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#!/usr/bin/python
# script to extract cluster sequences from brennecke et al table
# version 1 - 22-03-2013
# Usage piRNA_cluster_extracter.py <Dmfasta_genome> <coordinate reference table>
import sys
fasta_dic = {}
F = open (sys.argv[1], "r") # F the Dm fasta genome
for line in F:
if line[0] == ">":
try:
... | JuPeg/tools-artbio | unstable/local_tools/piRNA_cluster_extracter.py | Python | mit | 1,092 | [
"Bowtie"
] | fad1594ad8c3671c0ffed35cd9841f1aec4ab51f3f8bae65b52923ba63492192 |
# -- coding: utf-8 --
# Copyright 2018 Olivier Scholder <o.scholder@gmail.com>
"""
This module is used in order to align two different images.
Usually one from an SPM and the other from the ToF-SIMS.
This module also gives the ability to perform shift correction on images
which is used in order to align the differen... | scholi/pySPM | pySPM/align.py | Python | apache-2.0 | 10,513 | [
"Gaussian"
] | 7dcd8fcb46df9ed224bdb27d1f105c65d270e263f44ae6e60b369cb56dc0857d |
# sql/compiler.py
# Copyright (C) 2005-2014 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.com... | jessekl/flixr | venv/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py | Python | mit | 111,426 | [
"VisIt"
] | a86a8c177c777fe619a823c363d2374fda47d178627e912a01402e5a8851bc62 |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2011 Jose Fonseca
# All Rights Reserved.
#
# 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 th... | surround-io/apitrace | scripts/retracediff.py | Python | mit | 13,238 | [
"VisIt"
] | 88b8bc7dcb45bcc82d52a8d998752db0d3f9839373d634c115fddfb8b1668a99 |
#!/usr/bin/env python
#
# entries_tests.py: test the old entries API using entries-dump
#
# Subversion is a tool for revision control.
# See http://subversion.apache.org for more information.
#
# ====================================================================
# Licensed to the Apache Software Foundation (AS... | tux-mind/platform_external_subversion | subversion/tests/cmdline/entries_tests.py | Python | apache-2.0 | 9,744 | [
"BLAST"
] | f3f7afdeb38799fd2347ea7432c1064f1f0d86892a8697ef9ef6e516ea91136b |
import subprocess
import os
import click
import yaml
from Bio import SeqIO
from dgl import library_constants
@click.group()
def cli():
pass
@cli.command()
@click.argument('embl_gtf')
def parse_gtf(embl_gtf):
"""
organise embl gtf into genes
output in yaml format
"""
with open(embl_gtf) as fil... | DeskGen/dgcli | library_design/dgl/genome_remap.py | Python | gpl-2.0 | 18,256 | [
"BWA",
"Bowtie"
] | cc6fe8c8a15021b48a319e7cfee35abdf710c46b486576a99a89165a30ea08bf |
#!/usr/bin/env python
'''
Showing use of the parallelized CCSD with K-point sampling.
'''
import numpy as np
from pyscf import cc
from pyscf.pbc import cc as pbccc
from pyscf.pbc import scf as pbchf
from pyscf.pbc import gto
from pyscf.pbc.tools.pbc import super_cell
nmp = [1, 1, 2]
cell = gto.M(
unit='B',
a... | sunqm/pyscf | examples/pbc/24-k_points_vs_gamma.py | Python | apache-2.0 | 1,963 | [
"PySCF"
] | 18431457d7bdda254db8f7c2e1f4958eb99319ff48c3da58a5bb22603edf478f |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for the
IDL version is:
... | baklanovp/pystella | pystella/fit/mpfit.py | Python | mit | 89,365 | [
"Gaussian"
] | 634fa7bcb8b1820c6ec170df4af007788f33f425fe9e332ad08e597380d5cbc5 |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .sparse_gp import SparseGP
from numpy.linalg.linalg import LinAlgError
from ..inference.latent_function_inference.var_dtc_parallel import update_gradients, VarDTC_minibatch
imp... | dhhjx880713/GPy | GPy/core/sparse_gp_mpi.py | Python | bsd-3-clause | 5,130 | [
"Gaussian"
] | 4518bc942d1efd579c651df5352b24d04641868e349618cf93befba922a6a18e |
"""
This code provides a start to finish example of how to use emcee - the MCMC Hammer
For information on emcee - visit http://dan.iel.fm/emcee/current/
You may notice that this example is similar to the one on this site...
"""
#Start by importing some useful modules
import numpy as np
import emcee
import matplotlib.... | BU-PyCon/Meeting-3 | Programs/emcee_example.py | Python | mit | 7,623 | [
"Gaussian",
"VisIt"
] | 15e6b395570b1901ce8ed651013f21c11fc0bfa2982d770b42edd5646811ddab |
"""
Tests for ORA (Open Response Assessment) through the LMS UI.
