repo_name stringlengths 7 90 | path stringlengths 5 191 | copies stringlengths 1 3 | size stringlengths 4 6 | content stringlengths 976 581k | license stringclasses 15
values |
|---|---|---|---|---|---|
jdmcbr/blaze | blaze/compute/tests/test_bcolz_compute.py | 9 | 5874 | from __future__ import absolute_import, division, print_function
import pytest
bcolz = pytest.importorskip('bcolz')
from datashape import discover, dshape
import numpy as np
import pandas.util.testing as tm
from odo import into
from blaze import by
from blaze.expr import symbol
from blaze.compute.core import compu... | bsd-3-clause |
Garrett-R/scikit-learn | sklearn/decomposition/tests/test_dict_learning.py | 40 | 7535 | import numpy as np
from sklearn.utils.testing import assert_array_almost_equal
from sklearn.utils.testing import assert_array_equal
from sklearn.utils.testing import assert_equal
from sklearn.utils.testing import assert_true
from sklearn.utils.testing import assert_less
from sklearn.utils.testing import assert_raises
... | bsd-3-clause |
bobrock/eden | controllers/msg.py | 3 | 80604 | # -*- coding: utf-8 -*-
"""
Messaging Module - Controllers
"""
module = request.controller
resourcename = request.function
if not settings.has_module(module):
raise HTTP(404, body="Module disabled: %s" % module)
# -----------------------------------------------------------------------------
def index():
... | mit |
diegocavalca/Studies | phd-thesis/nilmtk/nilmtk/tests/test_elecmeter.py | 7 | 3716 | #!/usr/bin/python
from __future__ import print_function, division
import unittest
from os.path import join
import pandas as pd
from datetime import timedelta
from .testingtools import data_dir, WarningTestMixin
from ..datastore import HDFDataStore
from ..elecmeter import ElecMeter, ElecMeterID
from ..stats.tests.test_t... | cc0-1.0 |
zfrenchee/pandas | pandas/core/sparse/frame.py | 1 | 35133 | """
Data structures for sparse float data. Life is made simpler by dealing only
with float64 data
"""
from __future__ import division
# pylint: disable=E1101,E1103,W0231,E0202
import warnings
from pandas.compat import lmap
from pandas import compat
import numpy as np
from pandas.core.dtypes.missing import isna, notna... | bsd-3-clause |
weissj3/MWTools | SGRBHB/RADECCUTSParabolas.py | 1 | 9103 | import sys
sys.path.insert(0, '../Newby-tools/utilities')
import math as ma
import matplotlib.pyplot as plt
import astro_coordinates as ac
import operator
def Create_Line(x0, x1, y0, y1):
m = (y1 - y0)/(x1 - x0)
b = y1 - m * x1
return m,b
def ParabolaParams(x1, y1, x2, y2, x3, y3):
a = (x3*(y2-y1) + ... | mit |
ZhouJiaLinmumu/Grasp-and-lift-EEG-challenge | lvl1/genPreds_RNN.py | 4 | 6756 | # -*- coding: utf-8 -*-
"""
Created on Wed Jul 8 21:56:55 2015.
@author: rc, alex
"""
import os
import sys
if __name__ == '__main__' and __package__ is None:
filePath = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(filePath)
import pandas as pd
import numpy as np
import yaml
fro... | bsd-3-clause |
CristianCantoro/thes-discover | utils/graph.py | 1 | 2630 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#########################################################################
# Copyright (C) 2012 Cristian Consonni <cristian.consonni@gmail.com>.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | mit |
leaxp/mdl | LeNet/train_lenet.py | 1 | 2033 | # append the package folder to sys.path
import sys
sys.path.append("core")
# import the necessary packages
from core import LeNet
from sklearn.cross_validation import train_test_split
from sklearn.datasets.mldata import fetch_mldata
from keras.optimizers import SGD
from keras.utils import np_utils
import numpy as np
... | gpl-3.0 |
LCAV/pyroomacoustics | examples/adaptive_filter_stft_domain.py | 1 | 2975 | '''
Adaptive Filter in STFT Domain Example
======================================
In this example, we will run adaptive filters for system
identification, but in the frequeny domain.
'''
from __future__ import division, print_function
import numpy as np
from scipy.signal import fftconvolve
import matplotlib.pyplot a... | mit |
puruckertom/ubertool | ubertool/kabam/tests/test_kabam_integration.py | 1 | 58707 | from __future__ import division #brings in Python 3.0 mixed type calculation rules
import datetime
import inspect
import numpy.testing as npt
import os.path
import pandas as pd
import pkgutil
import sys
from tabulate import tabulate
import unittest
try:
from StringIO import StringIO
except ImportError:
from io... | unlicense |
ZENGXH/scikit-learn | examples/linear_model/plot_theilsen.py | 232 | 3615 | """
====================
Theil-Sen Regression
====================
Computes a Theil-Sen Regression on a synthetic dataset.
