made synthetic abundance scene generator method accessible in synth m…

…odule

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: b3e308d8506335cdbde9998bd9328cfb
+config: ba262d26c25120d2f9b242da7d115373
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/ramanspy/core.html

@@ -8,8 +8,12 @@
         <title>ramanspy.core - RamanSPy</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=135e06be" />
-    <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css?v=7f9a90b1" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
+    <link rel="stylesheet" type="text/css" href="../../_static/sg_gallery.css?v=61a4c737" />
+    <link rel="stylesheet" type="text/css" href="../../_static/sg_gallery-binder.css?v=f4aeca0c" />
+    <link rel="stylesheet" type="text/css" href="../../_static/sg_gallery-dataframe.css?v=2082cf3c" />
+    <link rel="stylesheet" type="text/css" href="../../_static/sg_gallery-rendered-html.css?v=1277b6f3" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo-extensions.css?v=36a5483c" />
 
 
@@ -205,7 +209,7 @@
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/vi-analysis/plot_iii_unmixing.html">Built-in unmixing methods</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/vi-analysis/plot_iv_integrative_svm.html">Integrative analysis: Support Vector Machine (SVM) classification</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/vi-analysis/plot_v_integrative_nn.html">Integrative analysis: Neural Network (NN) classification</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../../auto_tutorials/vii%20-%20synth/plot_i_generate_endmembers.html">Generate synthetic endmembers</a></li>
+<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>
@@ -316,8 +320,8 @@ <h1>Source code for ramanspy.core</h1><div class="highlight"><pre>
 <span class="sd">        raman_object = rp.SpectralContainer(spectral_data, spectral_axis)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">spectral_data</span><span class="p">,</span> <span class="n">spectral_axis</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">spectral_data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">spectral_data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">spectral_axis</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">spectral_axis</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">float32</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">spectral_data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</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="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">spectral_axis</span><span class="p">)</span>
 
         <span class="c1"># Order data and axis by shift number values</span>
         <span class="n">sorted_indices</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">spectral_axis</span><span class="o">.</span><span class="n">argsort</span><span class="p">()</span>
@@ -652,7 +656,9 @@ <h1>Source code for ramanspy.core</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=5929fcd5"></script>
+</div><script src="../../_static/jquery.js?v=5d32c60e"></script>
+    <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+    <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

docs/build/html/_sources/synth.rst.txt

@@ -9,11 +9,16 @@ Synthetic spectra
 .. autofunction:: generate_spectra
 
 
+Synthetic fractional abundance scenes
+=====================================
+.. autofunction:: generate_abundance_scene
+
+
 Synthetic mixtures
 ==================
 .. autofunction:: mix
 
 
 Synthetic mixture datasets
-==================
+==========================
 .. autofunction:: generate_mixture_image

docs/build/html/genindex.html

@@ -335,10 +335,12 @@ <h2>F</h2>
   <h2>G</h2>
   <table style="width: 100%" class="indextable genindextable"><tr>
     <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="synth.html#ramanspy.synth.generate_mixture_image">generate_mixture_image() (in module ramanspy.synth)</a>
+        <li><a href="synth.html#ramanspy.synth.generate_abundance_scene">generate_abundance_scene() (in module ramanspy.synth)</a>
 </li>
     </ul></td>
     <td style="width: 33%; vertical-align: top;"><ul>
+        <li><a href="synth.html#ramanspy.synth.generate_mixture_image">generate_mixture_image() (in module ramanspy.synth)</a>
+</li>
         <li><a href="synth.html#ramanspy.synth.generate_spectra">generate_spectra() (in module ramanspy.synth)</a>
 </li>
     </ul></td>

docs/build/html/loading.html

@@ -263,7 +263,7 @@
 <h1>Data loading<a class="headerlink" href="#data-loading" title="Link to this heading"></a></h1>
 <p><cite>RamanSPy</cite> can be used to easily load experimental Raman spectroscopic data from different instruments and manufacturers.
 This is enabled through the introduction of custom data loading functions, which can parse and load different data formats
-into the appropriate <a class="reference internal" href="auto_tutorials/index.html#data-containers"><span class="std std-ref">Data containers</span></a>.</p>
+into the appropriate <a class="reference internal" href="data_classes.html#data-containers"><span class="std std-ref">Data containers</span></a>.</p>
 <p>Loading methods are available within the <code class="xref py py-mod docutils literal notranslate"><span class="pre">ramanspy.load</span></code> module.</p>
 <section id="witec-suite-witec">
 <h2>WITec Suite (WITec)<a class="headerlink" href="#witec-suite-witec" title="Link to this heading"></a></h2>

docs/build/html/synth.html

@@ -296,6 +296,30 @@ <h2>Synthetic spectra<a class="headerlink" href="#synthetic-spectra" title="Link
 </div>
 </dd></dl>
 
