sheet_name='binary-svm')
# MULTI CLASS SVM
logging.info("Running SVM for multiclass classification")
# Train and predict for multi-class data using the linear svm from liblinear implementation
logging.info("Running SVM for multiclass classification with liblinear implementation")
svm.train(dataLoader.x_train, dataLoader.multi_y_train, dataLoader.x_test, dataLoader.multi_y_test, binary=False)
logging.info("Saving multiclass liblinear results")
svm.results.to_excel(writer_starcraft, sheet_name='multiclass-liblinear')
# Train for multi-class single run with these objects using the libsvm implementation
logging.info("Running SVM for multiclass classification with libsvm implementation")
svm.train(dataLoader.x_train, dataLoader.multi_y_train, dataLoader.x_test, dataLoader.multi_y_test, binary=False, linear=False)
logging.info("Saving multiclass libsvm results")
svm.results.to_excel(writer_starcraft, sheet_name='multiclass-libsvm')
# Train and test multi-class svm multiple times for all available multi-class variables
logging.info("Running SVM for multiclass classification for all available multi-class variables")
svm.train(dataLoader.x_train, dataLoader.multi_y_train, dataLoader.x_test, dataLoader.multi_y_test, iterate=True, binary=False)
logging.info("Saving multiclass multiple-runs results")
svm.results.to_excel(writer_starcraft, sheet_name='multiclass-multiple-variables')
# Train and test multi-class svm multiple times with KPCA-LDA
logging.info("Running SVM for multiclass classification with KPCA-LDA")
svm.train(dataLoader.x_train, dataLoader.multi_y_train, dataLoader.x_test, dataLoader.multi_y_test, iterate=True, binary=False, decomposition=True)
logging.info("Saving multiclass multiple-runs results")
svm.results.to_excel(writer_starcraft, sheet_name='multiclass-kpca-lda')
# KNN and NC
nearest(dataLoader.x_train, dataLoader.y_train, dataLoader.x_test, dataLoader.y_test, dataLoader.multi_y_train, dataLoader.multi_y_test, writer_starcraft)
"""
clustering(dataLoader.x_train, dataLoader.y_train, dataLoader.x_test,
dataLoader.y_test)
# Write all the results
writer_starcraft.save()
update_checkpoint_link([('epoch_%d.pt' % best_epoch, 'best.pt'),
('epoch_%d.pt' % epoch, 'last.pt')])
epoch += 1
cost_time = time.time() - since
print('Training complete in {:.0f}h{:.0f}m{:.0f}s'.format(
(cost_time // 60) // 60, (cost_time // 60) % 60, cost_time % 60))
return model, cost_time, best_acc, best_train_acc
if __name__ == '__main__':
loader = DataLoader(args.dataset,
batch_size=args.batch_size,
seed=args.seed)
dataloaders, dataset_sizes = loader.load_data(args.img_size)
num_classes = 10
if args.dataset == 'cifar-10':
num_classes = 10
if args.dataset == 'cifar-100':
num_classes = 100
if args.dataset == 'VOCpart':
num_classes = len(dataloaders['train'].dataset.classes)
assert args.img_size == 128, 'only supports --img_size 128'
model = resnet_std(depth=args.depth,
num_classes=num_classes,
ifmask=args.ifmask,
unique_name = 'stack_2406_2x_SumCorr_movie_DW'
#unique_name = 'stack_3025_2x_SumCorr_movie_DW'
coordinates = []
class_number = []
starfile = os.path.join(basepath, unique_name + new + '.star')
with open(starfile) as fin:
idx = 0
for l in fin:
idx += 1
if idx <= 5 or l.strip() == '':
continue
t = map(float, l.strip().split())
coordinates.append([int(t[0]), int(t[1])])
class_number.append(int(t[2]))
plot = 'test_plot_%d' % peek_cls + new + '.png'
filename = os.path.join(mrcpath, unique_name + '.mrc')
header, body = DataLoader.readMrcFile(filename)
n_col = header[0]
n_row = header[1]
print n_col, n_row
body_2d = np.array(body, dtype=np.float32).reshape(n_row, n_col, 1)
body_2d, bin_size = DataLoader.preprocess_micrograph(body_2d)
coordinates = np.array(coordinates)
coordinates = coordinates / bin_size
plot_circle_in_micrograph(body_2d,
coordinates,
class_number,
180 / bin_size,
plot,
color='white')
def analysis_pick_results(pick_results_file, reference_coordinate_dir, reference_coordinate_symbol, particle_size, minimum_distance_rate):
"""Load the picking results from a file of binary format and compare it with the reference coordinate.
