From 8f65210ed265c9ceac0791d0839464fea9d7c06c Mon Sep 17 00:00:00 2001 From: lan13005 Date: Thu, 26 Oct 2023 16:14:22 -0400 Subject: [PATCH] Update documentation --- _autosummary/PlotGen.html | 465 ----------------- _autosummary/PlotGenRDF.html | 465 ----------------- _autosummary/extract_ff.html | 465 ----------------- _autosummary/fit.html | 468 ----------------- _autosummary/mcmc.html | 474 ------------------ _autosummary/mcmcOptimalMoves.html | 465 ----------------- _sources/_autosummary/PlotGen.rst | 29 -- _sources/_autosummary/PlotGenRDF.rst | 29 -- _sources/_autosummary/extract_ff.rst | 29 -- _sources/_autosummary/fit.rst | 30 -- _sources/_autosummary/mcmc.rst | 32 -- _sources/_autosummary/mcmcOptimalMoves.rst | 29 -- _sources/api.rst | 26 + .../autosummary/module.rst} | 2 +- api.html | 221 +++++++- genindex.html | 89 ++-- notebooks.html | 2 +- objects.inv | 9 +- py-modindex.html | 447 ----------------- searchindex.js | 2 +- .../autosummary/module.html | 92 ++-- 21 files changed, 328 insertions(+), 3542 deletions(-) delete mode 100644 _autosummary/PlotGen.html delete mode 100644 _autosummary/PlotGenRDF.html delete mode 100644 _autosummary/extract_ff.html delete mode 100644 _autosummary/fit.html delete mode 100644 _autosummary/mcmc.html delete mode 100644 _autosummary/mcmcOptimalMoves.html delete mode 100644 _sources/_autosummary/PlotGen.rst delete mode 100644 _sources/_autosummary/PlotGenRDF.rst delete mode 100644 _sources/_autosummary/extract_ff.rst delete mode 100644 _sources/_autosummary/fit.rst delete mode 100644 _sources/_autosummary/mcmc.rst delete mode 100644 _sources/_autosummary/mcmcOptimalMoves.rst rename _sources/{_autosummary/modules.rst => templates/autosummary/module.rst} (79%) delete mode 100644 py-modindex.html rename _autosummary/modules.html => templates/autosummary/module.html (72%) diff --git a/_autosummary/PlotGen.html b/_autosummary/PlotGen.html deleted file mode 100644 index 50bd78f..0000000 --- a/_autosummary/PlotGen.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - - - - - - - PlotGen — PyAmpTools - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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PlotGen#

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PlotGen(plotGen, ofile[, ampString, ...])

Generates plots from a fit result file.

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PlotGenRDF#

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draw_histograms(results, hist_output_name, ...)

Draw booked histograms from RDataFrame

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extract_ff

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extract_ff#

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extract_ff(results[, outfileName, ...])

Regex merge is a useful tool to merge amplitudes that are related to each other (user-specified) For example waveset: D-2- D-1- D0- D1- D2- D-2+ D-1+ D0+ D1+ D2+ To remove the sign at the end (merge reflectivites) use = r'[-+]$' To remove first sign and number (merge M-projections) use = r'[-+]?(d+)' To remove numbers and signs to merge all D: use = r'[-+]?(d+)[-+]'

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fit

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fit#

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performFit(fitManager, seed_file_tag[, ...])

Performs a single fit

runFits(ati[, N, always_save_seed])

Performs N randomized fits, if N=0 then a single fit with no randomization is performed

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mcmc

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mcmc#

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LogProb(par_values, keys, ati, ...)

Definition of the (Log) Posterior distribution

createMovesMixtureFromDict(moves_dict)

Creates a mixture of moves for the emcee sampler

draw_corner(results, ofolder[, ...])

Draws a corner plot to visualize sampling and parameter correlations

perform_mcmc(ati, LoadParametersSampler[, ...])

