def test_pandas_rolling_expanding():
"""Test pandas.(Series|DataFrame).(rolling|expanding)"""
try:
from numpy.random import randint
import pandas as pd
except ImportError:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True)
series = pd.Series(randint(0, 50, (123,)))
res1 = series.rolling(10).progress_apply(lambda x: 1, raw=True)
res2 = series.rolling(10).apply(lambda x: 1, raw=True)
assert res1.equals(res2)
res3 = series.expanding(10).progress_apply(lambda x: 2, raw=True)
res4 = series.expanding(10).apply(lambda x: 2, raw=True)
assert res3.equals(res4)
expects = ['114it'] # 123-10+1
for exres in expects:
our_file.seek(0)
if our_file.getvalue().count(exres) < 2:
our_file.seek(0)
raise AssertionError(
"\nExpected:\n{0}\nIn:\n{1}\n".format(
exres + " at least twice.", our_file.read()))
def test_pandas_series():
"""Test pandas.Series.progress_apply and .progress_map"""
try:
from numpy.random import randint
import pandas as pd
except ImportError:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True)
series = pd.Series(randint(0, 50, (123,)))
res1 = series.progress_apply(lambda x: x + 10)
res2 = series.apply(lambda x: x + 10)
assert res1.equals(res2)
res3 = series.progress_map(lambda x: x + 10)
res4 = series.map(lambda x: x + 10)
assert res3.equals(res4)
expects = ['100%', '123/123']
for exres in expects:
our_file.seek(0)
if our_file.getvalue().count(exres) < 2:
our_file.seek(0)
raise AssertionError(
"\nExpected:\n{0}\nIn:\n{1}\n".format(
exres + " at least twice.", our_file.read()))
def test_pandas_groupby_apply():
""" Test pandas.DataFrame.groupby(...).progress_apply """
try:
from numpy.random import randint
import pandas as pd
except:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=False, ascii=True)
df = pd.DataFrame(randint(0, 50, (500, 3)))
df.groupby(0).progress_apply(lambda x: None)
dfs = pd.DataFrame(randint(0, 50, (500, 3)),
columns=list('abc'))
dfs.groupby(['a']).progress_apply(lambda x: None)
our_file.seek(0)
# don't expect final output since no `leave` and
# high dynamic `miniters`
nexres = '100%|##########|'
if nexres in our_file.read():
our_file.seek(0)
raise AssertionError("\nDid not expect:\n{0}\nIn:{1}\n".format(
nexres, our_file.read()))
def test_pandas_groupby_apply():
"""Test pandas.DataFrame.groupby(...).progress_apply"""
try:
from numpy.random import randint
import pandas as pd
except ImportError:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=False, ascii=True)
df = pd.DataFrame(randint(0, 50, (500, 3)))
df.groupby(0).progress_apply(lambda x: None)
dfs = pd.DataFrame(randint(0, 50, (500, 3)), columns=list('abc'))
dfs.groupby(['a']).progress_apply(lambda x: None)
our_file.seek(0)
# don't expect final output since no `leave` and
# high dynamic `miniters`
nexres = '100%|##########|'
if nexres in our_file.read():
our_file.seek(0)
raise AssertionError("\nDid not expect:\n{0}\nIn:{1}\n".format(
nexres, our_file.read()))
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True)
dfs = pd.DataFrame(randint(0, 50, (500, 3)), columns=list('abc'))
dfs.loc[0] = [2, 1, 1]
dfs['d'] = 100
expects = ['500/500', '1/1', '4/4', '2/2']
dfs.groupby(dfs.index).progress_apply(lambda x: None)
dfs.groupby('d').progress_apply(lambda x: None)
dfs.groupby(dfs.columns, axis=1).progress_apply(lambda x: None)
dfs.groupby([2, 2, 1, 1], axis=1).progress_apply(lambda x: None)
our_file.seek(0)
if our_file.read().count('100%') < 4:
our_file.seek(0)
raise AssertionError("\nExpected:\n{0}\nIn:\n{1}\n".format(
'100% at least four times', our_file.read()))
for exres in expects:
our_file.seek(0)
if our_file.getvalue().count(exres) < 1:
our_file.seek(0)
raise AssertionError(
"\nExpected:\n{0}\nIn:\n {1}\n".format(
exres + " at least once.", our_file.read()))
def test_pandas_setup():
"""Test tqdm.pandas()"""
try:
from numpy.random import randint
import pandas as pd
except ImportError:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True, total=123)
series = pd.Series(randint(0, 50, (100,)))
series.progress_apply(lambda x: x + 10)
res = our_file.getvalue()
assert '100/123' in res
def test_pandas_map():
""" Test pandas.Series.progress_map """
try:
from numpy.random import randint
import pandas as pd
except:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True)
dfs = pd.DataFrame(randint(0, 50, (500, 3)), columns=list("abc"))
dfs.a.progress_map(lambda x: None)
if our_file.getvalue().count("100%") < 1:
raise AssertionError("\nExpected:\n{0}\nIn:{1}\n".format("100% at least twice", our_file.getvalue()))
def map_translate(x):
print("Begining to translate")
tqdm.pandas(tqdm())
x['en_desc']=x['description'].progress_map(translate)
print("Done translating decription")
print("Begining to translate Title")
x['en_title']=x['title'].progress_map(translate)
print("Done translating")
print("Begining to translate region")
x['en_region']=x['region'].progress_map(translate)
print("Done translating")
print("Begining to translate city")
x['en_city']=x['city'].progress_map(translate)
print("Done translating")
print("Begining to translate category_name")
x['en_category_name']=x['category_name'].progress_map(translate)
print("Done translating")
return x
def test_pandas_leave():
""" Test pandas with `leave=True` """
try:
from numpy.random import randint
import pandas as pd
except:
raise SkipTest
with closing(StringIO()) as our_file:
df = pd.DataFrame(randint(0, 100, (1000, 6)))
tqdm.pandas(file=our_file, leave=True, ascii=True)
df.groupby(0).progress_apply(lambda x: None)
our_file.seek(0)
exres = "100%|##########| 101/101"
if exres not in our_file.read():
our_file.seek(0)
raise AssertionError("\nExpected:\n{0}\nIn:{1}\n".format(exres, our_file.read()))
def __debug_angle_error_per_number_of_bins_snr_and_samples():
from tqdm import tqdm
import pandas as pd
import numpy as np
tqdm.pandas()
# a = [[10, 100, 1000, 10000], [100, 300], [100, 1000, 10000], [None]]
# a = [[100], [100], [10000], [0.1, 0.01]]
# inx = pd.MultiIndex.from_product(a, names=['samples', 'hist_bins', 'snr', 'quant_size'])
a = dict(samples=[10, 100, 1000, 10000], hist_bins=[100, 300], snr=[100, 1000, 10000], quant_size=[0])
a = dict(samples=[100], hist_bins=[100], snr=[10000], quant_size=[0.2, 0.1, 0.01, 0.0001])
inx = pd.MultiIndex.from_product(a.values(), names=a.keys())
df = pd.DataFrame(index=inx).reset_index(drop=False).sample(frac=1)
df = pd.concat([df] * 10000, ignore_index=True)
df = df.join(df.progress_apply(lambda row: compare_sinogram_and_eigen_vector(**row.to_dict()), axis=1).apply(pd.Series))
df.to_csv('angle_error_by_sinogram.csv', header=None, mode='a')
# df.to_csv('angle_error_by_sinogram.csv', mode='w')
print(df.head())
def main():
# open
df_train = pd.read_csv('../middle/train_lemma_stem.csv')
df_test = pd.read_csv('../middle/test_lemma_stem.csv')
# drop None
df_train = df_train.replace(np.nan, ' ', regex=True)
df_test = df_test.replace(np.nan, ' ', regex=True)
# progress bars initialize
tqdm.pandas(desc="my bar!")
