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How to use test_interpolate method in molecule
Best Python code snippet using molecule_python
test_interpolate.py
Source:test_interpolate.py 
...16 self.n = 517 self.coefs = list((ra.random((self.n,)) * 0.5 - 1.0) * 2.0)18 self.x = ra.random((1,))[0]19 self.interpolate = interpolate.PolynomialInterpolate(self.coefs)20 def test_interpolate(self):21 self.assertTrue(np.isclose(np.polyval(self.coefs, self.x),22 self.interpolate(self.x)))23class TestPiecewiseLinearInterpolate(unittest.TestCase, BaseInterpolate):24 def setUp(self):25 self.validx = [-10.0, -2.0, 1.0, 2.0, 5.0, 15.0]26 self.invalidx_1 = [-2.0, -10.0, 1.0, 2.0, 5.0, 15.0]27 self.invalidx_2 = [-10.0, -2.0, 1.0, 2.0, 5.0]28 self.points = [50.0, -25.0, 1.0, 0.0, 0.0, 10.0]29 self.x = 17.030 self.valid = interpolate.PiecewiseLinearInterpolate(self.validx, 31 self.points)32 self.invalid1 = interpolate.PiecewiseLinearInterpolate(self.invalidx_1, 33 self.points)34 self.invalid2 = interpolate.PiecewiseLinearInterpolate(self.invalidx_2, 35 self.points)36 self.interpolate = self.valid37 def test_valid(self):38 self.assertTrue(self.valid.valid)39 self.assertFalse(self.invalid1.valid)40 self.assertFalse(self.invalid2.valid)41 def test_interpolate(self):42 testinter = inter.interp1d(self.validx, self.points,43 bounds_error = False)44 xs = np.linspace(-15.0,20.0)45 ys1 = [self.valid(x) for x in xs]46 ys2 = testinter(xs)47 ys2[xs < self.validx[0]] = self.points[0]48 ys2[xs > self.validx[-1]] = self.points[-1]49 self.assertTrue(np.allclose(ys1, ys2))50class TestGenericPiecewiseInterpolate(unittest.TestCase, BaseInterpolate):51 def setUp(self):52 self.xs = [1.0,5.0]53 self.cvs = [-1.0,5.0,-2.0]54 self.fns = [interpolate.ConstantInterpolate(cv) for cv in self.cvs]55 self.interpolate = interpolate.GenericPiecewiseInterpolate(self.xs,56 self.fns)57 self.x = 4.058 def test_interpolate(self):59 self.assertTrue(np.isclose(self.interpolate.value(0.0), self.cvs[0]))60 self.assertTrue(np.isclose(self.interpolate.value(4.0), self.cvs[1]))61 self.assertTrue(np.isclose(self.interpolate.value(10.0), self.cvs[2]))62class TestPiecewiseLogLinearInterpolate(unittest.TestCase, BaseInterpolate):63 def setUp(self):64 self.validx = [-10.0, -2.0, 1.0, 2.0, 5.0, 15.0]65 self.invalidx_1 = [-2.0, -10.0, 1.0, 2.0, 5.0, 15.0]66 self.invalidx_2 = [-10.0, -2.0, 1.0, 2.0, 5.0]67 self.points = [1.0e5, 1.0e0, 1.0e-1, 1.0e-6, 1.0e0, 1.0e2]68 self.invalidpoints = [1.0e5, 1.0e0, -1.0e-1, 1.0e-6, 1.0e0, 1.0e2]69 self.x = 17.070 self.valid = interpolate.PiecewiseLogLinearInterpolate(self.validx, 71 self.points)72 self.invalid1 = interpolate.PiecewiseLogLinearInterpolate(self.invalidx_1, 73 self.points)74 self.invalid2 = interpolate.PiecewiseLogLinearInterpolate(self.invalidx_2, 75 self.points)76 self.invalid3 = interpolate.PiecewiseLogLinearInterpolate(self.validx, 77 self.invalidpoints)78 self.interpolate = self.valid79 def test_valid(self):80 self.assertTrue(self.valid.valid)81 self.assertFalse(self.invalid1.valid)82 self.assertFalse(self.invalid2.valid)83 