scipy 1.16.2__cp314-cp314-win_arm64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scipy/__config__.py +161 -0
- scipy/__init__.py +150 -0
- scipy/_cyutility.cp314-win_arm64.lib +0 -0
- scipy/_cyutility.cp314-win_arm64.pyd +0 -0
- scipy/_distributor_init.py +18 -0
- scipy/_lib/__init__.py +14 -0
- scipy/_lib/_array_api.py +931 -0
- scipy/_lib/_array_api_compat_vendor.py +9 -0
- scipy/_lib/_array_api_no_0d.py +103 -0
- scipy/_lib/_bunch.py +229 -0
- scipy/_lib/_ccallback.py +251 -0
- scipy/_lib/_ccallback_c.cp314-win_arm64.lib +0 -0
- scipy/_lib/_ccallback_c.cp314-win_arm64.pyd +0 -0
- scipy/_lib/_disjoint_set.py +254 -0
- scipy/_lib/_docscrape.py +761 -0
- scipy/_lib/_elementwise_iterative_method.py +346 -0
- scipy/_lib/_fpumode.cp314-win_arm64.lib +0 -0
- scipy/_lib/_fpumode.cp314-win_arm64.pyd +0 -0
- scipy/_lib/_gcutils.py +105 -0
- scipy/_lib/_pep440.py +487 -0
- scipy/_lib/_sparse.py +41 -0
- scipy/_lib/_test_ccallback.cp314-win_arm64.lib +0 -0
- scipy/_lib/_test_ccallback.cp314-win_arm64.pyd +0 -0
- scipy/_lib/_test_deprecation_call.cp314-win_arm64.lib +0 -0
- scipy/_lib/_test_deprecation_call.cp314-win_arm64.pyd +0 -0
- scipy/_lib/_test_deprecation_def.cp314-win_arm64.lib +0 -0
- scipy/_lib/_test_deprecation_def.cp314-win_arm64.pyd +0 -0
- scipy/_lib/_testutils.py +373 -0
- scipy/_lib/_threadsafety.py +58 -0
- scipy/_lib/_tmpdirs.py +86 -0
- scipy/_lib/_uarray/LICENSE +29 -0
- scipy/_lib/_uarray/__init__.py +116 -0
- scipy/_lib/_uarray/_backend.py +707 -0
- scipy/_lib/_uarray/_uarray.cp314-win_arm64.lib +0 -0
- scipy/_lib/_uarray/_uarray.cp314-win_arm64.pyd +0 -0
- scipy/_lib/_util.py +1283 -0
- scipy/_lib/array_api_compat/__init__.py +22 -0
- scipy/_lib/array_api_compat/_internal.py +59 -0
- scipy/_lib/array_api_compat/common/__init__.py +1 -0
- scipy/_lib/array_api_compat/common/_aliases.py +727 -0
- scipy/_lib/array_api_compat/common/_fft.py +213 -0
- scipy/_lib/array_api_compat/common/_helpers.py +1058 -0
- scipy/_lib/array_api_compat/common/_linalg.py +232 -0
- scipy/_lib/array_api_compat/common/_typing.py +192 -0
- scipy/_lib/array_api_compat/cupy/__init__.py +13 -0
- scipy/_lib/array_api_compat/cupy/_aliases.py +156 -0
- scipy/_lib/array_api_compat/cupy/_info.py +336 -0
- scipy/_lib/array_api_compat/cupy/_typing.py +31 -0
- scipy/_lib/array_api_compat/cupy/fft.py +36 -0
- scipy/_lib/array_api_compat/cupy/linalg.py +49 -0
- scipy/_lib/array_api_compat/dask/__init__.py +0 -0
- scipy/_lib/array_api_compat/dask/array/__init__.py +12 -0
- scipy/_lib/array_api_compat/dask/array/_aliases.py +376 -0
- scipy/_lib/array_api_compat/dask/array/_info.py +416 -0
- scipy/_lib/array_api_compat/dask/array/fft.py +21 -0
- scipy/_lib/array_api_compat/dask/array/linalg.py +72 -0
- scipy/_lib/array_api_compat/numpy/__init__.py +28 -0
- scipy/_lib/array_api_compat/numpy/_aliases.py +190 -0
- scipy/_lib/array_api_compat/numpy/_info.py +366 -0
- scipy/_lib/array_api_compat/numpy/_typing.py +30 -0
- scipy/_lib/array_api_compat/numpy/fft.py +35 -0
- scipy/_lib/array_api_compat/numpy/linalg.py +143 -0
- scipy/_lib/array_api_compat/torch/__init__.py +22 -0
- scipy/_lib/array_api_compat/torch/_aliases.py +855 -0
- scipy/_lib/array_api_compat/torch/_info.py +369 -0
- scipy/_lib/array_api_compat/torch/_typing.py +3 -0
- scipy/_lib/array_api_compat/torch/fft.py +85 -0
- scipy/_lib/array_api_compat/torch/linalg.py +121 -0
- scipy/_lib/array_api_extra/__init__.py +38 -0
- scipy/_lib/array_api_extra/_delegation.py +171 -0
- scipy/_lib/array_api_extra/_lib/__init__.py +1 -0
- scipy/_lib/array_api_extra/_lib/_at.py +463 -0
- scipy/_lib/array_api_extra/_lib/_backends.py +46 -0
- scipy/_lib/array_api_extra/_lib/_funcs.py +937 -0
- scipy/_lib/array_api_extra/_lib/_lazy.py +357 -0
- scipy/_lib/array_api_extra/_lib/_testing.py +278 -0
- scipy/_lib/array_api_extra/_lib/_utils/__init__.py +1 -0
- scipy/_lib/array_api_extra/_lib/_utils/_compat.py +74 -0
- scipy/_lib/array_api_extra/_lib/_utils/_compat.pyi +45 -0
- scipy/_lib/array_api_extra/_lib/_utils/_helpers.py +559 -0
- scipy/_lib/array_api_extra/_lib/_utils/_typing.py +10 -0
- scipy/_lib/array_api_extra/_lib/_utils/_typing.pyi +105 -0
- scipy/_lib/array_api_extra/testing.py +359 -0
- scipy/_lib/cobyqa/__init__.py +20 -0
- scipy/_lib/cobyqa/framework.py +1240 -0
- scipy/_lib/cobyqa/main.py +1506 -0
- scipy/_lib/cobyqa/models.py +1529 -0
- scipy/_lib/cobyqa/problem.py +1296 -0
- scipy/_lib/cobyqa/settings.py +132 -0
- scipy/_lib/cobyqa/subsolvers/__init__.py +14 -0
- scipy/_lib/cobyqa/subsolvers/geometry.py +387 -0
- scipy/_lib/cobyqa/subsolvers/optim.py +1203 -0
- scipy/_lib/cobyqa/utils/__init__.py +18 -0
- scipy/_lib/cobyqa/utils/exceptions.py +22 -0
- scipy/_lib/cobyqa/utils/math.py +77 -0
- scipy/_lib/cobyqa/utils/versions.py +67 -0
- scipy/_lib/decorator.py +399 -0
- scipy/_lib/deprecation.py +274 -0
- scipy/_lib/doccer.py +366 -0
- scipy/_lib/messagestream.cp314-win_arm64.lib +0 -0
- scipy/_lib/messagestream.cp314-win_arm64.pyd +0 -0
- scipy/_lib/pyprima/__init__.py +212 -0
- scipy/_lib/pyprima/cobyla/__init__.py +0 -0
- scipy/_lib/pyprima/cobyla/cobyla.py +559 -0
- scipy/_lib/pyprima/cobyla/cobylb.py +714 -0
- scipy/_lib/pyprima/cobyla/geometry.py +226 -0
- scipy/_lib/pyprima/cobyla/initialize.py +215 -0
- scipy/_lib/pyprima/cobyla/trustregion.py +492 -0
- scipy/_lib/pyprima/cobyla/update.py +289 -0
- scipy/_lib/pyprima/common/__init__.py +0 -0
- scipy/_lib/pyprima/common/_bounds.py +34 -0
- scipy/_lib/pyprima/common/_linear_constraints.py +46 -0
- scipy/_lib/pyprima/common/_nonlinear_constraints.py +54 -0
- scipy/_lib/pyprima/common/_project.py +173 -0
- scipy/_lib/pyprima/common/checkbreak.py +93 -0
- scipy/_lib/pyprima/common/consts.py +47 -0
- scipy/_lib/pyprima/common/evaluate.py +99 -0
- scipy/_lib/pyprima/common/history.py +38 -0
- scipy/_lib/pyprima/common/infos.py +30 -0
- scipy/_lib/pyprima/common/linalg.py +435 -0
- scipy/_lib/pyprima/common/message.py +290 -0
- scipy/_lib/pyprima/common/powalg.py +131 -0
- scipy/_lib/pyprima/common/preproc.py +277 -0
- scipy/_lib/pyprima/common/present.py +5 -0
- scipy/_lib/pyprima/common/ratio.py +54 -0
- scipy/_lib/pyprima/common/redrho.py +47 -0
- scipy/_lib/pyprima/common/selectx.py +296 -0
- scipy/_lib/tests/__init__.py +0 -0
- scipy/_lib/tests/test__gcutils.py +110 -0
- scipy/_lib/tests/test__pep440.py +67 -0
- scipy/_lib/tests/test__testutils.py +32 -0
- scipy/_lib/tests/test__threadsafety.py +51 -0
- scipy/_lib/tests/test__util.py +641 -0
- scipy/_lib/tests/test_array_api.py +322 -0
- scipy/_lib/tests/test_bunch.py +169 -0
- scipy/_lib/tests/test_ccallback.py +196 -0
- scipy/_lib/tests/test_config.py +45 -0
- scipy/_lib/tests/test_deprecation.py +10 -0
- scipy/_lib/tests/test_doccer.py +143 -0
- scipy/_lib/tests/test_import_cycles.py +18 -0
- scipy/_lib/tests/test_public_api.py +482 -0
- scipy/_lib/tests/test_scipy_version.py +28 -0
- scipy/_lib/tests/test_tmpdirs.py +48 -0
- scipy/_lib/tests/test_warnings.py +137 -0
- scipy/_lib/uarray.py +31 -0
- scipy/cluster/__init__.py +31 -0
- scipy/cluster/_hierarchy.cp314-win_arm64.lib +0 -0
- scipy/cluster/_hierarchy.cp314-win_arm64.pyd +0 -0
- scipy/cluster/_optimal_leaf_ordering.cp314-win_arm64.lib +0 -0
- scipy/cluster/_optimal_leaf_ordering.cp314-win_arm64.pyd +0 -0
- scipy/cluster/_vq.cp314-win_arm64.lib +0 -0
- scipy/cluster/_vq.cp314-win_arm64.pyd +0 -0
- scipy/cluster/hierarchy.py +4348 -0
- scipy/cluster/tests/__init__.py +0 -0
- scipy/cluster/tests/hierarchy_test_data.py +145 -0
- scipy/cluster/tests/test_disjoint_set.py +202 -0
- scipy/cluster/tests/test_hierarchy.py +1238 -0
- scipy/cluster/tests/test_vq.py +434 -0
- scipy/cluster/vq.py +832 -0
- scipy/conftest.py +683 -0
- scipy/constants/__init__.py +358 -0
- scipy/constants/_codata.py +2266 -0
- scipy/constants/_constants.py +369 -0
- scipy/constants/codata.py +21 -0
- scipy/constants/constants.py +53 -0
- scipy/constants/tests/__init__.py +0 -0
- scipy/constants/tests/test_codata.py +78 -0
- scipy/constants/tests/test_constants.py +83 -0
- scipy/datasets/__init__.py +90 -0
- scipy/datasets/_download_all.py +71 -0
- scipy/datasets/_fetchers.py +225 -0
- scipy/datasets/_registry.py +26 -0
- scipy/datasets/_utils.py +81 -0
- scipy/datasets/tests/__init__.py +0 -0
- scipy/datasets/tests/test_data.py +128 -0
- scipy/differentiate/__init__.py +27 -0