"""
import json
from bok_choy.promise import fulfill, Promise
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.lms.course_info import CourseInfoPage
from ..pages.lms.tab_nav import TabNavPage
from ..pages.lms.course_nav import CourseNavPage... | pku9104038/edx-platform | common/test/acceptance/tests/test_ora.py | Python | agpl-3.0 | 14,853 | [
"VisIt"
] | 03b80b18baeb79212ccfdbdb2ec3196d6f6978e73a4b70c280a5be3e6e01e881 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a core class LammpsData for generating/parsing
LAMMPS data file, and other bridging classes to build LammpsData from
molecules. This module also implements a subclass CombinedData for... | mbkumar/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 59,476 | [
"LAMMPS",
"pymatgen"
] | d0a5a12e02495618e95a754f31067b2e40f277fc9dcab33a4a0ab760183a8ddf |
__author__ = 'Helder C. R. de Oliveira'
__email__ = 'heldercro@gmail.com'
__url__ = 'http://helderc.net'
"""
This is an improved implementation of SSIM, based on version of:
Antoine Vacavant, ISIT lab, antoine.vacavant@iut.u-clermont1.fr,
http://isit.u-clermont1.fr/~anvacava
References:
[1] Z.... | paulu/deepart | SSIM_Index.py | Python | mit | 3,099 | [
"Gaussian"
] | 01c9d0774b7fd47ad5fbeab203fb90dcb891bee31f1f6e19e9665544947b7c2f |
from django.utils.translation import ugettext_lazy as _
from horizon import tables
from django.core.urlresolvers import reverse
from crystal_dashboard.dashboards.crystal import exceptions as sdsexception
from django.utils.translation import ugettext_lazy as _
from django.utils.translation import ungettext_lazy
from hor... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/zones/tables.py | Python | gpl-3.0 | 2,413 | [
"CRYSTAL"
] | 89fdc03cd5bd6abb41e228ad8cb087847774ddb207acdf193aad22df600e79e1 |
#!/usr/bin/env python
"""
Copyright (C) 2015 Louis Dijkstra
This file is part of somatic-indel-calling
This program 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 o... | louisdijkstra/somatic-indel-calling | bin/extract-observations.py | Python | gpl-3.0 | 11,846 | [
"BWA",
"pysam"
] | 8722eaea5a5104bb9c2e190679de655bc6fffe779b9da32654528893ac9ac8b4 |
import pysam
import itertools
import sys
from collections import defaultdict
from django.conf import settings
MIN_MAPQ = settings.CL__MIN_MAPQ
MAX_DEPTH = settings.CL__MAX_DEPTH
MIN_DEPTH = settings.CL__MIN_DEPTH
MIN_LOWMAPQ_DEPTH = settings.CL__MIN_LOWMAPQ_DEPTH
MAX_LOWMAP_FRAC = settings.CL__MAX_LOWMAP_FRAC
MERGE_D... | woodymit/millstone | genome_designer/pipeline/callable_loci.py | Python | mit | 6,120 | [
"pysam"
] | 37b3d0c8f12d4df96c814b1bf9c307a38176c5b91e76c45c52c4b84cd855b502 |
""" This is a test of the chain
ProductionClient -> ProductionManagerHandler -> ProductionDB
It supposes that the DB is present, and that the service is running
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Core.Base.Script import p... | yujikato/DIRAC | tests/Integration/ProductionSystem/Test_Client_Production.py | Python | gpl-3.0 | 1,923 | [
"DIRAC"
] | 46a505c93f5a06a8af3403c7f24da62f84d41b03f8921f90a98372fa23570483 |
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 8 2018
@author: sserkez
"""
import logging
import ocelot
from ocelot.common.globals import *
from ocelot.optics.wave import imitate_sase_dfl, wigner_dfl, dfl_waistscan, generate_gaussian_dfl
from ocelot.gui.dfl_plot import plot_dfl, plot_wigner, plot_dfl_waistscan
from cop... | ocelot-collab/ocelot | demos/optics/1-radiation_field.py | Python | gpl-3.0 | 4,662 | [
"Gaussian"
] | ddef0f13c7eb48374e567e3e7660edd8e8177cbcac43fc654b2241f6248655ad |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | kepler-labelled-time-series-data/kepler-baseline.py | Python | mit | 2,949 | [
"Gaussian"
] | 136ed8198b6fdbf669f27dd7dcb03a67219a171b097e5f1cd923353b9dc1252a |
#
# Copyright 2014-2015, 2017, 2020-2021 Lars Pastewka (U. Freiburg)
# 2018-2021 Jan Griesser (U. Freiburg)
# 2020 Jonas Oldenstaedt (U. Freiburg)
# 2015 Adrien Gola (KIT)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https:/... | libAtoms/matscipy | matscipy/calculators/manybody/__init__.py | Python | lgpl-2.1 | 1,091 | [
"Matscipy"
] | 6ccbd9a769e5f2ffbac9e0d0a9cea159fff1dccc4b886f6c7ef00676907a0a26 |
"""
Python Interchangeable Virtual Instrument Library
Copyright (c) 2012-2016 Alex Forencich
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... | Diti24/python-ivi | ivi/agilent/agilent3000A.py | Python | mit | 6,792 | [
"Gaussian"
] | 8d654d88a5f725ce90568270f34beba570942e024ddc764078222a905e8b6040 |
""" ModuleBase - contains the base class for workflow modules. Defines several common utility methods.
The modules defined within this package are developed in a way to be executed by a DIRAC.Core.Worfklow.Worfklow.
In particular, a DIRAC.Core.Workflow.Worfklow object will only call the "execute" function, tha... | arrabito/DIRAC | Workflow/Modules/ModuleBase.py | Python | gpl-3.0 | 21,421 | [
"DIRAC"
] | 92e887a494e7d865e4b5d80e1ddeb4494f6a0fdcecb55e8179457d605dc496af |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/bibles/lib/biblestab.py | Python | gpl-2.0 | 26,262 | [
"Brian"
] | a268c0b66b6067c47ba853bc99dcb97fc96ccbb7a3bc259b7e0d3dc384849178 |
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 21 12:16:30 2013
@author: akusoka1
"""
import numpy as np
from matplotlib import pyplot as plt
import sys
print "Starting!"
