def set_nthreads(nthreads):
"""
set_nthreads(nthreads)
Sets the number of threads to be used during bcolz operation.
This affects to both Blosc and Numexpr (if available). If you want to
change this number only for Blosc, use `blosc_set_nthreads` instead.
Parameters
----------
nthreads : int
The number of threads to be used during bcolz operation.
Returns
-------
out : int
The previous setting for the number of threads.
See Also
--------
blosc_set_nthreads
"""
nthreads_old = bcolz.blosc_set_nthreads(nthreads)
if bcolz.numexpr_here:
bcolz.numexpr.set_num_threads(nthreads)
return nthreads_old
def set_nthreads(nthreads):
"""
set_nthreads(nthreads)
Sets the number of threads to be used during bcolz operation.
This affects to both Blosc and Numexpr (if available). If you want to
change this number only for Blosc, use `blosc_set_nthreads` instead.
Parameters
----------
nthreads : int
The number of threads to be used during bcolz operation.
Returns
-------
out : int
The previous setting for the number of threads.
See Also
--------
blosc_set_nthreads
"""
nthreads_old = bcolz.blosc_set_nthreads(nthreads)
if bcolz.numexpr_here:
bcolz.numexpr.set_num_threads(nthreads)
return nthreads_old
import time
from tqdm import tqdm
import h5py # for saving later usable files
import gc
from glob import glob
from sklearn.metrics import fbeta_score
from sklearn.model_selection import StratifiedKFold
import tensorflow as tf
import cv2
import bcolz
bcolz.blosc_set_nthreads(4)
bcolz.numexpr.set_num_threads(4)
#from joblib import Parallel, delayed
import image_ml_ext #modified ImageDataGenerator
import random
random_seed = 2017
random.seed(random_seed)
np.random.seed(random_seed)
def f2_score(y_true, y_pred):
# from https://www.kaggle.com/teasherm/keras-metric-for-f-score-tf-only
y_true = tf.cast(y_true, "int32")
y_pred = tf.cast(tf.round(y_pred),
"int32") # implicit 0.5 threshold via tf.round
"""
from __future__ import absolute_import
import os
import sys
sys.setrecursionlimit(8192)
import time
import re
import shutil
import zlib
import numpy as np
import bcolz
import numexpr as ne
bcolz.blosc_set_nthreads(2)
ne.set_num_threads(2)
import sqlalchemy as sql
from . import database
from . import compression
from .gemini_utils import get_gt_cols
def get_samples(metadata):
return [x['name'] for x in metadata.tables['samples'].select().order_by("sample_id").execute()]
def get_n_variants(cur):
return next(iter(cur.execute(sql.text("select count(*) from variants"))))[0]
def get_bcolz_dir(db):
if not "://" in db: