def main():
# define arg parser
parser = argparse.ArgumentParser()
parser.add_argument('--source_path', required=True)
parser.add_argument('--dest_path', default='da_movs.feather')
args = vars(parser.parse_args())
# define path
PROJ = Path()
DATA = PROJ / 'dados'
RAW = DATA / 'brutos'
PROCESSED = DATA / 'processados'
# load main data
dados = pd.read_feather(args['source_path'])
dados = dados.drop_duplicates('file_json')
paths = list(set(dados['file_json'].str[3:].to_list()))
paths = random.sample(paths, 1)
# execute loops to read, process and join files
kwargs = {'n_jobs': -2, 'verbose': 10}
movs = Parallel(**kwargs)(delayed(parse_lawsuits)(p) for p in paths)
movs = pd.concat(movs, ignore_index=True)
movs = movs.astype(str)
movs.to_feather(Path(args['dest_path']))
def spectral(x, sf, f, stype, dcomplex, cycle, width, n_jobs):
"""Extract spectral informations from data.
Parameters
----------
x : array_like
Array of data
sf : float
Sampling frequency
f : array_like
Frequency vector of shape (N, 2)
stype : string
Spectral informations to extract (use either 'pha' or 'amp')
dcomplex : string
Complex decomposition type. Use either 'hilbert' or 'wavelet'
cycle : int
Number of cycles to use for fir1 filtering.
width : int
Width of the wavelet.
n_jobs : int
Number of jobs to use. If jobs is -1, all of them are going to be
used.
"""
n_freqs = f.shape[0]
# Filtering + complex decomposition :
if dcomplex is 'hilbert':
# get filtering coefficients
b = []
a = np.zeros((n_freqs,), dtype=float)
forder = np.zeros((n_freqs,), dtype=int)
for k in range(n_freqs):
forder[k] = fir_order(sf, x.shape[-1], f[k, 0], cycle=cycle)
_b, a[k] = fir1(forder[k], f[k, :] / (sf / 2.))
b += [_b]
# Filt each time series :
xf = Parallel(n_jobs=n_jobs, **CONFIG['JOBLIB_CFG'])(delayed(filtfilt)(
b[k], a[k], x, padlen=forder[k], axis=-1) for k in range(n_freqs))
# Use hilbert for the complex decomposition :
xd = np.asarray(xf)
if stype is not None:
xd = hilbertm(xd)
elif dcomplex is 'wavelet':
f = f.mean(1) # centered frequencies
xd = Parallel(n_jobs=n_jobs, **CONFIG['JOBLIB_CFG'])(delayed(morlet)(
x, sf, k, width) for k in f)
# Extract phase / amplitude :
if stype is 'pha':
return np.angle(xd).astype(np.float64)
elif stype is 'amp':
return np.abs(xd).astype(np.float64)
elif stype is None:
return xd.astype(np.float64)
def extract_all_class_features(dataset, n_jobs=1, stride=5, patch_size=10):
"""Extract masked features from all dataset images, return features and labels"""
cns = []
labels = []
for (label, cls) in enumerate(dataset.classes):
print 'Extracting masked CNs from class {}'.format(cls)
hists = Parallel(n_jobs=n_jobs)(delayed(extract_masked_cns)(imname, maskname) for (imname, maskname) in dataset.get_class_images(cls))
hists = np.vstack(hists)
labels.append(label * np.ones((len(hists),), dtype=np.float32))
cns.append(hists.astype(np.float32))