- scipy/differentiate/_differentiate.py +1129 -0
- scipy/differentiate/tests/__init__.py +0 -0
- scipy/differentiate/tests/test_differentiate.py +694 -0
- scipy/fft/__init__.py +114 -0
- scipy/fft/_backend.py +196 -0
- scipy/fft/_basic.py +1650 -0
- scipy/fft/_basic_backend.py +197 -0
- scipy/fft/_debug_backends.py +22 -0
- scipy/fft/_fftlog.py +223 -0
- scipy/fft/_fftlog_backend.py +200 -0
- scipy/fft/_helper.py +348 -0
- scipy/fft/_pocketfft/LICENSE.md +25 -0
- scipy/fft/_pocketfft/__init__.py +9 -0
- scipy/fft/_pocketfft/basic.py +251 -0
- scipy/fft/_pocketfft/helper.py +249 -0
- scipy/fft/_pocketfft/pypocketfft.cp314-win_arm64.lib +0 -0
- scipy/fft/_pocketfft/pypocketfft.cp314-win_arm64.pyd +0 -0
- scipy/fft/_pocketfft/realtransforms.py +109 -0
- scipy/fft/_pocketfft/tests/__init__.py +0 -0
- scipy/fft/_pocketfft/tests/test_basic.py +1011 -0
- scipy/fft/_pocketfft/tests/test_real_transforms.py +505 -0
- scipy/fft/_realtransforms.py +706 -0
- scipy/fft/_realtransforms_backend.py +63 -0
- scipy/fft/tests/__init__.py +0 -0
- scipy/fft/tests/mock_backend.py +96 -0
- scipy/fft/tests/test_backend.py +98 -0
- scipy/fft/tests/test_basic.py +504 -0
- scipy/fft/tests/test_fftlog.py +215 -0
- scipy/fft/tests/test_helper.py +558 -0
- scipy/fft/tests/test_multithreading.py +84 -0
- scipy/fft/tests/test_real_transforms.py +247 -0
- scipy/fftpack/__init__.py +103 -0
- scipy/fftpack/_basic.py +428 -0
- scipy/fftpack/_helper.py +115 -0
- scipy/fftpack/_pseudo_diffs.py +554 -0
- scipy/fftpack/_realtransforms.py +598 -0
- scipy/fftpack/basic.py +20 -0
- scipy/fftpack/convolve.cp314-win_arm64.lib +0 -0
- scipy/fftpack/convolve.cp314-win_arm64.pyd +0 -0
- scipy/fftpack/helper.py +19 -0
- scipy/fftpack/pseudo_diffs.py +22 -0
- scipy/fftpack/realtransforms.py +19 -0
- scipy/fftpack/tests/__init__.py +0 -0
- scipy/fftpack/tests/fftw_double_ref.npz +0 -0
- scipy/fftpack/tests/fftw_longdouble_ref.npz +0 -0
- scipy/fftpack/tests/fftw_single_ref.npz +0 -0
- scipy/fftpack/tests/test.npz +0 -0
- scipy/fftpack/tests/test_basic.py +877 -0
- scipy/fftpack/tests/test_helper.py +54 -0
- scipy/fftpack/tests/test_import.py +33 -0
- scipy/fftpack/tests/test_pseudo_diffs.py +388 -0
- scipy/fftpack/tests/test_real_transforms.py +836 -0
- scipy/integrate/__init__.py +122 -0
- scipy/integrate/_bvp.py +1160 -0
- scipy/integrate/_cubature.py +729 -0
- scipy/integrate/_dop.cp314-win_arm64.lib +0 -0
- scipy/integrate/_dop.cp314-win_arm64.pyd +0 -0
- scipy/integrate/_ivp/__init__.py +8 -0
- scipy/integrate/_ivp/base.py +290 -0
- scipy/integrate/_ivp/bdf.py +478 -0
- scipy/integrate/_ivp/common.py +451 -0
- scipy/integrate/_ivp/dop853_coefficients.py +193 -0
- scipy/integrate/_ivp/ivp.py +755 -0
- scipy/integrate/_ivp/lsoda.py +224 -0
- scipy/integrate/_ivp/radau.py +572 -0
- scipy/integrate/_ivp/rk.py +601 -0
- scipy/integrate/_ivp/tests/__init__.py +0 -0
- scipy/integrate/_ivp/tests/test_ivp.py +1287 -0
- scipy/integrate/_ivp/tests/test_rk.py +37 -0
- scipy/integrate/_lebedev.py +5450 -0
- scipy/integrate/_lsoda.cp314-win_arm64.lib +0 -0
- scipy/integrate/_lsoda.cp314-win_arm64.pyd +0 -0
- scipy/integrate/_ode.py +1395 -0
- scipy/integrate/_odepack.cp314-win_arm64.lib +0 -0
- scipy/integrate/_odepack.cp314-win_arm64.pyd +0 -0
- scipy/integrate/_odepack_py.py +273 -0
- scipy/integrate/_quad_vec.py +674 -0
- scipy/integrate/_quadpack.cp314-win_arm64.lib +0 -0
- scipy/integrate/_quadpack.cp314-win_arm64.pyd +0 -0
- scipy/integrate/_quadpack_py.py +1283 -0
- scipy/integrate/_quadrature.py +1336 -0
- scipy/integrate/_rules/__init__.py +12 -0
- scipy/integrate/_rules/_base.py +518 -0
- scipy/integrate/_rules/_gauss_kronrod.py +202 -0
- scipy/integrate/_rules/_gauss_legendre.py +62 -0
- scipy/integrate/_rules/_genz_malik.py +210 -0
- scipy/integrate/_tanhsinh.py +1385 -0
- scipy/integrate/_test_multivariate.cp314-win_arm64.lib +0 -0
- scipy/integrate/_test_multivariate.cp314-win_arm64.pyd +0 -0
- scipy/integrate/_test_odeint_banded.cp314-win_arm64.lib +0 -0
- scipy/integrate/_test_odeint_banded.cp314-win_arm64.pyd +0 -0
- scipy/integrate/_vode.cp314-win_arm64.lib +0 -0
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- scipy/integrate/lsoda.py +15 -0
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- scipy/integrate/quadpack.py +23 -0
- scipy/integrate/tests/__init__.py +0 -0
- scipy/integrate/tests/test__quad_vec.py +211 -0
- scipy/integrate/tests/test_banded_ode_solvers.py +305 -0
- scipy/integrate/tests/test_bvp.py +714 -0
- scipy/integrate/tests/test_cubature.py +1375 -0
- scipy/integrate/tests/test_integrate.py +840 -0
- scipy/integrate/tests/test_odeint_jac.py +74 -0
- scipy/integrate/tests/test_quadpack.py +680 -0
- scipy/integrate/tests/test_quadrature.py +730 -0
- scipy/integrate/tests/test_tanhsinh.py +1171 -0
- scipy/integrate/vode.py +15 -0
- scipy/interpolate/__init__.py +228 -0
- scipy/interpolate/_bary_rational.py +715 -0
- scipy/interpolate/_bsplines.py +2469 -0
- scipy/interpolate/_cubic.py +973 -0
- scipy/interpolate/_dfitpack.cp314-win_arm64.lib +0 -0
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- scipy/io/_fast_matrix_market/__init__.py +600 -0
- scipy/io/_fast_matrix_market/_fmm_core.cp314-win_arm64.lib +0 -0
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- scipy/io/_harwell_boeing/__init__.py +7 -0
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"""
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Unit tests for optimization routines from minpack.py.
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"""
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import warnings
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import pytest
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import threading
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from numpy.testing import (assert_, assert_almost_equal, assert_array_equal,
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assert_array_almost_equal, assert_allclose,
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assert_warns, suppress_warnings)
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from pytest import raises as assert_raises
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import numpy as np
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from numpy import array, float64
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from multiprocessing.pool import ThreadPool
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from scipy import optimize, linalg
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from scipy.special import lambertw
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from scipy.optimize._minpack_py import leastsq, curve_fit, fixed_point
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from scipy.optimize import OptimizeWarning
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from scipy.optimize._minimize import Bounds
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class ReturnShape:
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"""
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A 1-D array of n flow rates [kg/s].
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A 1-D array of n valve coefficients [1/kg m].
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-------
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*flow_rates*. See `pressure_network` for the detailed
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description of parameters.
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-------
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and *f_i* and *Q_i* are described in the doc for `pressure_network`
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"""
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pressure_network_jacobian(flow_rates, Qtot, k))
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class TestFSolve:
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def test_pressure_network_no_gradient(self):
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# fsolve without gradient, equal pipes -> equal flows.
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k = np.full(4, 0.5)
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Qtot = 4
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initial_guess = array([2., 0., 2., 0.])