def normalize(X,Y):
N = X.shape[0]
X = X - np.tile(np.mean(X,0), (N,1))
X = X / np.tile(np.std(X,0), (N,1))
Y = Y - np.tile(np.m... | akusok/website-ibc | elm_prune.py | Python | gpl-2.0 | 2,716 | [
"NEURON"
] | 20612fe6bda85b52693b081d6b4e124e2f310e2d0c41b578e8db9c69913435b3 |
import string
import os
import sys
# ChemPy Simple Forcefield (CSFF) Generator Script
#
# A simplified force field based on Amber Parm99
# ===================================================
# This force field is designed to be used to answer
# general questions about shape and size of small
# conformationally constra... | gratefulfrog/lib | python/pymol/pymol_path/data/chempy/tinker/make_simple.py | Python | gpl-2.0 | 47,278 | [
"Amber",
"ChemPy",
"TINKER"
] | fb248c9481bb8f6e1832d52b51ffa6e2f9bf2b67a2155fedbe8a5e3488740824 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.7 on 2017-12-30 10:45
from __future__ import unicode_literals
import django.contrib.postgres.fields
from django.db import migrations, models
import geomat.stein.fields
import stdimage.models
class Migration(migrations.Migration):
dependencies = [
('stei... | GeoMatDigital/django-geomat | geomat/stein/migrations/0048_auto_20171230_1145.py | Python | bsd-3-clause | 4,672 | [
"CRYSTAL"
] | 3c04ce952c15b5e25283217300534a8353adc6298ec14f175e6231988abb4649 |
#-*- coding: utf-8 -*-
###########################################################################
## ##
## Copyrights Frédéric Rodrigo 2012 ##
## ... | tkas/osmose-backend | plugins/disabled/TagFix_Brand.py | Python | gpl-3.0 | 4,583 | [
"CASINO",
"Jaguar"
] | 2cba8f344f802191195297b5340ccb2f5b68e4e24a86f29f9c1ea6acbc858074 |
# -*- coding: utf-8 -*-
from __future__ import print_function
import gc
import time
import numpy as np
from scipy.optimize import leastsq
import acq4.Manager
import pyqtgraph as pg
from acq4.util import Qt
from acq4.util.HelpfulException import HelpfulException
from acq4.util.functions import blur
from acq4.util.ima... | acq4/acq4 | acq4/devices/Scanner/DeviceGui.py | Python | mit | 18,417 | [
"Gaussian"
] | 8431949c8a80c38e7d478e84a471d080f0f7355e6d9d5d82d5093ea25e2a6102 |
# -*- coding: utf-8 -*-
# PyNAM -- Python Neural Associative Memory Simulator and Evaluator
# Copyright (C) 2015 Andreas Stöckel
#
# This program 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, eit... | hbp-sanncs/pynam | pynam/experiment.py | Python | gpl-3.0 | 15,407 | [
"NEURON"
] | d3d10070ae2be48cd317a0c6c1e7843a40ac8d2843043e594d34332a51d5503d |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
import math
def main():
print ocl.revision()
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(-15, -8, 15)
myscreen.camera.SetFocalPoint(0,0, 0)
# axis arrows
camvtk.drawArrows(myscreen,center=(0,0,0))... | AlanZatarain/opencamlib | scripts/cutsim/cutsim_12.py | Python | gpl-3.0 | 3,193 | [
"VTK"
] | 5b87d6e3b5e01a994042cbcb7ff62e33c06176ef284394a54c91c71cabf2d7d2 |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute... | ashutoshvt/psi4 | doc/sphinxman/document_psifiles.py | Python | lgpl-3.0 | 3,196 | [
"Psi4"
] | a8bec72a6504a1774b8c916639259c8033f097a27fbc68014a35c0b2220934f6 |
#!/bin/env python
"""
Module openmm.unit.doctests
Lots of in-place doctests would no longer work after I rearranged
so that specific unit definitions are defined late. So those tests
are here.
Examples
>>> furlong = BaseUnit(length_dimension, "furlong", "fur")
Examples
>>> furlong_base_unit = Base... | mdtraj/mdtraj | mdtraj/utils/unit/doctests.py | Python | lgpl-2.1 | 21,553 | [
"OpenMM"
] | 4a509b2ed54054545e4576449d39445eb91e01d83bd5aa586c5a7085d5983628 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# servercomm - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms o... | heromod/migrid | mig/server/servercomm.py | Python | gpl-2.0 | 18,761 | [
"Brian"
] | 1e1916fcbcdf42fd0650cec754c62ea62bd242b9c08b403ecf897bf48b9fd335 |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# 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 applicable l... | eric-stanley/robotframework | src/robot/running/model.py | Python | apache-2.0 | 8,731 | [
"VisIt"
] | 4e13857a4f9b5caab37035de927d1ecdd7be048d604eb22a956def044b6d9b7c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from .__init__ import *
from .object import Object
from .control import Control
from gi.repository import Gtk
from gi.repository import Pango
from gi.repository import PangoCairo
class Table(Object):
"""This class represents a table"""
__name__ = "Table"... | jmouriz/sanaviron | sanaviron/objects/table.py | Python | apache-2.0 | 4,006 | [
"FLEUR"
] | c53fce62a3274ca7988aa831151aed327df7529a83ef1d852014f97e3ccb0a2e |
# -----------------------------------------------------------------------------
# Milky Way - Turn based strategy game from Milky Way galaxy
#
# URL: https://github.com/FedericoRessi/milkyway/
# License: GPL3
# -----------------------------------------------------------------------------
'''
@author: Federi... | FedericoRessi/milkyway | milkyway/ui/tests/__init__.py | Python | gpl-3.0 | 333 | [
"Galaxy"
] | 852d08f1211c4e20308b53772b424a0a6b4a020bfcef6d79d16d7493ee2aa185 |
