Merge pull request #10 from barahona-research-group/v0.2.7

V0.2.7
barahona-research-group · Dec 6, 2023 · b6005a9 · b6005a9
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diff --git a/docs/build/doctrees/_templates/autosummary/class.doctree b/docs/build/doctrees/_templates/autosummary/class.doctree
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diff --git a/docs/build/doctrees/auto_tutorials/i-classes/plot_iii_image_container.doctree b/docs/build/doctrees/auto_tutorials/i-classes/plot_iii_image_container.doctree
diff --git a/docs/build/doctrees/auto_tutorials/i-classes/plot_iv_volume_container.doctree b/docs/build/doctrees/auto_tutorials/i-classes/plot_iv_volume_container.doctree
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diff --git a/docs/build/doctrees/auto_tutorials/iv-viz/plot_iii_image.doctree b/docs/build/doctrees/auto_tutorials/iv-viz/plot_iii_image.doctree
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diff --git a/docs/build/doctrees/auto_tutorials/iv-viz/plot_vi_customisation.doctree b/docs/build/doctrees/auto_tutorials/iv-viz/plot_vi_customisation.doctree
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diff --git a/docs/build/doctrees/generated/analysis/decompose/ramanspy.analysis.decompose.NMF.doctree b/docs/build/doctrees/generated/analysis/decompose/ramanspy.analysis.decompose.NMF.doctree
diff --git a/docs/build/doctrees/generated/analysis/decompose/ramanspy.analysis.decompose.PCA.doctree b/docs/build/doctrees/generated/analysis/decompose/ramanspy.analysis.decompose.PCA.doctree
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diff --git a/docs/build/doctrees/generated/analysis/unmix/ramanspy.analysis.unmix.NFINDR.doctree b/docs/build/doctrees/generated/analysis/unmix/ramanspy.analysis.unmix.NFINDR.doctree
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diff --git a/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ARPLS.doctree b/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ARPLS.doctree
diff --git a/...d/doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ASLS.doctree b/...d/doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ASLS.doctree
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diff --git a/...s/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.CornerCutting.doctree b/...s/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.CornerCutting.doctree
diff --git a/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.DRPLS.doctree b/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.DRPLS.doctree
diff --git a/...d/doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.FABC.doctree b/...d/doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.FABC.doctree
diff --git a/...trees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Goldindec.doctree b/...trees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Goldindec.doctree
diff --git a/...doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IARPLS.doctree b/...doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IARPLS.doctree
diff --git a/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IASLS.doctree b/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IASLS.doctree
diff --git a/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IRSQR.doctree b/.../doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.IRSQR.doctree
diff --git a/...octrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ModPoly.doctree b/...octrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.ModPoly.doctree
diff --git a/...d/doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Poly.doctree b/...d/doctrees/generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Poly.doctree
diff --git a/...ctrees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Gaussian.doctree b/...ctrees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Gaussian.doctree
diff --git a/...doctrees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Kernel.doctree b/...doctrees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Kernel.doctree
diff --git a/...doctrees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.SavGol.doctree b/...doctrees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.SavGol.doctree
diff --git a/...trees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Whittaker.doctree b/...trees/generated/prepprocessing/denoising/ramanspy.preprocessing.denoise.Whittaker.doctree
diff --git a/...s/generated/prepprocessing/despiking/ramanspy.preprocessing.despike.WhitakerHayes.doctree b/...s/generated/prepprocessing/despiking/ramanspy.preprocessing.despike.WhitakerHayes.doctree
diff --git a/...es/generated/prepprocessing/misc/ramanspy.preprocessing.misc.BackgroundSubtractor.doctree b/...es/generated/prepprocessing/misc/ramanspy.preprocessing.misc.BackgroundSubtractor.doctree