+</section>
+<section id="synthetic-fractional-abundance-scenes">
+<h2>Synthetic fractional abundance scenes<a class="headerlink" href="#synthetic-fractional-abundance-scenes" title="Link to this heading"></a></h2>
+<dl class="py function">
+<dt class="sig sig-object py" id="ramanspy.synth.generate_abundance_scene">
+<span class="sig-prename descclassname"><span class="pre">ramanspy.synth.</span></span><span class="sig-name descname"><span class="pre">generate_abundance_scene</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_endmembers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scene_type</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/ramanspy/synth/synth.html#generate_abundance_scene"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#ramanspy.synth.generate_abundance_scene" title="Link to this definition"></a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>size</strong> (<em>int</em>) – The size of the abundance scene. Assumes a square scene (i.e. size x size).</p></li>
+<li><p><strong>num_endmembers</strong> (<em>int</em>) – The number of endmembers to use.</p></li>
+<li><p><strong>scene_type</strong> (<em>{'chessboard'</em><em>, </em><em>'gaussian'</em><em>, </em><em>'dirichlet'}</em>) – The type of scene to generate.</p></li>
+<li><p><strong>seed</strong> (<em>int</em><em>, </em><em>optional</em>) – The seed to use for the random number generator.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>image</strong> – The generated abundance image.</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>array_like, shape (size, size, num_endmembers)</p>
+</dd>
+</dl>
+</dd></dl>
+
 </section>
 <section id="synthetic-mixtures">
 <h2>Synthetic mixtures<a class="headerlink" href="#synthetic-mixtures" title="Link to this heading"></a></h2>
@@ -436,6 +460,10 @@ <h2>Synthetic mixture datasets<a class="headerlink" href="#synthetic-mixture-dat
 <li><a class="reference internal" href="#ramanspy.synth.generate_spectra"><code class="docutils literal notranslate"><span class="pre">generate_spectra()</span></code></a></li>
 </ul>
 </li>
+<li><a class="reference internal" href="#synthetic-fractional-abundance-scenes">Synthetic fractional abundance scenes</a><ul>
+<li><a class="reference internal" href="#ramanspy.synth.generate_abundance_scene"><code class="docutils literal notranslate"><span class="pre">generate_abundance_scene()</span></code></a></li>
+</ul>
+</li>
 <li><a class="reference internal" href="#synthetic-mixtures">Synthetic mixtures</a><ul>
 <li><a class="reference internal" href="#ramanspy.synth.mix"><code class="docutils literal notranslate"><span class="pre">mix()</span></code></a></li>
 </ul>

docs/source/synth.rst

@@ -9,11 +9,16 @@ Synthetic spectra
 .. autofunction:: generate_spectra
 
 
+Synthetic fractional abundance scenes
+=====================================
+.. autofunction:: generate_abundance_scene
+
+
 Synthetic mixtures
 ==================
 .. autofunction:: mix
 
 
 Synthetic mixture datasets
-==================
+==========================
 .. autofunction:: generate_mixture_image

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ramanspy"
-version = "0.2.3"
+version = "0.2.4"
 description = "RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis"
 readme = "README.md"
 authors = [{ name = "Dimitar Georgiev", email = "[email protected]" }]

src/ramanspy/synth/__init__.py

@@ -1,7 +1,8 @@
-from .synth import generate_spectra, mix, generate_mixture_image
+from .synth import generate_spectra, mix, generate_abundance_scene, generate_mixture_image
 
 __all__ = [
     "generate_spectra",
     "mix",
+    "generate_abundance_scene",
     "generate_mixture_image",
 ]

src/ramanspy/synth/synth.py

@@ -197,12 +197,12 @@ def mix(
     return mixtures
 
 
-def _generate_abundance_image(size, num_endmembers, scene_type, *, seed=None):
+def generate_abundance_scene(size, num_endmembers, scene_type, *, seed=None):
     """
     Parameters
     ----------
     size : int
-        The size of the abundance image. Assumes a square image.
+        The size of the abundance scene. Assumes a square scene (i.e. size x size).
     num_endmembers : int
         The number of endmembers to use.
     scene_type : {'chessboard', 'gaussian', 'dirichlet'}
@@ -326,7 +326,7 @@ def generate_mixture_image(
     """
 
     endmebers = generate_spectra(num_endmembers, num_spectral_bands, realistic=realistic_endmembers, seed=seed)
-    abundance_image = _generate_abundance_image(image_size, num_endmembers, image_type, seed=seed)
+    abundance_image = generate_abundance_scene(image_size, num_endmembers, image_type, seed=seed)
 
     mixture = mix(endmebers, abundance_image, mixture_mode=mixture_mode, noise=noise, noise_amplitude=noise_amplitude,
                   baseline=baseline, baseline_amplitude=baseline_amplitude, baseline_probability=baseline_probability,