loop_tuple1 = [('punct_re1', 'question1'), ('punct_re2', 'question2')]
loop_tuple2 = [('stem_q1', 'punct_re1'), ('stem_q2', 'punct_re2')]
loop_tuple3 = [('lemmas_q1', 'punct_re1'), ('lemmas_q2', 'punct_re2')]
# implement functions punct_re, spell_lemma, spell_stem to df_train and df_test dataframes
df_train, df_test = implement_fun(df_train, df_test, punct_re, loop_tuple1)
df_train, df_test = implement_fun(df_train, df_test, spell_lemma, loop_tuple2)
df_train, df_test = implement_fun(df_train, df_test, spell_stem, loop_tuple3)
def test_pandas_data_frame():
"""Test pandas.DataFrame.progress_apply and .progress_applymap"""
try:
from numpy.random import randint
import pandas as pd
except ImportError:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True)
df = pd.DataFrame(randint(0, 50, (100, 200)))
def task_func(x):
return x + 1
# applymap
res1 = df.progress_applymap(task_func)
res2 = df.applymap(task_func)
assert res1.equals(res2)
# apply
for axis in [0, 1, 'index', 'columns']:
res3 = df.progress_apply(task_func, axis=axis)
res4 = df.apply(task_func, axis=axis)
assert res3.equals(res4)
our_file.seek(0)
if our_file.read().count('100%') < 3:
our_file.seek(0)
raise AssertionError("\nExpected:\n{0}\nIn:\n{1}\n".format(
'100% at least three times', our_file.read()))
# apply_map, apply axis=0, apply axis=1
expects = ['20000/20000', '200/200', '100/100']
for exres in expects:
our_file.seek(0)
if our_file.getvalue().count(exres) < 1:
our_file.seek(0)
raise AssertionError(
"\nExpected:\n{0}\nIn:\n {1}\n".format(
exres + " at least once.", our_file.read()))
def test_pandas_apply():
""" Test pandas.DataFrame[.series].progress_apply """
try:
from numpy.random import randint
import pandas as pd
except:
raise SkipTest
with closing(StringIO()) as our_file:
tqdm.pandas(file=our_file, leave=True, ascii=True)
df = pd.DataFrame(randint(0, 50, (500, 3)))
df.progress_apply(lambda x: None)
dfs = pd.DataFrame(randint(0, 50, (500, 3)),
columns=list('abc'))
dfs.a.progress_apply(lambda x: None)
our_file.seek(0)
if our_file.read().count('100%') < 2:
our_file.seek(0)
raise AssertionError("\nExpected:\n{0}\nIn:{1}\n".format(
'100% at least twice', our_file.read()))
def postprocess(self, fps, sampling_rate=1, use_kalman=False):
"""
This function should be called after loading the data by loader
It performs the following steps:
-: check fps value, should be set and bigger than 0
-: check critical columns should exist in the table
-: update data types
-: fill 'groumates' if they are not set
-: checks if velocity do not exist, compute it for each agent
-: compute bounding box of trajectories
:param fps: video framerate
:param sampling_rate: if bigger than one, the data needs downsampling,
otherwise needs interpolation
:param use_kalman: for smoothing agent velocities
:return: None
"""
# check
for critical_column in self.critical_columns:
if critical_column not in self.data:
raise ValueError(
"Error! some critical columns are missing from trajectory dataset!"
)
# modify data types
self.data["frame_id"] = self.data["frame_id"].astype(int)
if str(self.data["agent_id"].iloc[0]).replace('.', '', 1).isdigit():
self.data["agent_id"] = self.data["agent_id"].astype(int)
self.data["pos_x"] = self.data["pos_x"].astype(float)
self.data["pos_y"] = self.data["pos_y"].astype(float)
self.data["label"] = self.data["label"].str.lower(
) # search with lower-case labels
# fill scene_id
if "scene_id" not in self.data:
self.data["scene_id"] = 0
self.fps = fps
# fill timestamps based on frame_id and video_fps
if "timestamp" not in self.data:
self.data["timestamp"] = self.data["frame_id"] / fps
# fill groupmates
agent_ids = pd.unique(self.data["agent_id"])
for agent_id in agent_ids:
if agent_id not in self.groupmates:
self.groupmates[agent_id] = []
# down/up sampling frames
if sampling_rate >= 2:
# FixMe: down-sampling
sampling_rate = int(sampling_rate)
self.data = self.data.loc[(self.data["frame_id"] %
sampling_rate) == 0]
self.data = self.data.reset_index()
elif sampling_rate < (1 - 1E-2):
# TODO: interpolation
pass
else:
pass
# remove the trajectories shorter than 2 frames
data_grouped = self.data.groupby(["scene_id", "agent_id"])
single_length_inds = data_grouped.head(1).index[
data_grouped.size() < 2]
self.data = self.data.drop(single_length_inds)
# fill velocities
if "vel_x" not in self.data:
data_grouped = self.data.groupby(["scene_id", "agent_id"])
dt = data_grouped["timestamp"].diff()
if (dt > 2).sum():
print('Warning! too big dt in [%s]' % self.title)
self.data["vel_x"] = (data_grouped["pos_x"].diff() /
dt).astype(float)
self.data["vel_y"] = (data_grouped["pos_y"].diff() /
dt).astype(float)
nan_inds = np.array(np.nonzero(dt.isnull().to_numpy())).reshape(-1)
self.data["vel_x"].iloc[nan_inds] = self.data["vel_x"].iloc[
nan_inds + 1].to_numpy()
self.data["vel_y"].iloc[nan_inds] = self.data["vel_y"].iloc[
nan_inds + 1].to_numpy()
# ============================================
if use_kalman:
def smooth(group):
if len(group) < 2: return group
dt = group["timestamp"].diff().iloc[1]
kf = KalmanModel(dt, n_dim=2, n_iter=7)
smoothed_pos, smoothed_vel = kf.smooth(
group[["pos_x", "pos_y"]].to_numpy())
group["pos_x"] = smoothed_pos[:, 0]
group["pos_y"] = smoothed_pos[:, 1]
group["vel_x"] = smoothed_vel[:, 0]
group["vel_y"] = smoothed_vel[:, 1]
return group
tqdm.pandas(desc="Smoothing trajectories (%s)" % self.title)
# print('Smoothing trajectories ...')
data_grouped = self.data.groupby(["scene_id", "agent_id"])
self.data = data_grouped.progress_apply(smooth)
# importando as bibliotecas
import pandas as pd
import numpy as np
from matplotlib import pyplot as plt
import seaborn as sns
from tqdm import tqdm
import pandas_profiling
%matplotlib inline
tqdm.pandas(desc="Operation Progress")
test_file = pd.read_csv("train.csv")
test_file = test_file.drop('ID_code',axis=1)
test_sample = test_file.sample(n=384,random_state=1)
# Definindo código para retornar features mais correlatas
# https://towardsdatascience.com/feature-selection-correlation-and-p-value-da8921bfb3cf
# Fazer df com amostra de 384
# Rodar os códigos abaixo e gerar um modelo fitando maiores correlações e rodando o predict
def get_redundant_pairs(test_sample):
'''Get diagonal and lower triangular pairs of correlation matrix'''
pairs_to_drop = set()
cols = test_sample.columns
for i in range(0, test_file.shape[1]):
for j in range(0, i+1):
pairs_to_drop.add((cols[i], cols[j]))
return pairs_to_drop
def get_top_abs_correlations(test_sample, n=5):
au_corr = test_file.corr().abs().unstack()
def spacy_tokenizer(sentence):
mytokens = parser(sentence)
mytokens = [
word.lemma_.lower().strip() if word.lemma_ != "-PRON-" else word.lower_
for word in mytokens
]
mytokens = [
word for word in mytokens
if word not in stopwords and word not in punctuations
]
mytokens = " ".join([i for i in mytokens])
return mytokens
# Applying the text-processing function on the body_text.
print(tqdm.pandas())
df["processed_text"] = df["body_text"].progress_apply(spacy_tokenizer)
# Let's take a look at word count in the papers
import seaborn as sns
sns.distplot(df['body_word_count'])
print(df['body_word_count'].describe())
sns.distplot(df['body_unique_words'])
print(df['body_unique_words'].describe())
# Vectorization
from sklearn.feature_extraction.text import TfidfVectorizer
# Sentence size range from 7 to 7944 characters.
# ### 3.1 NLP
# Now I will tokenize and lemmatize the sentences.
#
# Tokenization separates the sentences into a set of tokens.
#
# Lemmatization aims at reducing the inflectional forms of each word into a common base or root. Lemmatization, on the other hand, takes into consideration the morphological analysis of the words.
