text string |
|---|
<filename>prediction/bimod/BACs_and_TERF/cefprox_ccs_comparison.py
#!/Library/Frameworks/Python.framework/Versions/3.8/bin/python3
"""
"""
from matplotlib import pyplot as plt
import json
import numpy as np
from scipy.optimize import curve_fit
import sys
fset = sys.argv[1]
# set up plot fonts
from matplotlib impo... |
<gh_stars>0
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from scipy import signal
import time
import os
import argparse
parser = argparse.ArgumentParser(description='csv2txts')
parser.add_argument('--path', default='test2', type=str, metavar='PATH',help='csvs path')
args = parser.parse_args()... |
from __future__ import division
import refnx
from refnx.reflect import structure, ReflectModel, SLD
from refnx.dataset import ReflectDataset
from refnx.analysis import Transform, CurveFitter, Objective, GlobalObjective, Parameter
import numpy as np
import scipy
import matplotlib.pyplot as plt
import matplotlib.gridspe... |
<gh_stars>0
# -*- coding: utf-8 -*-
#"""Untitled1.ipynb
#Automatically generated by Colaboratory.
#Original file is located at
# https://colab.research.google.com/drive/105QoVdeDZbSv4YOPECOv3ZPRNU0Z1jhi
#"""
#from google.colab import drive
#drive.mount('/content/gdrive')
import sys
from bitarray import bitarray
... |
"""
A container for functions which aim to analyze or process gwas results, for some aim.
Author: <NAME>
Email: <EMAIL>
"""
import scipy as sp
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import warnings
import itertools as it
import random
import phenotypeData as pd
import math
def ca... |
"""
API resource class, retrieve attriubte data from database
Parameters can be passed with url using GET requests
required
:param attribute: attribute name(s)
:type attribute: string
:return The requested attribute details from the database
:rtype: JSON
OR
:param attributedata: attribute name(s)
:type... |
<reponame>dbstein/pybie2d
import numpy as np
import scipy as sp
import scipy.signal
import warnings
import os
from ..boundary import Boundary
from .laplace_slp_self_kress import Laplace_SLP_Self_Kress
from .stokes_slp_self_kress import Stokes_SLP_Self_Kress
from .laplace_cslp_self_kress import Laplace_CSLP_Self_Kress
... |
<gh_stars>10-100
"""
qtl.py contains wrappers around C++ Limix objects to streamline common tasks in GWAS.
"""
import scipy as SP
import scipy.stats as ST
import limix
import limix.utils.preprocess as preprocess
import limix.deprecated.modules.varianceDecomposition as VAR
import limix.utils.fdr as FDR
import time
#TO... |
import sys,os
import numpy as np
import pandas as pd
import h5py
import math
from scipy.stats import entropy
from collections import Counter
import pickle
# Get Euclidean Norm minus One
def get_ENMO(x,y,z):
enorm = np.sqrt(x*x + y*y + z*z)
ENMO = np.maximum(enorm-1.0, 0.0)
return ENMO
# Get tilt angles
def get_... |
<reponame>terhardt/DO-progression
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import joblib as jl
from code.model import linear_ramp
from code.plotting import parcolors
from scipy.stats import gaussian_kde
def calc_med_iqr(y, q=[5, 95], axis=None):
qs = np.percentile(y, [q[0], 50, q[-1]... |
"""
Python interface module for OSQP solver v0.6.2.post0
"""
from __future__ import print_function
from builtins import object
import rlqp._osqp as _osqp # Internal low level module
import numpy as np
import scipy.sparse as spa
from warnings import warn
from platform import system
import rlqp.codegen as cg
import rlqp... |
from .. import MagnetisationData
from . import plot_tools
import numpy as np
import click
import scipy.spatial as ss
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider
# import matplotlib
# from matplotlib import rcParams
from mpl_toolkits.axes_grid1 import make_axes_locatable
# -------------------... |
<filename>week_12_quantumChemistry1/utils2.py
import sys
version=sys.version_info.major
import os
import numpy as np
import scipy as sp
import scipy.linalg as spla
import matplotlib.pyplot as plt
import matplotlib.ticker as mtick
import matplotlib as mpl
try:
from colorama import Fore,Back,Style
from colorama i... |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 5 12:03:32 2020
Posprocessing functions
@author: jmon
"""
import numpy as np
from neepy import Neepy
import scipy.linalg as matrix
from functions_neepy import partial_trace, partial_trace_mul
from scipy.constants import k
sx = np.array([[0,1],[1,0]... |
""" Some common functions and constants for all of CLAM.