# Stack lists in numpy arrays.
return (cns, labels)
def main():
# define paths
PROJ = Path()
DATA = PROJ / 'dados'
RAW = DATA / 'brutos'
PROCESSED = DATA / 'processados'
# load digesto
fpath = [PROCESSED / f'processos0{i}_movs.csv' for i in range(1, 4)]
dados = pd.concat(
[pd.read_csv(fp, low_memory=False, dtype=str) for fp in fpath],
ignore_index=True)
dados['numero_cnj'] = dados['numero_cnj'].str.replace(r'\-|\.', '')
# load cnj inova
inova = pd.read_feather(PROCESSED / 'da_basic_transform.feather')
inova = inova[['file_json', 'rowid', 'numero']]
inova = inova.dropna(subset=['numero'])
# extrair os números cnj
numero_cnj = dados['numero_cnj'].to_list()
numero_cnj = set(numero_cnj)
# filter inova lawsuits for which we can recover text
inova = inova[inova['numero'].isin(numero_cnj)]
dados = dados[dados['numero_cnj'].isin(inova['numero'])]
# salvar as join keys e o banco do digesto
inova.to_csv(PROCESSED / 'join_keys.csv', index=False)
dados.to_csv(PROCESSED / 'movs_texto.csv', index=False, quoting=1)
# produce list for extracting info from cnj inova
inova = inova[['file_json', 'rowid']]
inova = inova.groupby('file_json')['rowid'].apply(list)
inova = inova.reset_index()
inova['file_json'] = inova['file_json'].str[3:]
inova = inova.itertuples(name=None, index=False)
# execute loops to read, process and join files
kwargs = {'n_jobs': -2, 'verbose': 10}
movs = Parallel(**kwargs)(delayed(parse_lawsuits)(*p) for p in inova)
movs = pd.concat(movs, ignore_index=True)
movs = movs.astype(str)
movs.to_csv(PROCESSED / 'movs_inova.csv', index=False, quoting=1)
def fit(i):
target = y_train[:, i].toarray().ravel()
if target.mean() == 0:
return np.zeros((X_test.shape[0],)) - 1
d = LogisticRegression(max_iter=10)
d.fit(X_train, target)
return (d.predict_proba(X_test)[:, 1])
preds = Parallel(n_jobs=8, verbose=50)(delayed(fit)(i) for i in range(y_train.shape[1]))
preds = np.vstack(preds).T
# To reduce memory usage
preds = preds.astype(np.float16)
num = int(np.ceil(num_users * 0.05))
# Let's take not random users, but the ones who viewed a lot
users = train.loc[mask_test].user_id.value_counts().index[:num]
ans_inds = np.argsort(preds[users])
test_inds_dict = {k: list(ans_inds[i, -5:]) for i,k in enumerate(users)}
scorer(y_val_dict, test_inds_dict, num_users=num_users)
# For each user find the categories, which we do not want to predict
last_3weeks = train.loc[mask_test].loc[train.loc[mask_test].date >= train.loc[mask_test].date.max() - 21 + 1]
y_not = last_3weeks.groupby('user_id').id3.apply(set)
y_pred = {}
def task7(args):
"""
Core logic for task7
"""
num_cores = multiprocessing.cpu_count()
k = int(args.k)
tensorFileName = "userImageLocation-tensor.npy"
factorMatricesFileName = "factor-matrices" + str(k) + ".npy"
cwd = os.getcwd()
# Load each object space into dictionary where d_obj = {'id': {'term': df, ...}, ...}
print("Loading User Space...")
userFile = '../Data/devset_textTermsPerUser.txt'
d_user = read_text_descriptor_files(userFile)
print("Loading Image Space...")
imageFile = '../Data/devset_textTermsPerImage.txt'
d_images = read_text_descriptor_files(imageFile)
print("Loading Location Space...")
locFile = '../Data/devset_textTermsPerPOI.txt'
d_locations = read_text_descriptor_files(locFile)
user_list = list(d_user.keys())
image_list = list(d_images.keys())
loc_list = list(d_locations.keys())
print(len(user_list), len(image_list), len(loc_list))
if os.path.exists(cwd + '/' + tensorFileName):
print("Loading Tensor...")
tensor = np.load(tensorFileName)
else:
print("Creating Tensor...")
