Update documentation

Author: lan13005

_sources/ift/iftpwa_exec.md

@@ -32,4 +32,6 @@ iftPwaPlot \
     --massIndepFit $base_directory/NiftyFits/.nifty_expanded.yaml
 # Draws some convergence plots to see global iteration dependence of resonance parameters, distributions, etc
 plotConvergence --inputFolder $base_directory/NiftyFits/fit_parameter_history --plotFolder $base_directory/NiftyFits/convergence_plots
+pa run_momentPlotter $yaml -n 10 # make a subdirectory at NiftyFits/plots/moments overlaying projected moments from nifty and amptools fits
+pa run_resultDump $yaml -n 10 # dump all results to csv files (if possible, it will calculate the moments also)
 ```

demos/fsroot_advanced.html

@@ -424,7 +424,10 @@ <h1>FSROOT Advanced Tutorial<a class="headerlink" href="#fsroot-advanced-tutoria
 atiSetup| Loading library libAmpTools.so ..............  ON
 atiSetup| Loading library libAmpPlotter.so ............  ON
 atiSetup| Loading library libAmpsDataIO.so ............  ON
-atiSetup| Loading library libFSRoot.so ................  ON
+atiSetup| Loading library libFSRoot.so ................
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>  ON
 atiSetup| Loading library libAmpsGen.so ...............  OFF
 
 
@@ -766,10 +769,7 @@ <h1>Draw second set of plots<a class="headerlink" href="#draw-second-set-of-plot
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.0
 </pre></div>
 </div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>fg Integral:
-</pre></div>
-</div>
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 499.999597944485
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>fg Integral: 499.999597944485
     FOUND HISTOGRAM...    FSRootHist:000011   101_1             OKAY           (entries = 36081)
     FOUND HISTOGRAM...    FSRootHist:000012   101_1             OKAY           (entries = 0)
     FOUND HISTOGRAM...    FSRootHist:000013   101_1             OKAY           (entries = 0)

demos/mcmc.html

@@ -430,7 +430,10 @@ <h1>Markov Chain Monte Carlo<a class="headerlink" href="#markov-chain-monte-carl
 atiSetup| Loading library libIUAmpTools.so ............  ON
 atiSetup| Loading library libAmpTools.so ..............  ON
 atiSetup| Loading library libAmpPlotter.so ............  ON
-atiSetup| Loading library libAmpsDataIO.so ............  ON
+atiSetup| Loading library libAmpsDataIO.so ............
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>  ON
 atiSetup| Loading library libFSRoot.so ................  OFF
 atiSetup| Loading library libAmpsGen.so ...............  OFF
 
@@ -704,7 +707,7 @@ <h1>Markov Chain Monte Carlo<a class="headerlink" href="#markov-chain-monte-carl
 burnIn: 0
 nsamples: 200
 params_dict: {}
-moves_mixture: [&lt;emcee.moves.stretch.StretchMove object at 0x7f57786ba2b0&gt;]
+moves_mixture: [&lt;emcee.moves.stretch.StretchMove object at 0x7f4fe3844340&gt;]
 sampler_kwargs: {&#39;progress&#39;: False}
  ========================================================================= 
 
@@ -713,10 +716,10 @@ <h1>Markov Chain Monte Carlo<a class="headerlink" href="#markov-chain-monte-carl
 </pre></div>
 </div>
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Calculating intensity with amplitudes dictionary:
-  resAmp1 -&gt; [&#39;etapi::reZ::resAmp1&#39;, &#39;etapi::imZ::resAmp1&#39;]
+  resAmp1 -&gt; [&#39;etapi::imZ::resAmp1&#39;, &#39;etapi::reZ::resAmp1&#39;]
+  resAmp2 -&gt; [&#39;etapi::reZ::resAmp2&#39;, &#39;etapi::imZ::resAmp2&#39;]
   resAmp3 -&gt; [&#39;etapi::reZ::resAmp3&#39;, &#39;etapi::imZ::resAmp3&#39;]
-  resAmp2 -&gt; [&#39;etapi::imZ::resAmp2&#39;, &#39;etapi::reZ::resAmp2&#39;]
-  total -&gt; [&#39;etapi::reZ::resAmp1&#39;, &#39;etapi::reZ::resAmp3&#39;, &#39;etapi::imZ::resAmp2&#39;, &#39;etapi::reZ::resAmp2&#39;, &#39;etapi::imZ::resAmp1&#39;, &#39;etapi::imZ::resAmp3&#39;]
+  total -&gt; [&#39;etapi::imZ::resAmp1&#39;, &#39;etapi::reZ::resAmp2&#39;, &#39;etapi::imZ::resAmp2&#39;, &#39;etapi::reZ::resAmp1&#39;, &#39;etapi::reZ::resAmp3&#39;, &#39;etapi::imZ::resAmp3&#39;]
 </pre></div>
 </div>
 <div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>The chain is shorter than 50 times the integrated autocorrelation time for 5 parameter(s). Use this estimate with caution and run a longer chain!
@@ -744,7 +747,7 @@ <h1>Markov Chain Monte Carlo<a class="headerlink" href="#markov-chain-monte-carl
 MCMC intensity samples saved to mcmc/samples_intensity.feather
   shape: (6400, 4)
 
-Fit time: 4.11643123626709 seconds
+Fit time: 4.4086549282073975 seconds
 </pre></div>
 </div>
 </div>

demos/mle.html

@@ -460,7 +460,7 @@ <h1>Maximum Likelihood Estimation<a class="headerlink" href="#maximum-likelihood
 Config file: /w/halld-scshelf2101/lng/WORK/PyAmpTools9/tests/samples/SIMPLE_EXAMPLE/fitInit.cfg
 Seed file: seed_file
 Number of random fits: 0
-Random seed: 1738864220
+Random seed: 1738867484
  ============================= 
 </pre></div>
 </div>

ift/iftpwa_exec.html

@@ -412,6 +412,8 @@ <h1>iftpwa - Default Execution<a class="headerlink" href="#iftpwa-default-execut
 <span class="w">    </span>--massIndepFit<span class="w"> </span><span class="nv">$base_directory</span>/NiftyFits/.nifty_expanded.yaml
 <span class="c1"># Draws some convergence plots to see global iteration dependence of resonance parameters, distributions, etc</span>
 plotConvergence<span class="w"> </span>--inputFolder<span class="w"> </span><span class="nv">$base_directory</span>/NiftyFits/fit_parameter_history<span class="w"> </span>--plotFolder<span class="w"> </span><span class="nv">$base_directory</span>/NiftyFits/convergence_plots
+pa<span class="w"> </span>run_momentPlotter<span class="w"> </span><span class="nv">$yaml</span><span class="w"> </span>-n<span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="c1"># make a subdirectory at NiftyFits/plots/moments overlaying projected moments from nifty and amptools fits</span>
+pa<span class="w"> </span>run_resultDump<span class="w"> </span><span class="nv">$yaml</span><span class="w"> </span>-n<span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="c1"># dump all results to csv files (if possible, it will calculate the moments also)</span>
 </pre></div>
 </div>
 </section>