#
# I still need to better understand about the stop words removal in the contaxt of Text Classification. I do believe (for now) that we should not remove the negative words at least. Some discussion [here](https://datascience.stackexchange.com/questions/31048/pros-cons-of-stop-word-removal), [here](https://www.researchgate.net/post/Does_Pre-processing_step_Remove_Stop_Word_effect_Sentiment_Analysis_result) and [here](https://stackoverflow.com/questions/40144473/do-we-need-to-use-stopwords-filtering-before-pos-tagging)
# In[17]:
tqdm.pandas()
# In[18]:
df['tokens'] = df['sentence'].progress_apply(lambda d: lemmatize_sent(d),
df.sentence, [])
# df['tokens'] = df.sentence.progress_apply(lambda d: lemmatize_sent(d), [i for i in df.sentence.values], [])
# flatten = lambda data: reduce(lambda x, y: x + y, data, [])
# In[19]:
df['tokens'][:3]
# In[20]:
sum(df['sentence'].isnull())
def urm_neg_score_user(mode,
_last_click_score=1,
_clicked_ref_score=1,
_impr_not_seen_score=0,
_seen_ref_score=1,
cluster='no_cluster'):
global impr_not_seen_score, last_click_score, seen_ref_score, clicked_ref_score
impr_not_seen_score = _impr_not_seen_score
last_click_score = _last_click_score
clicked_ref_score = _clicked_ref_score
seen_ref_score = _seen_ref_score
save_path = 'dataset/preprocessed/{}/{}/matrices/'.format(cluster, mode)
accomodations_array = data.accomodations_ids()
# load the dataframes according to the mode and cluster
train_df = data.train_df(mode=mode, cluster=cluster)
test_df = data.test_df(mode=mode, cluster=cluster)
# fill missing clickout_item on the test dataframe
test_df.fillna({'reference': -1}, inplace=True)
train_df.fillna({'reference': -1}, inplace=True)
# concatenate the train df and the test df mantaining only the columns of interest
df = pd.concat([train_df, test_df])[[
'session_id', 'user_id', 'action_type', 'reference', 'impressions'
]]
session_groups = df.groupby(['user_id'])
session_ids = list(session_groups.groups.keys())
rows_count = len(session_groups)
cols_count = len(accomodations_array)
# create dictionary (k: sessionId - v: urm row)
row_of_sessionid = {}
for i in range(len(session_ids)):
row_of_sessionid[session_ids[i]] = i
# create dictionary (k: accomodationId - v: urm col)
col_of_accomodation = {}
for i in range(cols_count):
col_of_accomodation[accomodations_array[i]] = i
print('dictionaries created\n')
tqdm.pandas()
sessions_score = session_groups.progress_apply(
_session_score_negative_value_seen_elem).values
print("apply function done\n")
# create the urm using data indeces and indptr
_data = []
indptr = [0]
indices = []
values_inserted = 0
for i in tqdm(range(rows_count)):
score_dict = sessions_score[i]
for k in score_dict.keys():
# TODO: FIND WHY THERE IS A KEY EQUAL -1
if k != -1:
indices.append(col_of_accomodation[k])
_data.append(score_dict[k])
values_inserted += 1
indptr.append(values_inserted)
_urm = sps.csr_matrix((_data, indices, indptr),
shape=(rows_count, cols_count))
print("URM created\n")
#check if the folder where to save exsist
cf.check_folder(save_path)
print('Saving urm matrix... ')
sps.save_npz('{}/urm_negative_user.npz'.format(save_path), _urm)
print('done!')
print('Saving row dictionary... ')
np.save('{}/dict_row_user.npy'.format(save_path), row_of_sessionid)
print('done!')
print('Saving col dictionary... ')
np.save('{}/dict_col_user.npy'.format(save_path), col_of_accomodation)
print('done!')
def loadCSVs(
self,
tokenFilename: str = "data_aspects_tokens.csv",
preprocessedFilename: str = "data_preprocessed.csv",
lexiconFilename: str = "sentiment_lexicon.csv",
) -> bool:
"""
load all necessary CSV for execution of the detector and set indices as appropriate
Args:
tokenFilename (str, optional): Defaults to "data_aspects_tokens.csv".
preprocessedFilename (str, optional): Defaults to "data_preprocessed.csv".
lexiconFilename (str, optional): Defaults to "sentiment_lexicon.csv".
Returns:
bool: successful execution
"""
try:
if self.df_aspect_tokens is None or self.df_aspect_tokens.empty:
self.df_aspect_tokens = PD.read_csv(self.path + tokenFilename)
self.df_aspect_tokens["polarity_strength"] = PD.NaT
self.df_aspect_tokens["polarity_strength"].fillna(
{i: []
for i in self.df_aspect_tokens.index}, inplace=True)
self.df_aspect_tokens["sentiment_words"] = PD.NaT
self.df_aspect_tokens["sentiment_words"].fillna(
{i: []
for i in self.df_aspect_tokens.index}, inplace=True)
self.df_aspect_tokens["intensifier_words"] = PD.NaT
self.df_aspect_tokens["intensifier_words"].fillna(
{i: []
for i in self.df_aspect_tokens.index}, inplace=True)
self.df_aspect_tokens["word_found"] = self.df_aspect_tokens[
"word_found"].str.replace(r"[^\w]*", "", regex=True)
# TODO remove after debugging
# self.df_aspect_tokens = self.df_aspect_tokens[:100]
if self.df_preprocessed is None or self.df_preprocessed.empty:
self.df_preprocessed = PD.read_csv(self.path +
preprocessedFilename)
# pandas read_csv does not read arrays correctly so we need to adjust those
tqdm.pandas(desc="Applying Datatype Transformations....")
self.df_preprocessed["tokens"] = self.df_preprocessed[
"tokens"].progress_apply(lambda x: json.loads(x))
if self.df_lexicon is None or self.df_lexicon.empty:
if not os.path.exists(self.path + lexiconFilename):
self.downloadLexicon()
self.df_lexicon = PD.read_csv(self.path + lexiconFilename)
self.df_lexicon.drop_duplicates(subset=["word", "qualifier"],
inplace=True)
self.df_lexicon.set_index("word", inplace=True)
self.df_lexicon.drop("%%")
return True
except IOError as e:
print(e)
return False
"""
import pickle
import os
import pandas as pd
import torch
import spacy
import re
from itertools import permutations
from tqdm import tqdm
from .preprocessing_funcs import load_dataloaders
from ..misc import save_as_pickle
import logging
tqdm.pandas(desc="prog-bar")
logging.basicConfig(format='%(asctime)s [%(levelname)s]: %(message)s', \
datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
logger = logging.getLogger('__file__')
def load_pickle(filename):
completeName = os.path.join(os.getcwd() + "/src/data/",\
filename)
with open(completeName, 'rb') as pkl_file:
data = pickle.load(pkl_file)
return data
class infer_from_trained(object):
def __init__(self, args=None, detect_entities=False):
if args is None:
self.args = load_pickle("args.pkl")
def annotate(self) -> None:
"""
function to call the "findAspects()" function for every row
"""
tqdm.pandas(desc="Finding Aspects!")
self.data.progress_apply(lambda x: self.findAspects(x), axis=1)
def run(self):
tqdm.pandas(tqdm)
kaggle_train_data = pandas.read_csv(
os.path.expanduser('~/Datasets/Kaggle-Quora/train.csv')).drop(
'id', 1)
a = kaggle_train_data.qid1.apply(
lambda v: mmh3.hash(str(v).encode('ascii'), 2213) % 128 > 1)
b = kaggle_train_data.qid2.apply(
lambda v: mmh3.hash(str(v).encode('ascii'), 6663) % 128 > 1)
print((a & b).sum(), np.invert(a).sum(), np.invert(b).sum())
print('Raw training questions')
kaggle_train_data['question1_raw'] = kaggle_train_data[
'question1'].fillna('')
kaggle_train_data['question2_raw'] = kaggle_train_data[
'question2'].fillna('')
print('Clean training tokens')
kaggle_train_data['question1_tokens'] = kaggle_train_data[
'question1_raw'].progress_apply(clean_text)
kaggle_train_data['question2_tokens'] = kaggle_train_data[
'question2_raw'].progress_apply(clean_text)
assert kaggle_train_data['question1_tokens'].str.len().max(
) > 0, 'No tokens 1 found'
assert kaggle_train_data['question2_tokens'].str.len().max(
) > 0, 'No tokens 2 found'
print('Clean training questions')
kaggle_train_data['question1_clean'] = kaggle_train_data[
'question1_tokens'].progress_apply(' '.join)
kaggle_train_data['question2_clean'] = kaggle_train_data[
'question2_tokens'].progress_apply(' '.join)
train_data = kaggle_train_data[a & b].reset_index(drop=True)
merge_data = kaggle_train_data[np.invert(b)].reset_index(drop=True)
valid_data = kaggle_train_data[np.invert(a)].reset_index(drop=True)
print('Writing training data')
self.output().makedirs()
train_data.to_msgpack('cache/dataset/train.msg')
merge_data.to_msgpack('cache/dataset/merge.msg')
valid_data.to_msgpack('cache/dataset/valid.msg')
del train_data, valid_data, kaggle_train_data
kaggle_test_data = pandas.read_csv(
os.path.expanduser('~/Datasets/Kaggle-Quora/test.csv'))
print('Raw testing questions')
kaggle_test_data['question1_raw'] = kaggle_test_data[
'question1'].fillna('')
kaggle_test_data['question2_raw'] = kaggle_test_data[
'question2'].fillna('')
print('Clean testing tokens')
kaggle_test_data['question1_tokens'] = kaggle_test_data[
'question1_raw'].progress_apply(clean_text)
kaggle_test_data['question2_tokens'] = kaggle_test_data[
'question2_raw'].progress_apply(clean_text)
print('Clean testing questions')
kaggle_test_data['question1_clean'] = kaggle_test_data[
'question1_tokens'].progress_apply(' '.join)
kaggle_test_data['question2_clean'] = kaggle_test_data[
'question2_tokens'].progress_apply(' '.join)
kaggle_test_data['is_duplicate'] = -1
kaggle_test_data.to_msgpack('cache/dataset/test.msg')
with self.output().open('w') as f:
f.write('done')
with open(fname, "r") as f:
for word in f:
english_long.add(word.strip())
# ## Create lists of stopwords, punctuation, and unicode characters
stop_words_list = stopwords_make(
) # Define old vocab file path if you want to remove first, dirty elements
unicode_list = unicode_make()
punctstr = punctstr_make()
print("Stopwords, Unicodes, Punctuations lists creation complete!")
#word2vec computation
whole_text_unnested = []
whole_text_nested = []
tqdm.pandas(desc="Cleaning text")
for school in tqdm(df['text'], desc="Cleaning text"):
doc = []
for chunk in school.split("\n"):
for sent in sent_tokenize(chunk):
sent = clean_sentence_apache(sent,
unhyphenate=True,
remove_propernouns=False,
remove_acronyms=False)
sent = [word for word in sent if word != '']
if len(sent) > 0:
whole_text_unnested.append(sent)
doc.append(sent)
whole_text_nested.append(doc)
def main():
print("Loading Data...")
names = ["OFFENSE_TYPE_ID", "OFFENSE_CATEGORY_ID", "FIRST_OCCURRENCE_DATE",
"REPORTED_DATE", "DISTRICT_ID", "PRECINCT_ID",
"NEIGHBORHOOD_ID", "IS_CRIME", "IS_TRAFFIC"]
filePath="crime.csv"
pd.set_option('display.float_format', '{:.2f}'.format)
fileExist=False
if(os.path.exists('crime-treated.csv')):
fileExist =True
filePath="crime-treated.csv"
names =["HOUR_REPORTED","DAY_REPORTED","WEEKDAY_REPORTED","MONTH_REPORTED","YEAR_REPORTED",
"OFFENSE_CATEGORY_ID","NEIGHBORHOOD_ID"]
data=pd.read_csv(filePath, parse_dates=True,usecols=names,nrows = None)
else:
data=pd.read_csv(filePath, parse_dates=True)
print("======================================================================DATA INFO======================================")
data.info()
print("===================================DATA INFO======================================")
if(not fileExist):
print(data.head(5))
display(data.groupby([data.OFFENSE_CODE,data.OFFENSE_CODE_EXTENSION,data.OFFENSE_TYPE_ID]).size())
temp=display(data.groupby([data.INCIDENT_ID,data.OFFENSE_CODE,data.OFFENSE_CODE_EXTENSION,data.OFFENSE_TYPE_ID]).size())
print(temp)
treatData(data)
crimesDict = {
'all-other-crimes': 1,
'larceny' : 1,
'theft-from-motor-vehicle' : 3,
'drug-alcohol' : 2,
'auto-theft' : 3,
'white-collar-crime': 1,
'burglary': 2,
'public-disorder' : 2,
'aggravated-assault': 3,
'other-crimes-against-persons' : 2,
'robbery' : 3,
'sexual-assault' : 3,
'murder': 3,
'arson': 2
}
tqdm.pandas()
print("Calculating Offense Weigh...")
data['OFFENSE_WEIGH'] = data.progress_apply(lambda row: crimesDict[row.OFFENSE_CATEGORY_ID], axis=1 )
dataCount = data.groupby(['MONTH_REPORTED','WEEKDAY_REPORTED','HOUR_REPORTED','NEIGHBORHOOD_ID']).MONTH_REPORTED.agg('count').to_frame('COUNT').reset_index()
dataClenad =data.groupby(['MONTH_REPORTED','WEEKDAY_REPORTED','HOUR_REPORTED','NEIGHBORHOOD_ID'], as_index=False).agg({'OFFENSE_WEIGH':'sum'})#['OFFENSE_WEIGH'].sum()['GEO_X'].mean()
dataClenad['COUNT'] = dataCount['COUNT']
print(dataClenad)
print("Calculating Safety ...")
medianCrime = dataClenad['OFFENSE_WEIGH'].median()
modeCrime = dataClenad['OFFENSE_WEIGH'].mode().values
modeQtd = dataClenad['COUNT'].mode().values
print("CRIME MODE: ",modeCrime)
dataClenad['SAFETY'] = dataClenad.progress_apply(lambda row: 1 if row.OFFENSE_WEIGH <= modeCrime and row.COUNT <= modeQtd else 0, axis=1 )
counts = dataClenad['SAFETY'].value_counts()
# CratGraph(dataClenad)
ExecuteKNN(dataClenad)
ExecuteDecisionTree(dataClenad)
le = LabelEncoder()
dataClenad = dataClenad.progress_apply(le.fit_transform)
x_columns = ['MONTH_REPORTED', 'WEEKDAY_REPORTED', 'HOUR_REPORTED', 'NEIGHBORHOOD_ID', 'OFFENSE_WEIGH', 'COUNT']
y_columns = ['SAFETY']
x_train, x_test = train_test_split(dataClenad[x_columns], test_size=0.3)
y_train, y_test = train_test_split(dataClenad[y_columns].values.ravel(), test_size=0.3)
bagging(5, 200, dataClenad, np.ravel(y_train, order='C'), x_train)
exit(0)
import re
import sys
import glob
import string
from pprint import pprint
from collections import Counter, OrderedDict
import spacy
nlp = spacy.load('en', disable=['parser', 'tagger', 'ner'])
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from tqdm import tqdm, tqdm_notebook, tnrange
tqdm.pandas(desc='Progress')
from sklearn.metrics import accuracy_score
from sklearn.preprocessing import LabelEncoder
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
from torch.utils.data import Dataset, DataLoader
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
from torch.autograd import Variable
import pickle
import math
import gensim.models
sep='\t'))
# create a dictionary locations : coordinates
df_loc = df_loc.sort_values(by=['ADM1'])
df_loc = df_loc.drop_duplicates(subset=['FULL_NAME_ND_RO'], keep='first')
loc_dict = dict(zip(df_loc.FULL_NAME_ND_RO, zip(df_loc.LAT, df_loc.LONG)))
loc_dict
import re, string
from tqdm import tqdm
tqdm.pandas(desc="progress")
from tqdm import tqdm_notebook
from fuzzywuzzy import process
from fuzzywuzzy import fuzz
remove_keywords = [
'nan', 'Planes de Emergencia', 'Cruz Roja', 'Media Luna Roja', 'Guatemala',
'Argentina', 'Japon', 'Juventud'
]
remove_keywords.extend(
['Malawi', 'Lebanon', 'لبنان', 'Nederland', 'Netherlands'])
import pandas as pd
import numpy as np
import csv
import difflib
from tqdm import tqdm
tqdm.pandas(desc="Fuzzy Match Progress")
patent_assignee_mapping = pd.read_csv("./patent_assignee/patent_assignee.tsv",
sep="\t",
low_memory=False)
patent_assignee_mapping.head()
patent_results = pd.read_csv(
"../Phase-1-Search-Term/green-technology/all-patent-green-terms-searches.csv",
dtype={
'Emerging low carbon-Additional energy sources': bool,
'Emerging low carbon-All-purpose': bool,
'Emerging low carbon-Alternative fuel': bool,
'Emerging low carbon-Alternative fuel vehicle': bool,
'Emerging low carbon-Battery': bool,
'Emerging low carbon-Building technologies': bool,
'Emerging low carbon-Carbon capture & storage': bool,
'Emerging low carbon-Electrochemical processes': bool,
'Emerging low carbon-Energy management': bool,
'Environmental-Air pollution': bool,
'Environmental-All-purpose': bool,
'Environmental-Biological treatment': bool,
'Environmental-Contaminated land reclamation & remediation': bool,
'"Environmental-Environmental monitoring': bool,
' instrumentation and analysis"': bool,
'Environmental-Marine pollution control': bool,
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 26 21:20:13 2018
@author: 徐嘉诚
"""
import pandas as pd
import numpy as np
import gc
#import os
import datetime
from sklearn.metrics import mean_squared_error
from tqdm import tqdm, tqdm_notebook
tqdm.pandas(tqdm_notebook)
#filelist = os.listdir('../data')
def get_beautiful_test(test):
test_rnd = np.round(test.iloc[:, 1:], 2)
ugly_indexes = []
non_ugly_indexes = []
for idx in tqdm(range(len(test))):
if not np.all(test_rnd.iloc[idx, :].values == test.iloc[idx,
1:].values):
ugly_indexes.append(idx)
else:
non_ugly_indexes.append(idx)
print(len(ugly_indexes), len(non_ugly_indexes))
np.save('test_ugly_indexes', np.array(ugly_indexes))
import torch
import numpy as np # linear algebra
import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)
from matplotlib import pyplot as plt
import cv2
from tqdm import tqdm
import multiprocessing as mp
from preprocessing import read_images
from prototypicalNet import PrototypicalNet, train_step, test_step
tqdm.pandas(desc="my bar!")