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final_flows, info, ier, mesg = optimize.fsolve(
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pressure_network, initial_guess, args=(Qtot, k),
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full_output=True)
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assert_array_almost_equal(final_flows, np.ones(4))
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assert_(ier == 1, mesg)
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def test_pressure_network_with_gradient(self):
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# fsolve with gradient, equal pipes -> equal flows
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k = np.full(4, 0.5)
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Qtot = 4
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initial_guess = array([2., 0., 2., 0.])
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final_flows = optimize.fsolve(
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pressure_network, initial_guess, args=(Qtot, k),
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fprime=pressure_network_jacobian)
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assert_array_almost_equal(final_flows, np.ones(4))
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def test_wrong_shape_func_callable(self):
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func = ReturnShape(1)
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# x0 is a list of two elements, but func will return an array with
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# length 1, so this should result in a TypeError.
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x0 = [1.5, 2.0]
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assert_raises(TypeError, optimize.fsolve, func, x0)
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def test_wrong_shape_func_function(self):
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# x0 is a list of two elements, but func will return an array with
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# length 1, so this should result in a TypeError.
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x0 = [1.5, 2.0]
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assert_raises(TypeError, optimize.fsolve, dummy_func, x0, args=((1,),))
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def test_wrong_shape_fprime_callable(self):
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func = ReturnShape(1)
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deriv_func = ReturnShape((2,2))
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assert_raises(TypeError, optimize.fsolve, func, x0=[0,1], fprime=deriv_func)
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def test_wrong_shape_fprime_function(self):
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def func(x):
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return dummy_func(x, (2,))
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def deriv_func(x):
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return dummy_func(x, (3, 3))
|
157
|
+
assert_raises(TypeError, optimize.fsolve, func, x0=[0,1], fprime=deriv_func)
|
158
|
+
|
159
|
+
def test_func_can_raise(self):
|
160
|
+
def func(*args):
|
161
|
+
raise ValueError('I raised')
|
162
|
+
|
163
|
+
with assert_raises(ValueError, match='I raised'):
|
164
|
+
optimize.fsolve(func, x0=[0])
|
165
|
+
|
166
|
+
def test_Dfun_can_raise(self):
|
167
|
+
def func(x):
|
168
|
+
return x - np.array([10])
|
169
|
+
|
170
|
+
def deriv_func(*args):
|
171
|
+
raise ValueError('I raised')
|
172
|
+
|
173
|
+
with assert_raises(ValueError, match='I raised'):
|
174
|
+
optimize.fsolve(func, x0=[0], fprime=deriv_func)
|
175
|
+
|
176
|
+
def test_float32(self):
|
177
|
+
def func(x):
|
178
|
+
return np.array([x[0] - 100, x[1] - 1000], dtype=np.float32) ** 2
|
179
|
+
p = optimize.fsolve(func, np.array([1, 1], np.float32))
|
180
|
+
assert_allclose(func(p), [0, 0], atol=1e-3)
|
181
|
+
|
182
|
+
def test_reentrant_func(self):
|
183
|
+
def func(*args):
|
184
|
+
self.test_pressure_network_no_gradient()
|
185
|
+
return pressure_network(*args)
|
186
|
+
|
187
|
+
# fsolve without gradient, equal pipes -> equal flows.
|
188
|
+
k = np.full(4, 0.5)
|
189
|
+
Qtot = 4
|
190
|
+
initial_guess = array([2., 0., 2., 0.])
|
191
|
+
final_flows, info, ier, mesg = optimize.fsolve(
|
192
|
+
func, initial_guess, args=(Qtot, k),
|
193
|
+
full_output=True)
|
194
|
+
assert_array_almost_equal(final_flows, np.ones(4))
|
195
|
+
assert_(ier == 1, mesg)
|
196
|
+
|
197
|
+
def test_reentrant_Dfunc(self):
|
198
|
+
def deriv_func(*args):
|
199
|
+
self.test_pressure_network_with_gradient()
|
200
|
+
return pressure_network_jacobian(*args)
|
201
|
+
|
202
|
+
# fsolve with gradient, equal pipes -> equal flows
|
203
|
+
k = np.full(4, 0.5)
|
204
|
+
Qtot = 4
|
205
|
+
initial_guess = array([2., 0., 2., 0.])
|
206
|
+
final_flows = optimize.fsolve(
|
207
|
+
pressure_network, initial_guess, args=(Qtot, k),
|
208
|
+
fprime=deriv_func)
|
209
|
+
assert_array_almost_equal(final_flows, np.ones(4))
|
210
|
+
|
211
|
+
def test_concurrent_no_gradient(self):
|
212
|
+
v = sequence_parallel([self.test_pressure_network_no_gradient] * 10)
|
213
|
+
assert all([result is None for result in v])
|
214
|
+
|
215
|
+
def test_concurrent_with_gradient(self):
|
216
|
+
v = sequence_parallel([self.test_pressure_network_with_gradient] * 10)
|
217
|
+
assert all([result is None for result in v])
|
218
|
+
|
219
|
+
|
220
|
+
class TestRootHybr:
|
221
|
+
def test_pressure_network_no_gradient(self):
|
222
|
+
# root/hybr without gradient, equal pipes -> equal flows
|
223
|
+
k = np.full(4, 0.5)
|
224
|
+
Qtot = 4
|
225
|
+
initial_guess = array([2., 0., 2., 0.])
|
226
|
+
final_flows = optimize.root(pressure_network, initial_guess,
|
227
|
+
method='hybr', args=(Qtot, k)).x
|
228
|
+
assert_array_almost_equal(final_flows, np.ones(4))
|
229
|
+
|
230
|
+
def test_pressure_network_with_gradient(self):
|
231
|
+
# root/hybr with gradient, equal pipes -> equal flows
|
232
|
+
k = np.full(4, 0.5)
|
233
|
+
Qtot = 4
|
234
|
+
initial_guess = array([[2., 0., 2., 0.]])
|
235
|
+
final_flows = optimize.root(pressure_network, initial_guess,
|
236
|
+
args=(Qtot, k), method='hybr',
|
237
|
+
jac=pressure_network_jacobian).x
|
238
|
+
assert_array_almost_equal(final_flows, np.ones(4))
|
239
|
+
|
240
|
+
def test_pressure_network_with_gradient_combined(self):
|
241
|
+
# root/hybr with gradient and function combined, equal pipes -> equal
|
242
|
+
# flows
|
243
|
+
k = np.full(4, 0.5)
|
244
|
+
Qtot = 4
|
245
|
+
initial_guess = array([2., 0., 2., 0.])
|
246
|
+
final_flows = optimize.root(pressure_network_fun_and_grad,
|
247
|
+
initial_guess, args=(Qtot, k),
|
248
|
+
method='hybr', jac=True).x
|
249
|
+
assert_array_almost_equal(final_flows, np.ones(4))
|
250
|
+
|
251
|
+
|
252
|
+
class TestRootLM:
|
253
|
+
def test_pressure_network_no_gradient(self):
|
254
|
+
# root/lm without gradient, equal pipes -> equal flows
|
255
|
+
k = np.full(4, 0.5)
|
256
|
+
Qtot = 4
|
257
|
+
initial_guess = array([2., 0., 2., 0.])
|
258
|
+
final_flows = optimize.root(pressure_network, initial_guess,
|
259
|
+
method='lm', args=(Qtot, k)).x
|
260
|
+
assert_array_almost_equal(final_flows, np.ones(4))
|
261
|
+
|
262
|
+
|
263
|
+
class TestNfev:
|
264
|
+
def setup_method(self):
|
265
|
+
self.nfev = threading.local()
|
266
|
+
|
267
|
+
def zero_f(self, y):
|
268
|
+
if not hasattr(self.nfev, 'c'):
|
269
|
+
self.nfev.c = 0
|
270
|
+
self.nfev.c += 1
|
271
|
+
return y**2-3
|
272
|
+
|
273
|
+
@pytest.mark.parametrize('method', ['hybr', 'lm', 'broyden1',
|
274
|
+
'broyden2', 'anderson',
|
275
|
+
'linearmixing', 'diagbroyden',
|
276
|
+
'excitingmixing', 'krylov',
|
277
|
+
'df-sane'])
|
278
|
+
def test_root_nfev(self, method):
|
279
|
+
self.nfev.c = 0
|
280
|
+
solution = optimize.root(self.zero_f, 100, method=method)
|
281
|
+
assert solution.nfev == self.nfev.c
|
282
|
+
|
283
|
+
def test_fsolve_nfev(self):
|
284
|
+
self.nfev.c = 0
|
285
|
+
x, info, ier, mesg = optimize.fsolve(self.zero_f, 100, full_output=True)
|
286
|
+
assert info['nfev'] == self.nfev.c
|
287
|
+
|
288
|
+
|
289
|
+
class TestLeastSq:
|
290
|
+
def setup_method(self):
|
291
|
+
x = np.linspace(0, 10, 40)
|
292
|
+
a,b,c = 3.1, 42, -304.2
|
293
|
+
self.x = x
|
294
|
+
self.abc = a,b,c
|
295
|
+
y_true = a*x**2 + b*x + c
|
296
|
+
np.random.seed(0)
|
297
|
+
self.y_meas = y_true + 0.01*np.random.standard_normal(y_true.shape)
|
298
|
+
|
299
|
+
def residuals(self, p, y, x):
|
300
|
+
a,b,c = p
|
301
|
+
err = y-(a*x**2 + b*x + c)
|
302
|
+
return err
|
303
|
+
|
304
|
+
def residuals_jacobian(self, _p, _y, x):
|
305
|
+
return -np.vstack([x**2, x, np.ones_like(x)]).T
|
306
|
+
|
307
|
+
def test_basic(self):
|
308
|
+
p0 = array([0,0,0])
|
309
|
+
params_fit, ier = leastsq(self.residuals, p0,
|
310
|
+
args=(self.y_meas, self.x))
|
311
|
+
assert_(ier in (1, 2, 3, 4), f'solution not found (ier={ier})')
|
312
|
+
# low precision due to random
|
313
|
+
assert_array_almost_equal(params_fit, self.abc, decimal=2)
|
314
|
+
|
315
|
+
def test_basic_with_gradient(self):
|
316
|
+
p0 = array([0,0,0])
|
317
|
+
params_fit, ier = leastsq(self.residuals, p0,
|
318
|
+
args=(self.y_meas, self.x),
|
319
|
+
Dfun=self.residuals_jacobian)
|
320
|
+
assert_(ier in (1, 2, 3, 4), f'solution not found (ier={ier})')
|
321
|
+
# low precision due to random
|
322
|
+
assert_array_almost_equal(params_fit, self.abc, decimal=2)
|
323
|
+
|
324
|
+
def test_full_output(self):
|
325
|
+
p0 = array([[0,0,0]])
|
326
|
+
full_output = leastsq(self.residuals, p0,
|
327
|
+
args=(self.y_meas, self.x),
|
328
|
+
full_output=True)
|
329
|
+
params_fit, cov_x, infodict, mesg, ier = full_output
|
330
|
+
assert_(ier in (1,2,3,4), f'solution not found: {mesg}')
|
331
|
+
|
332
|
+
def test_input_untouched(self):
|
333
|
+
p0 = array([0,0,0],dtype=float64)
|
334
|
+
p0_copy = array(p0, copy=True)
|
335
|
+
full_output = leastsq(self.residuals, p0,
|
336
|
+
args=(self.y_meas, self.x),
|
337
|
+
full_output=True)
|
338
|
+
params_fit, cov_x, infodict, mesg, ier = full_output
|
339
|
+
assert_(ier in (1,2,3,4), f'solution not found: {mesg}')
|
340
|
+
assert_array_equal(p0, p0_copy)
|
341
|
+
|
342
|
+
def test_wrong_shape_func_callable(self):
|
343
|
+
func = ReturnShape(1)