"""
SUBSAMPLE_LIMIT = 100
BATCH_SIZE = 10_000
EPSILON = 1e-8
def catch_normalization_mode(mode: str) -> None:
from typing import List
""" Make sure that the normalization mode is allowed. """
modes: List[str] = ['linear', 'gaussian', 'sigmoid']
... |
<reponame>LLNL/MaPPeRTrac<gh_stars>1-10
#!/usr/bin/env python3
import os,sys,glob,multiprocessing,time,csv,math,pprint,shutil,platform,fcntl,errno,tempfile,json,psutil,random
import scipy.io
import numpy as np
from parsl.app.app import python_app
from os.path import *
from mappertrac.subscripts import *
EDGE_LIST = 'd... |
import itertools
import os
import sys
import amici.petab_import
import git
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import petab
import petab.C as C
import pytest
import scipy.stats
import pyabc.petab
import pyabc.petab.base
@pytest.fixture(
params=itertools.product(
[petab... |
from skimage import io, filters, feature, measure, morphology, util
import numpy as np
from skimage.draw import polygon
from scipy import ndimage
from skimage.external.tifffile import TiffFile
import re
import alphashape
from joblib import Parallel, delayed
def bounding_box(viewer, img, DAPI_Ch=0):
z,x,y = img.sh... |
#!/usr/bin/env python3
# Linear programming bound on rank of different functions.
# This could almost certainly be simplified, but here we're
# trying to emphasize clarity.
# This includes several constraints; not all of them may be useful.
import numpy as np
import scipy.optimize
import scipy.special
class LpBound:... |
<reponame>GaffaSnobb/kshell-utilities
import sys, time, warnings
from typing import Union, Tuple, Optional
from fractions import Fraction
from itertools import chain
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import chi2
from scipy.optimize import curve_fit
from .parameters import flags
def cr... |
import numpy as np
from supporting_functions import p_stabilize
from plot_drawings import show_2d_array, quick_hist, correlation_plot
from chiffatools.dataviz import smooth_histogram
from scipy.stats import norm
# TODO: cell_drug_replicates analysis
# TODO: plate_specific noise level : correlation between T0 and TF di... |
import sys
import requests
import re
import discord
import logging
import argparse
import os
import random
from metno_locationforecast import Place, Forecast
import random
import giphy_client
from giphy_client.rest import ApiException
import xml.etree.ElementTree as ET
import datetime as dt
import statistics as s
impor... |
<gh_stars>1-10
from PyQt5.QtCore import *
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from SMLMUtil import SMLM
from scipy import ndimage
import numpy as np
import time, os
import matplotlib.pyplot as plt
# ********************************
# ******* resolution window ******
# ******************************... |
<filename>python/mxnet/gluon/probability/distributions/utils.py<gh_stars>1-10
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
#... |
# -*- coding: utf-8 -*-
import time as tim
import matplotlib.pyplot as plt
import numpy as np
from scipy.cluster.hierarchy import cut_tree, dendrogram, linkage
from scipy.constants import pi
from scipy.interpolate import interp1d as interp1d
from .boreholes import Borehole, _EquivalentBorehole, find_duplicates
from .... |
<reponame>linklab/link_rl<gh_stars>1-10
'''
Example taken from Balaji et al.