def main():
trainx, trainy = read_images('../input/omniglot/images_background/')
testx, testy = read_images('../input/omniglot/images_evaluation/')
use_gpu = torch.cuda.is_available()
trainx = torch.from_numpy(trainx).float()
testx = torch.from_numpy(testx).float()
if use_gpu:
trainx = trainx.cuda()
testx = testx.cuda()
print(trainx.size(), testx.size())
num_episode = 16000
frame_size = 1000
trainx = trainx.permute(0, 3, 1, 2)
testx = testx.permute(0, 3, 1, 2)
frame_loss = 0
frame_acc = 0
for i in range(num_episode):
loss, acc = train_step(trainx, trainy, 5, 60, 5)
frame_loss += loss.data
def urm_session_aware(mode,
action_score_dict,
cluster='no_cluster',
time_weight='lin'):
"""
Create the URM considering the whole session of a user and giving scores based on its interactions
:param train_df:
:param test_df:
:param time_weight:
:param save_path:
:param save:
:return:
"""
global tw
tw = time_weight
save_path = 'dataset/preprocessed/{}/{}/matrices/'.format(cluster, mode)
accomodations_array = data.accomodations_ids()
# load the dataframes according to the mode and cluster
train_df = data.train_df(mode=mode, cluster=cluster)
test_df = data.test_df(mode=mode, cluster=cluster)
# fill missing clickout_item on the test dataframe
test_df.fillna({'reference': -1}, inplace=True)
train_df.fillna({'reference': -1}, inplace=True)
# concatenate the train df and the test df mantaining only the columns of interest
df = pd.concat([train_df, test_df])[[
'session_id', 'user_id', 'action_type', 'reference', 'impressions'
]]
session_groups = df.groupby(['session_id', 'user_id'])
session_ids = list(session_groups.groups.keys())
rows_count = len(session_groups)
cols_count = len(accomodations_array)
# create dictionary (k: sessionId - v: urm row)
row_of_sessionid = {}
for i in range(len(session_ids)):
row_of_sessionid[session_ids[i]] = i
# create dictionary (k: accomodationId - v: urm col)
col_of_accomodation = {}
for i in range(cols_count):
col_of_accomodation[accomodations_array[i]] = i
print('dictionaries created\n')
tqdm.pandas()
sessions_score = session_groups.progress_apply(
_compute_session_score).values
print("apply function done\n")
# create the urm using data indeces and indptr
_data = []
indptr = [0]
indices = []
values_inserted = 0
for i in tqdm(range(rows_count)):
score_dict = sessions_score[i]
for k in score_dict.keys():
indices.append(col_of_accomodation[k])
_data.append(score_dict[k])
values_inserted += 1
indptr.append(values_inserted)
_urm = sps.csr_matrix((_data, indices, indptr),
shape=(rows_count, cols_count))
print("URM created\n")
#check if the folder where to save exsist
cf.check_folder(save_path)
print('Saving urm matrix... ')
sps.save_npz('{}/urm_session_aware1_{}.npz'.format(save_path, time_weight),
_urm)
print('done!')
print('Saving row dictionary... ')
np.save('{}/dict_row.npy'.format(save_path), row_of_sessionid)
print('done!')
print('Saving col dictionary... ')
np.save('{}/dict_col.npy'.format(save_path), col_of_accomodation)
print('done!')
import pandas as pd
import pandas_datareader as web
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import os
import re
from tqdm import tqdm
tqdm.pandas() # need to run in notebook
import warnings
warnings.filterwarnings(action='ignore')
pd.set_option('display.max_rows', 500)
pd.set_option('display.max_columns', 500)
#-----------sklearn----------------------------------------------------
from sklearn.metrics import log_loss
from sklearn.model_selection import train_test_split
#-----------other_models---------------------------------------------------
from xgboost import XGBClassifier
from lightgbm import LGBMClassifier
#-----------misc----------------------------------------------------
import gc
from datetime import datetime, timedelta
def create_urm(self):
# load the dataframes according to the mode and cluster
train_df = data.train_df(mode=self.mode, cluster=self.cluster)
test_df = data.test_df(mode=self.mode, cluster=self.cluster)
# fill missing clickout_item on the test dataframe
test_df.fillna({'reference': -1}, inplace=True)
train_df.fillna({'reference': -1}, inplace=True)
# concatenate the train df and the test df mantaining only the columns of interest
df = pd.concat([train_df, test_df])[[
'session_id', 'user_id', 'action_type', 'reference', 'impressions'
]]
if self.type == 'user':
session_groups = df.groupby(['user_id'])
if self.type == 'session':
session_groups = df.groupby(['user_id', 'session_id'])
# it coincides with the rows number
groups_keys = list(session_groups.groups.keys())
rows_count = len(groups_keys)
cols_count = len(self.accomodations_id)
"""
create ROW dictionary
if type == USER :
key: user_id -- value: row_urm
if type == SESSION :
key: (user_id, session_id) -- value: row_urm
"""
row_dict = {}
for i in range(rows_count):
row_dict[groups_keys[i]] = i
"""
create COL dictionary
key: accomodation_id -- value: col_urm
"""
col_dict = {}
for i in range(cols_count):
col_dict[self.accomodations_id[i]] = i
print('dictionaries created\n')
tqdm.pandas()
# compute the score
sessions_score = session_groups.progress_apply(
self._compute_session_score).values
print("apply function done\n")
# create the urm using data indeces and indptr
_data = []
indptr = [0]
indices = []
values_inserted = 0
for i in tqdm(range(rows_count)):
score_dict = sessions_score[i]
for k in score_dict.keys():
indices.append(col_dict[k])
_data.append(score_dict[k])
values_inserted += 1
indptr.append(values_inserted)
_urm = sps.csr_matrix((_data, indices, indptr),
shape=(rows_count, cols_count))
print("URM created\n")
print('Saving urm matrix... ')
sps.save_npz(f'{self.save_path}/{self.name}.npz', _urm)
print('done!')
print('Saving row dictionary... ')
np.save(f'{self.save_path}/{self.name}_dict_row.npy', row_dict)
print('done!')
print('Saving col dictionary... ')
np.save(f'{self.save_path}/{self.name}_dict_col.npy', col_dict)
print('done!')
'fuzz_token_sort_ratio_question': fuzz_token_sort_ratio_question,
'fuzz_token_sort_ratio_lemma1': fuzz_token_sort_ratio_lemma1,
'fuzz_token_sort_ratio_lemma2': fuzz_token_sort_ratio_lemma1,
'fuzz_token_set_ratio_question': fuzz_token_set_ratio_question,
'fuzz_token_set_ratio_lemma1': fuzz_token_set_ratio_lemma1,
'fuzz_token_set_ratio_lemma2': fuzz_token_set_ratio_lemma2
}
# read train dataframe
df_train = pd.read_csv('../../data/Quora_Question_Pairs/middle/train_lemma_stem.csv')
# implement function from calc_table to df_train
for name, fun in tqdm(calc_table.items()):
tqdm.pandas(desc=name)
df_train[name] = df_train.progress_apply(fun, axis=1)
# save result and delete df_train
df_train.to_csv("../../data/Quora_Question_Pairs/middle/train_lemma_stem.csv")
del df_train
# read test dataframe
df_test = pd.read_csv('../../data/Quora_Question_Pairs/middle/test_lemma_stem.csv')
# implement function from calc_table to df_train
for name, fun in tqdm(calc_table.items()):
tqdm.pandas(desc=name)
df_test[name] = df_test.progress_apply(fun, axis=1)
# save result df_test
def _createNewTrainingSetWithFeatureVariations(basicDf, newFeatureDf,
featureOfInterest,
variation_degree):
import pandas as pd
import numpy as np
from tqdm import tqdm
from utilities.pandasTools import suffixColumnsWithLabel
try:
# Create and register a new `tqdm` instance with `pandas`
# (can use tqdm_gui, optional kwargs, etc.)
tqdm.pandas()
print(
'_createNewTrainingSetWithFeatureVariations check point 1 >>> variation_degree >>> '
+ str(variation_degree))
featureVariants = [[
np.exp(
suffixColumnsWithLabel(newFeatureDf, '_exp_' + str(iterator)) *
iterator),
np.exp(
suffixColumnsWithLabel(newFeatureDf, '_exp_inv_' +
str(iterator)) * iterator * -1),
np.power(
suffixColumnsWithLabel(newFeatureDf, '_pow_' + str(iterator)),
iterator),
np.power(
suffixColumnsWithLabel(newFeatureDf, '_pow_inv_' +
str(iterator)).astype(float),
iterator * -1)
] for iterator in range(1, variation_degree + 1)]
print('_createNewTrainingSetWithFeatureVariations check point 2')
segmentCount, rowCount, colCount = len(featureVariants), len(
featureVariants[0]), len(featureVariants[0][0])
cummulativeListOfFeatures = np.empty(segmentCount, dtype=list)
print('_createNewTrainingSetWithFeatureVariations check point 3')
for segmentItr in range(0, segmentCount - 1):
cummulativeListOfFeatures[segmentItr] = pd.DataFrame([])
for rowItr in range(0, rowCount - 1):
cummulativeListOfFeatures[segmentItr] = pd.concat([
cummulativeListOfFeatures[segmentItr],
featureVariants[segmentItr][rowItr]
],
axis=1)
print('_createNewTrainingSetWithFeatureVariations check point 4')
cummulativeListOfFeatures = pd.concat(cummulativeListOfFeatures,
axis=1)
newTrainingSetDf = pd.concat(
[basicDf, newFeatureDf, cummulativeListOfFeatures], axis=1)
print('_createNewTrainingSetWithFeatureVariations check point 5')
return newTrainingSetDf
except:
print("Error executing method >>> ")
# exc_type, exc_obj, exc_tb = sys.exc_info()
# fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
# print("Unexpected error:", sys.exc_info())
# print(exc_type, fname, exc_tb.tb_lineno)
# http://docs.python.org/2/library/sys.html#sys.exc_info
exc_type, exc_value, exc_traceback = sys.exc_info(
) # most recent (if any) by default
'''
Reason this _can_ be bad: If an (unhandled) exception happens AFTER this,
or if we do not delete the labels on (not much) older versions of Py, the
reference we created can linger.
traceback.format_exc/print_exc do this very thing, BUT note this creates a
temp scope within the function.
'''
traceback_details = {
'filename': exc_traceback.tb_frame.f_code.co_filename,
'lineno': exc_traceback.tb_lineno,
'name': exc_traceback.tb_frame.f_code.co_name,
'type': exc_type.__name__,
'message': traceback.extract_tb(exc_traceback)
}
del (exc_type, exc_value, exc_traceback
) # So we don't leave our local labels/objects dangling
# This still isn't "completely safe", though!
# "Best (recommended) practice: replace all exc_type, exc_value, exc_traceback
# with sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2]
print
print(traceback.format_exc())
print
print(traceback_template % traceback_details)
print
#traceback.print_exception()
raise
def load_time_series_dataset(cfg, slide=None):
'''
Load the static and time series data from disk and join them. Create time series examples to form large dataset with
time series and static features. Partition into train/val/test sets. Normalize numerical data.
:param cfg: Project config (from config.yml)
:param slide: Int that controls how many recent dates to cut off from the dataset
:return: A dict of partitioned and normalized datasets, split into examples and labels
'''
# Load data info generated during preprocessing
data = {}
data['METADATA'] = {}
input_stream = open(cfg['PATHS']['DATA_INFO'], 'r')
data_info = yaml.full_load(input_stream)
data['METADATA']['N_WEEKS'] = data_info['N_WEEKS']
noncat_features = data_info[
'NON_CAT_FEATURES'] # Noncategorical features to be scaled
T_X = cfg['DATA']['TIME_SERIES']['T_X']
tqdm.pandas()
# Load data (before and after one-hot encoding)
df_ohe = pd.read_csv(cfg['PATHS']['PROCESSED_OHE_DATA'])
df = pd.read_csv(cfg['PATHS']['PROCESSED_DATA']
) # Static and dynamic data prior to one hot encoding
time_series_feats = [
f for f in df.columns if ('-Day_' in f) and (')' not in f)
]
# Partition dataset by date
unique_dates = np.flip(df_ohe['Date'].unique()).flatten()
val_split = cfg['TRAIN']['VAL_SPLIT']
if val_split * unique_dates.shape[0] < 1:
val_split = 1.0 / unique_dates.shape[
0] # Ensure validation set contains records from at least 1 time step
print("Val set split in config.yml is too small. Increased to " +
str(val_split))
test_split = cfg['TRAIN']['TEST_SPLIT']
if test_split * unique_dates.shape[0] < 1:
test_split = 1.0 / unique_dates.shape[
0] # Ensure test set contains records from at least 1 time step
print("Test set split in config.yml is too small. Increased to " +
str(test_split))
if slide is None:
test_df_dates = unique_dates[-int(test_split * unique_dates.shape[0]):]
val_df_dates = unique_dates[-int(
(test_split + val_split) *
unique_dates.shape[0]):-int(test_split * unique_dates.shape[0])]
train_df_dates = unique_dates[0:-int((test_split + val_split) *
unique_dates.shape[0])]
else:
test_split_size = max(int((test_split) * unique_dates.shape[0]), 1)
val_split_size = max(int((val_split) * unique_dates.shape[0]), 1)
offset = slide * test_split_size
if offset == 0:
test_df_dates = unique_dates[-(test_split_size):]
else:
test_df_dates = unique_dates[-(test_split_size + offset):-offset]
val_df_dates = unique_dates[-(val_split_size + test_split_size +
offset):-(test_split_size + offset)]
train_df_dates = unique_dates[0:-(val_split_size + test_split_size +
offset)]
train_df_ohe = df_ohe[df_ohe['Date'].isin(train_df_dates)]
val_df_ohe = df_ohe[df_ohe['Date'].isin(val_df_dates)]
test_df_ohe = df_ohe[df_ohe['Date'].isin(test_df_dates)]
train_df = df[df['Date'].isin(train_df_dates)]
test_df = df[df['Date'].isin(test_df_dates)]
print('Train set size = ' + str(train_df_ohe.shape[0]) +
'. Val set size = ' + str(val_df_ohe.shape[0]) +
'. Test set size = ' + str(test_df_ohe.shape[0]))
# Save train & test set for LIME
train_df.to_csv(cfg['PATHS']['TRAIN_SET'],
sep=',',
header=True,
index=False)
test_df.to_csv(cfg['PATHS']['TEST_SET'], sep=',', header=True, index=False)
# Anonymize clients
train_df_ohe.drop(['ClientID', 'Date'], axis=1, inplace=True)
val_df_ohe.drop(['ClientID', 'Date'], axis=1, inplace=True)
test_df_ohe.drop(['ClientID', 'Date'], axis=1, inplace=True)
# Get indices of noncategorical features
noncat_feat_idxs = [
test_df_ohe.columns.get_loc(c) for c in noncat_features
if c in test_df_ohe
]
# Separate ground truth from dataframe and convert to numpy arrays
data['Y_train'] = np.array(train_df_ohe.pop('GroundTruth'))
data['Y_val'] = np.array(val_df_ohe.pop('GroundTruth'))
data['Y_test'] = np.array(test_df_ohe.pop('GroundTruth'))
# Convert feature dataframes to numpy arrays
data['X_train'] = np.array(train_df_ohe)
data['X_val'] = np.array(val_df_ohe)
data['X_test'] = np.array(test_df_ohe)