self.assertFalse(self.invalid3.valid)84 def test_interpolate(self):85 testinter = inter.interp1d(self.validx, np.log(self.points),86 bounds_error = False)87 xs = np.linspace(-15.0,20.0)88 ys1 = [self.valid(x) for x in xs]89 yp = testinter(xs)90 yp[xs < self.validx[0]] = np.log(self.points[0])91 yp[xs > self.validx[-1]] = np.log(self.points[-1])92 ys2 = np.exp(yp)93 self.assertTrue(np.allclose(ys1, ys2))94class TestPiecewiseSemiLogXLinearInterpolate(unittest.TestCase, BaseInterpolate):95 def setUp(self):96 self.validx = [1e-2, 0.5, 1.0, 2.0, 5.0, 15.0]97 self.points = [10,20,30,40,50,60]98 self.x = 7.599 self.interpolate = interpolate.PiecewiseSemiLogXLinearInterpolate(self.validx, 100 self.points)101 def test_interpolate(self):102 testinter = inter.interp1d(np.log10(self.validx), self.points,103 bounds_error = False)104 xs = np.linspace(1e-3,20.0,500)105 ys1 = [self.interpolate(x) for x in xs]106 ys2 = testinter(np.log10(xs))107 ys2[xs < self.validx[0]] = self.points[0]108 ys2[xs > self.validx[-1]] = self.points[-1]109 self.assertTrue(np.allclose(ys1, ys2))110class TestConstantInterpolate(unittest.TestCase, BaseInterpolate):111 def setUp(self):112 self.v = ra.random((1,))[0]113 self.interpolate = interpolate.ConstantInterpolate(self.v)114 self.x = ra.random((1,))[0]115 def test_interpolate(self):116 self.assertTrue(np.isclose(self.v, self.interpolate(self.x)))117class TestExpInterpolate(unittest.TestCase, BaseInterpolate):118 def setUp(self):119 self.A = 1.2120 self.B = 5.1121 self.interpolate = interpolate.ExpInterpolate(self.A, self.B)122 self.x = 0.5123 def test_interpolate(self):124 self.assertTrue(np.isclose(self.A * np.exp(self.B/self.x),125 self.interpolate(self.x)))126class TestPowerLawInterpolate(unittest.TestCase, BaseInterpolate):127 def setUp(self):128 self.A = 5.1129 self.B = 0.3130 self.interpolate = interpolate.PowerLawInterpolate(self.A, self.B)131 self.x = 2.1132 def test_interpolate(self):133 self.assertTrue(np.isclose(self.A * self.x**self.B, 134 self.interpolate(self.x)))135class TestMTSShearInterpolate(unittest.TestCase, BaseInterpolate):136 def setUp(self):137 self.y0 = 100.0138 self.D = 50.0139 self.x0 = 200.0140 self.interpolate = interpolate.MTSShearInterpolate(self.y0, self.D, self.x0)141 self.x = 300.0142 def test_interpolate(self):143 should = self.y0 - self.D / (np.exp(self.x0 / self.x) - 1.0)144 act = self.interpolate(self.x)145 self.assertTrue(np.isclose(should, act))146class TestMTSInterpolate(unittest.TestCase, BaseInterpolate):147 def setUp(self):148 self.tau0 = 300.0149 self.g0 = 0.75150 E_poly = np.array([-3.94833389e-02, -5.20197047e+01, 1.95594836e+05])151 nu = 0.31152 self.mu = interpolate.PolynomialInterpolate(E_poly/(2*(1+nu)))153 self.k = 1.38064e-20154 self.b = 2.02e-7155 self.p = 0.8156 self.q = 0.9157 self.interpolate = interpolate.MTSInterpolate(self.tau0, self.g0, self.q, self.p, self.k, self.b, self.mu)158 self.x = 300.0159 def test_interpolate(self):160 should = self.tau0 * (1.0- (self.k*self.x/(self.mu(self.x)*self.b**3.0*self.g0))**(1.0/self.q))**(1.0/self.p) 161 act = self.interpolate(self.x)...
