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New: Linear fitting 2.0 #1462
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thomasaarholt
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thomasaarholt:Linear_fit
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New: Linear fitting 2.0 #1462
thomasaarholt
wants to merge
8
commits into
hyperspy:RELEASE_next_minor
from
thomasaarholt:Linear_fit
Commits on Jul 2, 2018
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Linearity attribute to parameters
Squashed commit containing most changes made to components Old commit message: Added linearity attributes (and cleared up two typos). I am uncertain about the correct approach to the expression component (currently set any parameter’s is_linear to False). I am also unsure about which parameters are linear for the heaviside, voigt, RC, PESCORELineShape (with shirley) and EELS_vignetting. "Better safe than sorry" attitude with linear components, but set heaviside linear. Fixed linearity of expression Temp fix for Expression, until removing is_linear = False attribute. I feel like an idiot for writing what I did. Parameters default to parameter.is_linear = False Removed parameter.is_linear = False in favour of default setting = False. Removed existance of .function method which existed for some reason in expression. Removed linear=False from heaviside. Fixed a typo on the Expression example Sympy now checks Expression for linear components Added tests Simplified sympy check and moved it out of class Better function name Now correct check of linearity Clarified code Added a test case Sympy extract constant part of expression with respect to variables Made is_linear protected Added constant term property to expression Added docstring Added check for only one linear parameter per component. + TIdy Fixed tests and "one linear" check Docstring + tidying Fixed missing _is_linear Offset is y=k, not y=k+x set Offset _is_linear True fixed (my) bug in Offset component Fixed test failing Added polynomial constant, needs a look Corrected expression constant extractor + tests indent typo Working with constant term Remove component._constant_parameters as it doesn't make sense if constant is free
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Linear model fitting functions
Added three linear fitters Added imports and docstring Added tests Some PEP changes Added bounds to lsq_linear Added test for bounded lsq_linear Ensure that linear components aren't initialised at zero Some formatting Ensure components don't get added twice Renamed "linear_lsq" to "linear" Reordering priority of fitters If fitter is None, use linear if model is linear Supports case of one component being inactive Fix fitting with inactive components for other fitters one file changed? check these changes Fixed for SI and changed warnings to logging INFO Removed print statement Cleared up some code, fixed a bug Cleaned code, fixed axis bug Fixed linear fitting with bounds made methods private deleted obsolete method fixed tests some language and cleanup Corrected binned signal fitting for linear fixed truedivide error Removed the other two forms of linear fitting. Can add later. minor cleaning up removed print statement Added preliminary support for convolved components Fixed transposing errors Removed old function and print statements fixed test error Fixed changed signal range breaking Removed remnants of other linear fitters More remnants autopep8 typo Working for convolved, nonconvolved, free and fixed components Add support for linear fitting with a free offset, by either component or parameter Update p0 and subtract free offsets from model, adding it as a type of component instead some tests code reduced, but slow? twinned case must be considered
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Documentation 2.0. Thanks @tjof2 clearer docs corrections to docs Deleted some unnecessary lines from linear fitting docs
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Commits on Jul 18, 2018
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Squash: Linear Model and EELS fitting
MODEL: Underscore bug MODEL: default fitter no longer from prefs MODEL: Working with twins but not in pseudocomponents fix twin situation fix twin situation moved test files removed old case for appending components Change test case to use artificial data add standard error Remove old code TEST: Add and remove test cases, and fix hydrogenic Cleaned up linear fitting procedure, simplified linear model estimation procedure and formatted code Removed unused code, cleaned up with pep8 moved error message Rewrote component function calls to support multidimensional models fixed small bugs with previous commits more fixes to the previous, now working made expression fix_free separation 2D-able corrected shape Add 2D model support for linear fitting Added test cases for model2D linear fitting model.py typo hotfix for Zanetta large multifit update - mostly working need to fix expression multi getting closer minor new twin tactic much changes beginning of EELS CL support further changes to eels modified convolve. Nearly there further GOS changes hello fixed Model2D
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Make most components multi-compatible
updated bleasdale to take parameters in function call remove print readied most comps for linear multifit minor fixing components and adding tests
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Commits on Jul 23, 2018
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remove unused code docstring and PEP improvements update docs remove old lsq_linear reference remove old import fixed fit_component and signal_range
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