diff --git a/.../build/doctrees/generated/prepprocessing/misc/ramanspy.preprocessing.misc.Cropper.doctree b/.../build/doctrees/generated/prepprocessing/misc/ramanspy.preprocessing.misc.Cropper.doctree
diff --git a/...build/doctrees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.AUC.doctree b/...build/doctrees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.AUC.doctree
diff --git a/...trees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MaxIntensity.doctree b/...trees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MaxIntensity.doctree
diff --git a/...ld/doctrees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MinMax.doctree b/...ld/doctrees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MinMax.doctree
diff --git a/...ld/doctrees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.Vector.doctree b/...ld/doctrees/generated/prepprocessing/norm/ramanspy.preprocessing.normalise.Vector.doctree
diff --git a/.../generated/prepprocessing/protocols/ramanspy.preprocessing.protocols.bergholt2016.doctree b/.../generated/prepprocessing/protocols/ramanspy.preprocessing.protocols.bergholt2016.doctree
diff --git a/...nerated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P1.doctree b/...nerated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P1.doctree
diff --git a/...nerated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P3.doctree b/...nerated/prepprocessing/protocols/ramanspy.preprocessing.protocols.georgiev2023_P3.doctree
diff --git a/docs/build/doctrees/preprocessing.doctree b/docs/build/doctrees/preprocessing.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
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 <li class="toctree-l1"><a class="reference internal" href="../plot.html">Data visualisation</a></li>
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+<li class="toctree-l2"><a class="reference internal" href="../generated/prepprocessing/misc/ramanspy.preprocessing.misc.Cropper.html">ramanspy.preprocessing.misc.Cropper</a></li>
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+<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>
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+<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>
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+<li class="toctree-l2"><a class="reference internal" href="../generated/prepprocessing/baseline/ramanspy.preprocessing.baseline.Poly.html">ramanspy.preprocessing.baseline.Poly</a></li>
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+<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>
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+<li class="toctree-l2"><a class="reference internal" href="../generated/prepprocessing/norm/ramanspy.preprocessing.normalise.MaxIntensity.html">ramanspy.preprocessing.normalise.MaxIntensity</a></li>
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+<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>
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+<li class="toctree-l2"><a class="reference internal" href="../generated/analysis/decompose/ramanspy.analysis.decompose.PCA.html">ramanspy.analysis.decompose.PCA</a></li>
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+<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>
@@ -258,13 +300,22 @@
         </div>
         <article role="main">
           <h1>All modules for which code is available</h1>
-<ul><li><a href="ramanspy/core.html">ramanspy.core</a></li>
+<ul><li><a href="ramanspy/analysis/cluster.html">ramanspy.analysis.cluster</a></li>
+<li><a href="ramanspy/analysis/decompose.html">ramanspy.analysis.decompose</a></li>
+<li><a href="ramanspy/analysis/unmix.html">ramanspy.analysis.unmix</a></li>
+<li><a href="ramanspy/core.html">ramanspy.core</a></li>
 <li><a href="ramanspy/datasets.html">ramanspy.datasets</a></li>
 <li><a href="ramanspy/load.html">ramanspy.load</a></li>
 <li><a href="ramanspy/metrics.html">ramanspy.metrics</a></li>
 <li><a href="ramanspy/plot/plot.html">ramanspy.plot.plot</a></li>
 <li><a href="ramanspy/preprocessing/Pipeline.html">ramanspy.preprocessing.Pipeline</a></li>
 <li><a href="ramanspy/preprocessing/Step.html">ramanspy.preprocessing.Step</a></li>
+<li><a href="ramanspy/preprocessing/baseline.html">ramanspy.preprocessing.baseline</a></li>
+<li><a href="ramanspy/preprocessing/denoise.html">ramanspy.preprocessing.denoise</a></li>
+<li><a href="ramanspy/preprocessing/despike.html">ramanspy.preprocessing.despike</a></li>
+<li><a href="ramanspy/preprocessing/misc.html">ramanspy.preprocessing.misc</a></li>
+<li><a href="ramanspy/preprocessing/normalise.html">ramanspy.preprocessing.normalise</a></li>
+<li><a href="ramanspy/preprocessing/protocols.html">ramanspy.preprocessing.protocols</a></li>
 <li><a href="ramanspy/synth/synth.html">ramanspy.synth.synth</a></li>
 </ul>
         </article>