# Normalize numerical data and save the scaler for prediction.
col_trans_scaler = ColumnTransformer(transformers=[
('col_trans_ordinal', StandardScaler(), noncat_feat_idxs)
],
remainder='passthrough')
data['X_train'] = col_trans_scaler.fit_transform(
data['X_train']) # Only fit train data to prevent data leakage
data['X_val'] = col_trans_scaler.transform(data['X_val'])
data['X_test'] = col_trans_scaler.transform(data['X_test'])
dump(col_trans_scaler,
cfg['PATHS']['SCALER_COL_TRANSFORMER'],
compress=True)
data['METADATA']['NUM_TS_FEATS'] = len(
time_series_feats) # Number of different time series features
data['METADATA']['T_X'] = T_X
return data
"""
@author - Mohsin
"""
import numpy as np
np.random.seed(786) # for reproducibility
import pandas as pd
from sklearn.model_selection import KFold
from sklearn.preprocessing import MinMaxScaler
from tqdm import tqdm
tqdm.pandas(tqdm)
from utils import *
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
if __name__ == "__main__":
LOGGER_FILE = "prepImageFeature3.log"
IMAGE_FILE_1 = "../utility/df_image_feats3.csv"
###################### Logger #########################################
handler = logging.FileHandler(LOGGER_FILE)
handler.setLevel(logging.INFO)
# create a logging format
formatter = logging.Formatter(
def get_variant_data(connection, limit=0, testRun = False):
'''
Get Variant data for Solr document.
'''
# Special variant IDs that represent
testAssociationId = [
42893, # Missing from solr slim
47195, # kgp ID
]
# function to retrieve further data from the database:
def get_more_variant_data(row):
# Extracting basic variant information:
resourcename = 'variant'
ID = row['ID']
rsID = row['RS_ID']
consequence = str(row['FUNCTIONAL_CLASS']).replace("_", " ").capitalize()
# Extracting association count:
association_count = variant_cls.get_association_count(ID)
# Extracting study count:
study_count = variant_cls.get_study_count(ID)
# We don't care about variants that have no associations:
if association_count == 0:
return(1)
# Extracting genomic location:
location = variant_cls.get_variant_location(ID)
# Extracting mapped genes:
mapped_genes_list = variant_cls.get_mapped_genes(ID)
mapped_genes_names = [x.split("|")[0] for x in mapped_genes_list]
mapped_genes_names = list(set(mapped_genes_names)) # GOCI-2475 - unique set of names are generated.
# Extracting merged rsID:
current_rsID = variant_cls.get_current_rsID(ID)
# Assign merged rsID and generate title:
title = ''
if current_rsID:
merged_rsID = rsID
title = "%s (%s)" %(current_rsID, merged_rsID)
else:
current_rsID = rsID
merged_rsID = ''
title = current_rsID
# Combining data into a dictionary:
varDoc = {
'resourcename' : resourcename,
'id' : "%s:%s" % (resourcename,ID),
'title' : title,
'rsID' : rsID,
'current_rsID' : current_rsID,
'merged_rsID' : merged_rsID,
'associationCount' : association_count,
'studyCount' : study_count,
'mappedGenes' : mapped_genes_list,
'consequence' : consequence,
}
# Adding only valid location indicated by integer position:
if isinstance(location['position'], int):
varDoc['chromosomeName'] = location['chromosome']
varDoc['chromosomePosition'] = location['position']
varDoc['region'] = location['region']
# Adding description to the document:
coordinates = '%s:%s' %(location['chromosome'], location['position'])
genes_str = ",".join(mapped_genes_names)
varDoc['description'] = "|".join([coordinates,
str(location['region']), consequence,genes_str])
# Adding to document list:
all_variant_data.append(varDoc)
# Initialize empty list for the documents:
all_variant_data = []
# Step 1: initialize variant object:
variant_cls = variant_sqls(connection)
# Step 2: retrieve all the variants in the database:
variants_df = variant_cls.get_snps()
# Inintialize progress bar:
tqdm.pandas(desc="Returning variant data")
# Step 3: Calling apply to retrieve all variant data:
if limit != 0:
variants_df[0:limit].progress_apply(get_more_variant_data, axis = 1)
elif testRun:
variants_df[variants_df['ID'].isin(testAssociationId)].progress_apply(get_more_variant_data, axis = 1)
else:
variants_df.progress_apply(get_more_variant_data, axis = 1)
return all_variant_data
wordcount[word] += 1
# function for replace every word in the lemmatized message with the most popular synonim
def build_new_sent(sent):
list_sent = []
for word in str(sent).split():
word_d = dict()
for syn in wordnet.synsets(word):
for lemma in syn.lemma_names():
word_d[lemma] = wordcount[lemma]
if len(word_d.items()):
list_sent.append(max(word_d.items(), key=operator.itemgetter(1))[0])
else:
list_sent.append(word)
return ' '.join(list_sent)
# implement build_new_sent function to the df_train and save results
tqdm.pandas("lemma_q1")
df_train['lemma_q1_new'] = df_train['lemma_q1'].progress_apply(build_new_sent)
tqdm.pandas("lemma_q2")
df_train['lemma_q2_new'] = df_train['lemma_q2'].progress_apply(build_new_sent)
df_train.to_csv("../middle/train_lemma_stem.csv", index=False)
# implement build_new_sent function to the df_test and save results
tqdm.pandas("lemma_q1")
df_test['lemma_q1_new'] = df_test['lemma_q1'].progress_apply(build_new_sent)
tqdm.pandas("lemma_q2")
df_test['lemma_q2_new'] = df_test['lemma_q2'].progress_apply(build_new_sent)
df_test.to_csv("../middle/test_lemma_stem.csv", index=False)
def main():
# open
df_train = pd.read_csv('../middle/train_lemma_stem.csv')
df_test = pd.read_csv('../middle/test_lemma_stem.csv')
# drop None
df_train = df_train.replace(np.nan, ' ', regex=True)
df_test = df_test.replace(np.nan, ' ', regex=True)
# tuple of input and output columns names
name_tuple = [('lemma_q1', 'lemma1doc'), ('lemma_q2', 'lemma2doc'), ('lemma_q1_new', 'lemma1doc_syn'), ('lemma_q2_new', 'lemma2doc_syn')]
# apply spacy_doc function for columns from name_tuple to df_train
for t in name_tuple:
tqdm.pandas(desc=t[0]+'train')
df_train[t[1]] = df_train[t[0]].progress_apply(spacy_doc)
# find similarity in df_train
tqdm.pandas(desc='spacy_similarity_lem+train')
df_train['spacy_sim_lem'] = df_train.progress_apply(spacy_similarity_lem, axis=1)
tqdm.pandas(desc='spacy_similarity_syn+train')
df_train['spacy_sim_syn'] = df_train.progress_apply(spacy_similarity_syn, axis=1)
df_train.to_csv('../middle/train_lemma_stem.csv')
# apply spacy_doc function for columns from name_tuple to df_test
for t in name_tuple:
tqdm.pandas(desc=t[0]+'test')
df_test[t[1]] = df_test[t[0]].progress_apply(spacy_doc)
# find similarity in df_test
tqdm.pandas(desc='spacy_similarity_lem+test')
df_test['spacy_sim_lem'] = df_test.progress_apply(spacy_similarity_lem, axis=1)
tqdm.pandas(desc='spacy_similarity_syn+test')
df_test['spacy_sim_syn'] = df_test.progress_apply(spacy_similarity_syn, axis=1)
df_test.to_csv('../middle/test_lemma_stem.csv', index=False)
def mapUniProt(geneIndexFile):
#fills in the uniProt column of the geneIndex dataframe by calling the uniprot mapping server
tqdm.pandas(desc="mapping entrez to uniProt")
indexFrame = pd.read_pickle(geneIndexFile)
indexFrame['uniProt'] = indexFrame['Entrez_Gene_Id'].progress_apply(lambda entrez: getUniprot(entrez))