Paper: https://arxiv.org/abs/1911.10641
GitHub: https://github.com/awslabs/or-rl-benchmarks
'''
import gym
from gym import spaces
import or_gym
from or_gym.utils import assign_env_config
import random
import numpy as np
from scipy.stats import... |
<gh_stars>1-10
# -*- coding: utf-8 -*-
#
"""
<NAME>,
Approximate Calculation of Multiple Integrals,
Prentice Hall, 1971.
"""
from __future__ import division
import numpy
import sympy
from . import rabinowitz_richter
from . import stroud_secrest
from ..helpers import untangle
def _gen4_1(symbolic):
frac = sympy.... |
"""
Set of functions to generate synthetic data for experiments as in
the paper "Clustering network layers with the strata multilayer
stochastic block model"
"""
import numpy as np
import numpy.random as npr
import sys
import pickle
import time
import pdb
from random import randint
import scipy as sp
from scipy.stats i... |
"""
Implementation of the method proposed in the paper:
'Adversarial Attacks on Graph Neural Networks via Meta Learning'
by <NAME>, <NAME>
Published at ICLR 2019 in New Orleans, USA.
Copyright (C) 2019
<NAME>
Technical University of Munich
"""
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import numpy as ... |
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
u"""
Created by <NAME> at 2021.03.16
This is migrated from Zhou's code
"""
import numpy as np
import scipy.stats as sts
from matplotlib import pylab
from plot.utils import *
def plot_sideplot(
read_depth_object,
sample_info,
graph_coords,
ax_var,
fon... |
<filename>cosmos/latex_ocr/img2latex.py
import sys, os
sys.path.append(os.path.dirname(__file__))
import random
import re
from scipy.misc import imread
import PIL
from PIL import Image
import os
import uuid
from imgaug import augmenters as iaa
from model.img2seq import Img2SeqModel
from model.utils.general import Conf... |
import streamlit as st
from streamlit_ace import st_ace
import types
import sympy as sm
from sympy.abc import *
from pchem import solve
# See
# https://discuss.streamlit.io/t/take-code-input-from-user/6413/2?u=ryanpdwyer
# import random, string
# import importlib
# import os
# def import_code(code, name):
# ... |
<reponame>jessicaleete/numerical_computing
import matplotlib
matplotlib.rcParams = matplotlib.rc_params_from_file('../../matplotlibrc')
from matplotlib import pyplot as plt
import numpy as np
from scipy import linalg as la
from scipy import optimize as opt
def newtonsMethod1d(f, df, ddf, x, niter=10):
'''
Per... |
<reponame>jifengting1/fastpliFork
# -*- coding: utf-8 -*-
"""
Methods for calculating and applying affine transformation to coordinates and images.
"""
import numpy as np
import scipy.interpolate
import numba
def _replace_mat_row(B, r, d):
return np.linalg.det(np.delete(np.vstack([r, B]), (d + 1), axis=0))
@n... |
<filename>examples/pinn_inverse/Navier_Stokes_inverse.py
"""Backend supported: tensorflow.compat.v1, tensorflow, pytorch
An inverse problem of the Navier-Stokes equation of incompressible flow around cylinder with Re=100
References: https://doi.org/10.1016/j.jcp.2018.10.045 Section 4.1.1
"""
import deepxde as dde
im... |
<filename>demo.py
#!/usr/bin/env python
from random import random
from sympy import *
class Supply:
def __init__(self, file):
self.pair = {}
self.satisfy_demand = {}
with open(file, 'r') as f:
for line in f:
line = line.strip()
if line.startswi... |
<gh_stars>1-10
import numpy as np
import math as mth
import matplotlib.pyplot as plt
from mpl_toolkits import axes_grid1
from astropy.io import fits
import math as m
import sys
from scipy.optimize import curve_fit
import astropy.units as u
import astropy.coordinates as coord
from astropy.wcs import WCS
def fit(x,y,y... |
<gh_stars>0
import functools
import warnings
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import pandas as pd
import os
from scipy.stats import poisson
from scipy.special import logsumexp
from sklearn.neighbors import DistanceMetric
from sklearn.decomposition import PCA, NMF
from sklearn.me... |