#
# Copyright 2015 The AMP HTML 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 applic... | gumgum/amphtml | validator/validator_gen_js.py | Python | apache-2.0 | 37,179 | [
"VisIt"
] | 7ac5e69502106fe460aafcbefd55fbd70a98b89fc0e583e1443d5c9e11ce4c9b |
"""Planning (Chapters 10-11)"""
import copy
import itertools
from collections import deque, defaultdict
from functools import reduce as _reduce
import numpy as np
import search
from csp import sat_up, NaryCSP, Constraint, ac_search_solver, is_constraint
from logic import FolKB, conjuncts, unify_mm, associate, SAT_pl... | Chipe1/aima-python | planning.py | Python | mit | 81,006 | [
"VisIt"
] | 72fbc781a0f60a7b2edd5b103d09fe6005c2f14a5d91d52c45034a0fd4ceb478 |
import datetime as dt
import decimal
import random
import math
from collections import namedtuple, OrderedDict
import simplejson as json
import pytest
from marshmallow import (
Schema,
fields,
utils,
validates,
validates_schema,
EXCLUDE,
INCLUDE,
RAISE,
class_registry,
)
from mars... | marshmallow-code/marshmallow | tests/test_schema.py | Python | mit | 91,595 | [
"Brian"
] | c75950681a37f0647189e8dce13ce469084cbfb25ae0d9a1062145a22956a554 |
import numpy
import unittest
import numpy.testing as nptst
import logging
from sandbox.predictors.DecisionTreeLearner import DecisionTreeLearner
from sandbox.data.ExamplesGenerator import ExamplesGenerator
from sandbox.data.Standardiser import Standardiser
from sandbox.util.Sampling import Sampling
from sklearn.tr... | charanpald/sandbox | sandbox/predictors/test/DecisionTreeLearnerTest.py | Python | gpl-3.0 | 19,150 | [
"Gaussian"
] | 9977012b37388627fdcf62f2e2970f7e33198ba9eea50f7f4391f20935c0f44d |
###############################################################################
##
## Copyright (C) 2011-2013 Tavendo GmbH
##
## 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
##
## h... | claws/AutobahnPython | autobahn/autobahn/websocket/useragent.py | Python | apache-2.0 | 9,842 | [
"Galaxy"
] | 6e294b615fc25bbeac21ca50b27cf51549e353d4637be567ec61c5bc4738b7a6 |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
from six.moves import reduce, xrange, zip, zip_longest
import itertools
import math
import warnings
import numpy as np
from numpy import ma
import matplotlib
from matplotlib import unpack_labeled_... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/axes/_axes.py | Python | bsd-2-clause | 284,309 | [
"Gaussian"
] | f54b7efef33b461040569aeadc935937df3ab3a108cd6e5c6aad436635ccf0ba |
from os.path import abspath, exists, isdir, isfile, walk, join, basename, expanduser, getsize
import io
from utils.pubsub import PubSub
import struct
from wire.ttypes import TBinaryProtocol
from wire.ttypes import Message
from thrift.transport import TTransport
class DataLocation:
"""A DataLocation represents whe... | InspectorB/3Dami-python | src/raw/load.py | Python | gpl-3.0 | 5,632 | [
"VisIt"
] | d8fef31af77bf498664437f8ae0acd25611fbee6a6a51be5a63ea1ed79a9e136 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-cnvkit/package.py | Python | lgpl-2.1 | 2,241 | [
"Biopython",
"pysam"
] | d6f5f7fded18edc0fe03ebadefc46b024ea1db03396e9df799f4661b3d0376a3 |
"""Configure file for PyMorph. Authors: Vinu Vikram, Yogesh Wadadekar and Ajit Kembhavi (IUCAA) 2008, Alan Meert (UPenn)"""
###----Specify the input images and Catalogues----###
imagefile = 'tot.fits'
whtfile = 'tot_rms.fits'
#whtfile = 'j8f643-1-1_drz_rms.fits' #The weight image. If it contains the
... | vvinuv/pymorph | examples/full_image/expected_results/config.py | Python | gpl-2.0 | 5,739 | [
"Galaxy"
] | 9b595d428804dad1c318799708a39efe3b8bec6f146d6a5e34fa31c43e920d28 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import pytest
import warnings
def has_pyvista():
"""Check that pyvista ... | Teekuningas/mne-python | mne/viz/backends/tests/_utils.py | Python | bsd-3-clause | 1,360 | [
"Mayavi"
] | 061c9f59e4a08d9c8704ba9ab62986a6068e6aa6714d329fba196012af248a3b |
"""
Core visualization operations based on Mayavi.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric... | bloyl/mne-python | mne/viz/backends/_pysurfer_mayavi.py | Python | bsd-3-clause | 22,504 | [
"Mayavi",
"VTK"
] | 34f780f5698ebc25c671c1d6800712c7d948b8710a8bd46df44f8e20a6b9a75a |
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 10 13:30:56 2016
@author: armeev
"""
import numpy as np
from general_functions import box_transform_1channel, Distribution, squarte_box
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
class Gel(object):
def __init__(self, path_to_image):
se... | satary/pyGEL | pyGEL.py | Python | gpl-3.0 | 4,687 | [
"Gaussian"
] | 110b5580240536c49b0a49e04a90faba3eef32bb39482d9bb9ace76f2ce58bff |
import sys
import abc
import os
import commands
import re
import urllib2
import logging
import glob
import shutil
import collections
import socket
import xml.sax
from os.path import abspath, join, dirname
from seance.filetypes import SffFile, FastqFile
from seance.datatypes import IUPAC
from seance.progress import Pro... | ajm/seance | seance/tools.py | Python | gpl-3.0 | 25,041 | [
"BLAST",
"Biopython"