This function analysis the picking results with reference coordinate and calculate the recall, precision and the deviation from the center.
Args:
pick_results_file: string, the file name of the pre-picked results.
reference_mrc_dir: string, the directory of the mrc file dir.
reference_coordinate_symbol: the symbol of the coordinate, like '_manualpick'
particle_size: int, the size of particle
minimum_distance_rate: float, the default is 0.2, a picked coordinate is considered to be a true positive only when the distance between the picked coordinate and the reference coordinate is less than minimum_distance_rate mutiplicate particle_size.
"""
with open(pick_results_file, 'rb') as f:
coordinate = pickle.load(f)
"""
coordinate: a list, the length of it stands for the number of picked micrograph file.
Each element is a list too, which contains all coordinates from the same micrograph.
The length of the list stands for the number of the particles.
And each element in the list is a small list of length of 4.
The first element in the small list is the coordinate x-aixs.
The second element in the small list is the coordinate y-aixs.
The third element in the small list is the prediction score.
The fourth element in the small list is the micrograh name.
"""
tp = 0
total_pick = 0
total_reference = 0
coordinate_total = []
for i in range(len(coordinate)):
mrc_filename = os.path.basename(coordinate[i][0][3])
#print(mrc_filename)
reference_coordinate_file = mrc_filename.replace('.mrc', reference_coordinate_symbol+'.star')
reference_coordinate_file = os.path.join(reference_coordinate_dir, reference_coordinate_file)
#print(reference_coordinate_file)
if os.path.isfile(reference_coordinate_file):
reference_coordinate = DataLoader.read_coordinate_from_star(reference_coordinate_file)
"""
reference_coordinate: a list, the length of it stands for the number of picked particles.
And each element in the list is a small list of length of 2.
The first element in the small list is the coordinate x-aixs.
The second element in the small list is the coordinate y-aixs.
"""
tp_sigle, average_distance = AutoPicker.calculate_tp(coordinate[i], reference_coordinate, particle_size*minimum_distance_rate)
#print("tp:",tp_sigle)
#print("average_distance:",average_distance)
# calculate the number of true positive, when the threshold is set to 0.5
tp_sigle = 0
total_reference = total_reference + len(reference_coordinate)
for j in range(len(coordinate[i])):
coordinate_total.append(coordinate[i][j])
if coordinate[i][j][2]>0.5:
total_pick = total_pick + 1
if coordinate[i][j][4] == 1:
tp = tp + 1
tp_sigle = tp_sigle + 1
print(tp_sigle/len(reference_coordinate))
else:
print("Can not find the reference coordinate:"+reference_coordinate_file)
precision = tp/total_pick
recall = tp/total_reference
print("(threshold 0.5)precision:%f recall:%f"%(precision, recall))