<reponame>robbje/eis
#!/usr/bin/env python2
import json
import numpy as np
import scipy.signal
from scipy.optimize import leastsq
import matplotlib.pyplot as plt
from copy import deepcopy
class Spectrum(object):
def __init__(self):
self.omega = []
self.Z = []
@classmethod
def fromExperim... |
<reponame>mherde/modAL<gh_stars>0
import numpy as np
import itertools
from scipy.special import factorial, gammaln
from modAL.utils.parzen_window_classifier import PWC
from typing import Tuple
import numpy as np
from scipy.stats import entropy
from sklearn.exceptions import NotFittedError
from sklearn.base import Ba... |
# -*- coding: utf-8 -*-
# Copyright 2020 the HERA Project
# Licensed under the MIT License
"""
abscal.py
---------
Calibrate measured visibility
data to a visibility model using
linearizations of the (complex)
antenna-based calibration equation:
V_ij,xy^data = g_i_x * conj(g_j_y) * V_ij,xy^model.
Complex-valued para... |
"""
:author:
<NAME> (<EMAIL>)
2021
:License:
This package is published under Simplified BSD License.
"""
"""
This script extracts and converts audio samples from Common Voice.
"""
import os
import pydub
import argparse
from threading import Thread
import numpy as np
import scipy.io.wavfile as wav
import shutil
from... |
import math
from statistics import mean
from pm4py.objects.conversion.log import converter
from pm4pymdl.algo.mvp.utils import succint_mdl_to_exploded_mdl
from collections import Counter
def apply(df, parameters=None):
if parameters is None:
parameters = {}
stream = get_stream_from_dataframe(df, pa... |
<gh_stars>10-100
import scipy.signal
import numpy as np
def _spectrogram(samplerate, signal, window="hamming", winlen=0.02, winstep=0.01, nfft=512):
nperseg = int(winlen * samplerate)
noverlap = int(winstep * samplerate)
f, t, Sxx = scipy.signal.spectrogram(signal, samplerate, window, nperseg=nperseg, noverlap=n... |
from load import ROOT as R
import gna.constructors as C
import numpy as N
from collections import OrderedDict
from gna.bundle import *
from scipy.interpolate import interp1d
class reactor_anu_freemodel_v01(TransformationBundleLegacy):
debug = False
def __init__(self, *args, **kwargs):
super(reactor_an... |
""" This contains Thiel analysis plots """
from os import read, path
# import px4tools
import numpy as np
import math
import io
import os
import sys
import errno
import base64
from db_entry import *
import pickle
import simstats # this the module that you can modify to add your own stats
#import thiel_analysis
fr... |
<gh_stars>0
import clamp_ephys
import pandas as pd
import os
import scipy
import matplotlib
%matplotlib
import matplotlib.pyplot as plt
import numpy as np
'''####################### SET PROPER PATH_TO_DATA_NOTES ########################## '''
data_path = os.path.join(os.getcwd(), 'test_data', 'p2_data_notes.csv')
'''... |
<filename>openhgnn/models/HPN.py
"""
This model shows an example of using dgl.metapath_reachable_graph on the original heterogeneous
graph.
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import dgl
from scipy import sparse as sp
from . import BaseModel, register_model
from d... |
<filename>ML/gtsdb/semantic_seg.py
#!/usr/bin/env python
"""Semantic Segmentation experiment."""
from keras.models import load_model
from keras.models import Model
from keras.layers import UpSampling2D
import scipy.misc
import numpy as np
from PIL import Image
import logging
import sys
logging.basicConfig(format='%(... |
<gh_stars>1-10
import statistics
import ast
import os
import matplotlib.pyplot as plt
import numpy as np
import urllib.request
from bs4 import BeautifulSoup
script_directory = str(os.path.dirname(os.path.realpath(__file__)))
file_name = "prelimsavefile.txt"
path_to_file = script_directory + '\\' + file_name
"""
READM... |
import numpy as np
# import scipy.stats
# import scipy.special
from scipy.special import gammaln
try:
import xarray as xr
except ImportError:
xr = None
class NegativeBinomial:
r"""
Negative binomial distribution.
