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barahona-research-group · Mar 15, 2024 · 8b8d88f · 8b8d88f
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diff --git a/docs/build/doctrees/data_classes.doctree b/docs/build/doctrees/data_classes.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b9011271c24b0197b8ccf2f8ebd0aeb4
+config: 8dc05dbcadf16d0c72d16703e32690b0
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -329,7 +329,7 @@ <h1>All modules for which code is available</h1>
         <div class="bottom-of-page">
           <div class="left-details">
             <div class="copyright">
-                Copyright &#169; 2023, Dimitar Georgiev
+                Copyright &#169; 2024, Dimitar Georgiev
             </div>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>

diff --git a/docs/build/html/_modules/ramanspy/core.html b/docs/build/html/_modules/ramanspy/core.html
@@ -175,13 +175,55 @@
 <li class="toctree-l1"><a class="reference internal" href="../../datasets.html">Datasets</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../metrics.html">Metrics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../plot.html">Data visualisation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../preprocessing.html">Preprocessing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../analysis.html">Analysis</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../preprocessing.html">Preprocessing</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Preprocessing</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/misc/ramanspy.preprocessing.misc.Cropper.html">ramanspy.preprocessing.misc.Cropper</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/misc/ramanspy.preprocessing.misc.BackgroundSubtractor.html">ramanspy.preprocessing.misc.BackgroundSubtractor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/despiking/ramanspy.preprocessing.despike.WhitakerHayes.html">ramanspy.preprocessing.despike.WhitakerHayes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.SavGol.html">ramanspy.preprocessing.denoise.SavGol</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Whittaker.html">ramanspy.preprocessing.denoise.Whittaker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Kernel.html">ramanspy.preprocessing.denoise.Kernel</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Gaussian.html">ramanspy.preprocessing.denoise.Gaussian</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ASLS.html">ramanspy.preprocessing.baseline.ASLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IASLS.html">ramanspy.preprocessing.baseline.IASLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.AIRPLS.html">ramanspy.preprocessing.baseline.AIRPLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ARPLS.html">ramanspy.preprocessing.baseline.ARPLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.DRPLS.html">ramanspy.preprocessing.baseline.DRPLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IARPLS.html">ramanspy.preprocessing.baseline.IARPLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ASPLS.html">ramanspy.preprocessing.baseline.ASPLS</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Poly.html">ramanspy.preprocessing.baseline.Poly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ModPoly.html">ramanspy.preprocessing.baseline.ModPoly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Poly.html">ramanspy.preprocessing.baseline.Poly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ModPoly.html">ramanspy.preprocessing.baseline.ModPoly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Goldindec.html">ramanspy.preprocessing.baseline.Goldindec</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IRSQR.html">ramanspy.preprocessing.baseline.IRSQR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.CornerCutting.html">ramanspy.preprocessing.baseline.CornerCutting</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.FABC.html">ramanspy.preprocessing.baseline.FABC</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/norm/ramanspy.preprocessing.normalise.Vector.html">ramanspy.preprocessing.normalise.Vector</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MinMax.html">ramanspy.preprocessing.normalise.MinMax</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MaxIntensity.html">ramanspy.preprocessing.normalise.MaxIntensity</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/norm/ramanspy.preprocessing.normalise.AUC.html">ramanspy.preprocessing.normalise.AUC</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P1.html">ramanspy.preprocessing.protocols.georgiev2023_P1</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P3.html">ramanspy.preprocessing.protocols.georgiev2023_P3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P3.html">ramanspy.preprocessing.protocols.georgiev2023_P3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/prepprocessing/protocols/ramanspy.preprocessing.protocols.bergholt2016.html">ramanspy.preprocessing.protocols.bergholt2016</a></li>
+</ul>
+</li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../analysis.html">Analysis</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of Analysis</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/decompose/ramanspy.analysis.decompose.PCA.html">ramanspy.analysis.decompose.PCA</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/decompose/ramanspy.analysis.decompose.NMF.html">ramanspy.analysis.decompose.NMF</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/decompose/ramanspy.analysis.decompose.ICA.html">ramanspy.analysis.decompose.ICA</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/cluster/ramanspy.analysis.cluster.KMeans.html">ramanspy.analysis.cluster.KMeans</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/unmix/ramanspy.analysis.unmix.PPI.html">ramanspy.analysis.unmix.PPI</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/unmix/ramanspy.analysis.unmix.FIPPI.html">ramanspy.analysis.unmix.FIPPI</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/unmix/ramanspy.analysis.unmix.NFINDR.html">ramanspy.analysis.unmix.NFINDR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../generated/analysis/unmix/ramanspy.analysis.unmix.VCA.html">ramanspy.analysis.unmix.VCA</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="../../synth.html">Synthetic data</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Gallery:</span></p>
 <ul>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../auto_tutorials/index.html">Tutorials</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><div class="visually-hidden">Toggle navigation of Tutorials</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../auto_tutorials/index.html">Tutorials</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" role="switch" type="checkbox"/><label for="toctree-checkbox-3"><div class="visually-hidden">Toggle navigation of Tutorials</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/i-classes/plot_i_generic_container.html">Storing generic data</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/i-classes/plot_ii_spectrum_container.html">Storing spectra</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/i-classes/plot_iii_image_container.html">Storing imaging data</a></li>
@@ -212,7 +254,7 @@
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/vii-synth/plot_i_endmembers.html">Generate synthetic spectra</a></li>
 </ul>
 </li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../auto_examples/index.html">Examples</a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><div class="visually-hidden">Toggle navigation of Examples</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../auto_examples/index.html">Examples</a><input class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" role="switch" type="checkbox"/><label for="toctree-checkbox-4"><div class="visually-hidden">Toggle navigation of Examples</div><i class="icon"><svg><use href="#svg-arrow-right"></use></svg></i></label><ul>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_examples/plot_i_package_overview.html">Cell phenotyping</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_examples/plot_i_preprocessing_pipelines.html">Preprocessing pipelines</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_examples/plot_ii_dl_denoising.html">AI-based denoising</a></li>
@@ -444,6 +486,17 @@ <h1>Source code for ramanspy.core</h1><div class="highlight"><pre>
 
         <span class="c1"># Return the slice across that band</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">spectral_data</span><span class="p">[</span><span class="o">...</span><span class="p">,</span> <span class="n">closest_band_index</span><span class="p">]</span></div>
+
+
+<div class="viewcode-block" id="SpectralContainer.tolist">
+<a class="viewcode-back" href="../../data_classes.html#ramanspy.SpectralContainer.tolist">[docs]</a>
+    <span class="k">def</span> <span class="nf">tolist</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">Spectrum</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the spectral object as a list of Spectrum objects.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">unfolded_spectral_data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">spectral_data</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">spectral_length</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">[</span><span class="n">Spectrum</span><span class="p">(</span><span class="n">spectral_data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">spectral_axis</span><span class="p">)</span> <span class="k">for</span> <span class="n">spectral_data</span> <span class="ow">in</span> <span class="n">unfolded_spectral_data</span><span class="p">]</span></div>
 </div>
 
 
@@ -637,7 +690,7 @@ <h1>Source code for ramanspy.core</h1><div class="highlight"><pre>
         <div class="bottom-of-page">
           <div class="left-details">
             <div class="copyright">
-                Copyright &#169; 2023, Dimitar Georgiev
+                Copyright &#169; 2024, Dimitar Georgiev
             </div>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>