|
344
|
+
# x0 is a list of two elements, but func will return an array with
|
345
|
+
# length 1, so this should result in a TypeError.
|
346
|
+
x0 = [1.5, 2.0]
|
347
|
+
assert_raises(TypeError, optimize.leastsq, func, x0)
|
348
|
+
|
349
|
+
def test_wrong_shape_func_function(self):
|
350
|
+
# x0 is a list of two elements, but func will return an array with
|
351
|
+
# length 1, so this should result in a TypeError.
|
352
|
+
x0 = [1.5, 2.0]
|
353
|
+
assert_raises(TypeError, optimize.leastsq, dummy_func, x0, args=((1,),))
|
354
|
+
|
355
|
+
def test_wrong_shape_Dfun_callable(self):
|
356
|
+
func = ReturnShape(1)
|
357
|
+
deriv_func = ReturnShape((2,2))
|
358
|
+
assert_raises(TypeError, optimize.leastsq, func, x0=[0,1], Dfun=deriv_func)
|
359
|
+
|
360
|
+
def test_wrong_shape_Dfun_function(self):
|
361
|
+
def func(x):
|
362
|
+
return dummy_func(x, (2,))
|
363
|
+
def deriv_func(x):
|
364
|
+
return dummy_func(x, (3, 3))
|
365
|
+
assert_raises(TypeError, optimize.leastsq, func, x0=[0,1], Dfun=deriv_func)
|
366
|
+
|
367
|
+
def test_float32(self):
|
368
|
+
# Regression test for gh-1447
|
369
|
+
def func(p,x,y):
|
370
|
+
q = p[0]*np.exp(-(x-p[1])**2/(2.0*p[2]**2))+p[3]
|
371
|
+
return q - y
|
372
|
+
|
373
|
+
x = np.array([1.475,1.429,1.409,1.419,1.455,1.519,1.472, 1.368,1.286,
|
374
|
+
1.231], dtype=np.float32)
|
375
|
+
y = np.array([0.0168,0.0193,0.0211,0.0202,0.0171,0.0151,0.0185,0.0258,
|
376
|
+
0.034,0.0396], dtype=np.float32)
|
377
|
+
p0 = np.array([1.0,1.0,1.0,1.0])
|
378
|
+
p1, success = optimize.leastsq(func, p0, args=(x,y))
|
379
|
+
|
380
|
+
assert_(success in [1,2,3,4])
|
381
|
+
assert_((func(p1,x,y)**2).sum() < 1e-4 * (func(p0,x,y)**2).sum())
|
382
|
+
|
383
|
+
def test_func_can_raise(self):
|
384
|
+
def func(*args):
|
385
|
+
raise ValueError('I raised')
|
386
|
+
|
387
|
+
with assert_raises(ValueError, match='I raised'):
|
388
|
+
optimize.leastsq(func, x0=[0])
|
389
|
+
|
390
|
+
def test_Dfun_can_raise(self):
|
391
|
+
def func(x):
|
392
|
+
return x - np.array([10])
|
393
|
+
|
394
|
+
def deriv_func(*args):
|
395
|
+
raise ValueError('I raised')
|
396
|
+
|
397
|
+
with assert_raises(ValueError, match='I raised'):
|
398
|
+
optimize.leastsq(func, x0=[0], Dfun=deriv_func)
|
399
|
+
|
400
|
+
def test_reentrant_func(self):
|
401
|
+
def func(*args):
|
402
|
+
self.test_basic()
|
403
|
+
return self.residuals(*args)
|
404
|
+
|
405
|
+
p0 = array([0,0,0])
|
406
|
+
params_fit, ier = leastsq(func, p0,
|
407
|
+
args=(self.y_meas, self.x))
|
408
|
+
assert_(ier in (1, 2, 3, 4), f'solution not found (ier={ier})')
|
409
|
+
# low precision due to random
|
410
|
+
assert_array_almost_equal(params_fit, self.abc, decimal=2)
|
411
|
+
|
412
|
+
def test_reentrant_Dfun(self):
|
413
|
+
def deriv_func(*args):
|
414
|
+
self.test_basic()
|
415
|
+
return self.residuals_jacobian(*args)
|
416
|
+
|
417
|
+
p0 = array([0,0,0])
|
418
|
+
params_fit, ier = leastsq(self.residuals, p0,
|
419
|
+
args=(self.y_meas, self.x),
|
420
|
+
Dfun=deriv_func)
|
421
|
+
assert_(ier in (1, 2, 3, 4), f'solution not found (ier={ier})')
|
422
|
+
# low precision due to random
|
423
|
+
assert_array_almost_equal(params_fit, self.abc, decimal=2)
|
424
|
+
|
425
|
+
def test_concurrent_no_gradient(self):
|
426
|
+
v = sequence_parallel([self.test_basic] * 10)
|
427
|
+
assert all([result is None for result in v])
|
428
|
+
|
429
|
+
def test_concurrent_with_gradient(self):
|
430
|
+
v = sequence_parallel([self.test_basic_with_gradient] * 10)
|
431
|
+
assert all([result is None for result in v])
|
432
|
+
|
433
|
+
def test_func_input_output_length_check(self):
|
434
|
+
|
435
|
+
def func(x):
|
436
|
+
return 2 * (x[0] - 3) ** 2 + 1
|
437
|
+
|
438
|
+
with assert_raises(TypeError,
|
439
|
+
match='Improper input: func input vector length N='):
|
440
|
+
optimize.leastsq(func, x0=[0, 1])
|
441
|
+
|
442
|
+
|
443
|
+
class TestCurveFit:
|
444
|
+
def setup_method(self):
|
445
|
+
self.y = array([1.0, 3.2, 9.5, 13.7])
|
446
|
+
self.x = array([1.0, 2.0, 3.0, 4.0])
|
447
|
+
|
448
|
+
def test_one_argument(self):
|
449
|
+
def func(x,a):
|
450
|
+
return x**a
|
451
|
+
popt, pcov = curve_fit(func, self.x, self.y)
|
452
|
+
assert_(len(popt) == 1)
|
453
|
+
assert_(pcov.shape == (1,1))
|
454
|
+
assert_almost_equal(popt[0], 1.9149, decimal=4)
|
455
|
+
assert_almost_equal(pcov[0,0], 0.0016, decimal=4)
|
456
|
+
|
457
|
+
# Test if we get the same with full_output. Regression test for #1415.
|
458
|
+
# Also test if check_finite can be turned off.
|
459
|
+
res = curve_fit(func, self.x, self.y,
|
460
|
+
full_output=1, check_finite=False)
|
461
|
+
(popt2, pcov2, infodict, errmsg, ier) = res
|
462
|
+
assert_array_almost_equal(popt, popt2)
|
463
|
+
|
464
|
+
def test_two_argument(self):
|
465
|
+
def func(x, a, b):
|
466
|
+
return b*x**a
|
467
|
+
popt, pcov = curve_fit(func, self.x, self.y)
|
468
|
+
assert_(len(popt) == 2)
|
469
|
+
assert_(pcov.shape == (2,2))
|
470
|
+
assert_array_almost_equal(popt, [1.7989, 1.1642], decimal=4)
|
471
|
+
assert_array_almost_equal(pcov, [[0.0852, -0.1260], [-0.1260, 0.1912]],
|
472
|
+
decimal=4)
|
473
|
+
|
474
|
+
def test_func_is_classmethod(self):
|
475
|
+
class test_self:
|
476
|
+
"""This class tests if curve_fit passes the correct number of
|
477
|
+
arguments when the model function is a class instance method.
