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Allow plotting parameters against Q^2 - #271
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Analysis.plot_parameters and ParameterAnalysis.plot take an x_axis
argument ('Q' or 'Q^2'). The values at each Q are unchanged; only the
plotted coordinate is transformed, via the shared add_x_axis_coord
helper and its Q_AXIS_TRANSFORMS table, so further axes are one entry.
Closes #205
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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* update pixi (#266) * Adding Chudley-Elliott Jump Diffusion Model (#246) * Add ChudleyElliotJumpDiffusion model and corresponding tests * Enhance ChudleyElliotJumpDiffusion model documentation and tests; all checks passed * Fix: replace Chudley-Elliot with Chudley-Elliott (propegated from spelling mistake in Mantid documentation) * Fix: Add missing ChudleyElliottJumpDiffusion to public API and module exports * Fix: Improve test clarity and update unit handling in ChudleyElliottJumpDiffusion tests * Fix: Implement minimum width for residence time in ChudleyElliottJumpDiffusion model and update tests * Fix: Update error handling in ChudleyElliottJumpDiffusion model and improve test assertions * chore: pixi update and linting * Add jump diffusion tutorials and Chudley-Elliott citation - Add Jump Translational and Chudley-Elliott sections to diffusion_model.ipynb, with subheaders for each model - Name the models in the Diffusion model entry of the tutorials index - Add the Chudley and Elliott (1961) reference and "See also the tutorials" to the ChudleyElliottJumpDiffusion docstring - Remove the tutorials TODO (#273) * Speed up StretchedExponential evaluation (#268) * Speed up StretchedExponential quadrature 3-4x Evaluate the exp-sinh quadrature in cache-sized blocks with in-place temporaries, and drop nodes whose decaying exponent provably underflows exp to exactly zero. Results are unchanged to rounding and stay bitwise independent of block boundaries. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Interpolate the StretchedExponential profile by default Add an interpolate flag (default True) that evaluates G_beta from a cached cubic-spline table of log(G / G(0)) on y = asinh(w / w_ref) instead of running the quadrature at every energy. Tables are cached per beta and grow on a fixed lattice, so fits stay smooth under finite-difference Jacobian steps. Accuracy is ~1e-7 of the peak for all beta; interpolate=False keeps the ~1e-11 quadrature. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Add example, run pixi update --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> * Allow plotting parameters against Q^2 (#271) * Allow plotting parameters against Q^2 Analysis.plot_parameters and ParameterAnalysis.plot take an x_axis argument ('Q' or 'Q^2'). The values at each Q are unchanged; only the plotted coordinate is transformed, via the shared add_x_axis_coord helper and its Q_AXIS_TRANSFORMS table, so further axes are one entry. Closes #205 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Show the Lorentzian width against Q^2 in tutorial 1 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> * Align the data and residuals axes in plots with residuals (#270) slicerplot_with_residuals drew the residuals in a second Matplotlib figure below the main one. Each figure was tight_layout'ed on its own, so the axes' left edges depended on each panel's y tick label and y label widths and did not line up. Draw both panels as two axes of one figure with a shared x axis, so they are laid out together and share x limits, scale and zoom. figsize now sizes the whole figure, and the residuals panel hides its log buttons, since logX is shared and logY does not suit residuals. Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> --------- Co-authored-by: easyscience[bot] <2476259+easyscience[bot]@users.noreply.github.com> Co-authored-by: Henrik Jacobsen <henrik.jacobsen.fys@gmail.com> Co-authored-by: mark <191927387+markbujehein@users.noreply.github.com> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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Closes #205.
Diffusion models are usually read off a plot of the widths against Q², where Fickian diffusion (Γ = D·Q²) is a straight line. Both parameter plots now take an
x_axisargument:The default is
'Q', so existing calls are unchanged.How it works
coords=[x_axis]. The axis label and unit follow from scipp (Q^2 [1/Å^2]).easydynamics.utils.plotting:Q_AXIS_TRANSFORMSmaps each axis name to a function of Q.add_x_axis_coord(data, x_axis)checks the name and returns a copy of the Dataset with that coordinate added.'1/Q', is one entry inQ_AXIS_TRANSFORMS. Both plot methods pick it up automatically.Tutorial 1 now plots the Lorentzian width against Q² before fitting the Brownian diffusion model.
Notes for review
x_axisis placed afternames, so positional calls that already passednamesstill work.test_plot_parametersintest_analysis.pyused placeholder objects instead of data. It now uses a realsc.Dataset, since the method reads its Q coordinate.plot_parameters' docstring said kwargs go toplopp.slicer; it now saysplopp.plot, which is where they go.ParameterAnalysis.plotof a D·Q² model: data points and model line both land at x = Q² and form a straight line.🤖 Generated with Claude Code