test_utils.py
Source:test_utils.py
1# -*- coding: utf-8 -*-2import unittest3import os4from advanced_ssh_config.utils import (safe_makedirs, value_interpolate,5 construct_proxy_commands, shellquote,6 shellquotemultiple)7from advanced_ssh_config.exceptions import ConfigError8from . import PREFIX9class TestContructProxyCommand(unittest.TestCase):10 def test_no_arg(self):11 self.assertRaises(TypeError, construct_proxy_commands)12 def test_empty_arg(self):13 self.assertRaises(ValueError, construct_proxy_commands, {})14 def test_minimal_valid(self):15 command = construct_proxy_commands({16 'hostname': 'aaa',17 'port': 42,18 })19 self.assertEqual(20 command, [['nc', '-w', 180, '-G', 5, 'aaa', 42], ['nc', 'aaa', 42]]21 )22 def test_minimal_nc(self):23 command = construct_proxy_commands({24 'hostname': 'aaa',25 'proxy_type': 'nc',26 'port': 42,27 })28 self.assertEqual(29 command, [['nc', '-w', 180, '-G', 5, 'aaa', 42], ['nc', 'aaa', 42]]30 )31 def test_full_nc(self):32 command = construct_proxy_commands({33 'hostname': 'aaa',34 'port': 42,35 'verbose': True,36 'proxy_type': 'nc',37 'timeout': 45,38 })39 self.assertEqual(40 command, [41 ['nc', '-v', '-w', 45, '-G', 5, 'aaa', 42],42 ['nc', 'aaa', 42]43 ]44 )45 def test_invalid_proxy_type(self):46 args = {47 'hostname': 'aaa',48 'port': 42,49 'proxy_type': 'fake',50 }51 self.assertRaises(ValueError, construct_proxy_commands, args)52 def test_minimal_socat(self):53 command = construct_proxy_commands({54 'hostname': 'aaa',55 'proxy_type': 'socat',56 'port': 42,57 })58 self.assertEqual(command, [['socat', 'STDIN', 'TCP:aaa:42']])59 def test_minimal_socat_http_proxy(self):60 command = construct_proxy_commands({61 'hostname': 'aaa',62 'proxy_type': 'socat_http_proxy',63 'http_proxy_host': 'bbb',64 'http_proxy_port': 43,65 'port': 42,66 })67 self.assertEqual(68 command, [['socat', 'STDIN', 'PROXY:bbb:aaa:42,proxyport=43']]69 )70 def test_minimal_socat_socks(self):71 command = construct_proxy_commands({72 'hostname': 'aaa',73 'proxy_type': 'socat_socks',74 'socks_host': 'bbb',75 'socks_port': 43,76 'port': 42,77 })78 self.assertEqual(79 command, [['socat', 'STDIN', 'SOCKS:bbb:aaa:42,socksport=43']]80 )81 # FIXME: test_custom_handler82class TestSafeMakedirs(unittest.TestCase):83 def setUp(self):84 if os.path.exists(PREFIX):85 os.system('rm -rf {}'.format(PREFIX))86 os.makedirs(PREFIX)87 def test_already_exists(self):88 safe_makedirs('{}/dir'.format(PREFIX))89 safe_makedirs('{}/dir'.format(PREFIX))90 def test_invalid(self):91 for path in ('/dev/null/test',):92 self.assertRaises(OSError, safe_makedirs, path)93 def test_makedirs_on_file(self):94 open('{}/file'.format(PREFIX), 'w').write('hello')95 