See :ref:`theil_sen_regression` for more information on the regressor.
Compared to the OLS (ordinary least squares) estimator, the Theil-Sen
estimator is robust against outliers. It has a breakd... | bsd-3-clause |
agiliq/django-graphos | graphos/renderers/matplotlib_renderer.py | 1 | 1757 | #Named such to not clash with matplotlib
from .base import BaseChart
import matplotlib
matplotlib.use('Agg') # http://stackoverflow.com/a/4706614/202168
import matplotlib.pyplot as plt
from matplotlib.ticker import FormatStrFormatter
try:
# python 2
from StringIO import StringIO
except ImportError:
# pyt... | bsd-2-clause |
hlin117/scikit-learn | sklearn/setup.py | 69 | 3201 | import os
from os.path import join
import warnings
from sklearn._build_utils import maybe_cythonize_extensions
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
import numpy
lib... | bsd-3-clause |
Xeralux/tensorflow | tensorflow/python/estimator/canned/dnn_linear_combined_test.py | 11 | 33691 | # Copyright 2017 The TensorFlow Authors. 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | apache-2.0 |
edonyM/emthesis | code/pca.py | 1 | 3616 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
# .---. .-----------
# / \ __ / ------
# / / \( )/ ----- (`-') _ _(`-') <-. (`-')_
# ////// '\/ ` --- ( OO).-/( (OO ).-> .-> \( OO) ) .->
# //// / // : : --- (,------... | mit |
SnowWalkerJ/quantlib | quant/common/decorators.py | 1 | 4754 | import os
from inspect import signature
from types import FunctionType
from functools import wraps, singledispatch, update_wrapper
import pandas as pd
from tables.exceptions import HDF5ExtError
from ..common.settings import DATA_PATH
from ..common.logging import Logger
class Localizer:
"""
把DataFrame缓存到本地hdf5... | gpl-3.0 |
fenech/aubio | python/demos/demo_keyboard.py | 14 | 2095 | #! /usr/bin/env python
def get_keyboard_edges(firstnote = 21, lastnote = 108):
octaves = 10
# build template of white notes
scalew = 12/7.
xw_temp = [i*scalew for i in range(0,7)]
# build template of black notes
scaleb = 6/7.
xb_temp = [i*scaleb for i in [1,3,7,9,11]]
xb,xw = [],[]
... | gpl-3.0 |
paulmorio/grusData | gradientDescent/example.py | 1 | 1349 | """
Example function that we want to minimize/maximize
"""
def sum_of_squares(v):
"""
Computers the sum of squared elemetns in v
"""
return sum(v_i ** 2 for v_i in v)
# Estimating the gradient
def difference_quotient(f, x, h):
return (f(x+h) - f(x))/h
# as h approaches 0
# now for some basic understanding of d... | mit |
sergpolly/Thermal_adapt_scripts | BOOTSTRAPS/compare_codon_bias.py | 2 | 6501 | import re
import os
import sys
from Bio import Seq
from Bio import SeqIO
from Bio import SeqUtils
import numpy as np
import pandas as pd
import cairi
from multiprocessing import Pool
import matplotlib.pyplot as plt
#MAYBE WE DONT NEED THAT ANYMORE ...
# # STUPID FIX TO AVOID OLDER PANDAS HERE ...
# # PYTHONPATH seems ... | mit |
donK23/shed01 | PyBeispiele/SherlockRec/simulate_ratings.py | 1 | 3646 | """
Name: simulate_ratings
Purpose: Create dummy data for a recommendation system based on collaborative filtering
Author: Thomas Treml (datadonk23@gmail.com)
Date: 31.08.2015
"""
import numpy as np
import pandas as pd
from sqlalchemy import create_engine, MetaData, Table, Column, Integer, VARCHAR, TIMESTAMP
""" DB ... | apache-2.0 |
jplourenco/bokeh | bokeh/compat/mplexporter/renderers/vega_renderer.py | 54 | 5284 | import warnings
import json
import random
from .base import Renderer
from ..exporter import Exporter
class VegaRenderer(Renderer):
def open_figure(self, fig, props):
self.props = props
self.figwidth = int(props['figwidth'] * props['dpi'])
self.figheight = int(props['figheight'] * props['dp... | bsd-3-clause |
mbayon/TFG-MachineLearning | vbig/lib/python2.7/site-packages/pandas/io/clipboard/__init__.py | 14 | 3443 | """
Pyperclip
A cross-platform clipboard module for Python. (only handles plain text for now)
By Al Sweigart al@inventwithpython.com
BSD License
Usage:
import pyperclip
pyperclip.copy('The text to be copied to the clipboard.')
spam = pyperclip.paste()
if not pyperclip.copy:
print("Copy functionality unav... | mit |
liyu1990/sklearn | sklearn/metrics/pairwise.py | 8 | 45133 | # -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | bsd-3-clause |
r39132/airflow | airflow/contrib/operators/hive_to_dynamodb.py | 21 | 4084 | # -*- coding: utf-8 -*-
#
# 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
# to you under the Apache License, Version 2.0 (the
#... | apache-2.0 |
lucidfrontier45/scikit-learn | examples/cluster/plot_dbscan.py | 5 | 2629 | # -*- coding: utf-8 -*-
"""
===================================
Demo of DBSCAN clustering algorithm
===================================
Finds core samples of high density and expands clusters from them.