# sort the coordinate based on prediction score in a descending order.
coordinate_total = sorted(coordinate_total, key = itemgetter(2), reverse = True)
total_tp = []
total_recall = []
total_precision = []
total_probability = []
total_average_distance = []
total_distance = 0
tp_tem = 0
for i in range(len(coordinate_total)):
if coordinate_total[i][4] == 1:
tp_tem = tp_tem + 1
total_distance = total_distance + coordinate_total[i][5]
precision = tp_tem/(i+1)
recall = tp_tem/total_reference
total_tp.append(tp_tem)
total_recall.append(recall)
total_precision.append(precision)
total_probability.append(coordinate_total[i][2])
if tp_tem==0:
average_distance = 0
else:
average_distance = total_distance/tp_tem
total_average_distance.append(average_distance)
# write the list results in file
directory_pick = os.path.dirname(pick_results_file)
total_results_file = os.path.join(directory_pick, 'results.txt')
f = open(total_results_file, 'w')
# write total_tp
f.write(','.join(map(str, total_tp))+'\n')
f.write(','.join(map(str, total_recall))+'\n')
f.write(','.join(map(str, total_precision))+'\n')
f.write(','.join(map(str, total_probability))+'\n')
f.write(','.join(map(str, total_average_distance))+'\n')
f.write('#total autopick number:%d\n'%(len(coordinate_total)))
f.write('#total manual pick number:%d\n'%(total_reference))
f.write('#the first row is number of true positive\n')
f.write('#the second row is recall\n')
f.write('#the third row is precision\n')
f.write('#the fourth row is probability\n')
f.write('#the fiveth row is distance\n')
# show the recall and precision
times_of_manual = len(coordinate_total)//total_reference + 1
for i in range(times_of_manual):
print('autopick_total sort, take the head number of total_manualpick * ratio %d'%(i+1))
f.write('#autopick_total sort, take the head number of total_manualpick * ratio %d \n'%(i+1))
if i==times_of_manual-1:
print('precision:%f \trecall:%f'%(total_precision[-1], total_recall[-1]))
f.write('precision:%f \trecall:%f \n'%(total_precision[-1], total_recall[-1]))
else:
print('precision:%f \trecall:%f'%(total_precision[(i+1)*total_reference-1], total_recall[(i+1)*total_reference-1]))
f.write('precision:%f \trecall:%f \n'%(total_precision[(i+1)*total_reference-1], total_recall[(i+1)*total_reference-1]))
f.close()
def train(self):
training_data = DataLoader.load_nmist_train_data()
self.__train(self.n, training_data)
def Run_SRNN_NormalCase(args, no_dataset):
data_path, graph_path = Data_path(no_dataset)
log_path = Log_path(no_dataset)
# Construct the DataLoader object that loads data
dataloader = DataLoader(args)
dataloader.load_data(data_path)
# Construct the ST-graph object that reads graph
stgraph = ST_GRAPH(args)
stgraph.readGraph(dataloader.num_sensor, graph_path)
# Initialize net
net = SRNN(args)
net.setStgraph(stgraph)
print('- Number of trainable parameters:',
sum(p.numel() for p in net.parameters() if p.requires_grad))
# optimizer = torch.optim.Adam(net.parameters(), lr=args.learning_rate)
# optimizer = torch.optim.RMSprop(net.parameters(), lr=args.learning_rate, momentum=0.0001, centered=True)
optimizer = torch.optim.Adagrad(net.parameters())
best_eval_loss = 10000
best_epoch = 0
print('')
print('---- Train and Evaluation ----')
eval_loss_res = np.zeros((args.num_epochs + 1, 2))
for e in range(args.num_epochs):
epoch = e + 1
#### Training ####
print('-- Training, epoch {}/{}'.format(epoch, args.num_epochs))
loss_epoch = 0
# For each batch
for b in range(dataloader.num_batches_train):
batch = b + 1
start = time.time()
# Get batch data
x = dataloader.next_batch_train()
# Loss for this batch
loss_batch = 0
# For each sequence in the batch
for sequence in range(dataloader.batch_size):
# put node and edge features
stgraph.putSequenceData(x[sequence])
# get data to feed
data_nodes, data_temporalEdges, data_spatialEdges = stgraph.getSequenceData(
)
# put a sequence to net
loss_output, data_nodes, outputs = forward(
net, optimizer, args, stgraph, data_nodes,
data_temporalEdges, data_spatialEdges)
loss_output.backward()
loss_batch += loss_RMSE(data_nodes[-1], outputs[-1],
dataloader.scaler)
# Clip gradients
torch.nn.utils.clip_grad_norm_(net.parameters(),
args.grad_clip)
# Update parameters
optimizer.step()
end = time.time()
loss_batch = loss_batch / dataloader.batch_size
loss_epoch += loss_batch
print('Train: {}/{}, train_loss = {:.3f}, time/batch = {:.3f}'.