] | ae80e39f784b1599f68084525d3e947641ddc0e6596a416b7e2b265c2f6b60a4 |
########################################################################
# This example demonstrates a multiscale bistable model.
# In the low state there is no spiking, no Ca entry, and the KA channel
# is unophosporylated and hence active. This keeps the potential low.
# In the high state, there is sustained spikin... | BhallaLab/moose | moose-examples/tutorials/Rdesigneur/ex8.0_multiscale_KA_phosph.py | Python | gpl-3.0 | 2,316 | [
"MOOSE"
] | 88538a2fa31b9bee70239accf6bf84c70cec9eb8e1f912d1d90e81fb7cc22b62 |
#!/Users/student/anaconda/bin/python
'''
.. module:: PDBUtil
:platform: Unix, Windows
:synopsis: Contains miscellaneous utilities for dealing with parsed PDB files. *Consider putting PDBParse in here.*
.. moduleauthor:: Amelia F. Antrim <amelia.f.antrim@gmail.com>
'''
import numpy
from Bio.PDB import *
from co... | afantrim/epitope_mapping | src/SequentialPairs/PDBUtil.py | Python | gpl-2.0 | 2,313 | [
"Biopython"
] | 866f3fb76b5e83d576f612b624c5aa8b9115f7b958893fdd4ec2bd88ccae7dc6 |
"""
The main client API you'll be working with most often. You'll need to
configure a dropbox.session.DropboxSession for this to work, but otherwise
it's fairly self-explanatory.
"""
import re
import json
from efforia.dropbox.rest import ErrorResponse
from efforia.dropbox.rest import RESTClient
def format_path(path... | efforia/eos-dashboard | pandora-ckz/pandora/dropbox/client.py | Python | lgpl-3.0 | 29,289 | [
"VisIt"
] | 5327c3055c87f4853aef99e3cd29d404ef51da18dbda331d6899819201de70fc |
## Copyright (c) 2015 Ryan Koesterer GNU General Public License v3
##
## This program 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 l... | rmkoesterer/uga | uga/RunSnvgroup.py | Python | gpl-3.0 | 13,158 | [
"pysam"
] | 1b10254234359373e5e1b71b8fde0e8a72d54370f35ad796fac384c3a180541b |
### Neural Photo Editor
# A Brock, 2016
### Imports
from Tkinter import * # Note that I dislike the * on the Tkinter import, but all the tutorials seem to do that so I stuck with it.
from tkColorChooser import askcolor # This produces an OS-dependent color selector. I like the windows one best, and can't stand the li... | ajbrock/Neural-Photo-Editor | NPE.py | Python | mit | 15,369 | [
"Gaussian"
] | 0652acde8d8e2338d71aa9e6c4e933d692381d7c3c4ec659e42ef018a1dcc485 |
from six import assertRaisesRegex
from unittest import TestCase
from tempfile import mkstemp
from os import close, unlink, write
from contextlib import contextmanager
from io import StringIO
from json import dumps, loads
import numpy as np
from pysam import CHARD_CLIP, CMATCH
from dark.reads import Read, ReadFilter
f... | acorg/dark-matter | test/test_sam.py | Python | mit | 69,806 | [
"pysam"
] | 29132a696fafaedae2049ae13001696df44b6959238f3f74b0434cd51a70fecd |
# Copyright (c) 2012-2014, Max Zwiessele, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
__doc__ = """
Inference over Gaussian process latent functions
In all our GP models, the consistency propery means that we have a Gaussian
prior over a finite set of points f. This prior is
math:: N(... | ysekky/GPy | GPy/inference/latent_function_inference/__init__.py | Python | bsd-3-clause | 4,032 | [
"Gaussian"
] | 173286914cef13d3c2a8551ab5fae9706cdcb5ddd73e977ef3bd7e956ff12ec1 |
# -*- coding: UTF-8 -*-
# Copyright 2013-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
"""
Database models for :mod:`lino_welfare.modlib.reception`.
.. autosummary::
"""
from builtins import str
import logging
logger = logging.getLogger(__name__)
from django.db import models
from django.conf im... | lsaffre/lino-welfare | lino_welfare/modlib/reception/models.py | Python | agpl-3.0 | 13,950 | [
"VisIt"
] | 2783d73c26a02ad7a459178310bce9cd621f21fecc5a33182214eda5c1d68e9a |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/event.py | Python | lgpl-2.1 | 7,615 | [
"MDTraj"
] | bd495d67ac85f02527f4fbce1f2ab69ac5c2cfd6d55370fcc4107b73afc5a390 |
import codecs
import contextlib
import io
import locale
import sys
import unittest
import warnings
import encodings
from test import support
if sys.platform == 'win32':
VISTA_OR_LATER = (sys.getwindowsversion().major >= 6)
else:
VISTA_OR_LATER = False
try:
import ctypes
except ImportError:
ctypes = N... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.5.9/Python-3.5.9/Lib/test/test_codecs.py | Python | apache-2.0 | 121,644 | [
"FEFF"
] | c20cd754a10be685958128dba2d08a8fe3fefddae3b9d1b2a836ab44f581bc18 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | michaelrup/scancode-toolkit | tests/packagedcode/test_maven.py | Python | apache-2.0 | 21,551 | [
"VisIt"
] | 7019e72c91d232c96dc8a1f67e5768307cf167743d478755bfd1fd502ac82225 |
# Copyright 2016 Autodesk Inc.
#
# 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 applicable law or agreed to in writing... | tkzeng/molecular-design-toolkit | moldesign/parameters.py | Python | apache-2.0 | 9,366 | [
"PySCF"
] | 2fc29bc0bc9a687f05e9ad348ac64339d8cc480a33a10cff49187fa8acf4cd98 |
from lettuce import step, world
from salad.logger import logger
try:
from lettuce.django import django_url
@step(r'(?:visit|access|open) the django url "(.*)"')
def go_to_the_url(step, url):
world.response = world.browser.visit(django_url(url))
except:
try:
# Only complain if it seems ... | adw0rd/salad-py3 | salad/steps/djangoify.py | Python | bsd-3-clause | 456 | [
"VisIt"
] | d0205a65c2a7968d75aedebd88cd1314d95953c64a3259fa42dde1df15f83531 |
#! /usr/bin/env python
from hermes2d import Mesh, MeshView, H1Shapeset, PrecalcShapeset, H1Space, \
LinSystem, WeakForm, DummySolver, Solution, ScalarView, VonMisesFilter
from hermes2d.examples.c07 import set_bc, set_forms
from hermes2d.examples import get_sample_mesh
mesh = Mesh()
mesh.load(get_sample_mesh(... | solin/hermes2d | python/examples/07.py | Python | gpl-2.0 | 1,300 | [
"Mayavi"
] | 0c770f054023494c5c6b07243ede1b39f380952e61c87e3fac391e5aa12a3862 |
__copyright__ = """This code is licensed under the 3-clause BSD license.
Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
See LICENSE.txt for details.