"""
print __doc__
import numpy as np
from scipy.spatial import distance
from sklearn.cluster import DBSCAN
from sk... | bsd-3-clause |
cactusbin/nyt | matplotlib/lib/matplotlib/compat/subprocess.py | 4 | 2622 | """
A replacement wrapper around the subprocess module, with a number of
work-arounds:
- Provides the check_output function (which subprocess only provides from Python
2.7 onwards).
- Provides a stub implementation of subprocess members on Google App Engine
(which are missing in subprocess).
Instead of importing s... | unlicense |
mizzao/ggplot | ggplot/scales/scale_colour_gradient.py | 12 | 2017 | from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .scale import scale
from copy import deepcopy
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap, rgb2hex, ColorConverter
def colors_at_breaks(cmap, breaks=[0, 0.25, 0.5... | bsd-2-clause |
tdhopper/scikit-learn | sklearn/datasets/tests/test_20news.py | 280 | 3045 | """Test the 20news downloader, if the data is available."""
import numpy as np
import scipy.sparse as sp
from sklearn.utils.testing import assert_equal
from sklearn.utils.testing import assert_true
from sklearn.utils.testing import SkipTest
from sklearn import datasets
def test_20news():
try:
data = dat... | bsd-3-clause |
andrewnc/scikit-learn | sklearn/linear_model/tests/test_passive_aggressive.py | 169 | 8809 | import numpy as np
import scipy.sparse as sp
from sklearn.utils.testing import assert_less
from sklearn.utils.testing import assert_greater
from sklearn.utils.testing import assert_array_almost_equal, assert_array_equal
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.testing import assert_rais... | bsd-3-clause |
unnikrishnankgs/va | venv/lib/python3.5/site-packages/IPython/lib/latextools.py | 3 | 6248 | # -*- coding: utf-8 -*-
"""Tools for handling LaTeX."""
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
from io import BytesIO, open
import os
import tempfile
import shutil
import subprocess
from base64 import encodebytes
from IPython.utils.process import find_cmd... | bsd-2-clause |
bsipocz/astropy | astropy/units/tests/test_quantity.py | 1 | 53631 | # coding: utf-8
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Test the Quantity class and related.
"""
import copy
import pickle
import decimal
import numbers
from fractions import Fraction
import pytest
import numpy as np
from numpy.testing import (assert_allclose, assert_array_equal,
... | bsd-3-clause |
biofilos/cluster_genomics | cluster_strips.py | 1 | 4981 | import pandas as pd
from bokeh.plotting import figure, output_file, show, ColumnDataSource
from bokeh.io import export_svgs
from bokeh.models import HoverTool
from bokeh import palettes
import sys
"""
Cluster Strips
Goal: Plot clusters of several species
In order to reduce the clutter, information
of every gene will b... | gpl-3.0 |
CVML/scikit-learn | sklearn/linear_model/omp.py | 127 | 30417 | """Orthogonal matching pursuit algorithms
"""
# Author: Vlad Niculae
#
# License: BSD 3 clause
import warnings
from distutils.version import LooseVersion
import numpy as np
from scipy import linalg
from scipy.linalg.lapack import get_lapack_funcs
from .base import LinearModel, _pre_fit
from ..base import RegressorM... | bsd-3-clause |
HolgerPeters/scikit-learn | sklearn/externals/joblib/parallel.py | 33 | 32728 | """
Helpers for embarrassingly parallel code.
"""
# Author: Gael Varoquaux < gael dot varoquaux at normalesup dot org >
# Copyright: 2010, Gael Varoquaux
# License: BSD 3 clause
from __future__ import division
import os
import sys
from math import sqrt
import functools
import time
import threading
import itertools
fr... | bsd-3-clause |
ylow/SFrame | oss_src/unity/python/sframe/test/test_sarray_sketch.py | 5 | 12151 | '''
Copyright (C) 2016 Turi
All rights reserved.
This software may be modified and distributed under the terms
of the BSD license. See the LICENSE file for details.