self.assertRaises(OSError, safe_makedirs, '{}/file/dir'.format(PREFIX))96class TestValueInterpolate(unittest.TestCase):97 def setUp(self):98 if os.environ.get('TEST_INTERPOLATE'):99 del os.environ['TEST_INTERPOLATE']100 def test_interpolate_success(self):101 os.environ['TEST_INTERPOLATE'] = 'titi'102 self.assertEquals(value_interpolate('$TEST_INTERPOLATE'), 'titi')103 def test_interpolate_no_match(self):104 self.assertEquals(105 value_interpolate('$TEST_INTERPOLATE'), '$TEST_INTERPOLATE'106 )107 def test_interpolate_not_interpolable(self):108 os.environ['TEST_INTERPOLATE'] = 'titi'109 self.assertEquals(110 value_interpolate('TEST_INTERPOLATE'), 'TEST_INTERPOLATE'111 )112 def test_interpolate_interpolate_recursive(self):113 os.environ['TEST_INTERPOLATE'] = '$TEST_INTERPOLATE_2'114 os.environ['TEST_INTERPOLATE_2'] = '$TEST_INTERPOLATE_3'115 os.environ['TEST_INTERPOLATE_3'] = '$TEST_INTERPOLATE_4'116 os.environ['TEST_INTERPOLATE_4'] = 'tutu'117 self.assertEquals(value_interpolate('$TEST_INTERPOLATE'), 'tutu')118 def test_interpolate_interpolate_loop(self):119 os.environ['TEST_INTERPOLATE'] = '$TEST_INTERPOLATE'120 self.assertRaises(ConfigError, value_interpolate, '$TEST_INTERPOLATE')121 def test_interpolate_interpolate_loop_complex(self):122 os.environ['TEST_INTERPOLATE'] = '$TEST_INTERPOLATE_2'123 os.environ['TEST_INTERPOLATE_2'] = '$TEST_INTERPOLATE_3'124 os.environ['TEST_INTERPOLATE_3'] = '$TEST_INTERPOLATE'125 self.assertRaises(ConfigError, value_interpolate, '$TEST_INTERPOLATE')126class TestShellQuote(unittest.TestCase):127 def test_shellquote_simple(self):128 self.assertEquals(shellquote(["aaa"]), 'aaa')129 self.assertEquals(shellquote(["aaa", "bbb"]), 'aaa bbb')130 self.assertEquals(shellquote(["aaa", "bbb", 42]), 'aaa bbb 42')131 def test_shellquote_empty(self):132 self.assertEquals(shellquote([]), '')133 def test_shellquote_escape(self):134 self.assertEquals(shellquote(["test'test"]), "'test\\'test'")135 self.assertEquals(shellquote(["test\\test"]), "'test\\\\test'")136 self.assertEquals(shellquote(["test\"test"]), "test\"test")137 def test_shellquote_complex(self):138 self.assertEquals(139 shellquote(["ssh", "manfred's imac", '-p', 4242]),140 "ssh 'manfred\\'s imac' -p 4242"141 )142 def test_shellquote_not_list(self):143 self.assertRaises(ValueError, shellquote, 'aaa')144class TestShellQuoteMultiple(unittest.TestCase):145 def test_shellquote_multiple_simple(self):146 self.assertEquals(147 shellquotemultiple([['aaa', 'bbb', 42], ['ccc', 'ddd', 43]]),148 '(aaa bbb 42 2>/dev/null || ccc ddd 43)'149 )150 def test_shellquote_not_list_of_list(self):151 self.assertRaises(ValueError, shellquotemultiple, [42, 42])152 self.assertRaises(ValueError, shellquotemultiple, 42)...