format(e * dataloader.num_batches_train + batch,
args.num_epochs * dataloader.num_batches_train,
loss_batch, end - start))
# Compute loss for the entire epoch
loss_epoch /= dataloader.num_batches_train
print('(epoch {}), train_loss = {:.3f}'.format(epoch, loss_epoch))
# Save the model after each epoch
save_path = Save_path(no_dataset, epoch)
print('Saving model to ' + save_path)
torch.save(
{
'epoch': epoch,
'state_dict': net.state_dict(),
'optimizer_state_dict': optimizer.state_dict()
}, save_path)
#### Evaluation ####
print('-- Evaluation, epoch {}/{}'.format(epoch, args.num_epochs))
loss_epoch = 0
for b in range(dataloader.num_batches_eval):
batch = b + 1
start = time.time()
# Get batch data
x = dataloader.next_batch_eval()
# Loss for this batch
loss_batch = 0
for sequence in range(dataloader.batch_size):
# put node and edge features
stgraph.putSequenceData(x[sequence])
# get data to feed
data_nodes, data_temporalEdges, data_spatialEdges = stgraph.getSequenceData(
)
# put a sequence to net
_, data_nodes, outputs = forward(net, optimizer, args, stgraph,
data_nodes,
data_temporalEdges,
data_spatialEdges)
loss_batch += loss_RMSE(data_nodes[-1], outputs[-1],
dataloader.scaler)
end = time.time()
loss_batch = loss_batch / dataloader.batch_size
loss_epoch += loss_batch
print(
'Eval: {}/{}, eval_loss = {:.3f}, time/batch = {:.3f}'.format(
e * dataloader.num_batches_eval + batch,
args.num_epochs * dataloader.num_batches_eval, loss_batch,
end - start))
loss_epoch /= dataloader.num_batches_eval
eval_loss_res[e] = (epoch, loss_epoch)
# Update best validation loss until now
if loss_epoch < best_eval_loss:
best_eval_loss = loss_epoch
best_epoch = epoch
print('(epoch {}), eval_loss = {:.3f}'.format(epoch, loss_epoch))
# Record the best epoch and best validation loss overall
print('Best epoch: {}, Best evaluation loss {:.3f}'.format(
best_epoch, best_eval_loss))
eval_loss_res[-1] = (best_epoch, best_eval_loss)
np.savetxt(log_path, eval_loss_res, fmt='%d, %.3f')
print('- Eval result has been saved in ', log_path)
print('')
def integrated_benchmark(dataset_path):
"""
Variables:
Dataset size: number of columns
Dataset distribution: column length distribution
threshold
query column
"""
loader = DataLoader("")
dataset = loader.load_dataset(dataset_path)
bf_lists, lsh_list = init(dataset)
print("""
Benchmark 1
Goal: Measure scalability of different methods
Variable:
the size of datasets. size: 400, 600, 800, 1000
Fix:
threshold = 0.6
query column = median col
Output:
Runtime
precision, recall, f1
""")
labels = ["bloom filter", "lsh", "lsh ensemble", "lsh + bloom filter"]
time_for_each_size = np.empty((len(dataset), len(labels)), dtype=float)
x_axis = np.empty(len(dataset), dtype=int)
for i, cols in enumerate(dataset):
candidate_index = len(cols) // 2 # median col
brute_force_result = brute_force(candidate_index, cols, 0.6)
print("brute_force finished\n")
time = benchmark(cols, candidate_index, 0.6, bf_lists[i], lsh_list[i],
brute_force_result,
"Benchmark-1-cols-size-" + str(len(cols)))
time_for_each_size[i] = time
x_axis[i] = len(cols)
fig, ax = plt.subplots()
for i in range(len(labels)):
ax.plot(x_axis, time_for_each_size[:, i], 'o-', label=labels[i])
ax.legend()
ax.set_title("Benchmark-1-cols-size")
ax.set_xticks(x_axis)
ax.set_xlabel("size")
ax.set_ylabel("time(s)")
fig.tight_layout()
# plt.show()
fig.savefig("./bench_results/Benchmark-1-cols-size")
print("""
Benchmark 2
Goal: Measure the effect of threshold
Variable:
threshold: 0.1 0.3 0.5 0.7 0.9
Fix:
dataset size = median col
Output
Runtime
precision, recall, f1
""")
threshold_list = [0.1, 0.3, 0.5, 0.7, 0.9]
time_for_each_threshold = np.empty((len(threshold_list), len(labels)),
dtype=float)
x_axis = np.empty(len(threshold_list), dtype=float)
cols_index = len(dataset) // 2
cols = dataset[cols_index]
for i in range(len(threshold_list)):
threshold = threshold_list[i]
candidate_index = len(cols) // 2 # median col