This class supports re-parameterising, sampling and calculation of
probabilities... |
<filename>corems/molecular_id/calc/math_distance.py
import numpy as np
import scipy.stats
'''exploratory module based on Yuanyue Li code at
TODO add GitHub and Paper here'''
def entropy_distance(v, y):
merged = v + y
entropy_increase = 2 * scipy.stats.entropy(merged) - scipy.stats.entropy(v) - scipy.stats.en... |
from sympy import Eq, Symbol, Derivative, Basic
from compartor.compartments import Moment, Expectation, _getNumSpecies, get_missing_moments
from IPython.core.display import display, Markdown
###################################################
#
# Displaying reaction networks and moment equations
# in jupyter notebook... |
<reponame>princeton-computational-imaging/NLOSFeatureEmbeddings
import numpy as np
import cv2
from helper import definePsf, resamplingOperator
##########################################################
def lct(meas_hxwxt, wall_size, crop, bin_len):
c = 3e8
width = wall_size / 2.0;
bin_resolution = ... |
<gh_stars>0
from os import path
import json, time, numpy as np, pandas as pd, datetime, copy, re, traceback, multiprocessing as mp
from scipy.spatial import distance
# function for solving instance
def meta_zone(zone):
m = re.match('[A-Z]+(?=-)', zone)
higher_meta = m.group(0) if m else zone
m_ = re... |
import json
import collections
import numpy as np
from scipy.stats import multivariate_normal
# import matplotlib.pyplot as plt
def parse_json_parameters(func):
def inner(*args, **kwargs):
print(args, kwargs)
args = [json.loads(value) if type(value) is str else value
... |
# -------------------------------------------------------------------
# ibool reader.
#
# Author: <NAME>
# Email: <EMAIL>
# -------------------------------------------------------------------
from seisgen.util_SPECFEM3D import NGLLX, NGLLY, NGLLZ, CONSTANT_INDEX_27_GLL
from scipy.io import FortranFile
import numpy as ... |
<gh_stars>0
from mpmath import *
from sympy import *
def k_1(func, k, n, f, t0):
for i in range(k, n+1):
k0 = func.subs([(y,f[0]),(t,t0)])
y_prox = f[0] + h* k0
f[0] = y_prox
print (str(i) + ' ' + str(y_prox))
t0=t0+h
def k_2(func, k, n, f, t0):
for i in... |
<filename>gprpy/mergeProfiles.py
import gprpy.gprpy as gp
import numpy as np
from scipy.ndimage import zoom
def mergeProfiles(file1,file2,outfile,gapfill=0):
'''
Merges two GPR profiles by placing the second one at the end
of the first one.
Make sure you preprocessed them in GPRPy and save ... |
import argparse
import csv
import logging
import math
import time
from datetime import datetime
from pathlib import Path
from statistics import mean, stdev
import numpy as np
import fem
from feat import mesh
def main():
# argument parser creation and setup
desc = (
"Complete an RVE analysis for the ... |
# -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 <NAME>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of... |
import numpy as np
import matplotlib.pyplot as plt
import random
from scipy.signal import convolve2d
import math
from scipy import misc
import os
from PIL import Image
from numba import jit
import cv2
import scipy.misc
np.set_printoptions(threshold=np.inf)
def S_UNIWARD(coverPath, payload):
sgm = 1
## Get 2D ... |
<filename>pyNastran/op2/op2_interface/random_results.py
from typing import Dict, Any
import numpy as np
class RandomObjects:
prefix = ''
postfix = ''
def __init__(self):
self.displacements = {}
self.velocities = {}
self.accelerations = {}
self.load_vectors = {}
self.... |
<gh_stars>0
# qa_images.py
import os
import logging
import numpy as np
def do_diff(test, mast, nodata=False):
"""Do image diff, break if the grids are not the same size.