Interpolation.py
Source:Interpolation.py
...8""" Interpolation holds classes and functions important for interpolating data.9 Examples10--------11 #!python12 >>test_interpolate()13 <h3><a href="../../../Examples/html/Interpolation_Example.html">Interpolation Example</a></h3>14Requirements15------------16+ [sys](https://docs.python.org/2/library/sys.html)17+ [os](https://docs.python.org/2/library/os.html)18+ [types](https://docs.python.org/2/library/types.html)19+ [numpy](https://docs.scipy.org/doc/)20+ [scipy](https://docs.scipy.org/doc/)21Help22---------------23<a href="./index.html">`pyMez.Code.Analysis`</a>24<div>25<a href="../../../pyMez_Documentation.html">Documentation Home</a> |26<a href="../../index.html">API Documentation Home</a> |27<a href="../../../Examples/html/Examples_Home.html">Examples Home</a> |28<a href="../../../Reference_Index.html">Index</a>29</div>30 """31#-----------------------------------------------------------------------------32# Standard Imports33import os34import sys35from types import *36#-----------------------------------------------------------------------------37# Third Party Imports38sys.path.append(os.path.join(os.path.dirname( __file__ ), '..','..'))39try:40 import numpy as np41except:42 print("Numpy was not imported")43 raise44try:45 from scipy.interpolate import interp1d46except:47 print("The function scipy.interpolate.interp1d did not import properly,"48 "please check that scipy is on the python path and that it is not in an error state")49 raise50#-----------------------------------------------------------------------------51# Module Constants52#-----------------------------------------------------------------------------53# Module Functions54def interpolate_data(data_list,**options):55 """interpolate data takes a list of data in [[x,y1,y2,..yn]..] format and56 returns a list of interpolation functions [f1(x),f2(x),f3(x)...fn(x)]"""57 out_list=[]58 # reorganize the list to [[x,..xm],[y,...ym]]59 vector_list=[]60 for index,column in enumerate(data_list[0]):61 vector=[row[index] for row in data_list]62 vector_list.append(vector)63 # now each function is interp1d of64 for vector in vector_list[1:]:65 f=interp1d(vector_list[0],vector,**options)66 out_list.append(f)67 return out_list68def build_interpolated_data_set(x_list,interpolated_function_list):69 """build_interpolated_data_set takes an input independent variable and a list70 of interpolation functions and returns a data set of the form [..[xi,f1(xi),..fn(xi)]]71 it is meant to create a synthetic data set after using interpolate_data"""72 out_data=[]73 for x in x_list:74 new_row=[]75 new_row.append(x)76 for function in interpolated_function_list:77 # to list is needed if the function returns np.array78 if type(function(x)) in [np.ndarray]:79 new_row.append(function(x).tolist())80 else:81 new_row.append(function(x))82 out_data.append(new_row)83 return out_data84def interpolate_table(table,independent_variable_list):85 """Returns a copy of the table interpolated to the independent variable list86 Assumes there is a single independent variable in the first column"""87 functions=interpolate_data(table.data)88 new_data=build_interpolated_data_set(independent_variable_list,functions)89 new_table=table.copy()90 new_table.data=new_data91 return new_table92#-----------------------------------------------------------------------------93# Module Classes94#-----------------------------------------------------------------------------95# Module Scripts96def test_interpolate(data_set=None):97 if data_set is None:98 data_set=[[i,i**2,i**3] for i in range(100)]99 interpolation_functions=interpolate_data(data_set)100 type_of_f=type(interpolation_functions[0](1))101 print(("The types of of the function results are {0}".format(type_of_f)))102 print(("type(f(x)) == numpy.ndarray is {0}".format(type_of_f in [np.ndarray,"<type 'numpy.ndarray'>"])))103 new_x=[i for i in range(100)]104 interpolated_data=build_interpolated_data_set(new_x,interpolation_functions)105 print("Testing interpolation of data set")106 print(("*"*80))107 print(("the old data set is {0} ".format(data_set)))108 print(("*"*80))109 print(("the new data set is {0}".format(interpolated_data)))110#-----------------------------------------------------------------------------111# Module Runner112if __name__ == '__main__':113 test_interpolate()...
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