"""
import importlib.util
import os
import sys
from pathlib import Path
from distutils import ccompiler, sysconfig
# Step 1: Load the python bind... | qcscine/utilities | src/Utils/Python/pkginit.py | Python | bsd-3-clause | 2,229 | [
"Gaussian",
"ORCA"
] | f308e5f79a0b6651fffb8ce27e31be85b1f0ff4d0f380d3438aaf9a42549ef5d |
# -*- coding: utf-8 -*-
import logging
import os
import re
import shlex
import shutil
import subprocess
import tempfile
import unicodedata
from pyparsing import Combine, FollowedBy, Group, LineEnd, LineStart, Literal, \
OneOrMore, Optional, SkipTo, StringEnd, StringStart, Suppress, Word
from .models import _d
... | kcl-ddh/chopin-online | catalogue/pdf_parser.py | Python | gpl-3.0 | 5,063 | [
"ADF"
] | e4df06f9e063e8b89c2258a2c5ff4e6af51bd35699c2162ac78a2c7fa286835f |
"""
ASSET is a statistical method [1] for the detection of repeating sequences
of synchronous spiking events in parallel spike trains.
Given a list `sts` of spike trains, the analysis comprises the following
steps:
1) Build the intersection matrix `imat` (optional) and the associated
probability matrix `pmat` with ... | carloscanova/elephant | elephant/asset.py | Python | bsd-3-clause | 69,319 | [
"NEURON"
] | 86be34ab119ecbb16fb99946e05dd09b851619895baaa910f608e058f1e363c7 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
class_names = '''tench, Tinca tinca
goldfish, Carassius auratus
great white shark, white shark, man-eater, man-eating shark, Carcharodon carcharias
tiger shark, Galeocerdo cuvieri
hammerhead, hammerhead shark
electric ray, crampfish, numbfish, torpedo
stingray
cock
hen
ostric... | zsdonghao/tensorlayer | tensorlayer/models/imagenet_classes.py | Python | apache-2.0 | 21,751 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | 2c858b0f320b194d027783a798be3b0b9fda2dc5f9f6103a481108b0b5c04dc0 |
import datetime
from authentication.models import Account
from posts.models import Post
from posts.views import AccountPostsViewSet
def initialize_calendar(data):
post_new_years = Post()
post_new_years.author = Account.objects.get(username = data['username'])
post_new_years.content = 'New Year\'s Day'
... | bewallyt/Classy | posts/initial_calendar.py | Python | mit | 13,788 | [
"COLUMBUS"
] | d937abfb30c007a52534fac4801906943ddcf9e67aea069611ac4956431fb0fa |
"""
@name: Modules/Computer/Web/web_irrigation.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2020 by D. Brian Kimmel
@note: Created on Aug 22, 2016
@license: MIT License
@summary:
"""
__updated__ = '2019-12-30'
# Import system type stuff
import os
# Import PyMh ... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Web/web_irrigation.py | Python | mit | 1,855 | [
"Brian"
] | 93dbfa42549816b229545aa4169eee9d3002da1e643882c3b93c38fd19ef0836 |
#Copyright (C) 2013 Alex Nitz
#
# This program 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.
#
# This program is distributed in the h... | cmbiwer/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 76,756 | [
"Gaussian"
] | 6897f10f57c81081d550385b5c0e35720985da23b64f0153c4a36013be300a36 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/subservices.py | Python | gpl-2.0 | 5,496 | [
"VisIt"
] | 441efca68c15364794bc8710621586d717543cd86b24abca5c799ec1aa9c130d |
"""Read and write notebook files as XML.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed a... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/IPython/nbformat/v2/nbxml.py | Python | mit | 6,819 | [
"Brian"
] | efeea7aa3f7cdab2e54d5f152f61920127f381ee3346235c8639ef35a491d73f |
"""
Gridded data is already aggregated by month
therefore we don't have daily gridded data, but this is
importing to the same basic table type as if it were daily.
So:
Don't make a daily table
Record what monthly aggregations are available
We only use monthly aggregations on the map and ... | flavour/eden | modules/templates/historic/Climate/ClimateDataPortal/import_NetCDF_readings.py | Python | mit | 12,346 | [
"NetCDF"
] | da21ec1b9746db9041f9283c189532b8a0d341a029048f04493e3fcdb265cb03 |
DEVICE_ALIASES = {
# Popular devices - generic name points to latest version
"iPad": "Apple iPad 4",
"iPad mini": "Apple iPad mini 3",
"iPhone": "Apple iPhone 6",
"Galaxy": "Samsung Galaxy S4",
"Nexus": "Motorola Nexus 6",
"Nexus 10": "Samsung Nexus 10",
... | DistilledLtd/heimdall | heimdall/devices.py | Python | apache-2.0 | 5,381 | [
"Galaxy"
] | a7123e7a0c31e08941d1ded0f0a30cbcf8dd53c30d01a29da59a8a9a32354c7c |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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 ... | lahnerml/espresso | tools/blockfile.py | Python | gpl-3.0 | 7,534 | [
"ESPResSo"
] | f1d748a7fe3d00b8e4b2d37ad2716e375ccbd9263a91ee64340b3a48c1ba502e |
import math
import random
"""FILTER"""
#**** STEP 1 = AWARENESS OF ARAVIND SOLUTION ***
#TO PUT IN PEOPLE.PY
"""
def generate_person():
#To add to person generation, after classification
if classification = 'Urban':
city_center_distance = urban_radius*random.random()
if classification = 'Rural':
... | rkawauchi/IHK | health_thibault.py | Python | bsd-3-clause | 17,216 | [
"Gaussian"
] | 81371472070d221f8d0234622a8402d7b414a8894c93aa4f2b8d5ddf716399c2 |
# encoding: utf-8
"""
Context managers for adding things to sys.path temporarily.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license... | marcoantoniooliveira/labweb | oscar/lib/python2.7/site-packages/IPython/utils/syspathcontext.py | Python | bsd-3-clause | 2,028 | [
"Brian"