|
478
|
+
"""
|
479
|
+
|
480
|
+
def func(self, x, a, b):
|
481
|
+
return b * x**a
|
482
|
+
|
483
|
+
test_self_inst = test_self()
|
484
|
+
popt, pcov = curve_fit(test_self_inst.func, self.x, self.y)
|
485
|
+
assert_(pcov.shape == (2,2))
|
486
|
+
assert_array_almost_equal(popt, [1.7989, 1.1642], decimal=4)
|
487
|
+
assert_array_almost_equal(pcov, [[0.0852, -0.1260], [-0.1260, 0.1912]],
|
488
|
+
decimal=4)
|
489
|
+
|
490
|
+
def test_regression_2639(self):
|
491
|
+
# This test fails if epsfcn in leastsq is too large.
|
492
|
+
x = [574.14200000000005, 574.154, 574.16499999999996,
|
493
|
+
574.17700000000002, 574.18799999999999, 574.19899999999996,
|
494
|
+
574.21100000000001, 574.22199999999998, 574.23400000000004,
|
495
|
+
574.245]
|
496
|
+
y = [859.0, 997.0, 1699.0, 2604.0, 2013.0, 1964.0, 2435.0,
|
497
|
+
1550.0, 949.0, 841.0]
|
498
|
+
guess = [574.1861428571428, 574.2155714285715, 1302.0, 1302.0,
|
499
|
+
0.0035019999999983615, 859.0]
|
500
|
+
good = [5.74177150e+02, 5.74209188e+02, 1.74187044e+03, 1.58646166e+03,
|
501
|
+
1.0068462e-02, 8.57450661e+02]
|
502
|
+
|
503
|
+
def f_double_gauss(x, x0, x1, A0, A1, sigma, c):
|
504
|
+
return (A0*np.exp(-(x-x0)**2/(2.*sigma**2))
|
505
|
+
+ A1*np.exp(-(x-x1)**2/(2.*sigma**2)) + c)
|
506
|
+
popt, pcov = curve_fit(f_double_gauss, x, y, guess, maxfev=10000)
|
507
|
+
assert_allclose(popt, good, rtol=1e-5)
|
508
|
+
|
509
|
+
def test_pcov(self):
|
510
|
+
xdata = np.array([0, 1, 2, 3, 4, 5])
|
511
|
+
ydata = np.array([1, 1, 5, 7, 8, 12])
|
512
|
+
sigma = np.array([1, 2, 1, 2, 1, 2])
|
513
|
+
|
514
|
+
def f(x, a, b):
|
515
|
+
return a*x + b
|
516
|
+
|
517
|
+
for method in ['lm', 'trf', 'dogbox']:
|
518
|
+
popt, pcov = curve_fit(f, xdata, ydata, p0=[2, 0], sigma=sigma,
|
519
|
+
method=method)
|
520
|
+
perr_scaled = np.sqrt(np.diag(pcov))
|
521
|
+
assert_allclose(perr_scaled, [0.20659803, 0.57204404], rtol=1e-3)
|
522
|
+
|
523
|
+
popt, pcov = curve_fit(f, xdata, ydata, p0=[2, 0], sigma=3*sigma,
|
524
|
+
method=method)
|
525
|
+
perr_scaled = np.sqrt(np.diag(pcov))
|
526
|
+
assert_allclose(perr_scaled, [0.20659803, 0.57204404], rtol=1e-3)
|
527
|
+
|
528
|
+
popt, pcov = curve_fit(f, xdata, ydata, p0=[2, 0], sigma=sigma,
|
529
|
+
absolute_sigma=True, method=method)
|
530
|
+
perr = np.sqrt(np.diag(pcov))
|
531
|
+
assert_allclose(perr, [0.30714756, 0.85045308], rtol=1e-3)
|
532
|
+
|
533
|
+
popt, pcov = curve_fit(f, xdata, ydata, p0=[2, 0], sigma=3*sigma,
|
534
|
+
absolute_sigma=True, method=method)
|
535
|
+
perr = np.sqrt(np.diag(pcov))
|
536
|
+
assert_allclose(perr, [3*0.30714756, 3*0.85045308], rtol=1e-3)
|
537
|
+
|
538
|
+
# infinite variances
|
539
|
+
|
540
|
+
def f_flat(x, a, b):
|
541
|
+
return a*x
|
542
|
+
|
543
|
+
pcov_expected = np.array([np.inf]*4).reshape(2, 2)
|
544
|
+
|
545
|
+
with suppress_warnings() as sup:
|
546
|
+
sup.filter(OptimizeWarning,
|
547
|
+
"Covariance of the parameters could not be estimated")
|
548
|
+
popt, pcov = curve_fit(f_flat, xdata, ydata, p0=[2, 0], sigma=sigma)
|
549
|
+
popt1, pcov1 = curve_fit(f, xdata[:2], ydata[:2], p0=[2, 0])
|
550
|
+
|
551
|
+
assert_(pcov.shape == (2, 2))
|
552
|
+
assert_array_equal(pcov, pcov_expected)
|
553
|
+
|
554
|
+
assert_(pcov1.shape == (2, 2))
|
555
|
+
assert_array_equal(pcov1, pcov_expected)
|
556
|
+
|
557
|
+
def test_array_like(self):
|
558
|
+
# Test sequence input. Regression test for gh-3037.
|
559
|
+
def f_linear(x, a, b):
|
560
|
+
return a*x + b
|
561
|
+
|
562
|
+
x = [1, 2, 3, 4]
|
563
|
+
y = [3, 5, 7, 9]
|
564
|
+
assert_allclose(curve_fit(f_linear, x, y)[0], [2, 1], atol=1e-10)
|
565
|
+
|
566
|
+
@pytest.mark.thread_unsafe
|
567
|
+
def test_indeterminate_covariance(self):
|
568
|
+
# Test that a warning is returned when pcov is indeterminate
|
569
|
+
xdata = np.array([1, 2, 3, 4, 5, 6])
|
570
|
+
ydata = np.array([1, 2, 3, 4, 5.5, 6])
|
571
|
+
assert_warns(OptimizeWarning, curve_fit,
|
572
|
+
lambda x, a, b: a*x, xdata, ydata)
|
573
|
+
|
574
|
+
def test_NaN_handling(self):
|
575
|
+
# Test for correct handling of NaNs in input data: gh-3422
|
576
|
+
|
577
|
+
# create input with NaNs
|
578
|
+
xdata = np.array([1, np.nan, 3])
|
579
|
+
ydata = np.array([1, 2, 3])
|
580
|
+
|
581
|
+
assert_raises(ValueError, curve_fit,
|
582
|
+
lambda x, a, b: a*x + b, xdata, ydata)
|
583
|
+
assert_raises(ValueError, curve_fit,
|
584
|
+
lambda x, a, b: a*x + b, ydata, xdata)
|
585
|
+
|
586
|
+
assert_raises(ValueError, curve_fit, lambda x, a, b: a*x + b,
|
587
|
+
xdata, ydata, **{"check_finite": True})
|
588
|
+
|
589
|
+
@staticmethod
|
590
|
+
def _check_nan_policy(f, xdata_with_nan, xdata_without_nan,
|
591
|
+
ydata_with_nan, ydata_without_nan, method):
|
592
|
+
kwargs = {'f': f, 'xdata': xdata_with_nan, 'ydata': ydata_with_nan,
|
593
|
+
'method': method, 'check_finite': False}
|
594
|
+
# propagate test
|
595
|
+
error_msg = ("`nan_policy='propagate'` is not supported "
|
596
|
+
"by this function.")
|
597
|
+
with assert_raises(ValueError, match=error_msg):
|
598
|
+
curve_fit(**kwargs, nan_policy="propagate", maxfev=2000)
|
599
|
+
|
600
|
+
# raise test
|
601
|
+
with assert_raises(ValueError, match="The input contains nan"):
|
602
|
+
curve_fit(**kwargs, nan_policy="raise")
|
603
|
+
|
604
|
+
# omit test
|
605
|
+
result_with_nan, _ = curve_fit(**kwargs, nan_policy="omit")
|
606
|
+
kwargs['xdata'] = xdata_without_nan
|
607
|
+
kwargs['ydata'] = ydata_without_nan
|
608
|
+
result_without_nan, _ = curve_fit(**kwargs)
|
609
|
+
assert_allclose(result_with_nan, result_without_nan)
|
610
|
+
|
611
|
+
# not valid policy test
|
612
|
+
# check for argument names in any order
|
613
|
+
error_msg = (r"nan_policy must be one of \{(?:'raise'|'omit'|None)"
|
614
|
+
r"(?:, ?(?:'raise'|'omit'|None))*\}")
|
615
|
+
with assert_raises(ValueError, match=error_msg):
|
616
|
+
curve_fit(**kwargs, nan_policy="hi")
|
617
|
+
|
618
|
+
@pytest.mark.parametrize('method', ["lm", "trf", "dogbox"])
|
619
|
+
def test_nan_policy_1d(self, method):
|
620
|
+
def f(x, a, b):
|
621
|
+
return a*x + b
|
622
|
+
|
623
|
+
xdata_with_nan = np.array([2, 3, np.nan, 4, 4, np.nan])
|
624
|
+
ydata_with_nan = np.array([1, 2, 5, 3, np.nan, 7])
|
625
|
+
xdata_without_nan = np.array([2, 3, 4])
|
626
|
+
ydata_without_nan = np.array([1, 2, 3])
|
627
|
+
|
628
|
+
self._check_nan_policy(f, xdata_with_nan, xdata_without_nan,
|
629
|
+
ydata_with_nan, ydata_without_nan, method)
|
630
|
+
|
631
|
+
@pytest.mark.parametrize('method', ["lm", "trf", "dogbox"])
|
632
|
+
def test_nan_policy_2d(self, method):
|
633
|
+
def f(x, a, b):
|
634
|
+
x1 = x[0, :]
|
635
|
+
x2 = x[1, :]
|
636
|
+
return a*x1 + b + x2
|
637
|
+
|
638
|
+
xdata_with_nan = np.array([[2, 3, np.nan, 4, 4, np.nan, 5],
|
639
|
+
[2, 3, np.nan, np.nan, 4, np.nan, 7]])
|
640
|
+
ydata_with_nan = np.array([1, 2, 5, 3, np.nan, 7, 10])
|
641
|
+
xdata_without_nan = np.array([[2, 3, 5], [2, 3, 7]])
|
642
|
+
ydata_without_nan = np.array([1, 2, 10])
|
643
|
+
|
644
|
+
self._check_nan_policy(f, xdata_with_nan, xdata_without_nan,
|
645
|
+
ydata_with_nan, ydata_without_nan, method)
|
646
|
+
|
647
|
+
@pytest.mark.parametrize('n', [2, 3])
|
648
|
+
@pytest.mark.parametrize('method', ["lm", "trf", "dogbox"])
|
649
|
+
def test_nan_policy_2_3d(self, n, method):
|
650
|
+
def f(x, a, b):
|
651
|
+
x1 = x[..., 0, :].squeeze()
|
652
|
+
x2 = x[..., 1, :].squeeze()
|
653
|
+
return a*x1 + b + x2
|
654
|
+
|
655
|
+
xdata_with_nan = np.array([[[2, 3, np.nan, 4, 4, np.nan, 5],
|
656
|
+
[2, 3, np.nan, np.nan, 4, np.nan, 7]]])
|
657
|
+
xdata_with_nan = xdata_with_nan.squeeze() if n == 2 else xdata_with_nan
|
658
|
+
ydata_with_nan = np.array([1, 2, 5, 3, np.nan, 7, 10])
|
659
|
+
xdata_without_nan = np.array([[[2, 3, 5], [2, 3, 7]]])
|
660
|
+
ydata_without_nan = np.array([1, 2, 10])
|
661
|
+
|
662
|
+
self._check_nan_policy(f, xdata_with_nan, xdata_without_nan,
|
663
|
+
ydata_with_nan, ydata_without_nan, method)
|
664
|
+
|
665
|
+
def test_empty_inputs(self):
|
666
|
+
# Test both with and without bounds (regression test for gh-9864)
|
667
|
+
assert_raises(ValueError, curve_fit, lambda x, a: a*x, [], [])
|
668
|
+
assert_raises(ValueError, curve_fit, lambda x, a: a*x, [], [],
|
669
|
+
bounds=(1, 2))
|
670
|
+
assert_raises(ValueError, curve_fit, lambda x, a: a*x, [1], [])
|
671
|
+
assert_raises(ValueError, curve_fit, lambda x, a: a*x, [2], [],
|
672
|
+
bounds=(1, 2))
|
673
|
+
|
674
|
+
def test_function_zero_params(self):
|
675
|
+
# Fit args is zero, so "Unable to determine number of fit parameters."
|
676
|
+
assert_raises(ValueError, curve_fit, lambda x: x, [1, 2], [3, 4])
|
677
|
+
|
678
|
+
def test_None_x(self): # Added in GH10196
|
679
|
+
popt, pcov = curve_fit(lambda _, a: a * np.arange(10),
|
680
|
+
None, 2 * np.arange(10))
|
681
|
+
assert_allclose(popt, [2.])