'''
# from nose import with_setup
# -*- coding: utf-8 -*-
from ..data_structures.sarray import SArray
import pandas as pd
import numpy as np
import unitte... | bsd-3-clause |
sonnyhu/scikit-learn | sklearn/linear_model/tests/test_base.py | 83 | 15089 | # Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
#
# License: BSD 3 clause
import numpy as np
from scipy import sparse
from scipy import linalg
from itertools import product
from sklearn.utils.testing import assert_array_almost_equal
from sklearn.utils... | bsd-3-clause |
nixingyang/Kaggle-Competitions | Shelter Animal Outcomes/XGBoost.py | 1 | 7423 | from copy import deepcopy
from sklearn.cross_validation import StratifiedKFold, StratifiedShuffleSplit
from xgboost.sklearn import XGBClassifier
import numpy as np
N_FOLDS = 5
CV_NUM = 1
EVAL_METRIC = "mlogloss"
EARLY_STOPPING_ROUNDS = 100
N_ESTIMATORS = 1000000
OBJECTIVE = "multi:softprob"
GET_BEST_SCORE_INDEX = np.a... | mit |
giorgiop/scikit-learn | examples/mixture/plot_gmm_sin.py | 103 | 6101 | """
=================================
Gaussian Mixture Model Sine Curve
=================================
This example demonstrates the behavior of Gaussian mixture models fit on data
that was not sampled from a mixture of Gaussian random variables. The dataset
is formed by 100 points loosely spaced following a noisy ... | bsd-3-clause |
costypetrisor/scikit-learn | examples/semi_supervised/plot_label_propagation_digits.py | 268 | 2723 | """
===================================================
Label Propagation digits: Demonstrating performance
===================================================
This example demonstrates the power of semisupervised learning by
training a Label Spreading model to classify handwritten digits
with sets of very few labels.... | bsd-3-clause |
samsammurphy/ee-atmcorr-timeseries | atmcorr/plots.py | 1 | 1623 | import pandas as pd
from matplotlib import pylab as plt
import matplotlib.dates as mdates
def figure_plotting_space():
"""
defines the plotting space
"""
fig = plt.figure(figsize=(10,10))
bar_height = 0.04
mini_gap = 0.03
gap = 0.05
graph_height = 0.24
axH = fig.add_axes([0.1,ga... | apache-2.0 |
aestrivex/mne-python | examples/realtime/rt_feedback_server.py | 8 | 4955 | """
==============================================
Real-time feedback for decoding :: Server Side
==============================================
This example demonstrates how to setup a real-time feedback
mechanism using StimServer and StimClient.
The idea here is to display future stimuli for the class which
is pred... | bsd-3-clause |
iandriver/RNA-sequence-tools | RNA_Seq_analysis/cluster.py | 2 | 33129 | import cPickle as pickle
import numpy as np
import pandas as pd
import os
from subprocess import call
import matplotlib
matplotlib.use('QT4Agg')
import matplotlib.pyplot as plt
from matplotlib.ticker import LinearLocator
import scipy
import json
from sklearn.decomposition import PCA as skPCA
from scipy.spatial.distance... | mit |
SuLab/scheduled-bots | scheduled_bots/civic/make_drug_list.py | 1 | 1969 | from collections import defaultdict
import requests
from tqdm import tqdm
import json
r = requests.get('https://civic.genome.wustl.edu/api/variants?count=999999999')
variants_data = r.json()
records = variants_data['records']
all_data = dict()
for record in tqdm(records):
variant_id = str(record['id'])
r = r... | mit |
JeanKossaifi/scikit-learn | examples/decomposition/plot_ica_vs_pca.py | 306 | 3329 | """
==========================
FastICA on 2D point clouds
==========================
This example illustrates visually in the feature space a comparison by
results using two different component analysis techniques.
:ref:`ICA` vs :ref:`PCA`.
Representing ICA in the feature space gives the view of 'geometric ICA':
ICA... | bsd-3-clause |
cbrunet/fibermodes | plots/sio2geo2.py | 2 | 1764 | """Plot refractive index as function of concentration and wavelength.
Updated: 2015-10-15
"""
from fibermodes.fiber.material import SiO2GeO2, Silica, Germania
from fibermodes.fiber.material.sio2geo2cm import SiO2GeO2 as SiO2GeO2CM
import numpy
from matplotlib import pyplot
def n_fx():
pyplot.figure()
X = n... | gpl-3.0 |
aemerick/galaxy_analysis | examples/plot_time_series.py | 1 | 9996 | import numpy as np
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import glob
import deepdish as dd
import sys
import os
# some general plot styles for consistency
from galaxy_analysis.plot import plot_styles as ps
from galaxy_analysis.utilities import utilities
colors = {'Disk' : ps.black,
... | mit |
DavidLutton/EngineeringProject | examples/sweep.py | 1 | 5327 | #!/usr/bin/env python3
# Standard modules
import logging # https://docs.python.org/3/library/logging.html
import time # https://docs.python.org/3/library/time.html
import statistics # https://docs.python.org/3/library/statistics.html
# Functions or Classes from standard modules
from pprint import pprint # https:/... | mit |
meerkat-code/meerkat_api | meerkat_api/resources/completeness.py | 1 | 21570 | """
Data resource for completeness data
"""
import json
import pandas as pd
import meerkat_abacus.util as abacus_util
from datetime import datetime, timedelta
from dateutil.parser import parse
from flask import jsonify, request, g
from flask_restful import Resource, abort
from pandas.tseries.offsets import CustomBusin... | mit |
stuckeyr/sharkmap | sharkmap.py | 1 | 6902 | #!/usr/bin/env python
import itertools
import pandas as pd
import numpy as np
import re
import sys
import time
from geopy.geocoders import GoogleV3
from geopy.geocoders import Nominatim
reload(sys)
sys.setdefaultencoding('utf8')
# Clean our Fatal column up
def clean_Fatal(x):
if x == 'Y':
return True
... | mit |
lucidfrontier45/scikit-learn | examples/cluster/plot_lena_compress.py | 5 | 2192 | #!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=========================================================
