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11 | | - <title>Integrated fitting workflow (pesfit.fitter) — pesfit 0.5.0 documentation</title> |
| 11 | + <title>Integrated fitting workflow (pesfit.fitter) — pesfit 0.5.2 documentation</title> |
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35 | 35 | <link rel="index" title="Index" |
36 | 36 | href="genindex.html"/> |
37 | 37 | <link rel="search" title="Search" href="search.html"/> |
38 | | - <link rel="top" title="pesfit 0.5.0 documentation" href="index.html"/> |
| 38 | + <link rel="top" title="pesfit 0.5.2 documentation" href="index.html"/> |
39 | 39 | <link rel="next" title="Utility functions (pesfit.utils)" href="utils.html"/> |
40 | 40 | <link rel="prev" title="Complex lineshape models (pesfit.lineshape)" href="lineshape.html"/> |
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66 | 66 |
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67 | 67 |
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68 | 68 | <div class="version"> |
69 | | - 0.5.0 |
| 69 | + 0.5.2 |
70 | 70 | </div> |
71 | 71 |
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72 | 72 |
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182 | 182 |
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183 | 183 | <dl class="py method"> |
184 | 184 | <dt id="pesfit.fitter.ParallelPatchFitter.parallel_fit"> |
185 | | -<code class="sig-name descname">parallel_fit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">varkeys</span><span class="o">=</span><span class="default_value">['value', 'vary']</span></em>, <em class="sig-param"><span class="n">other_initvals</span><span class="o">=</span><span class="default_value">[True]</span></em>, <em class="sig-param"><span class="n">compute_kwds</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">scheduler</span><span class="o">=</span><span class="default_value">'processes'</span></em>, <em class="sig-param"><span class="n">backend</span><span class="o">=</span><span class="default_value">'dask'</span></em>, <em class="sig-param"><span class="n">ret</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwds</span></em><span class="sig-paren">)</span><a class="headerlink" href="#pesfit.fitter.ParallelPatchFitter.parallel_fit" title="Permalink to this definition">¶</a></dt> |
186 | | -<dd><p>Parallel line fitting of the data patch.</p> |
| 185 | +<code class="sig-name descname">parallel_fit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">varkeys</span><span class="o">=</span><span class="default_value">['value', 'vary']</span></em>, <em class="sig-param"><span class="n">other_initvals</span><span class="o">=</span><span class="default_value">[True]</span></em>, <em class="sig-param"><span class="n">para_kwds</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">scheduler</span><span class="o">=</span><span class="default_value">'processes'</span></em>, <em class="sig-param"><span class="n">backend</span><span class="o">=</span><span class="default_value">'multiprocessing'</span></em>, <em class="sig-param"><span class="n">ret</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwds</span></em><span class="sig-paren">)</span><a class="headerlink" href="#pesfit.fitter.ParallelPatchFitter.parallel_fit" title="Permalink to this definition">¶</a></dt> |
| 186 | +<dd><p>Parallel pointwise spectrum fitting of the data patch.</p> |
| 187 | +<p><strong>Parameters</strong></p> |
| 188 | +<p>varkeys: list/tuple | [‘value’, ‘vary’] |
| 189 | +other_initvals: list/tuple | [True] |
| 190 | +para_kwds: dic | {} |
| 191 | +scheduler: str | ‘processes’ |
| 192 | +backend: str | ‘multiprocessing’ |
| 193 | +ret: bool | False |
| 194 | +<a href="#id1"><span class="problematic" id="id2">**</span></a>kwds: keyword arguments</p> |
187 | 195 | </dd></dl> |
188 | 196 |
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189 | 197 | <dl class="py method"> |
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235 | 243 | </dd> |
236 | 244 | <dt>ftype: str | ‘h5’</dt><dd><p>File type to load.</p> |
237 | 245 | </dd> |
238 | | -<dt><a href="#id1"><span class="problematic" id="id2">**</span></a>kwds: keywords argument</dt><dd><p>Additional arguments for <code class="docutils literal notranslate"><span class="pre">pesfit.fitter.load_file()</span></code>.</p> |