brute_force_result = brute_force(candidate_index, cols, threshold)
print("brute_force finished\n")
time = benchmark(
cols, candidate_index, threshold, bf_lists[cols_index],
lsh_list[cols_index], brute_force_result,
"Benchmark-2-threshold-" + str(int(threshold * 100)) + "%")
time_for_each_threshold[i] = time
x_axis[i] = threshold
fig, ax = plt.subplots()
for i in range(len(labels)):
ax.plot(x_axis, time_for_each_threshold[:, i], 'o-', label=labels[i])
ax.legend()
ax.set_title("Benchmark-2-threshold")
ax.set_xticks(x_axis)
ax.set_xlabel("threshold")
ax.set_ylabel("time(s)")
fig.tight_layout()
# plt.show()
fig.savefig("./bench_results/Benchmark-2-threshold")
print("""
Benchmark 3
Goal: Measure the effect of query column
Variable:
query column = small col, median col, large col
Fix:
dataset size = median size cols
threshold = 0.6
Output
Runtime
precision, recall, f1
""")
cols_index = len(dataset) // 2
cols = dataset[cols_index]
label = ["small-col", "median-col", "large-col"]
for i, candidate_index in enumerate([0, len(cols) // 2, len(cols) - 1]):
brute_force_result = brute_force(candidate_index, cols, 0.6)
benchmark(cols, candidate_index, 0.6, bf_lists[cols_index],
lsh_list[cols_index], brute_force_result,
"Benchmark-3-candidate-" + label[i])
def main(pretrain_checkpoint_dir,
train_summary_writer,
vocab: Vocab,
dataloader: DataLoader,
batch_size: int = 64,
embedding_dim: int = 256,
seq_length: int = 3000,
gen_seq_len: int = 3000,
gen_rnn_units: int = 1024,
disc_rnn_units: int = 1024,
epochs: int = 40000,
pretrain_epochs: int = 4000,
learning_rate: float = 1e-4,
rollout_num: int = 2,
gen_pretrain: bool = False,
disc_pretrain: bool = False,
load_gen_weights: bool = False,
load_disc_weights: bool = False,
save_gen_weights: bool = True,
save_disc_weights: bool = True,
disc_steps: int = 3):
gen = Generator(dataloader=dataloader,
vocab=vocab,
batch_size=batch_size,
embedding_dim=embedding_dim,
seq_length=seq_length,
checkpoint_dir=pretrain_checkpoint_dir,
rnn_units=gen_rnn_units,
start_token=0,
learning_rate=learning_rate)
if load_gen_weights:
gen.load_weights()
if gen_pretrain:
gen_pre_trainer = GenPretrainer(gen,
dataloader=dataloader,
vocab=vocab,
pretrain_epochs=pretrain_epochs,
tb_writer=train_summary_writer,
learning_rate=learning_rate)
print('Start pre-training generator...')
gen_pre_trainer.pretrain(gen_seq_len=gen_seq_len,
save_weights=save_gen_weights)
disc = Discriminator(vocab_size=vocab.vocab_size,
embedding_dim=embedding_dim,
rnn_units=disc_rnn_units,
batch_size=batch_size,
checkpoint_dir=pretrain_checkpoint_dir,
learning_rate=learning_rate)
if load_disc_weights:
disc.load_weights()
if disc_pretrain:
disc_pre_trainer = DiscPretrainer(disc,
gen,
dataloader=dataloader,
vocab=vocab,
pretrain_epochs=pretrain_epochs,
tb_writer=train_summary_writer,
learning_rate=learning_rate)
print('Start pre-training discriminator...')
disc_pre_trainer.pretrain(save_disc_weights)
rollout = Rollout(generator=gen,
discriminator=disc,
vocab=vocab,
batch_size=batch_size,
seq_length=seq_length,
rollout_num=rollout_num)
with tqdm(desc='Epoch: ', total=epochs, dynamic_ncols=True) as pbar:
for epoch in range(epochs):
fake_samples = gen.generate()
rewards = rollout.get_reward(samples=fake_samples)
gen_loss = gen.train_step(fake_samples, rewards)
real_samples, _ = dataloader.get_batch(shuffle=shuffle,
seq_length=seq_length,
batch_size=batch_size,
training=True)
disc_loss = 0
for i in range(disc_steps):
disc_loss += disc.train_step(fake_samples,
real_samples) / disc_steps
with train_summary_writer.as_default():
tf.summary.scalar('gen_train_loss', gen_loss, step=epoch)
tf.summary.scalar('disc_train_loss', disc_loss, step=epoch)
tf.summary.scalar('total_train_loss',
disc_loss + gen_loss,
step=epoch)
pbar.set_postfix(gen_train_loss=tf.reduce_mean(gen_loss),
disc_train_loss=tf.reduce_mean(disc_loss),
total_train_loss=tf.reduce_mean(gen_loss +
disc_loss))
if (epoch + 1) % 5 == 0 or (epoch + 1) == 1:
print('保存weights...')