Performs MCMC sampling

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mcmcOptimalMoves

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mcmcOptimalMoves#

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Classes

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Objective(conditions)

Modified objective function (Class) for Optuna that takes an initialization list

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- - - - - - - - \ No newline at end of file diff --git a/_sources/_autosummary/PlotGen.rst b/_sources/_autosummary/PlotGen.rst deleted file mode 100644 index fa211c0..0000000 --- a/_sources/_autosummary/PlotGen.rst +++ /dev/null @@ -1,29 +0,0 @@ -PlotGen -======= - -.. automodule:: PlotGen - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - PlotGen - - - - - - - - - - - - - diff --git a/_sources/_autosummary/PlotGenRDF.rst b/_sources/_autosummary/PlotGenRDF.rst deleted file mode 100644 index e9a8b98..0000000 --- a/_sources/_autosummary/PlotGenRDF.rst +++ /dev/null @@ -1,29 +0,0 @@ -PlotGenRDF -========== - -.. automodule:: PlotGenRDF - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - draw_histograms - - - - - - - - - - - - - diff --git a/_sources/_autosummary/extract_ff.rst b/_sources/_autosummary/extract_ff.rst deleted file mode 100644 index 8a974e2..0000000 --- a/_sources/_autosummary/extract_ff.rst +++ /dev/null @@ -1,29 +0,0 @@ -extract\_ff -=========== - -.. automodule:: extract_ff - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - extract_ff - - - - - - - - - - - - - diff --git a/_sources/_autosummary/fit.rst b/_sources/_autosummary/fit.rst deleted file mode 100644 index dd50d05..0000000 --- a/_sources/_autosummary/fit.rst +++ /dev/null @@ -1,30 +0,0 @@ -fit -=== - -.. automodule:: fit - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - performFit - runFits - - - - - - - - - - - - - diff --git a/_sources/_autosummary/mcmc.rst b/_sources/_autosummary/mcmc.rst deleted file mode 100644 index 54e5071..0000000 --- a/_sources/_autosummary/mcmc.rst +++ /dev/null @@ -1,32 +0,0 @@ -mcmc -==== - -.. automodule:: mcmc - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - LogProb - createMovesMixtureFromDict - draw_corner - perform_mcmc - - - - - - - - - - - - - diff --git a/_sources/_autosummary/mcmcOptimalMoves.rst b/_sources/_autosummary/mcmcOptimalMoves.rst deleted file mode 100644 index 1472f02..0000000 --- a/_sources/_autosummary/mcmcOptimalMoves.rst +++ /dev/null @@ -1,29 +0,0 @@ -mcmcOptimalMoves -================ - -.. automodule:: mcmcOptimalMoves - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - Objective - - - - - - - - - diff --git a/_sources/api.rst b/_sources/api.rst index d7d054e..e8c1b69 100644 --- a/_sources/api.rst +++ b/_sources/api.rst @@ -1,4 +1,30 @@ +.. autosummary:: + :toctree: _autosummary + :template: autosummary/module.rst + Detailed API documentation ========================== +fit +--- +.. autofunction:: fit.performFit +.. autofunction:: fit.runFits + +mcmc +---- +.. autofunction:: mcmc.LogProb +.. autofunction:: mcmc.createMovesMixtureFromDict +.. autofunction:: mcmc.perform_mcmc +.. autofunction:: mcmc.draw_corner + +extract_ff +---------- .. autofunction:: extract_ff.extract_ff + +PlotGen +------- +.. autofunction:: PlotGen.PlotGen + +PlotGenRDF +---------- +.. autofunction:: PlotGenRDF.draw_histograms \ No newline at end of file diff --git a/_sources/_autosummary/modules.rst b/_sources/templates/autosummary/module.rst similarity index 79% rename from _sources/_autosummary/modules.rst rename to _sources/templates/autosummary/module.rst index 7f5c2d8..49741c3 100644 --- a/_sources/_autosummary/modules.rst +++ b/_sources/templates/autosummary/module.rst @@ -3,5 +3,5 @@ .. automodule:: {{ name }} :members: - :inherited-members: + :undoc-members: :show-inheritance: diff --git a/api.html b/api.html index 88c7c08..9d9bd00 100644 --- a/api.html +++ b/api.html @@ -341,7 +341,9 @@ `); - + @@ -357,6 +359,18 @@

Detailed API documentation

+
+

Contents

+
+
@@ -366,8 +380,145 @@

Detailed API documentation

-
+ + + +
+

Detailed API documentation#

+
+

fit#

+
+
+performFit(fitManager, seed_file_tag, always_save_seed: bool = False)#
+

Performs a single fit

+
+
Parameters:
+
    +

  • fitManager – MinuitMinimizationManager

    • +

  • seed_file_tag – Tag to append to output file names

    • +
+
+
Returns:
+

Bool indicating if fit failed +NLL: Negative log likelihood

+
+
Return type:
+

bFitFailed

+
+
+
+ +
+
+runFits(ati, N: int = 0, always_save_seed: bool = False)#
+

Performs N randomized fits, if N=0 then a single fit with no randomization is performed