def processInput(i):
# Create a slice of 3-D tensor (combinations of loc & image per user)
print('Started for user' + str(i))
user = user_list[i]
array = [[0 for _ in range(len(loc_list))]
for _ in range(len(image_list))]
for j in range(len(image_list)):
for l in range(len(loc_list)):
image = image_list[j]
loc = loc_list[l]
# Number of terms shared by all three entities
union_words = d_user[user].keys() & d_images[image].keys(
) & d_locations[loc].keys()
array[j][l] += len(union_words)
print('Ended for user' + str(i))
return array
tensor = Parallel(n_jobs=num_cores - 1)(delayed(processInput)(i)
for i in range(len(user_list)))
tensor = np.array(tensor)
print(tensor.shape)
np.save(tensorFileName, tensor)
print('Tensor created')
if not os.path.exists(cwd + '/' + factorMatricesFileName):
# Perform CP decomposition via ALS
tensor = tensor.astype(float)
print("Performing CP Decomposition...")
factors = parafac(tensor=tensor, rank=k, n_iter_max=150, init='random')
np.save(factorMatricesFileName, factors)
else:
factors = np.load(factorMatricesFileName)
print("Factor Matrices created")
indexToSpaceIds = {0: user_list, 1: image_list, 2: loc_list}
def createGroups(factor_index):
# Create k non-overlapping groups
f_matrix = factors[factor_index] # factor matrix to be used
groups = []
for i in range(k):
groups.append([])
for j in range(f_matrix.shape[0]):
# Assign object to one of k groups/latent-features that it has highest membership towards
object_id = indexToSpaceIds[factor_index][
j] # Map indices back to user/image/location id's
group_index = np.argmax(f_matrix[j])
groups[group_index].append(object_id)
return groups
groupsList = Parallel(n_jobs=num_cores - 1)(delayed(createGroups)(i)
for i in [0, 1, 2])
# Output Results
with open("task7_output.txt", "w") as f:
userGroups = groupsList[0]
f.write("\n********** K-USER GROUPS **********\n")
for i in range(k):
printGroups(userGroups, i, f)
imageGroups = groupsList[1]
f.write("\n********** K-IMAGE GROUPS **********\n")
for i in range(k):
printGroups(imageGroups, i, f)
locGroups = groupsList[2]
f.write("\n********** K-LOCATION GROUPS **********\n")
for i in range(k):
printGroups(locGroups, i, f)
def inferred_bsa(job, dataset_name, cdd, cores=NUM_WORKERS):
job.log("INF CDD {}".format(cdd))
cdd_bsa_path = os.path.join(get_interfaces_path(dataset_name),
"by_superfamily", str(int(cdd)), str(int(cdd)))
if not os.path.isfile(cdd_bsa_path + "_bsa.h5"):
job.log("observed bsa must exist")
return
print("Reading obs bsa")
store = pd.HDFStore(unicode(cdd_bsa_path + "_bsa.h5"))
# if "/inferred" in store.keys():
# return
try:
cdd_obs_bsa = store.get("/observed")
except KeyError:
raise RuntimeError("Must calculate observed BSAs first")
try:
cdd_obs_bsa = cdd_obs_bsa[[
"obs_int_id", "bsa", "c1_asa", "c2_asa", "face1_asa", "face2_asa",
"complex_asa", "ppi_type"
]]
except KeyError:
job.log("Failed due to column select {}".format(cdd_obs_bsa.columns))
raise
cdd_obs_bsa = cdd_obs_bsa.rename(
columns={
"obs_int_id": "nbr_obs_int_id",
"bsa": "obs_bsa",
"c1_asa": "c1_asa_obs",
"face1_asa": "face1_asa_obs",
"complex_asa": "complex_asa_obs",
"ppi_type": "ppi_type_obs"
})
inf_interactome_path = unicode(cdd_bsa_path + ".inferred_interactome")
try:
print("Reading inf interactome")