| 246 | +<dt><a href="#id3"><span class="problematic" id="id4">**</span></a>kwds: keywords argument</dt><dd><p>Additional arguments for <code class="docutils literal notranslate"><span class="pre">pesfit.fitter.load_file()</span></code>.</p> |
239 | 247 | </dd> |
240 | 248 | </dl> |
241 | 249 | </dd></dl> |
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284 | 292 | </dd> |
285 | 293 | <dt>pbenv: str | ‘notebook’</dt><dd><p>Progress bar environment (‘notebook’ for Jupyter notebook or ‘classic’ for command line).</p> |
286 | 294 | </dd> |
287 | | -<dt><a href="#id3"><span class="problematic" id="id4">**</span></a>kwds: keywords arguments</dt><dd><dl class="simple"> |
| 295 | +<dt><a href="#id5"><span class="problematic" id="id6">**</span></a>kwds: keywords arguments</dt><dd><dl class="simple"> |
288 | 296 | <dt>nspec: int | <code class="docutils literal notranslate"><span class="pre">self.nspec</span></code></dt><dd><p>Number of spectra for fitting.</p> |
289 | 297 | </dd> |
290 | 298 | <dt>additional arguments:</dt><dd><p>See <code class="docutils literal notranslate"><span class="pre">pesfit.fitter.pointwise_fitting()</span></code>.</p> |
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331 | 339 | </dd> |
332 | 340 | <dt>varkeys: list/tuple | [‘value’]</dt><dd><p>Keyword specified for the parameter (‘value’, ‘min’, ‘max’, ‘vary’).</p> |
333 | 341 | </dd> |
334 | | -<dt><a href="#id5"><span class="problematic" id="id6">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
| 342 | +<dt><a href="#id7"><span class="problematic" id="id8">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
335 | 343 | <dt>lpnames: list/tuple | None</dt><dd><p>Collection of namestrings (or prefixes) for lineshapes.</p> |
336 | 344 | </dd> |
337 | 345 | <dt>parvals: list/tuple | None</dt><dd><p>Collection of values for parameters.</p> |
|
357 | 365 | </dd> |
358 | 366 | <dt>background: str | ‘None’</dt><dd><p>Background model name. All possible models see <code class="docutils literal notranslate"><span class="pre">lmfit.models</span></code>.</p> |
359 | 367 | </dd> |
360 | | -<dt><a href="#id7"><span class="problematic" id="id8">**</span></a>kwds: keyword arguments</dt><dd><p>Additional keyword arguments for <code class="docutils literal notranslate"><span class="pre">pesfit.lineshape.MultipeakModel</span></code> class.</p> |
| 368 | +<dt><a href="#id9"><span class="problematic" id="id10">**</span></a>kwds: keyword arguments</dt><dd><p>Additional keyword arguments for <code class="docutils literal notranslate"><span class="pre">pesfit.lineshape.MultipeakModel</span></code> class.</p> |
361 | 369 | </dd> |
362 | 370 | </dl> |
363 | 371 | <p><strong>Return</strong></p> |
|
389 | 397 | </dd> |
390 | 398 | <dt>ret: bool | False</dt><dd><p>Option to return the graphical elements.</p> |
391 | 399 | </dd> |
392 | | -<dt><a href="#id9"><span class="problematic" id="id10">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
| 400 | +<dt><a href="#id11"><span class="problematic" id="id12">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
393 | 401 | <dt>figsize: list/tuple | [10, 6]</dt><dd><p>Default size of the figure.</p> |
394 | 402 | </dd> |
395 | 403 | </dl> |
|
411 | 419 | </dd> |
412 | 420 | <dt>downsamp: int | 1</dt><dd><p>Level of downsampling of the data (1 means no downsampling).</p> |
413 | 421 | </dd> |
414 | | -<dt><a href="#id11"><span class="problematic" id="id12">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
| 422 | +<dt><a href="#id13"><span class="problematic" id="id14">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
415 | 423 | <dt>figsize: list/tuple | [8, 5]</dt><dd><p>Default size of the figure.</p> |
416 | 424 | </dd> |
417 | 425 | </dl> |
|
445 | 453 | <p><code class="docutils literal notranslate"><span class="pre">'result'</span></code>: returns the fitting result</p> |
446 | 454 | <p><code class="docutils literal notranslate"><span class="pre">'all'</span></code>: returns the fitting result and evaluated lineshape components.</p> |
447 | 455 | </dd> |
448 | | -<dt><a href="#id13"><span class="problematic" id="id14">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