Vector Quantization Example
=========================================================
The classic image processing example, Lena, an 8-bit grayscale
bit-depth, 512 x 512 sized image, is used here to illustrate
how `... | bsd-3-clause |
stetie/postpic | postpic/datahandling.py | 1 | 89783 | #
# This file is part of postpic.
#
# postpic is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# postpic is distributed in the hope th... | gpl-3.0 |
croxis/SpaceDrive | spacedrive/renderpipeline/rpcore/mount_manager.py | 1 | 12750 | """
RenderPipeline
Copyright (c) 2014-2016 tobspr <tobias.springer1@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the right... | mit |
dssg/wikienergy | disaggregator/build/pandas/pandas/tseries/tests/test_plotting.py | 3 | 41563 | from datetime import datetime, timedelta, date, time
import nose
from pandas.compat import lrange, zip
import numpy as np
from numpy.testing.decorators import slow
from numpy.testing import assert_array_equal
from pandas import Index, Series, DataFrame
from pandas.tseries.index import date_range, bdate_range
from p... | mit |
zorojean/scikit-learn | sklearn/metrics/metrics.py | 233 | 1262 | import warnings
warnings.warn("sklearn.metrics.metrics is deprecated and will be removed in "
"0.18. Please import from sklearn.metrics",
DeprecationWarning)
from .ranking import auc
from .ranking import average_precision_score
from .ranking import label_ranking_average_precision_score
fro... | bsd-3-clause |
yarikoptic/pystatsmodels | statsmodels/datasets/sunspots/data.py | 3 | 2000 | """Yearly sunspots data 1700-2008"""
__docformat__ = 'restructuredtext'
COPYRIGHT = """This data is public domain."""
TITLE = __doc__
SOURCE = """
http://www.ngdc.noaa.gov/stp/SOLAR/ftpsunspotnumber.html
The original dataset contains monthly data on sunspot activity in the file
./src/sunspots_yearly.dat... | bsd-3-clause |
MJuddBooth/pandas | pandas/tests/io/test_compression.py | 2 | 4797 | import contextlib
import os
import warnings
import pytest
import pandas as pd
import pandas.util.testing as tm
import pandas.io.common as icom
@contextlib.contextmanager
def catch_to_csv_depr():
# Catching warnings because Series.to_csv has
# been deprecated. Remove this context when
# Series.to_csv ha... | bsd-3-clause |
Wilee999/panda3d | makepanda/makepanda.py | 1 | 322800 | #!/usr/bin/env python
########################################################################
#
# Caution: there are two separate, independent build systems:
# 'makepanda', and 'ppremake'. Use one or the other, do not attempt
# to use both. This file is part of the 'makepanda' system.
#
# To build panda using this s... | bsd-3-clause |
zihua/scikit-learn | examples/linear_model/plot_sgd_comparison.py | 112 | 1819 | """
==================================
Comparing various online solvers
==================================
An example showing how different online solvers perform
on the hand-written digits dataset.