+
+
Parameters:
+

N – Number of randomized fits to perform

+
+
Returns:
+

Minimum negative log likelihood

+
+
Return type:
+

minNLL

+
+
+
+ +
+
+

mcmc#

+
+
+LogProb(par_values, keys, ati, LoadParametersSampler)#
+

Definition of the (Log) Posterior distribution

+
+
Parameters:
+
    +

  • par_values – Flattened (complex-to-Real/Imag) Parameter values. ~ [real1, imag1, real2, imag2, …]

    • +

  • keys – Flattened Parameter names. ~ [amp1, amp1, amp2, amp2, …]

    • +

  • ati – AmpToolsInterface

    • +

  • LoadParametersSampler – LoadParameters class to manage parameters

    • +
+
+
Returns:
+

Log posterior probability

+
+
Return type:
+

log_prob

+
+
+
+ +
+
+createMovesMixtureFromDict(moves_dict)#
+

Creates a mixture of moves for the emcee sampler

+
+
Parameters:
+

moves_dict – { move: {kwargs: {}, probability} }

+
+
Returns:
+

[ (emcee.moves.{move}(kwargs), probability) ]

+
+
Return type:
+

moves_mixture

+
+
+
+ +
+
+perform_mcmc(ati, LoadParametersSampler, ofolder: str = 'mcmc', ofile: str = 'mcmc.h5', nwalkers: int = 32, burnIn: int = 100, nsamples: int = 1000, params_dict={}, moves_mixture=[<emcee.moves.stretch.StretchMove object>])#
+

Performs MCMC sampling

+
+
Parameters:
+
    +

  • ati – AmpToolsInterface class

    • +

  • LoadParametersSampler – LoadParameters class

    • +

  • ofolder – output folder name

    • +

  • ofile – output file name

    • +

  • nwalkers – number of walkers

    • +

  • burnIn – number of burn-in steps

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  • nsamples – number of samples

    • +

  • params_dict – ~ {par: value} or {par: [value, min, max]} Sample from [min, max] for walker initialization

    • +

  • moves_mixture – Move mixture for sampler

    • +
+
+
Returns:
+

Dictionary containing results of MCMC sampling (samples, MAP, acceptance fraction, autocorrelation time, etc.)

+
+
Return type:
+

results

+
+
+
+ +
+
+draw_corner(results, ofolder, corner_ofile='corner.png', save=True, kwargs={})#
+

Draws a corner plot to visualize sampling and parameter correlations

+
+
Parameters:
+
    +

  • results – Dictionary containing results of MCMC sampling (samples, MAP, acceptance fraction, autocorrelation time, etc.)

    • +

  • ofolder – output folder name

    • +

  • save – Save the figure to a file or return figure. Default True = Save

    • +
+
+
Returns:
+

Figure object (or None)

+
+
Return type:
+

fig

+
+
+
+ +
+
+

extract_ff#

extract_ff(results, outfileName='', acceptanceCorrect=True, fmt='.5f', regex_merge=None)#
@@ -392,6 +543,54 @@

Detailed API documentation +

PlotGen#

+
+
+PlotGen(plotGen, ofile, ampString='all', keepAllAmps=False, plotAllVars=False, plotGenHists=False, doAccCorr=True)#
+

Generates plots from a fit result file. The plots are saved to a root file.

+
+
Parameters:
+
    +

  • plotGen – Sub-classed PlotGenerator instance.

    • +

  • plotfile – name of output root file.

    • +

  • ampString – Semicolon separated list of coherent sums to plot. Sums are underscore separated amplitudes. Empty string will plot sum of all waves.

    • +

  • keepAllAmps – If True, all amplitudes are summed and plotted. If False, only the amplitudes specified in ampString will be plotted.

    • +

  • plotAllVars – If True, all variables will be plotted.

    • +

  • plotGenHists – If True, generated histograms will be plotted.

    • +

  • doAccCorr – If True, acceptance correction will be applied to the histograms.

    • +
+
+
Returns:
+

None

+
+
+
+ +

+
+

PlotGenRDF#

+
+
+draw_histograms(results, hist_output_name, particles, HISTS_TO_BOOK)#
+

Draw booked histograms from RDataFrame

+
+
Parameters:
+
    +

  • results (FitResults) – FitResults object

    • +

  • hist_output_name (str) – Output file name, do not include file type

    • +

  • particles (List[str]) – List of particles in reaction

    • +

  • HISTS_TO_BOOK (Dict[str, List]) – Dictionary of histograms to book. See book_histogram() for details

    • +
+
+
Returns:
+

None

+
+
+
+ +
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