int_store = pd.HDFStore(unicode(cdd_bsa_path +
".inferred_interactome"))
if "/table" not in int_store.keys():
return
m = re.search("nrows->(\d+)", int_store.info())
if not m:
int_store.close()
job.log("Unable to read inferred interactome")
return
if int(m.group(1)) > 1000000:
int_store.close()
return inferred_bsa_dask(cdd_obs_bsa, cdd_bsa_path)
inf_interactome = int_store.get(
"/table"
) #pd.read_hdf(unicode(cdd_bsa_path+".inferred_interactome"), "table").reset_index()
except MemoryError:
return inferred_bsa_dask(cdd_obs_bsa, cdd_bsa_path)
if inf_interactome.shape[0] > 1000000:
int_store.close()
del inf_interactome
return inferred_bsa_dask(cdd_obs_bsa, cdd_bsa_path)
inf_interactome = pd.merge(inf_interactome,
cdd_obs_bsa,
how="left",
on="nbr_obs_int_id")
#Remove redundant interfaces
inf_interactome = inf_interactome.groupby(
["mol_sdi", "nbr_obs_int_id", "mol_sdi_from", "mol_sdi_to"],
as_index=False).nth(0).reset_index(drop=True).copy()
bsa = Parallel(n_jobs=NUM_WORKERS)(delayed(get_asa)(group) for _, group in \
inf_interactome.groupby(["mol_sdi", "nbr_obs_int_id"], as_index=False))
bsa = pd.concat(bsa, axis=1).T
bsa = bsa.astype({
"mol_sdi": np.float64,
"nbr_obs_int_id": np.float64,
"c1_asa": np.float64,
"face1_asa": np.float64,
"bsa": np.float64,
"complex_asa": np.float64,
"pred_ratio": np.float64,
"ppi_type": str
})
inf_interactome = pd.merge(inf_interactome,
bsa,
how="left",
on=["mol_sdi", "nbr_obs_int_id"])
inf_interactome.to_hdf(unicode(cdd_bsa_path + "_bsa.h5"),
"inferred",
format='table',
append=True,
complevel=9,
complib="bzip2")
print(unicode(cdd_bsa_path + "_bsa.h5"))
int_store.close()
def observed_bsa(job, dataset_name, cdd, cores=NUM_WORKERS):
job.log("CDD {}".format(cdd))
prefix = os.path.join(get_interfaces_path(dataset_name), "by_superfamily",
str(int(cdd)), str(int(cdd)))
# if os.path.isfile(prefix+"_bsa.h5"):
# store = pd.HDFStore(unicode(prefix+"_bsa.h5"))
# if "/observed" in store.keys():
# store.close()
# return
# store.close()
cdd_interactome_path = prefix + ".observed_interactome"
cdd_interactome = pd.read_hdf(unicode(cdd_interactome_path), "table")
if cdd_interactome.shape[0] == 0:
job.log("CDD observed interactome is empty -- FIX!!!")
return
if cdd_interactome.shape[0] == 0:
job.log(
"CDD observed interactome contains intra-chain PPI, skipped -- FIX!!!"
)
return
#Remove redundant interfaces
cdd_interactome = cdd_interactome.groupby(
["obs_int_id", "mol_sdi_from", "mol_sdi_to"],
as_index=False).nth(0).reset_index(drop=True).copy()
if "mol_sdi" in cdd_interactome:
key = "mol_sdi"
elif "mol_sdi_id" in cdd_interactome:
key = "mol_sdi_id"
else:
raise RuntimeError("sdi not in df")
bsa = Parallel(n_jobs=NUM_WORKERS)(delayed(get_bsa)(group) for _, group in \
cdd_interactome.groupby(key, as_index=False))
bsa = pd.concat(bsa, axis=1).T
bsa[key] = bsa[key].astype(int)
bsa = bsa.astype({
"bsa": np.float64,
"c1_asa": np.float64,
"c2_asa": np.float64,
"complex_asa": np.float64,
"face1_asa": np.float64,
"face2_asa": np.float64,
"ppi_type": str
})
cdd_interactome = pd.merge(cdd_interactome, bsa, how="left", on=key)
cdd_interactome.to_hdf(unicode(prefix + "_bsa.h5"),
"observed",
table=True,
format='table',
complevel=9,
complib="bzip2")
print(unicode(prefix + "_bsa.h5"))