"""
# Author: Rob Zinkov <rob at zinkov dot com>
# License: BSD 3 clause
import numpy as np
import matplotlib.pyplot a... | bsd-3-clause |
maubarsom/maars-shotgun | scripts/extract_samples.py | 1 | 1368 | """
Script to create a directory structure from selected samples
and link the appropriate fastq files
"""
#!/usr/bin/python
import os
import subprocess
import os.path
import sys
import pandas as pd
import glob
if len(sys.argv) != 4:
sys.stderr.write("Number of arguments: {}\n".format(len(sys.argv)))
sys.stderr... | apache-2.0 |
JeroenZegers/Nabu-MSSS | nabu/postprocessing/reconstructors/deepattractornet_noisefilter_reconstructor.py | 1 | 4275 | '''@file deepclustering_reconstructor.py
contains the reconstor class using deep clustering'''
from sklearn.cluster import KMeans
import mask_reconstructor
from nabu.postprocessing import data_reader
import numpy as np
import os
import pdb
class DeepattractornoisefilterReconstructor(mask_reconstructor.MaskReconstruct... | mit |
idlead/scikit-learn | examples/calibration/plot_calibration.py | 33 | 4794 | """
======================================
Probability calibration of classifiers
======================================
When performing classification you often want to predict not only
the class label, but also the associated probability. This probability
gives you some kind of confidence on the prediction. However,... | bsd-3-clause |
MarcSpitz/ldebroux_kjadin_masters-thesis_2014 | src/addition_removal_time.py | 1 | 6966 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @author: Debroux Léonard <leonard.debroux@gmail.com>
# @author: Jadin Kevin <contact@kjadin.com>
import sys, os
from utils import Utils
from setup import Setup
import logging as log
from pylab import savefig, figure, plot, subplots, gca, tight_layout
from matplotl... | gpl-2.0 |
kevin-intel/scikit-learn | sklearn/linear_model/_passive_aggressive.py | 2 | 17461 | # Authors: Rob Zinkov, Mathieu Blondel
# License: BSD 3 clause
from ._stochastic_gradient import BaseSGDClassifier
from ._stochastic_gradient import BaseSGDRegressor
from ._stochastic_gradient import DEFAULT_EPSILON
class PassiveAggressiveClassifier(BaseSGDClassifier):
"""Passive Aggressive Classifier
Read ... | bsd-3-clause |
napjon/moocs_solution | Data_Science/project_1/custom_heuristics/assignment.py | 1 | 3203 | from __future__ import division
import numpy
import pandas
import statsmodels.api as sm
import sys
def custom_heuristic(file_path):
'''
You are given a list of Titantic passengers and their associating
information. More information about the data can be seen at the link below:
http://www.kaggle.com/c/... | mit |
Vimos/scikit-learn | examples/neural_networks/plot_mlp_training_curves.py | 58 | 3692 | """
========================================================
Compare Stochastic learning strategies for MLPClassifier
========================================================
This example visualizes some training loss curves for different stochastic
learning strategies, including SGD and Adam. Because of time-constrai... | bsd-3-clause |
spallavolu/scikit-learn | examples/decomposition/plot_image_denoising.py | 181 | 5819 | """
=========================================
Image denoising using dictionary learning
=========================================
An example comparing the effect of reconstructing noisy fragments
of the Lena image using firstly online :ref:`DictionaryLearning` and
various transform methods.
The dictionary is fitted o... | bsd-3-clause |
dkaylor/datasciencebowl | train.py | 1 | 9102 | import os
import numpy as np
from data import load_images
from realtime_augment import RealtimeAugment
from pylearn2.datasets import preprocessing
from pylearn2.training_algorithms import sgd, learning_rule
from pylearn2.termination_criteria import EpochCounter
from pylearn2.datasets.dense_design_matrix import DenseDe... | mit |
dougthor42/OWT_WM_View | build_executables.py | 1 | 4362 | # -*- coding: utf-8 -*-
"""
Created on Mon Jun 22 13:08:24 2015
@author: dthor
"""
# ---------------------------------------------------------------------------
### Imports
# ---------------------------------------------------------------------------
# Standard Library
import sys
import logging
import os... | gpl-3.0 |
drammock/mne-python | examples/stats/fdr_stats_evoked.py | 20 | 2740 | """
=======================================
FDR correction on T-test on sensor data
=======================================
One tests if the evoked response significantly deviates from 0.
Multiple comparison problem is addressed with
False Discovery Rate (FDR) correction.
"""
# Authors: Alexandre Gramfort <alexandre.... | bsd-3-clause |
tavo91/NER-WNUT17 | common/utilities.py | 1 | 15371 | import re
import string
import csv
import numpy as np
import matplotlib.pyplot as plt
from collections import Counter
from collections import defaultdict as ddict
from embeddings.twitter.word2vecReader import Word2Vec
from itertools import groupby
from keras import backend as K
from keras.preprocessing.text import Tok... | mit |
liangz0707/scikit-learn | examples/svm/plot_separating_hyperplane_unbalanced.py | 329 | 1850 | """
=================================================
SVM: Separating hyperplane for unbalanced classes
=================================================
Find the optimal separating hyperplane using an SVC for classes that
are unbalanced.
We first find the separating plane with a plain SVC and then plot
(dashed) the ... | bsd-3-clause |
Hemisphere-Project/Telemir-DatabitMe | Telemir-EEG/pyacq/pyacq/gui/timefreq.py | 1 | 22106 | # -*- coding: utf-8 -*-
from PyQt4 import QtCore,QtGui
import pyqtgraph as pg
import zmq
import time
from .tools import RecvPosThread, MultiChannelParamsSetter
from .guiutil import *
from .multichannelparam import MultiChannelParam
from matplotlib.cm import get_cmap
from matplotlib.colors import ColorConverter
fro... | gpl-2.0 |
JackDandy/SickGear | lib/dateutil/parser/_parser.py | 2 | 60702 | # -*- coding: utf-8 -*-
"""
This module offers a generic date/time string parser which is able to parse
most known formats to represent a date and/or time.