] | 91c4b5a8bc287808b36545202b3db5079a631b190fe868b9547520211310b5f8 |
import json
import logging
import os
import re
from ece2cmor3 import cmor_utils
# Logger instance.
log = logging.getLogger(__name__)
# Base class for cmor source objects, which represent variables produced by a model
class cmor_source(object):
def __init__(self):
pass
def variable(self):
p... | goord/ece2cmor3 | ece2cmor3/cmor_source.py | Python | apache-2.0 | 9,988 | [
"NetCDF"
] | 1d30aee22bd6c97c9578d21d2dd19f1059eade73ed7173dcccc8da8037b0aa00 |
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space 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 2 of the License, or
# (... | dahaic/outerspace | server/lib/ige/ospace/IPlanet.py | Python | gpl-2.0 | 55,054 | [
"Galaxy"
] | 12728f3c924cc446952f169bb02e44d98c4310f60d6034cfbcc86b6c91e0e624 |
import sympy.mpmath
from sympy.mpmath import *
from sympy.mpmath.libmp import *
import random
import sys
try:
long = long
except NameError:
long = int
def test_type_compare():
assert mpf(2) == mpc(2,0)
assert mpf(0) == mpc(0)
assert mpf(2) != mpc(2, 0.00001)
assert mpf(2) == 2.0
assert mpf... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sympy/mpmath/tests/test_basic_ops.py | Python | agpl-3.0 | 15,195 | [
"Gaussian"
] | 70244eca5642fab79c1d0b2447b35c26ebafd42d42775d9d3aab7f3c5d71080c |
import abc
import datetime
import enum
import typing
import jsii
import jsii.compat
import publication
from jsii.python import classproperty
import aws_cdk.aws_cloudwatch
import aws_cdk.aws_iam
import aws_cdk.aws_kms
import aws_cdk.core
__jsii_assembly__ = jsii.JSIIAssembly.load("@aws-cdk/aws-sqs", "1.15.0", __name_... | randyzingle/tools | kub/services/archive/cdk/python/sample-app/.env/lib/python3.6/site-packages/aws_cdk/aws_sqs/__init__.py | Python | apache-2.0 | 103,200 | [
"CDK"
] | 05e4396230103958ca25a41ce12b43a7a47963060fe9bc7bbf2f53d7c3604509 |
# Install setuptools if not installed.
try:
import setuptools
except ImportError:
from ez_setup import use_setuptools
use_setuptools()
from setuptools import setup, find_packages
# read README as the long description
with open('README.rst', 'r') as f:
long_description = f.read()
setup(
name='urb... | SANDAG/urbansim | setup.py | Python | bsd-3-clause | 1,300 | [
"ORCA"
] | 5cddd843506f26f15681940b082c56ce87cea0cca22d2d3a7edeb2181d5caff1 |
from traits.api import HasTraits, Button, Instance, List, Str, Enum, Float, File, Int
#from traitsui.api import View, Item, VGroup, HSplit, CheckListEditor, HGroup, Group, FileEditor
from traitsui.api import View, Item, VGroup, HSplit, HGroup, FileEditor
from tvtk.pyface.scene_editor import SceneEditor
from mayavi.tool... | xinglunju/tdviz | TDViz.py | Python | mit | 14,736 | [
"Mayavi"
] | 916e7b642d944f3d3aaec11b7368ec60898d1d26bbf364a9725593999205a4fa |
#!/usr/bin/env python
from __future__ import print_function, division #, unicode_literals
import sys
import os
import platform
import shelve
from os.path import join as pj, abspath as absp, basename
from socket import gethostname
from warnings import warn
import logging
logger = logging.getLogger(__name__)
try:
... | SamKChang/abinit-7.10.5_multipole | tests/testbot.py | Python | gpl-3.0 | 18,557 | [
"ABINIT"
] | f7f689f24640bc31099080301d54a319103d3984cad08f65c2b83edf51a9a3a5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import six
from pymatgen.electronic_structure.core import Spin, Orbital
from pymatgen.core.periodic_table import get_el_sp
from pymatgen.co... | xhqu1981/pymatgen | pymatgen/electronic_structure/dos.py | Python | mit | 17,289 | [
"Gaussian",
"VASP",
"pymatgen"
] | 60cdfa8cd50e86c0ffad8c80345f180f7464f8eeb5aa9949d83299616cff67fc |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | yashdsaraf/scancode-toolkit | src/licensedcode/tokenize.py | Python | apache-2.0 | 8,305 | [
"VisIt"
] | 3a055523de150fffaffbba8816da6b6e6a021e3446f50c73c9264d91485ff007 |
# -*- coding: utf-8 -*-
"""Handles creating a release PR"""
import base64
import json
import os
import tempfile
import textwrap
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from pathlib import Path
from typing import Tuple
import httplib2
from apiclient import discovery
from git ... | Avira/tox | tasks/notify.py | Python | mit | 5,605 | [
"VisIt"
] | b8df9cfc6015a8e3025e8297e78943beee528f40f88c73d16f39fc5af59a5674 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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 versio... | psci2195/espresso-ffans | testsuite/scripts/tutorials/test_04-lattice_boltzmann_part4_solution.py | Python | gpl-3.0 | 1,604 | [
"ESPResSo"
] | fd29abfe361acca2a7b404956c75182d9023a9b82bd8c95c5268d84d3b35b684 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
import tensorflow as tf
from niftynet.layer.base_layer import Layer
from niftynet.layer.layer_util import \
expand_spatial_params, infer_spatial_rank
from niftynet.utilities.util_common import look_up_operations
"""
This cla... | NifTK/NiftyNet | niftynet/layer/approximated_smoothing.py | Python | apache-2.0 | 3,416 | [
"Gaussian"
] | 9fff8409fdf61c4c41dc70bb9cd21478778bd16b3cc571a7d5d467ec3b033df1 |
from dipy.align import floating
import numpy as np
import numpy.linalg as npl
import scipy.ndimage.filters as filters
class ScaleSpace(object):
def __init__(self, image, num_levels,
image_grid2world=None,
input_spacing=None,
sigma_factor=0.2,
mas... | StongeEtienne/dipy | dipy/align/scalespace.py | Python | bsd-3-clause | 17,207 | [
"Gaussian"
] | 37f078abc6cd616d92967dcd5e32e957d53b54a6112f35edaaa89636c40392da |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2015 CERN.