|
682
|
+
|
683
|
+
def test_method_argument(self):
|
684
|
+
def f(x, a, b):
|
685
|
+
return a * np.exp(-b*x)
|
686
|
+
|
687
|
+
xdata = np.linspace(0, 1, 11)
|
688
|
+
ydata = f(xdata, 2., 2.)
|
689
|
+
|
690
|
+
for method in ['trf', 'dogbox', 'lm', None]:
|
691
|
+
popt, pcov = curve_fit(f, xdata, ydata, method=method)
|
692
|
+
assert_allclose(popt, [2., 2.])
|
693
|
+
|
694
|
+
assert_raises(ValueError, curve_fit, f, xdata, ydata, method='unknown')
|
695
|
+
|
696
|
+
def test_full_output(self):
|
697
|
+
def f(x, a, b):
|
698
|
+
return a * np.exp(-b * x)
|
699
|
+
|
700
|
+
xdata = np.linspace(0, 1, 11)
|
701
|
+
ydata = f(xdata, 2., 2.)
|
702
|
+
|
703
|
+
for method in ['trf', 'dogbox', 'lm', None]:
|
704
|
+
popt, pcov, infodict, errmsg, ier = curve_fit(
|
705
|
+
f, xdata, ydata, method=method, full_output=True)
|
706
|
+
assert_allclose(popt, [2., 2.])
|
707
|
+
assert "nfev" in infodict
|
708
|
+
assert "fvec" in infodict
|
709
|
+
if method == 'lm' or method is None:
|
710
|
+
assert "fjac" in infodict
|
711
|
+
assert "ipvt" in infodict
|
712
|
+
assert "qtf" in infodict
|
713
|
+
assert isinstance(errmsg, str)
|
714
|
+
assert ier in (1, 2, 3, 4)
|
715
|
+
|
716
|
+
def test_bounds(self):
|
717
|
+
def f(x, a, b):
|
718
|
+
return a * np.exp(-b*x)
|
719
|
+
|
720
|
+
xdata = np.linspace(0, 1, 11)
|
721
|
+
ydata = f(xdata, 2., 2.)
|
722
|
+
|
723
|
+
# The minimum w/out bounds is at [2., 2.],
|
724
|
+
# and with bounds it's at [1.5, smth].
|
725
|
+
lb = [1., 0]
|
726
|
+
ub = [1.5, 3.]
|
727
|
+
|
728
|
+
# Test that both variants of the bounds yield the same result
|
729
|
+
bounds = (lb, ub)
|
730
|
+
bounds_class = Bounds(lb, ub)
|
731
|
+
for method in [None, 'trf', 'dogbox']:
|
732
|
+
popt, pcov = curve_fit(f, xdata, ydata, bounds=bounds,
|
733
|
+
method=method)
|
734
|
+
assert_allclose(popt[0], 1.5)
|
735
|
+
|
736
|
+
popt_class, pcov_class = curve_fit(f, xdata, ydata,
|
737
|
+
bounds=bounds_class,
|
738
|
+
method=method)
|
739
|
+
assert_allclose(popt_class, popt)
|
740
|
+
|
741
|
+
# With bounds, the starting estimate is feasible.
|
742
|
+
popt, pcov = curve_fit(f, xdata, ydata, method='trf',
|
743
|
+
bounds=([0., 0], [0.6, np.inf]))
|
744
|
+
assert_allclose(popt[0], 0.6)
|
745
|
+
|
746
|
+
# method='lm' doesn't support bounds.
|
747
|
+
assert_raises(ValueError, curve_fit, f, xdata, ydata, bounds=bounds,
|
748
|
+
method='lm')
|
749
|
+
|
750
|
+
def test_bounds_p0(self):
|
751
|
+
# This test is for issue #5719. The problem was that an initial guess
|
752
|
+
# was ignored when 'trf' or 'dogbox' methods were invoked.
|
753
|
+
def f(x, a):
|
754
|
+
return np.sin(x + a)
|
755
|
+
|
756
|
+
xdata = np.linspace(-2*np.pi, 2*np.pi, 40)
|
757
|
+
ydata = np.sin(xdata)
|
758
|
+
bounds = (-3 * np.pi, 3 * np.pi)
|
759
|
+
for method in ['trf', 'dogbox']:
|
760
|
+
popt_1, _ = curve_fit(f, xdata, ydata, p0=2.1*np.pi)
|
761
|
+
popt_2, _ = curve_fit(f, xdata, ydata, p0=2.1*np.pi,
|
762
|
+
bounds=bounds, method=method)
|
763
|
+
|
764
|
+
# If the initial guess is ignored, then popt_2 would be close 0.
|
765
|
+
assert_allclose(popt_1, popt_2)
|
766
|
+
|
767
|
+
def test_jac(self):
|
768
|
+
# Test that Jacobian callable is handled correctly and
|
769
|
+
# weighted if sigma is provided.
|
770
|
+
def f(x, a, b):
|
771
|
+
return a * np.exp(-b*x)
|
772
|
+
|
773
|
+
def jac(x, a, b):
|
774
|
+
e = np.exp(-b*x)
|
775
|
+
return np.vstack((e, -a * x * e)).T
|
776
|
+
|
777
|
+
xdata = np.linspace(0, 1, 11)
|
778
|
+
ydata = f(xdata, 2., 2.)
|
779
|
+
|
780
|
+
# Test numerical options for least_squares backend.
|
781
|
+
for method in ['trf', 'dogbox']:
|
782
|
+
for scheme in ['2-point', '3-point', 'cs']:
|
783
|
+
popt, pcov = curve_fit(f, xdata, ydata, jac=scheme,
|
784
|
+
method=method)
|
785
|
+
assert_allclose(popt, [2, 2])
|
786
|
+
|
787
|
+
# Test the analytic option.
|
788
|
+
for method in ['lm', 'trf', 'dogbox']:
|
789
|
+
popt, pcov = curve_fit(f, xdata, ydata, method=method, jac=jac)
|
790
|
+
assert_allclose(popt, [2, 2])
|
791
|
+
|
792
|
+
# Now add an outlier and provide sigma.
|
793
|
+
ydata[5] = 100
|
794
|
+
sigma = np.ones(xdata.shape[0])
|
795
|
+
sigma[5] = 200
|
796
|
+
for method in ['lm', 'trf', 'dogbox']:
|
797
|
+
popt, pcov = curve_fit(f, xdata, ydata, sigma=sigma, method=method,
|
798
|
+
jac=jac)
|
799
|
+
# Still the optimization process is influenced somehow,
|
800
|
+
# have to set rtol=1e-3.
|
801
|
+
assert_allclose(popt, [2, 2], rtol=1e-3)
|
802
|
+
|
803
|
+
def test_maxfev_and_bounds(self):
|
804
|
+
# gh-6340: with no bounds, curve_fit accepts parameter maxfev (via leastsq)
|
805
|
+
# but with bounds, the parameter is `max_nfev` (via least_squares)
|
806
|
+
x = np.arange(0, 10)
|
807
|
+
y = 2*x
|
808
|
+
popt1, _ = curve_fit(lambda x,p: p*x, x, y, bounds=(0, 3), maxfev=100)
|
809
|
+
popt2, _ = curve_fit(lambda x,p: p*x, x, y, bounds=(0, 3), max_nfev=100)
|
810
|
+
|
811
|
+
assert_allclose(popt1, 2, atol=1e-14)
|
812
|
+
assert_allclose(popt2, 2, atol=1e-14)
|
813
|
+
|
814
|
+
@pytest.mark.parametrize("sigma_dim", [0, 1, 2])
|
815
|
+
def test_curvefit_omitnan(self, sigma_dim):
|
816
|
+
def exponential(x, a, b):
|
817
|
+
return b * np.exp(a * x)
|
818
|
+
|
819
|
+
rng = np.random.default_rng(578285731148908)
|
820
|
+
N = 100
|
821
|
+
x = np.linspace(1, 10, N)
|
822
|
+
y = exponential(x, 0.2, 0.5)
|
823
|
+
|
824
|
+
if (sigma_dim == 0):
|
825
|
+
sigma = 0.05
|
826
|
+
y += rng.normal(0, sigma, N)
|
827
|
+
|
828
|
+
elif (sigma_dim == 1):
|
829
|
+
sigma = x * 0.05
|
830
|
+
y += rng.normal(0, sigma, N)
|
831
|
+
|
832
|
+
elif (sigma_dim == 2):
|
833
|
+
# The covariance matrix must be symmetric positive-semidefinite
|
834
|
+
a = rng.normal(0, 2, (N, N))
|
835
|
+
sigma = a @ a.T
|
836
|
+
y += rng.multivariate_normal(np.zeros_like(x), sigma)
|
837
|
+
else:
|
838
|
+
assert False, "The sigma must be a scalar, 1D array or 2D array."