| 456 | +<dt><a href="#id15"><span class="problematic" id="id16">**</span></a>kwds: keyword arguments</dt><dd><dl class="simple"> |
449 | 457 | <dt>shifts: list/tuple/numpy array | np.arange(0.1, 1.1, 0.1)</dt><dd><p>The choices of random shifts to apply to the peak position initialization (energy in eV unit). The shifts are only operational when <code class="docutils literal notranslate"><span class="pre">jitter_init=True</span></code>.</p> |
450 | 458 | </dd> |
451 | 459 | <dt>other arguments</dt><dd><p>See details in <code class="docutils literal notranslate"><span class="pre">pesfit.fitter.random_varshift()</span></code>.</p> |
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463 | 471 |
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464 | 472 | <dl class="py function"> |
465 | 473 | <dt id="pesfit.fitter.random_varshift"> |
466 | | -<code class="sig-prename descclassname">pesfit.fitter.</code><code class="sig-name descname">random_varshift</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">fitres</span></em>, <em class="sig-param"><span class="n">model</span></em>, <em class="sig-param"><span class="n">params</span></em>, <em class="sig-param"><span class="n">shifts</span></em>, <em class="sig-param"><span class="n">yvals</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">xvals</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">parnames</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwds</span></em><span class="sig-paren">)</span><a class="headerlink" href="#pesfit.fitter.random_varshift" title="Permalink to this definition">¶</a></dt> |
| 474 | +<code class="sig-prename descclassname">pesfit.fitter.</code><code class="sig-name descname">random_varshift</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">fitres</span></em>, <em class="sig-param"><span class="n">model</span></em>, <em class="sig-param"><span class="n">params</span></em>, <em class="sig-param"><span class="n">shifts</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">yvals</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">xvals</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">parnames</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwds</span></em><span class="sig-paren">)</span><a class="headerlink" href="#pesfit.fitter.random_varshift" title="Permalink to this definition">¶</a></dt> |
467 | 475 | <dd><p>Recursively apply a random shift value to certain key variables to get a better fit. Execution of the function terminates when either (1) the fitting results are sufficiently good (measured by its chi-squared metric) or (2) the trials exhaust all choices of shift parameters.</p> |
468 | 476 | <p><strong>Parameters</strong></p> |
469 | 477 | <dl class="simple"> |
|
473 | 481 | </dd> |
474 | 482 | <dt>params: instance of <code class="docutils literal notranslate"><span class="pre">lmfit.parameter.Parameters</span></code></dt><dd><p>Lineshape model parameters.</p> |
475 | 483 | </dd> |
| 484 | +<dt>shifts: list/tuple/array | []</dt><dd><p>Different random shifts to apply to the initial conditions.</p> |
| 485 | +</dd> |
476 | 486 | <dt>xvals, yvals: numpy array, numpy array | None, None</dt><dd><p>Horizontal and vertical axis values for the lineshape fitting.</p> |
477 | 487 | </dd> |
478 | 488 | <dt>parnames: list | []</dt><dd><p>List of names of the parameters to update initial conditions.</p> |
479 | 489 | </dd> |
480 | 490 | <dt>verbose: bool | True</dt><dd><p>Option for printout of the chi-squared value.</p> |
481 | 491 | </dd> |
| 492 | +<dt><a href="#id17"><span class="problematic" id="id18">**</span></a>kwds: keyword arguments</dt><dd><p>Extra keywords passed to the <code class="docutils literal notranslate"><span class="pre">Model.fit()</span></code> method.</p> |
| 493 | +</dd> |
482 | 494 | </dl> |
483 | 495 | </dd></dl> |
484 | 496 |
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543 | 555 | <script type="text/javascript"> |
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546 | | - VERSION:'0.5.0', |
| 558 | + VERSION:'0.5.2', |
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548 | 560 | FILE_SUFFIX:'.html', |
549 | 561 | HAS_SOURCE: true, |
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