This module attempts to be forgiving with regards to unlikely input formats,
returning a datetime object even for dates which are ambiguous. If an element
o... | gpl-3.0 |
GaZ3ll3/scikit-image | skimage/viewer/canvastools/recttool.py | 43 | 8886 | from matplotlib.widgets import RectangleSelector
from ...viewer.canvastools.base import CanvasToolBase
from ...viewer.canvastools.base import ToolHandles
__all__ = ['RectangleTool']
class RectangleTool(CanvasToolBase, RectangleSelector):
"""Widget for selecting a rectangular region in a plot.
After making ... | bsd-3-clause |
umuzungu/zipline | tests/test_history.py | 1 | 65003 | from textwrap import dedent
from numbers import Real
from nose_parameterized import parameterized
import numpy as np
from numpy import nan
from numpy.testing import assert_almost_equal
import pandas as pd
from six import iteritems
from zipline import TradingAlgorithm
from zipline._protocol import handle_non_market_m... | apache-2.0 |
MaterialsDiscovery/PyChemia | pychemia/code/abinit/task/static.py | 1 | 3422 | import os
import json
import numpy as np
from pychemia.crystal import KPoints
from ...tasks import Task
from ..abinit import AbinitJob
__author__ = 'Guillermo Avendano-Franco'
class StaticCalculation(Task):
def __init__(self, structure, workdir='.', executable='abinit', ecut=50, kpoints=None, kp_density=1E4):
... | mit |
n-west/gnuradio | gr-filter/examples/synth_filter.py | 58 | 2552 | #!/usr/bin/env python
#
# Copyright 2010,2012,2013 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or (at your ... | gpl-3.0 |
rajat1994/scikit-learn | sklearn/feature_selection/tests/test_from_model.py | 244 | 1593 | import numpy as np
import scipy.sparse as sp
from nose.tools import assert_raises, assert_true
from sklearn.utils.testing import assert_less
from sklearn.utils.testing import assert_greater
from sklearn.datasets import load_iris
from sklearn.linear_model import LogisticRegression
from sklearn.linear_model import SGD... | bsd-3-clause |
bit-jmm/ttarm | result/plots/error_bar.py | 1 | 1372 | """
Demo of the errorbar function, including upper and lower limits
"""
import numpy as np
import matplotlib.pyplot as plt
# example data
x = np.arange(0.5, 5.5, 0.5)
y = np.exp(-x)
xerr = 0.1
yerr = 0.2
ls = 'dotted'
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
# standard error bars
plt.errorbar(x, y, xerr=xerr... | gpl-2.0 |
nburn42/tensorflow | tensorflow/python/estimator/inputs/queues/feeding_queue_runner_test.py | 116 | 5164 | # Copyright 2017 The TensorFlow Authors. 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | apache-2.0 |
mmacgilvray18/Phospho_Network | python/Kullback_Leibler_Module_toEachKinase.py | 1 | 11649 | import pandas as pd
import numpy as np
import glob
import math
'''This script is comparing each PWM from Mok et al to to each Module PWM using a method called Kullback-Leibler divergence (KLD).
KLD(X,Y) = 1/2 (E Xalog(Xa/Ya) + E Yalog(Ya/Xa))
Where ‘X’ represents a query PWM position and ‘Y’ a comparison PWM posi... | gpl-3.0 |
miloharper/neural-network-animation | matplotlib/tests/test_path.py | 9 | 2261 | from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import numpy as np
from matplotlib.path import Path
from matplotlib.patches import Polygon
from nose.tools import assert_raises
from matplotlib.testing.decorators import image_comparison
import mat... | mit |
DJArmstrong/autovet | Features/Centroiding/Centroiding_RDX.py | 1 | 50983 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 14 18:25:52 2016
@author:
Maximilian N. Guenther
Battcock Centre for Experimental Astrophysics,
Cavendish Laboratory,
JJ Thomson Avenue
Cambridge CB3 0HE
Email: mg719@cam.ac.uk
"""
import warnings
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patch... | gpl-3.0 |
crichardson17/starburst_atlas | Low_resolution_sims/DustFree_LowRes/Geneva_Rot_inst/Geneva_Rot_inst_age4/UV2.py | 33 | 7365 | import csv
import matplotlib.pyplot as plt
from numpy import *
import scipy.interpolate
import math
from pylab import *
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
import matplotlib.patches as patches
from matplotlib.path import Path
import os
# --------------------------------------------------... | gpl-2.0 |
equialgo/scikit-learn | examples/feature_selection/plot_feature_selection.py | 95 | 2847 | """
===============================
Univariate Feature Selection
===============================
An example showing univariate feature selection.