|
839
|
+
|
840
|
+
p0 = [0.1, 1.0]
|
841
|
+
|
842
|
+
# Choose indices to place NaNs.
|
843
|
+
i_x = rng.integers(N, size=5)
|
844
|
+
i_y = rng.integers(N, size=5)
|
845
|
+
|
846
|
+
# Add NaNs and compute result using `curve_fit`
|
847
|
+
x[i_x] = np.nan
|
848
|
+
y[i_y] = np.nan
|
849
|
+
res_opt, res_cov = curve_fit(exponential, x, y, p0=p0, sigma=sigma,
|
850
|
+
nan_policy="omit")
|
851
|
+
|
852
|
+
# Manually remove elements that should be eliminated, and
|
853
|
+
# calculate reference using `curve_fit`
|
854
|
+
i_delete = np.unique(np.concatenate((i_x, i_y)))
|
855
|
+
x = np.delete(x, i_delete, axis=0)
|
856
|
+
y = np.delete(y, i_delete, axis=0)
|
857
|
+
|
858
|
+
sigma = np.asarray(sigma)
|
859
|
+
if sigma.ndim == 1:
|
860
|
+
sigma = np.delete(sigma, i_delete)
|
861
|
+
elif sigma.ndim == 2:
|
862
|
+
sigma = np.delete(sigma, i_delete, axis=0)
|
863
|
+
sigma = np.delete(sigma, i_delete, axis=1)
|
864
|
+
ref_opt, ref_cov = curve_fit(exponential, x, y, p0=p0, sigma=sigma)
|
865
|
+
|
866
|
+
assert_allclose(res_opt, ref_opt, atol=1e-14)
|
867
|
+
assert_allclose(res_cov, ref_cov, atol=1e-14)
|
868
|
+
|
869
|
+
def test_curvefit_simplecovariance(self):
|
870
|
+
|
871
|
+
def func(x, a, b):
|
872
|
+
return a * np.exp(-b*x)
|
873
|
+
|
874
|
+
def jac(x, a, b):
|
875
|
+
e = np.exp(-b*x)
|
876
|
+
return np.vstack((e, -a * x * e)).T
|
877
|
+
|
878
|
+
np.random.seed(0)
|
879
|
+
xdata = np.linspace(0, 4, 50)
|
880
|
+
y = func(xdata, 2.5, 1.3)
|
881
|
+
ydata = y + 0.2 * np.random.normal(size=len(xdata))
|
882
|
+
|
883
|
+
sigma = np.zeros(len(xdata)) + 0.2
|
884
|
+
covar = np.diag(sigma**2)
|
885
|
+
|
886
|
+
for jac1, jac2 in [(jac, jac), (None, None)]:
|
887
|
+
for absolute_sigma in [False, True]:
|
888
|
+
popt1, pcov1 = curve_fit(func, xdata, ydata, sigma=sigma,
|
889
|
+
jac=jac1, absolute_sigma=absolute_sigma)
|
890
|
+
popt2, pcov2 = curve_fit(func, xdata, ydata, sigma=covar,
|
891
|
+
jac=jac2, absolute_sigma=absolute_sigma)
|
892
|
+
|
893
|
+
assert_allclose(popt1, popt2, atol=1e-14)
|
894
|
+
assert_allclose(pcov1, pcov2, atol=1e-14)
|
895
|
+
|
896
|
+
def test_curvefit_covariance(self):
|
897
|
+
|
898
|
+
def funcp(x, a, b):
|
899
|
+
rotn = np.array([[1./np.sqrt(2), -1./np.sqrt(2), 0],
|
900
|
+
[1./np.sqrt(2), 1./np.sqrt(2), 0],
|
901
|
+
[0, 0, 1.0]])
|
902
|
+
return rotn.dot(a * np.exp(-b*x))
|
903
|
+
|
904
|
+
def jacp(x, a, b):
|
905
|
+
rotn = np.array([[1./np.sqrt(2), -1./np.sqrt(2), 0],
|
906
|
+
[1./np.sqrt(2), 1./np.sqrt(2), 0],
|
907
|
+
[0, 0, 1.0]])
|
908
|
+
e = np.exp(-b*x)
|
909
|
+
return rotn.dot(np.vstack((e, -a * x * e)).T)
|
910
|
+
|
911
|
+
def func(x, a, b):
|
912
|
+
return a * np.exp(-b*x)
|
913
|
+
|
914
|
+
def jac(x, a, b):
|
915
|
+
e = np.exp(-b*x)
|
916
|
+
return np.vstack((e, -a * x * e)).T
|
917
|
+
|
918
|
+
rng = np.random.RandomState(0)
|
919
|
+
xdata = np.arange(1, 4)
|
920
|
+
y = func(xdata, 2.5, 1.0)
|
921
|
+
ydata = y + 0.2 * rng.normal(size=len(xdata))
|
922
|
+
sigma = np.zeros(len(xdata)) + 0.2
|
923
|
+
covar = np.diag(sigma**2)
|
924
|
+
# Get a rotation matrix, and obtain ydatap = R ydata
|
925
|
+
# Chisq = ydata^T C^{-1} ydata
|
926
|
+
# = ydata^T R^T R C^{-1} R^T R ydata
|
927
|
+
# = ydatap^T Cp^{-1} ydatap
|
928
|
+
# Cp^{-1} = R C^{-1} R^T
|
929
|
+
# Cp = R C R^T, since R^-1 = R^T
|
930
|
+
rotn = np.array([[1./np.sqrt(2), -1./np.sqrt(2), 0],
|
931
|
+
[1./np.sqrt(2), 1./np.sqrt(2), 0],
|
932
|
+
[0, 0, 1.0]])
|
933
|
+
ydatap = rotn.dot(ydata)
|
934
|
+
covarp = rotn.dot(covar).dot(rotn.T)
|
935
|
+
|
936
|
+
for jac1, jac2 in [(jac, jacp), (None, None)]:
|
937
|
+
for absolute_sigma in [False, True]:
|
938
|
+
popt1, pcov1 = curve_fit(func, xdata, ydata, sigma=sigma,
|
939
|
+
jac=jac1, absolute_sigma=absolute_sigma)
|
940
|
+
popt2, pcov2 = curve_fit(funcp, xdata, ydatap, sigma=covarp,
|
941
|
+
jac=jac2, absolute_sigma=absolute_sigma)
|
942
|
+
|
943
|
+
assert_allclose(popt1, popt2, rtol=1.2e-7, atol=1e-14)
|
944
|
+
assert_allclose(pcov1, pcov2, rtol=1.2e-7, atol=1e-14)
|
945
|
+
|
946
|
+
@pytest.mark.parametrize("absolute_sigma", [False, True])
|
947
|
+
def test_curvefit_scalar_sigma(self, absolute_sigma):
|
948
|
+
def func(x, a, b):
|
949
|
+
return a * x + b
|
950
|
+
|
951
|
+
x, y = self.x, self.y
|
952
|
+
_, pcov1 = curve_fit(func, x, y, sigma=2, absolute_sigma=absolute_sigma)
|
953
|
+
# Explicitly building the sigma 1D array
|
954
|
+
_, pcov2 = curve_fit(
|
955
|
+
func, x, y, sigma=np.full_like(y, 2), absolute_sigma=absolute_sigma
|
956
|
+
)
|
957
|
+
assert np.all(pcov1 == pcov2)
|
958
|
+
|
959
|
+
def test_dtypes(self):
|
960
|
+
# regression test for gh-9581: curve_fit fails if x and y dtypes differ
|
961
|
+
x = np.arange(-3, 5)
|
962
|
+
y = 1.5*x + 3.0 + 0.5*np.sin(x)
|
963
|
+
|
964
|
+
def func(x, a, b):
|
965
|
+
return a*x + b
|
966
|
+
|
967
|
+
for method in ['lm', 'trf', 'dogbox']:
|
968
|
+
for dtx in [np.float32, np.float64]:
|
969
|
+
for dty in [np.float32, np.float64]:
|
970
|
+
x = x.astype(dtx)
|
971
|
+
y = y.astype(dty)
|
972
|
+
|
973
|
+
with warnings.catch_warnings():
|
974
|
+
warnings.simplefilter("error", OptimizeWarning)
|
975
|
+
p, cov = curve_fit(func, x, y, method=method)
|
976
|
+
|
977
|
+
assert np.isfinite(cov).all()
|
978
|
+
assert not np.allclose(p, 1) # curve_fit's initial value
|
979
|
+
|
980
|
+
def test_dtypes2(self):
|
981
|
+
# regression test for gh-7117: curve_fit fails if
|
982
|
+
# both inputs are float32
|
983
|
+
def hyperbola(x, s_1, s_2, o_x, o_y, c):
|
984
|
+
b_2 = (s_1 + s_2) / 2
|
985
|
+
b_1 = (s_2 - s_1) / 2
|
986
|
+
return o_y + b_1*(x-o_x) + b_2*np.sqrt((x-o_x)**2 + c**2/4)
|
987
|
+
|
988
|
+
min_fit = np.array([-3.0, 0.0, -2.0, -10.0, 0.0])
|
989
|
+
max_fit = np.array([0.0, 3.0, 3.0, 0.0, 10.0])
|
990
|
+
guess = np.array([-2.5/3.0, 4/3.0, 1.0, -4.0, 0.5])
|
991
|
+
|
992
|
+
params = [-2, .4, -1, -5, 9.5]
|
993
|
+
xdata = np.array([-32, -16, -8, 4, 4, 8, 16, 32])
|
994
|
+
ydata = hyperbola(xdata, *params)
|
995
|
+
|
996
|
+
# run optimization twice, with xdata being float32 and float64
|
997
|
+
popt_64, _ = curve_fit(f=hyperbola, xdata=xdata, ydata=ydata, p0=guess,
|
998
|
+
bounds=(min_fit, max_fit))
|
999
|
+
|
1000
|
+
xdata = xdata.astype(np.float32)
|
1001
|
+
ydata = hyperbola(xdata, *params)
|
1002
|
+
|
1003
|
+
popt_32, _ = curve_fit(f=hyperbola, xdata=xdata, ydata=ydata, p0=guess,
|
1004
|
+
bounds=(min_fit, max_fit))
|
1005
|
+
|
1006
|
+
assert_allclose(popt_32, popt_64, atol=2e-5)
|
1007
|
+
|
1008
|
+
def test_broadcast_y(self):
|
1009
|
+
xdata = np.arange(10)
|
1010
|
+
target = 4.7 * xdata ** 2 + 3.5 * xdata + np.random.rand(len(xdata))
|
1011
|
+
def fit_func(x, a, b):
|
1012
|
+
return a * x ** 2 + b * x - target
|
1013
|
+
for method in ['lm', 'trf', 'dogbox']:
|
1014
|
+
popt0, pcov0 = curve_fit(fit_func,
|
1015
|
+