# 保存weights
gen.model.save_weights(gen.checkpoint_prefix)
disc.model.save_weights(disc.checkpoint_prefix)
# gen.model.save('gen.h5')
# disc.model.save('disc.h5')
# 测试 disc
fake_samples = gen.generate(gen_seq_len)
real_samples = dataloader.get_batch(shuffle=shuffle,
seq_length=gen_seq_len,
batch_size=batch_size,
training=False)
disc_loss = disc.test_step(fake_samples, real_samples)
# 测试 gen
gen_loss = gen.test_step()
# 得到bleu_score
# bleu_score = get_bleu_score(true_seqs=real_samples, genned_seqs=fake_samples)
genned_sentences = vocab.extract_seqs(fake_samples)
# print(genned_sentences)
# print(vocab.idx2char[fake_samples[0]])
# 记录 test losses
with train_summary_writer.as_default():
tf.summary.scalar('disc_test_loss',
tf.reduce_mean(disc_loss),
step=epoch)
tf.summary.scalar('gen_test_loss',
tf.reduce_mean(gen_loss),
step=epoch)
# tf.summary.scalar('bleu_score', tf.reduce_mean(bleu_score), step=epoch + gen_pretrain * pretrain_epochs)
pbar.update()
def train():
parser = OptionParser()
parser.add_option("--train_good",
dest="train_good",
help="Input good particles ",
metavar="FILE")
parser.add_option("--train_bad",
dest="train_bad",
help="Input bad particles",
metavar="FILE")
parser.add_option("--particle_number",
type="int",
dest="train_number",
help="Number of positive samples to train.",
metavar="VALUE",
default=-1)
parser.add_option("--bin_size",
type="int",
dest="bin_size",
help="image size reduction",
metavar="VALUE",
default=3)
parser.add_option(
"--coordinate_symbol",
dest="coordinate_symbol",
help="The symbol of the coordinate file, like '_manualPick'",
metavar="STRING")
parser.add_option("--particle_size",
type="int",
dest="particle_size",
help="the size of the particle.",
metavar="VALUE",
default=-1)
parser.add_option("--validation_ratio",
type="float",
dest="validation_ratio",
help="the ratio.",
metavar="VALUE",
default=0.1)
parser.add_option(
"--model_retrain",
action="store_true",
dest="model_retrain",
help=
"train the model using the pre-trained model as parameters initialization .",
default=False)
parser.add_option("--model_load_file",
dest="model_load_file",
help="pre-trained model",
metavar="FILE")
parser.add_option("--logdir",
dest="logdir",
help="directory of logfiles",
metavar="DIRECTORY",
default="Logfile")
parser.add_option("--model_save_file",
dest="model_save_file",
help="save the model to file",
metavar="FILE")
(opt, args) = parser.parse_args()
np.random.seed(1234)
# define the input size of the model
model_input_size = [100, 64, 64, 1]
num_classes = 2 # the number of output classes
batch_size = model_input_size[0]
if not os.access(opt.logdir, os.F_OK):
os.mkdir(opt.logdir)
# load training dataset
dataLoader = DataLoader()
train_data, train_label, eval_data, eval_label = dataLoader.load_trainData_From_RelionStarFile(
opt.train_good, opt.particle_size, model_input_size,
opt.validation_ratio, opt.train_number, opt.bin_size)
# Check if train_data exist
try:
train_data
except NameError:
print("ERROR: in function load.loadInputTrainData.")
return None
else:
print("Load training data successfully!")