Noisy (non informative) features are added to the iris data and
univariate feature selection is applied. For each feature, we plot the
p-values for the univariate feature s... | bsd-3-clause |
jaeminSon/V-GAN | codes/utils.py | 1 | 16560 | import os
import sys
from PIL import Image, ImageEnhance
from keras.preprocessing.image import Iterator
from scipy.ndimage import rotate
from skimage import filters
from sklearn.metrics import auc
from sklearn.metrics import confusion_matrix
from sklearn.metrics import roc_curve, roc_auc_score, precision_recall_curve
... | mit |
julietbravo/microhh | kernel_tuner/statistics.py | 5 | 1185 | import matplotlib.pyplot as pl
import numpy as np
import json
import glob
pl.close('all')
pl.ion()
def get_timings(kernel_name, gridsizes):
dt = np.zeros_like(gridsizes, dtype=float)
for i,gridsize in enumerate(gridsizes):
with open( '{0}_{1:03d}.json'.format(kernel_name, gridsize) ) as f:
... | gpl-3.0 |
sudikrt/costproML | cost.py | 1 | 1547 | import pandas
import numpy as np
import matplotlib.pyplot as plt
from sklearn.cross_validation import train_test_split
from sklearn.metrics import mean_squared_error
from sklearn.linear_model import LinearRegression
from sklearn.naive_bayes import GaussianNB
from sklearn.svm import SVC
from datetime import timedelta
... | apache-2.0 |
sigmaroles/bpred | mlpredict.py | 1 | 1388 | import sys
import numpy as np
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import train_test_split
from sklearn.metrics import confusion_matrix, accuracy_score, classification_report
if __name__=='__main__':
fname = sys.argv[1]
data = []
labels = []
with op... | gpl-3.0 |
JWDebelius/scikit-bio | skbio/stats/distance/tests/test_mantel.py | 1 | 22066 | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | bsd-3-clause |
dsquareindia/scikit-learn | sklearn/metrics/tests/test_regression.py | 49 | 8058 | from __future__ import division, print_function
import numpy as np
from itertools import product
from sklearn.utils.testing import assert_raises, assert_raises_regex
from sklearn.utils.testing import assert_equal
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.testing import assert_array_equa... | bsd-3-clause |
chrsrds/scikit-learn | examples/classification/plot_lda_qda.py | 25 | 5449 | """
====================================================================
Linear and Quadratic Discriminant Analysis with covariance ellipsoid
====================================================================
This example plots the covariance ellipsoids of each class and
decision boundary learned by LDA and QDA. The... | bsd-3-clause |
ephes/scikit-learn | examples/mixture/plot_gmm_sin.py | 248 | 2747 | """
=================================
Gaussian Mixture Model Sine Curve
=================================
This example highlights the advantages of the Dirichlet Process:
complexity control and dealing with sparse data. The dataset is formed
by 100 points loosely spaced following a noisy sine curve. The fit by
the GMM... | bsd-3-clause |
lucashtnguyen/wqio | wqio/algo/ros.py | 1 | 16320 | from __future__ import division
import pdb
import os
import sys
if sys.version_info.major == 3:
from io import StringIO
else:
from StringIO import StringIO
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as stats
import pandas
__all__ = ['rosSort', 'MR']
def rosSort(dataframe, resco... | bsd-3-clause |
BhallaLab/moose-examples | tutorials/Electrophys/ephys1_cable.py | 2 | 6794 | ########################################################################
# This example demonstrates a cable
# Copyright (C) Upinder S. Bhalla NCBS 2018
# Released under the terms of the GNU Public License V3.
########################################################################
import matplotlib.pyplot as plt
impor... | gpl-2.0 |
maxlikely/scikit-learn | sklearn/datasets/twenty_newsgroups.py | 4 | 10030 | """Caching loader for the 20 newsgroups text classification dataset
The description of the dataset is available on the official website at:
http://people.csail.mit.edu/jrennie/20Newsgroups/
Quoting the introduction:
The 20 Newsgroups data set is a collection of approximately 20,000
newsgroup documents,... | bsd-3-clause |
LohithBlaze/scikit-learn | examples/cluster/plot_color_quantization.py | 297 | 3443 | # -*- coding: utf-8 -*-
"""
==================================
Color Quantization using K-Means
==================================
Performs a pixel-wise Vector Quantization (VQ) of an image of the summer palace
(China), reducing the number of colors required to show the image from 96,615
unique colors to 64, while pre... | bsd-3-clause |
rsivapr/scikit-learn | sklearn/feature_selection/tests/test_feature_select.py | 5 | 18632 | """
Todo: cross-check the F-value with stats model
"""
import itertools
import numpy as np
from scipy import stats, sparse
import warnings
from nose.tools import assert_equal, assert_raises, assert_true
from numpy.testing import assert_array_equal, assert_array_almost_equal
from sklearn.utils.testing import assert_no... | bsd-3-clause |
jungla/ICOM-fluidity-toolbox | Detectors/plot_Hovmuller_v.py | 1 | 4493 | #!~/python
import fluidity_tools
import matplotlib as mpl
mpl.use('ps')
import matplotlib.pyplot as plt
import numpy as np
import vtktools
import myfun
import os
import spectrum
exp = 'r_3k_B_1F0_s'
filename ='/tamay2/mensa/fluidity/'+exp+'/ring_checkpoint.detectors'
#filename2 = '/tamay2/mensa/fluidity/'+exp+'/ring_... | gpl-2.0 |
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