Args:
test <numpy.ndarray>: array of test raster
mast <numpy.ndarray>: array of master raster
"""
if nodata:
... |
<reponame>gianmatharu/Aniso
import numpy as np
from scipy.ndimage.filters import gaussian_filter
# math utilities
def eigsorted(A):
"""
Return sorted eigenvalues and eigenvec... |
<filename>cognigraph/gui/source_obj.py
"""Base class for objects of type source."""
from warnings import warn
import logging
import numpy as np
from scipy.spatial.distance import cdist
from vispy import scene
from vispy.scene import visuals
import vispy.visuals.transforms as vist
# from ._projection import _project_s... |
from __future__ import division, print_function
from scipy.special import logsumexp
from ._global_imports import *
from . import _precision
from getdist.plots import getSubplotPlotter
from getdist.mcsamples import MCSamples
try:
from nestcheck.ns_run_utils import get_logw, get_w_rel
from nestcheck.plots im... |
<filename>particlezoo/parsers/transform.py
from __future__ import annotations
from particlezoo.builders.lagrangian import Lagrangian
from sympy import sympify, Matrix
from liesym import SU, SO, U1, Sp, Z, E, Group, LieGroup
from typing import Dict, Union
from ..builders import (SymmetryGroup, Symmetry,
... |
<gh_stars>0
"""
Module for performing two-dimensional coaddition of spectra.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
import os
import copy
from IPython import embed
import numpy as np
from scipy import ndimage
from matplotlib import pyplot as plt
... |
"""
localization_detection.py
This script contains all methods used for localization and detection.
- parse_annotations: groundtruth localization, based on metadata annotation parsing
- ld_oracle: wrapper for parse_annotations methor
- ld_basic: diffuseness mask and simple event grouping by temporal continuity
- ld_ba... |
<reponame>vishaltiwari/XNet<filename>tools/thermo/plot_expansion_no_parser.py
import os,sys,itertools
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker as plticker
import matplotlib.gridspec as gridspec
import matplotlib.axes as plax
from datetime import datetime
from scipy import inter... |
<filename>miditoolkit/pianoroll/parser.py
import numpy as np
from copy import deepcopy
from scipy.sparse import csc_matrix
import miditoolkit.midi.containers as ct
PITCH_RANGE = 128
# def get_onsets_pianoroll():
# pass
# def get_offsets_pianoroll():
# pass
def notes2pianoroll(
note_stream_ori,
... |
from mmdet.apis import init_detector, inference_detector
import mmcv
import cv2
import numpy as np
from scipy import ndimage
config_file = '../configs/solov2/solov2_r50_fpn_8gpu_1x___.py'
# download the checkpoint from model zoo and put it in `checkpoints/`
checkpoint_file = '../work_dirs/solov2_12/epoch_12.pth'
# b... |
from dgdynamic.utils.project_utils import LogMixin, make_directory
from dgdynamic.config.settings import config
from dgdynamic.utils.plotter import matplotlib_plot
from scipy.interpolate import interpolate
import threading
import time
import csv
import matplotlib.pyplot as plt
import os.path
import enum
import collecti... |
<gh_stars>1-10
import statistics
import pytest
from telliot_feed_examples.feeds.eth_jpy_feed import eth_jpy_median_feed
@pytest.mark.asyncio
async def test_AssetPriceFeed():
"""Retrieve median ETH/JPY price."""