# Keywords X
# Legend:
# X = Complete
# V = Currently Void
# P = Partially Stabalized
# ------------------------------------------------------------------------------------------------------------
# United Kingdom
# ------------------------------------------------------------------------------------------------------------
os.chdir(MAIN_FOLDER + "/Data/Governmental_Science_Funding/UK")
uk_df = pd.read_csv("uk_funding_data.csv")
# Start tqdm
tqdm.pandas(desc="status")
# Limit to Research Grants
uk_df = uk_df[uk_df['ProjectCategory'] == 'Research Grant'].reset_index(drop=True)
# Drop unneeded columns
to_drop = ['ProjectReference',
'EndDate',
'Status',
'PIOtherNames',
'PI ORCID iD',
'StudentSurname',
'StudentFirstName',
'StudentOtherNames',
'Student ORCID iD',
'GTRProjectUrl',
# 'pos_max': negative sentiment (strongest sentiment statement)',
# 'comp_max': composite sentiment (strongest sentiment statement)',
# Import dependencies
from statistics import mean
import pandas as pd
from nltk.sentiment.vader import SentimentIntensityAnalyzer
from nltk import sent_tokenize
import numpy as np
from tqdm import tqdm
import collections
# load data
review = pd.read_csv('C:/Users/adamb/Desktop/vader/yelp_review.csv')
tqdm.pandas() # progress bar
analyser = SentimentIntensityAnalyzer() # create analyser
# Function to get scores
def sentiment_analyzer_scores(text):
"""Calculates sentiment scores for each text review
Parameters
----------
text : str
Text to analyze
Returns
----------
list of float:
from molmaps import distances, calculator, summary
import pandas as pd
import numpy as np
from rdkit import Chem
from tqdm import tqdm
tqdm.pandas(ascii=True)
def caldis(data, idx, tag, methods=['correlation', 'cosine', 'jaccard']):
##############################################################
Nf = len(feature.fingerprint.Extraction().bitsinfo)
data0 = loadnpy('./data/fingerprint_8206960.npy', N=Nf, dtype=np.bool)
groups = data0.sum(axis=1)
from sklearn.model_selection import GroupKFold
G = GroupKFold(n_splits=10)
sp = G.split(X=data0, groups=groups)
spl = list(sp)
sidx = spl[0][1]
del data0
print(len(sidx))
data = data[sidx]
data = data.astype(np.float32, copy=False)
#############################################################
for method in methods:
res = calculator.pairwise_distance(data, n_cpus=16, method=method)
res = np.nan_to_num(res, copy=False)
df = pd.DataFrame(res, index=idx, columns=idx)
df = df.astype('float32')
import random
import numpy as np
import pandas as pd
from nltk.corpus import stopwords
from nltk.tokenize.regexp import regexp_tokenize
from sklearn.linear_model import LogisticRegression
from sklearn.metrics import accuracy_score, classification_report
from sklearn.model_selection import train_test_split
from tqdm import tqdm
tqdm.pandas(desc="progress-bar")
import re
from gensim.models import Doc2Vec, doc2vec
from sklearn import utils
from sklearn.utils import shuffle
import classifierutils
import dataread
headers = dataread.read_file('top_sectionheaders_5000.txt')
results = []
for header in headers:
ret_val = []
for item in header_corpus[header]['labelled_tokenised'].TEXT:
logreg.predict([model_dbow.infer_vector(item)])
def apply_preprocessing(df):
tqdm.pandas()
df['reviewClean_sw'], df['noun_adjective'] = zip(
*df['reviewText'].progress_apply(text_preprocessing))
return df
import pandas as pd import numpy as np from tqdm import tqdm df = pd.DataFrame(np.random.randint(0, 100, (100000, 6))) # Register `pandas.progress_apply` and `pandas.Series.map_apply` with `tqdm` # (can use `tqdm_gui`, `tqdm_notebook`, optional kwargs, etc.) tqdm.pandas(desc="my bar!") # Now you can use `progress_apply` instead of `apply` # and `progress_map` instead of `map` df.progress_apply(lambda x: x**2) # can also groupby: # df.groupby(0).progress_apply(lambda x: x**2) # -- Source code for `tqdm_pandas` (really simple!) # def tqdm_pandas(t): # from pandas.core.frame import DataFrame # def inner(df, func, *args, **kwargs): # t.total = groups.size // len(groups) # def wrapper(*args, **kwargs): # t.update(1) # return func(*args, **kwargs) # result = df.apply(wrapper, *args, **kwargs) # t.close() # return result # DataFrame.progress_apply = inner
import networkx as nx
import numpy as np
import pandas as pd
from tqdm import tqdm
from feature_engineering.tools import lit_eval_nan_proof
# this script computes the features authors_citation and coauthor score by considering the graph of coauthorship and
# the author's graph of citations.
# the script takes approximately 5 minutes to run
# progress bar for pandas
tqdm.pandas(tqdm())
# path
path_to_data = "data/"
# loading data
converter_dict = {
'authors': lit_eval_nan_proof,
'journal': lit_eval_nan_proof,
'title': lit_eval_nan_proof,
'abstract': lit_eval_nan_proof
}
nodes = pd.read_csv(path_to_data + "nodes_preprocessed.csv",
converters=converter_dict)
nodes.set_index("id", inplace=True)
training = pd.read_csv(path_to_data + "training_features.txt")
training.set_index("my_index", inplace=True)
testing = pd.read_csv(path_to_data + "testing_features.txt")
testing.set_index("my_index", inplace=True)
import numpy as np
import pandas as pd
pd.set_option("display.max_columns",1000) # don’t put … instead of multi columns
pd.set_option('expand_frame_repr',False) # for not wrapping columns if you have many
from optparse import OptionParser
from tqdm import tqdm
tqdm.pandas()
from sys import platform
import plotly as py
import cufflinks
import sys
sys.path.append('../')
sys.path.append('../../')
sys.path.append('../../../')
import int_force
if __name__ == '__main__':
timer=int_force.global_imports.timer()
help_text='''
examples:
seq 0 40 |xargs -I ^ echo python3 "%prog" -s ^ \&
sbatch --mem=1800m -c1 --time=0:50:0 --array=0-399 --wrap 'python3 %prog -s ${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID}'
sbatch --mem=1800m -c1 --time=0:50:0 --array=0-199 --wrap 'python3 %prog -s ${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID} -q "[0,3,150]" -b "[5,17,19,10001]" -m 15'
'''
parser = OptionParser(usage=help_text, version="%prog 1.0 beta")
parser.add_option("-n", dest="samples", type="int", default=1000, help='number of dots X2 because you have x and y. for example 1000. you better use 5 [default: %default]')
parser.add_option("-s", dest="split_id", type="str", default='0', help='the split unique id so it will not override old output [default: %default]')
from timeit import default_timer as timer
import pandas as pd
import numpy as np
from umap import UMAP
from ivis import Ivis
from evaluation import Doc2VecModel
from tqdm import tqdm
from pyod.models.ocsvm import OCSVM
from pyod.models.hbos import HBOS
from pyod.models.pca import PCA
from itertools import permutations
from utils import next_path, product_dict, get_scores, reject_outliers, sample_data, remove_short_texts
tqdm.pandas(desc="progess: ")
class IQROutlier:
def __init__(self, contamination=0.1):
self.contamination = contamination
def fit(self, X, y=None):
pcnt = self.contamination / 2
qlow, self.median, qhigh = np.quantile(X, [pcnt, 0.50, 1-pcnt])
self.iqr = qhigh - qlow
return self
def transform(self, X, thresh_factor=1.0):
iqr = self.iqr*thresh_factor
preds = ((np.abs(X - self.median)) >= iqr/2)