xdata=xdata,
|
1016
|
+
ydata=np.zeros_like(xdata),
|
1017
|
+
method=method)
|
1018
|
+
popt1, pcov1 = curve_fit(fit_func,
|
1019
|
+
xdata=xdata,
|
1020
|
+
ydata=0,
|
1021
|
+
method=method)
|
1022
|
+
assert_allclose(pcov0, pcov1)
|
1023
|
+
|
1024
|
+
def test_args_in_kwargs(self):
|
1025
|
+
# Ensure that `args` cannot be passed as keyword argument to `curve_fit`
|
1026
|
+
|
1027
|
+
def func(x, a, b):
|
1028
|
+
return a * x + b
|
1029
|
+
|
1030
|
+
with assert_raises(ValueError):
|
1031
|
+
curve_fit(func,
|
1032
|
+
xdata=[1, 2, 3, 4],
|
1033
|
+
ydata=[5, 9, 13, 17],
|
1034
|
+
p0=[1],
|
1035
|
+
args=(1,))
|
1036
|
+
|
1037
|
+
def test_data_point_number_validation(self):
|
1038
|
+
def func(x, a, b, c, d, e):
|
1039
|
+
return a * np.exp(-b * x) + c + d + e
|
1040
|
+
|
1041
|
+
with assert_raises(TypeError, match="The number of func parameters="):
|
1042
|
+
curve_fit(func,
|
1043
|
+
xdata=[1, 2, 3, 4],
|
1044
|
+
ydata=[5, 9, 13, 17])
|
1045
|
+
|
1046
|
+
@pytest.mark.filterwarnings('ignore::RuntimeWarning')
|
1047
|
+
def test_gh4555(self):
|
1048
|
+
# gh-4555 reported that covariance matrices returned by `leastsq`
|
1049
|
+
# can have negative diagonal elements and eigenvalues. (In fact,
|
1050
|
+
# they can also be asymmetric.) This shows up in the output of
|
1051
|
+
# `scipy.optimize.curve_fit`. Check that it has been resolved.giit
|
1052
|
+
def f(x, a, b, c, d, e):
|
1053
|
+
return a*np.log(x + 1 + b) + c*np.log(x + 1 + d) + e
|
1054
|
+
|
1055
|
+
rng = np.random.default_rng(408113519974467917)
|
1056
|
+
n = 100
|
1057
|
+
x = np.arange(n)
|
1058
|
+
y = np.linspace(2, 7, n) + rng.random(n)
|
1059
|
+
p, cov = optimize.curve_fit(f, x, y, maxfev=100000)
|
1060
|
+
assert np.all(np.diag(cov) > 0)
|
1061
|
+
eigs = linalg.eigh(cov)[0] # separate line for debugging
|
1062
|
+
# some platforms see a small negative eigevenvalue
|
1063
|
+
assert np.all(eigs > -1e-2)
|
1064
|
+
assert_allclose(cov, cov.T)
|
1065
|
+
|
1066
|
+
def test_gh4555b(self):
|
1067
|
+
# check that PR gh-17247 did not significantly change covariance matrix
|
1068
|
+
# for simple cases
|
1069
|
+
rng = np.random.default_rng(408113519974467917)
|
1070
|
+
|
1071
|
+
def func(x, a, b, c):
|
1072
|
+
return a * np.exp(-b * x) + c
|
1073
|
+
|
1074
|
+
xdata = np.linspace(0, 4, 50)
|
1075
|
+
y = func(xdata, 2.5, 1.3, 0.5)
|
1076
|
+
y_noise = 0.2 * rng.normal(size=xdata.size)
|
1077
|
+
ydata = y + y_noise
|
1078
|
+
_, res = curve_fit(func, xdata, ydata)
|
1079
|
+
# reference from commit 1d80a2f254380d2b45733258ca42eb6b55c8755b
|
1080
|
+
ref = [[+0.0158972536486215, 0.0069207183284242, -0.0007474400714749],
|
1081
|
+
[+0.0069207183284242, 0.0205057958128679, +0.0053997711275403],
|
1082
|
+
[-0.0007474400714749, 0.0053997711275403, +0.0027833930320877]]
|
1083
|
+
# Linux_Python_38_32bit_full fails with default tolerance
|
1084
|
+
assert_allclose(res, ref, 2e-7)
|
1085
|
+
|
1086
|
+
def test_gh13670(self):
|
1087
|
+
# gh-13670 reported that `curve_fit` executes callables
|
1088
|
+
# with the same values of the parameters at the beginning of
|
1089
|
+
# optimization. Check that this has been resolved.
|
1090
|
+
|
1091
|
+
rng = np.random.default_rng(8250058582555444926)
|
1092
|
+
x = np.linspace(0, 3, 101)
|
1093
|
+
y = 2 * x + 1 + rng.normal(size=101) * 0.5
|
1094
|
+
|
1095
|
+
def line(x, *p):
|
1096
|
+
assert not np.all(line.last_p == p)
|
1097
|
+
line.last_p = p
|
1098
|
+
return x * p[0] + p[1]
|
1099
|
+
|
1100
|
+
def jac(x, *p):
|
1101
|
+
assert not np.all(jac.last_p == p)
|
1102
|
+
jac.last_p = p
|
1103
|
+
return np.array([x, np.ones_like(x)]).T
|
1104
|
+
|
1105
|
+
line.last_p = None
|
1106
|
+
jac.last_p = None
|
1107
|
+
p0 = np.array([1.0, 5.0])
|
1108
|
+
curve_fit(line, x, y, p0, method='lm', jac=jac)
|
1109
|
+
|
1110
|
+
@pytest.mark.parametrize('method', ['trf', 'dogbox'])
|
1111
|
+
def test_gh20155_error_mentions_x0(self, method):
|
1112
|
+
# `curve_fit` produced an error message that referred to an undocumented
|
1113
|
+
# variable `x0`, which was really `p0`. Check that this is resolved.
|
1114
|
+
def func(x,a):
|
1115
|
+
return x**a
|
1116
|
+
message = "Initial guess is outside of provided bounds"
|
1117
|
+
with pytest.raises(ValueError, match=message):
|
1118
|
+
curve_fit(func, self.x, self.y, p0=[1], bounds=(1000, 1001),
|
1119
|
+
method=method)
|
1120
|
+
|
1121
|
+
|
1122
|
+
class TestFixedPoint:
|
1123
|
+
|
1124
|
+
def test_scalar_trivial(self):
|
1125
|
+
# f(x) = 2x; fixed point should be x=0
|
1126
|
+
def func(x):
|
1127
|
+
return 2.0*x
|
1128
|
+
x0 = 1.0
|
1129
|
+
x = fixed_point(func, x0)
|
1130
|
+
assert_almost_equal(x, 0.0)
|
1131
|
+
|
1132
|
+
def test_scalar_basic1(self):
|
1133
|
+
# f(x) = x**2; x0=1.05; fixed point should be x=1
|
1134
|
+
def func(x):
|
1135
|
+
return x**2
|
1136
|
+
x0 = 1.05
|
1137
|
+
x = fixed_point(func, x0)
|
1138
|
+
assert_almost_equal(x, 1.0)
|
1139
|
+
|
1140
|
+
def test_scalar_basic2(self):
|
1141
|
+
# f(x) = x**0.5; x0=1.05; fixed point should be x=1
|
1142
|
+
def func(x):
|
1143
|
+
return x**0.5
|
1144
|
+
x0 = 1.05
|
1145
|
+
x = fixed_point(func, x0)
|
1146
|
+
assert_almost_equal(x, 1.0)
|
1147
|
+
|
1148
|
+
def test_array_trivial(self):
|
1149
|
+
def func(x):
|
1150
|
+
return 2.0*x
|
1151
|
+
x0 = [0.3, 0.15]
|
1152
|
+
with np.errstate(all='ignore'):
|
1153
|
+
x = fixed_point(func, x0)
|
1154
|
+
assert_almost_equal(x, [0.0, 0.0])
|
1155
|
+
|
1156
|
+
def test_array_basic1(self):
|
1157
|
+
# f(x) = c * x**2; fixed point should be x=1/c
|
1158
|
+
def func(x, c):
|
1159
|
+
return c * x**2
|
1160
|
+
c = array([0.75, 1.0, 1.25])
|
1161
|
+
x0 = [1.1, 1.15, 0.9]
|
1162
|
+
with np.errstate(all='ignore'):
|
1163
|
+
x = fixed_point(func, x0, args=(c,))
|
1164
|
+
assert_almost_equal(x, 1.0/c)
|
1165
|
+
|
1166
|
+
def test_array_basic2(self):
|
1167
|
+
# f(x) = c * x**0.5; fixed point should be x=c**2
|
1168
|
+
def func(x, c):
|
1169
|
+
return c * x**0.5
|
1170
|
+
c = array([0.75, 1.0, 1.25])
|
1171
|
+
x0 = [0.8, 1.1, 1.1]
|
1172
|
+
x = fixed_point(func, x0, args=(c,))
|
1173
|
+
assert_almost_equal(x, c**2)
|
1174
|
+
|
1175
|
+
def test_lambertw(self):
|
1176
|
+
# python-list/2010-December/594592.html
|
1177
|
+
xxroot = fixed_point(lambda xx: np.exp(-2.0*xx)/2.0, 1.0,
|
1178
|
+
args=(), xtol=1e-12, maxiter=500)
|
1179
|
+
assert_allclose(xxroot, np.exp(-2.0*xxroot)/2.0)
|
1180
|
+
assert_allclose(xxroot, lambertw(1)/2)
|
1181
|
+
|
1182
|
+
def test_no_acceleration(self):
|
1183
|
+
# GitHub issue 5460
|
1184
|
+
ks = 2
|
1185
|
+
kl = 6
|
1186
|
+
m = 1.3
|
1187
|
+
n0 = 1.001
|
1188
|
+
i0 = ((m-1)/m)*(kl/ks/m)**(1/(m-1))
|
1189
|
+
|
1190
|
+
def func(n):
|
1191
|
+
return np.log(kl/ks/n) / np.log(i0*n/(n - 1)) + 1
|
1192
|
+
|
1193
|
+
n = fixed_point(func, n0, method='iteration')
|
1194
|
+
assert_allclose(n, m)
|