v, _ = await eth_jpy_median_feed.source.fetch_new_datapoint()
assert v is not None
asser... |
<filename>scripts/gauge_comparison.py
#!/usr/bin/env python
import os
import sys
import datetime
import scipy.io
import numpy as np
# Plot customization
import matplotlib
# Markers and line widths
matplotlib.rcParams['lines.linewidth'] = 2.0
matplotlib.rcParams['lines.markersize'] = 6
matplotlib.rcParams['lines.mar... |
from lrasm.homoscedasticity_tst import homoscedasticity_test
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn import linear_model
from matplotlib.pyplot import figure
from scipy import stats
def test_homoscedasticity_test():
"""Test homoscedasticity test outputs from dataset"""
... |
<reponame>sreichl/genomic_region_enrichment
#!/bin/env python
import pandas as pd
import pickle
import os
import numpy as np
import gseapy as gp
# utils for manual odds ratio calculation
def overlap_converter(overlap_str, bg_n, gene_list_n):
overlap_n, gene_set_n = str(overlap_str).split('/')
return odds_rati... |
#!/usr/bin/env python3
from itertools import accumulate, chain, combinations, groupby, permutations, product
from collections import deque, Counter
from bisect import bisect_left, bisect_right
from math import gcd, sqrt, sin, cos, tan, degrees, radians, ceil, floor
from fractions import Fraction
from decimal import Dec... |
<reponame>psteinb/HINT
import numpy as np
import torch
import time
import os
import matplotlib.pyplot as plt
import pickle
from tqdm import tqdm
from scipy.spatial import distance_matrix
from data import FourierCurveModel
# Choose data set
dataset = ('fourier_curve', 'fourier-curve')
# dataset = ('plus_shape', 'plus-... |
import warnings
import sympy
from xarray import DataArray
from weldx.asdf.types import WeldxConverter
from weldx.constants import META_ATTR
from weldx.core import MathematicalExpression
__all__ = ["MathematicalExpression", "MathematicalExpressionConverter"]
class MathematicalExpressionConverter(WeldxConverter):
... |
# -*- coding: utf-8 -*-
# @Time : 2021/4/12 12:59 上午
# @Author : <NAME>
# @FileName: main.py
# @Software: PyCharm
# @Blog ：https://lesliewongcv.github.io/
import numpy as np
import os
from scipy.io import loadmat
from sklearn.model_selection import KFold
def sigmoid(a, b, x):
return 1.0 / (1 + np.exp(-1... |
<reponame>QuESt-Calculator/pyscf
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apac... |
import time
import requests
import shutil
import os
import numpy as np
import matplotlib.pyplot as plt
import scipy.io.wavfile as wavfile
def download_file(file_url, headers, output_path):
args = {
"url": file_url,
}
url = "https://api.dolby.com/media/output"
# Create a request to download ... |
#! /usr/bin/env python3
import os
import gensim
import pickle
import string
import numpy as np
import pandas as pd
from scipy.stats import pearsonr
from nltk.corpus import stopwords
from gensim.models import Word2Vec
from nltk import word_tokenize
from nltk.stem import SnowballStemmer
from sklearn.feature_extraction.te... |
<reponame>Sumit1673/Projects
from matplotlib.colors import ListedColormap
import numpy as np
from random import seed
from math import exp
from random import random
import matplotlib.pyplot as plt
# Activation functions
sigmoid_functn = lambda x: 1/(1+ np.exp(-x))
sigmoid_derivative = lambda x: x * (1-x)
# Question(a... |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Oct 07 2019
@author: <NAME> <<EMAIL>>
"""
from typing import Union
import numpy as np
from scipy import sparse
from sknetwork.linalg import SVDSolver, LanczosSVD
from sknetwork.ranking.base import BaseRanking
from sknetwork.utils.check import check_format... |
<filename>src/eddington/fit_result.py
"""Fitting result class that will be returned by the fitting algorithm."""
from dataclasses import dataclass, field
from typing import Optional
import numpy as np
import scipy.stats as stats
from eddington.print_util import to_precise_string
@dataclass(repr=False) # pylint: di... |
<filename>cats/data_modules/combine.py<gh_stars>1-10
import numpy as np
from astropy import units as u
import matplotlib.pyplot as plt
from copy import deepcopy
from scipy.optimize import curve_fit
from scipy.ndimage.filters import gaussian_filter1d
from scipy.interpolate import RegularGridInterpolator
from astropy.nd... |
"""
A suite of functions for finding sources in images.