# shuffle training data
train_data, train_label = shuffle_in_unison_inplace(
train_data, train_label)
eval_data, eval_label = shuffle_in_unison_inplace(eval_data, eval_label)
train_x = train_data.reshape(train_data.shape[0], 64, 64, 1)
test_x = eval_data.reshape(eval_data.shape[0], 64, 64, 1)
print("shape of training data: ", train_x.shape, test_x.shape)
train_y = to_categorical(train_label, 2)
test_y = to_categorical(eval_label, 2)
print(train_y.shape, test_y.shape)
datagen = ImageDataGenerator(featurewise_center=True,
featurewise_std_normalization=True,
rotation_range=20,
width_shift_range=0.0,
height_shift_range=0.0,
horizontal_flip=True,
vertical_flip=True)
datagen.fit(train_x)
model = Sequential()
model.add(
Conv2D(32,
kernel_size=(8, 8),
strides=(1, 1),
activation='relu',
input_shape=(64, 64, 1)))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Conv2D(64, kernel_size=(8, 8), activation='relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Conv2D(128, kernel_size=(3, 3), activation='relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Flatten())
model.add(Dense(1024, activation='relu'))
model.add(Dense(num_classes, activation='softmax'))
for layer in model.layers:
print(layer.name, layer.output_shape)
logdir = opt.logdir + '/' + datetime.now().strftime("%Y%m%d-%H%M%S")
tensorboard_callback = TensorBoard(log_dir=logdir)
checkpoint = ModelCheckpoint('best_model.h5',
monitor='val_acc',
verbose=1,
save_best_only=True,
period=1)
reduce_lr_plateau = ReduceLROnPlateau(monitor='val_acc',
patience=10,
verbose=1)
callbacks = [checkpoint, reduce_lr_plateau, tensorboard_callback]
model.compile(optimizer=SGD(0.01),
loss="binary_crossentropy",
metrics=["accuracy"])
model.fit_generator(datagen.flow(train_x, train_y, batch_size=batch_size),
steps_per_epoch=len(train_x) / 32,
epochs=30,
validation_data=(test_x, test_y),
callbacks=callbacks)
model.save(opt.model_save_file)
accuracy = model.evaluate(x=test_x, y=test_y, batch_size=batch_size)
print("Accuracy:", accuracy[1])
from dataLoader import DataLoader
from crfBrandDetector import CrfBrandDetector
if __name__ == '__main__':
print('Preparing Data...')
df = DataLoader().get_data()
print('Building Model...')
crf_model = CrfBrandDetector()
print('Fitting...')
x_train, x_test, y_train, y_test = crf_model.train_test_split(df)
crf_model.fit(x_train, y_train)
crf_model.report_classification(x_test, y_test)
print('Accuracy: {}'.format(crf_model.evaluate(x_test, y_test)))
pred = crf_model.predict(x_test)
pred.to_csv('./pred.csv', index=False)
'loss': loss,
}, os.path.join(args.exp_dir , 'unfinished_model.pt'))
epoch += 1
cost_time = time.time() - since
print ('Training complete in {:.0f}m {:.0f}s'.format(cost_time//60,cost_time%60))
print ('Best Train Acc is {:.4f}'.format(best_train_acc))
print ('Best Val Acc is {:.4f}'.format(best_acc))
model.load_state_dict(best_model)
return model,cost_time,best_acc,best_train_acc
if __name__ == '__main__':
print ('DataSets: '+args.dataset)
print ('ResNet Depth: '+str(args.depth))
loader = DataLoader(args.dataset,batch_size=args.batch_size)
dataloaders,dataset_sizes = loader.load_data()
num_classes = 10
if args.dataset == 'cifar-10':
num_classes = 10
if args.dataset == 'cifar-100':
num_classes = 100
model = resnet_cifar(depth=args.depth, num_classes=num_classes)
optimizer = torch.optim.SGD(model.parameters(), lr=0.1,
momentum=0.9, nesterov=True, weight_decay=1e-4)
# define loss and optimizer
criterion = nn.CrossEntropyLoss()
scheduler = MultiStepLR(optimizer, milestones=[args.epoch*0.4, args.epoch*0.6, args.epoch*0.8], gamma=0.1)
from dataLoader import DataLoader
loader = DataLoader()
loader.loadAll()
fileobj = open("csv/subjectAreaDump.csv", 'w')
for id, paper in loader.papers.iteritems():
if paper.accepted:
fileobj.write("%s|%d|%s" % (
paper.primarySpecificSubjectArea, id, paper.title))
for subj in paper.specificSubjectAreas:
fileobj.write("|" + subj)
fileobj.write("\n")
fileobj.close()