#
# Invenio 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 2 of the
# License, or (at your option) any later... | eamonnmag/invenio-search | invenio_search/walkers/elasticsearch.py | Python | gpl-2.0 | 6,499 | [
"VisIt"
] | f685a92b005fef7ab8c093b6a1f03f3267729ddf5add2e69ac41903c40767e4e |
#!/usr/bin/python
import sys
import os
from oauth2client import client
import gflags
import httplib2
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import OAuth2WebServerFlow
from oauth2client.tools import run
from datetime import datetime, date, time, timed... | arnau-prat/My-Raspersonal-assistant | assets/modules/calendar.py | Python | mit | 18,280 | [
"VisIt"
] | 63ccef8503e462ba1e7e79af627f089ad2b80bffa25d7e01db17ceb4bbd46427 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_phi1.0a.py | Python | gpl-3.0 | 2,479 | [
"VTK"
] | aa96dd0b0357a4a2ebd13d4b90e44731f68e71d6eb04630d02a5074cbb95b14e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import httplib as http
import logging
import unittest
import markupsafe
import mock
from nose.tools import * # flake8: noqa (PEP8 asserts)
import re
from framework.mongo.utils import to_mongo_key
from framework.auth import cas
from f... | mluke93/osf.io | tests/webtest_tests.py | Python | apache-2.0 | 40,398 | [
"VisIt"
] | 3d0cc6c2e1dfe73840c6bb0dd1a1056bfb2d93091208338f0039bf41303347ef |
import os
import warnings
import numpy as np
from astropy.convolution import Gaussian1DKernel, Gaussian2DKernel
from astropy.io import fits
from astropy import wcs
import astropy
import multiprocessing
from .. import cubes, Cube, CubeStack
from ...spectrum.models import n2hp, ammonia_constants
from ...spectrum.models.... | e-koch/pyspeckit | pyspeckit/cubes/tests/test_cubetools.py | Python | mit | 15,381 | [
"Gaussian"
] | a9144bb5c374e03fb380929bb2f3946f0817f5ad18076dbadcf6b3f3c31afb12 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTexturedSphereSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkTexturedSphereSource.py | Python | bsd-3-clause | 487 | [
"VTK"
] | 72c47a86835be1a32c348b0a92fbe04f4e27891e19a12b01f7c5358431920e34 |
# Built-in modules #
import multiprocessing
# Internal modules #
from seqenv.seqsearch.blast import BLASTquery
from seqenv.seqsearch.vsearch import VSEARCHquery
from seqenv.common.cache import property_cached
from seqenv.common.autopaths import FilePath
# Third party modules #
#######################################... | xapple/seqenv | seqenv/seqsearch/__init__.py | Python | mit | 4,079 | [
"BLAST"
] | 93453f0917d316a70c6c0d78f84571638ffd8f4debe5c183586bd84aa07fd2cc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vgridforum - Access VGrid private forum for owners and members
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the... | heromod/migrid | mig/shared/functionality/vgridworkflows.py | Python | gpl-2.0 | 10,824 | [
"Brian"
] | 8db46e6b97985f1e75e15f6da4c95d0ab7c14d211e8596ec2e29f4e8694c1731 |
"""
This file is part of the cygnet project.
Copyright 2017 Anna-Christina Eilers.
"""
import matplotlib
matplotlib.use('Agg')
import numpy as np
import matplotlib.pyplot as plt
from astropy.table import Table
import seaborn as sns
import pickle
from datetime import datetime
from astropy.table import Column
import co... | aceilers/cygnet | hmf.py | Python | mit | 12,397 | [
"Amber"
] | d826bee07f51186fa2241db0e69e6770fd38b005e3c16efa7a95e43577ce6ec1 |
""" Plot the meteor PSF profile from the detection and FF file. """
import os
import matplotlib.pyplot as plt
import numpy as np
import scipy.ndimage
import scipy.optimize
from RMS.Formats.FFfile import read as readFF
from RMS.Formats.FTPdetectinfo import readFTPdetectinfo
def mapCoordinatesToRotatedImage(img, ... | apevec/RMS | Utils/PlotMeteorPSFProfile.py | Python | gpl-3.0 | 6,883 | [
"Gaussian"
] | ca641e1d224a354fff2ad673bd4c292000d5bb76d8fe5171358552f4d79b18d8 |
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