:Authors: <NAME>, <NAME>
:License: :doc:`LICENSE`
"""
import sys
import math
import numpy as np
from scipy import signal, ndimage
import stsci.imagestats as imagestats
from . import cdriz
__all__ = ['gaussian1', 'gausspars', 'gaussian', 'moments', 'errfunc'... |
import numpy as np
from scipy.interpolate import LinearNDInterpolator, interp1d, griddata
from scipy.spatial import cKDTree
from numpy import matlib
import discretize
from discretize import TensorMesh
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib import ticker
import warnings
from ....data i... |
<filename>src/utils.py
import time
import pathlib
import numpy as np
import json
from .log import logger
# Timing and Performance
import hdbscan
import umap
import umap.plot
import numpy as np
import pandas as pd
from scipy.spatial.distance import cdist
def timing_info(method):
def wrapper(*args, **kw):
s... |
import numpy as np
import cv2
from scipy import ndimage
def flow_visualization(u, v, dil_size=0):
H = u.shape[0]
W = u.shape[1]
hsv = np.zeros((H, W, 3))
# convert from cartesian to polar
mag, ang = cv2.cartToPolar(u, v)
hsv[:, :, 0] = ang * 180 / np.pi / 2
hsv[:, :, 2] = cv2.normalize(m... |
# noinspection PyPackageRequirements
import datawrangler as dw
import os
import sys
import numpy as np
import pandas as pd
import ast
import json
import datetime
import quail
import nltk
import warnings
import pickle
import datetime as dt
# noinspection PyPackageRequirements
from spellchecker import SpellChecker
from ... |
<gh_stars>10-100
from pylab import *
import argparse
import packages.primitive as primitive
import scipy.signal
parser = argparse.ArgumentParser(description='Generate polar view of the lines directions.')
parser.add_argument('primitivefile')
parser.add_argument('--shownormals', action="store_true", help="Shows the nor... |
import numpy as np
import pandas as pd
import scipy.integrate as integrate
import scipy.optimize as optimize
def simulate_JM_base(I, obstime, miss_rate=0.1, opt="none", seed=None):
if seed is not None:
np.random.seed(seed)
J = len(obstime)
#### longitudinal submodel... |
<reponame>joye1503/Distributed-Computing-Scripts
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Automatic assignment handler for Mlucas and CUDALucas.
[*] Revised by <NAME> and <NAME> for CUDALucas (2020)
Original Authorship(s):
* # EWM: adapted from https://github.com/MarkRose/primetools/blob/master/mfloo... |
<reponame>leggedrobotics/DeLORA
#!/usr/bin/env python3
# Copyright 2021 by <NAME>, Robotic Systems Lab, ETH Zurich.
# All rights reserved.
# This file is released under the "BSD-3-Clause License".
# Please see the LICENSE file that has been included as part of this package.
import scipy.spatial
class KDTreeBuilder:
... |
import pandas as pd
import numpy as np
import math
import statistics
import api.recrudescence_utils as recrudescence_utils
def calculate_frequencies3(genotypedata, alleles_definitions):
'''
Calculate frequencies of alleles
Using the input data table and alleles_definition
which contains the lower and upper break... |
### Diffusion_1D
# Time-stamp: <2015-07-21 09:33:37 marine>
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
## Tri Diagonal Matrix Algorithm(a.k.a Thomas algorithm) solver
def TDMAsolver(a, b, c, d):
'''
Solve the equation ax_{i-1}+bx_{i}+cx_{i+1}=d_{i} for x
TDMA solver, a b c d ca... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.